Hindawi International Journal of Genomics Volume 2017, Article ID 6876393, 17 pages https://doi.org/10.1155/2017/6876393

Research Article Mapping QTL for Root and Shoot Morphological Traits in a Durum Wheat×T. dicoccum Segregating Population at Seedling Stage Anna Iannucci,1 Daniela Marone,1 Maria Anna Russo,1 Pasquale De Vita,1 Vito Miullo,1 Pina Ferragonio,1 Antonio Blanco,2 Agata Gadaleta,2 and Anna Maria Mastrangelo1 1

Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), SS 673 km 25.2, 71122 Foggia, Italy 2 Department of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, University of Bari Aldo Moro, Via G. Amendola 165/A, 70126 Bari, Italy Correspondence should be addressed to Anna Maria Mastrangelo; [email protected] Received 12 January 2017; Revised 12 May 2017; Accepted 21 June 2017; Published 6 August 2017 Academic Editor: Mohamed Salem Copyright © 2017 Anna Iannucci et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. A segregating population of 136 recombinant inbred lines derived from a cross between the durum wheat cv. “Simeto” and the T. dicoccum accession “Molise Colli” was grown in soil and evaluated for a number of shoot and root morphological traits. A total of 17 quantitative trait loci (QTL) were identified for shoot dry weight, number of culms, and plant height and for root dry weight, volume, length, surface area, and number of forks and tips, on chromosomes 1B, 2A, 3A, 4B, 5B, 6A, 6B, and 7B. LODs were 2.1 to 21.6, with percent of explained phenotypic variability between 0.07 and 52. Three QTL were mapped to chromosome 4B, one of which corresponds to the Rht-B1 locus and has a large impact on both shoot and root traits (LOD 21.6). Other QTL that have specific effects on root morphological traits were also identified. Moreover, meta-QTL analysis was performed to compare the QTL identified in the “Simeto” × “Molise Colli” segregating population with those described in previous studies in wheat, with three novel QTL defined. Due to the complexity of phenotyping for root traits, further studies will be helpful to validate these regions as targets for breeding programs for optimization of root function for field performance.

1. Introduction The root system architecture defines the shape and spatial arrangements of the root structure within the soil [1]. A number of factors contribute to the definition of the morphology of the root system, such as the angle and rate of root growth, and the diameters of the individual roots. The development of the root structure depends on interactions between the genetic features of a plant and the environment in which the roots grow (i.e., soil type and composition, water and nutrient availability, and microorganism profile). The main challenge in studying root traits is the need for robust and high-throughput methods for phenotypic evaluation

that can provide a proxy for field performance, because the measurement of root traits under open field conditions can be very difficult. This is particularly the case for genetic studies that require analysis of large sets of samples. For this reason, various hydroponic culture techniques have been adopted, together with experimental systems with soilbased growth substrates that can offer better tools to predict plant behavior under field conditions, for example [2–5]. Once young seedlings have been grown in the laboratory or in glasshouses with various methods [6, 7], scanner-based image analysis can make root analysis less time consuming. Therefore, although there is the limitation of the early growth stage of the plants analyzed, this represents a

2 decisive tool, as it allows the evaluation of large sets of genotypes, as in the case of segregating populations or association-mapping panels. Many studies have been carried out to dissect out the genetic basis of root system architectures. For cereals, quantitative trait loci (QTL) for root traits have been mapped in rice (Oryza sativa L.) [8–14], maize (Zea mays L.) [15–17], sorghum [18], and bread and durum wheat [4, 5, 19–37]. Linkage mapping has largely been used to map QTL for root traits in biparental populations, although recently, association mapping with germplasm collections has also been used in durum wheat [35, 37]. Altogether, these studies have shown relatively complex genetic control for root traits and strong environmental effects, with only a few examples of QTL that can individually explain up to 30% of the phenotypic variation in rice [38, 39] and maize [40] and up to 50% in wheat [4]. In most cases, root traits are regulated by a suite of small-effect loci [41]. Uptake of water and nutrients, anchorage in the soil, and interactions with microorganisms are among the main functions of the root structure, and these are responsible for crop performance, in terms of yield and quality. Indeed, some studies have shown overlap of QTL for root features with QTL for traits related to productivity [35, 37, 42–45]. Moreover, despite the complexity of the genetic control of root traits, there are some examples in which marker-assisted selection for root QTL has been successfully exploited to improve the root-system architecture and yield in rice [45, 46] and maize [40, 47]. Grain yield in wheat has been greatly improved over the last century, with the introduction of semidwarf wheat cultivars that are characterized by higher harvest index compared to taller genotypes [48]. Many studies have focused on the relationships between above-ground biomass and root growth; nevertheless, controversial results have been reported. In general, recent studies have indicated the absence of a clear correlation between shoot and root growth in wheat, with shoot and root traits reported to be controlled by different sets of genetic loci [21, 49–51]. Different conclusions have been reported in other studies. Miralles et al. [52] indicated that spring wheat plants with dwarfing genes are characterized by reduced plant height but increased root length and dry weight. More recently, Kabir et al. [36] analyzed two bread-wheat segregating populations and defined a negative correlation between root traits and plant height in both of the populations. On the contrary, Subira et al. [53] indicated that the Rht-B1b dwarfing allele is effective in reducing both aerial and root biomass in durum wheat. In the present study, a durum wheat (Triticum turgidum L. var. durum) population of 136 recombinant inbred lines (RILs) was grown in soil under controlled conditions to identify the chromosome regions that are involved in the control of their root and shoot architecture.

2. Materials and Methods 2.1. Genetic Materials. The RIL population of 136 F6 lines that was used in the present study was developed from a cross between the Italian durum wheat cv. “Simeto” (Capeiti/ Valnova) and a cultivar of T. dicoccum known as “Molise Colli”

International Journal of Genomics that was selected within the framework of a local population of T. dicoccum (from the Regional Agency for Development and Innovation of Agriculture of the Molise Region (Agenzia Regionale per lo Sviluppo e l’Innovazione dell’Agricoltura della Regione Molise)). 2.2. Plant Growth and Soil Sampling. The RIL population and the parents were grown in plastic cylinders containing a soil mixture (soil: sand, 50 : 50; v/v). Before the pot experiments, soil with a history of exposure to annual cereal species was collected (in July 2013) from the experimental farming station of the Cereal Research Centre in Foggia (Italy; 41°28′ N, 15°34′ E; 76 m a.s.l.). The samples were collected from the upper 30 cm of the soil profile and air dried for 1 week. They were then thoroughly mixed, passed through a 2 mm sieve (to remove gravel fragments), cleaned of plant debris, and stored in a cold room (4°C) until further use. This soil was an unsterilized loam soil (USDA classification system) with the following characteristics: 21% clay, 43% silt, 36% sand, pH 8 (in H2O), 15 mg/kg available phosphorous (Olsen method), 800 mg/kg exchangeable potassium (NH4Ac), and 21 g/kg organic matter (Walkey-Black method). Silica sand with a grain size that ranged from 0.4 mm to 0.1 mm was used. The soil mixture is hereinafter referred to as “soil.” Before sowing the seeds, they were surface sterilized by soaking them in 2% sodium hypochlorite for 5 min and then rinsed several times with distilled water. The seeds were put into Petri dishes with one sheet of filter paper (Whatman number 1) that was moistened with 5 mL distilled water, and these were kept in a dark incubator at a constant temperature of 20°C for 48 h. Three germinated wheat seeds (roots, 4.5 mm. 2.4. Statistical Analysis. The means, standard deviations, coefficients of variation, and ranges of each measured morphological trait were separately calculated for each genotype. The data were also analyzed using ANOVA, and the homogeneity of the phenotypic variance between the replications was verified, with the means separated by Fischer’s protected least-significant difference at P < 0 05 for all of the traits, to test the differences across the RILs and the two parents (i.e., “Molise Colli” and “Simeto”). The heritability (H) was estimated for each trait, as in H=

σb 2 , σt 2

1

where σb 2 and σt 2 are the between-line variance (as an estimate of the genotypic variance) and the total variance (as an estimate of the phenotypic variance), respectively, as estimated from the mean squares of the analysis of variance. To obtain a general comprehensive characterization of the samples, the root traits were subjected to principal component analysis (PCA) based on correlations, followed by factor analysis. To overcome differences in size during recording, the data for the different traits were standardized to a mean of zero and variance of one [55]. The components that represented the original variables (traits) were also extracted. Only those with eigenvalues ≥ 3.0 were considered as having a major contribution to the total variation [56]. The first and second principal component axis scores were plotted to aid the visualization of the genotype differences. All of the statistical analyses were performed using the JMP software (version 8.0; SAS Institute Inc.). Genome-wide QTL searches were conducted on the “Simeto” × “Molise Colli” linkage map that was described

by Russo et al. [57]. Briefly, the map covers all of the 14 chromosomes of the durum wheat genome with 9040 markers on 2879.3 cM. The “Simeto” × “Molise Colli” segregating population (SMC) was also genotyped with the markers BF-MR1 and BF-WR1, to infer the presence of the alleles Rht-B1b and Rht-B1a, respectively [58]. The inclusive composite interval mapping method [59] was used for the QTL mapping, with the QGene 4.0 software [60]. The scanning interval of 2 cM between markers and putative QTL with a window size of 10 cM were used to detect QTL. The marker cofactors for background control were set by single marker regression and simple interval analysis, with a maximum of five controlling markers. Putative QTL were defined as two or more linked markers that were associated with a trait at a log10 odds ratio (LOD) ≥ 3. Suggestive QTL at the subthreshold of 2.0 < LOD < 3.0 are reported for further investigations [61]. For the main QTL effects, the positive and negative signs of the estimates indicated that “Simeto” and “Molise Colli,” respectively, contributed toward higher value alleles for the traits. The proportion of phenotypic variance explained by a single QTL was determined by the square of the partial correlation coefficient (R2 ). Finally, the 95% confidence intervals of the QTL were estimated using the approach of Darvasi and Soller [62], as given in

Conf idence interval =

163 , N × R2

2

where N is the population size and R2 is the proportion of the phenotypic variance explained by the QTL. 2.5. Meta-QTL Analysis. Twelve previously published studies were identified that reported QTL for root traits (see Supplementary Table S1 available online at https://doi.org/10.1155/ 2017/6876393). An integrated map of the A and B genomes was constructed using the wheat map developed with a 90K single-nucleotide polymorphism (SNP) array [63] on which a durum-wheat linkage map was projected, based on the SNP and simple sequence repeat (SSR) markers (“Ciccio” × “Svevo”) by Colasuonno et al. [64], together with the SMC genetic map. The map obtained was used as the reference map for merging another wheat consensus map that included diversity array technology (DArT) and PCR-based markers, as described in Marone et al. [65, 66]. The chromosomal regions that contained QTL for root traits retrieved in the literature were also integrated. All of the calculations for both the creation of the integrated map and the QTL projections were performed with the Biomercator software v.4. For n individual QTL, the Biomercator software tests the most likely assumption between 1, 2, 3, 4, and n QTL. The Akaike information criterion (AIC) was considered to select the best QTL model that indicated the number of meta (M) QTL. The model with the lowest AIC was considered the best fit. When the n model was the most likely model, the meta-analysis was performed again, choosing a subset of the QTL. The MQTL were obtained from the midpoint positions of the overlapping QTL.

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International Journal of Genomics Table 1: Details of all of the traits for which a QTL was identified in the present study.

Trait Crossing number Shoot number per plant Plant height Shoot dry weight Root dry weight Length Length, diameter class 0.0 < d ≤ 0.5 mm Length, diameter class 0.5 < d ≤ 1.0 mm Length, diameter class 1.0 < d ≤ 1.5 mm Length, diameter class 1.5 < d ≤ 2.0 mm Length, diameter class 2.0 < d ≤ 2.5 mm Length, diameter class 2.5 < d ≤ 3.0 mm Length, diameter class 4.0 < d ≤ 4.5 mm Surface area Surface area, diameter class 0.0 < d ≤ 0.5 mm Surface area, diameter class 0.5 < d ≤ 1.0 mm Surface area, diameter class 1.0 < d ≤ 1.5 mm Surface area, diameter class 1.5 < d ≤ 2.0 mm Surface area, diameter class 2.0 < d ≤ 2.5 mm Surface area, diameter class 2.5 < d ≤ 3.0 mm Surface area, diameter class 4.0 < d ≤ 4.5 mm Volume Volume, diameter class 0.0 < d ≤ 0.5 mm Volume, diameter class 0.5 < d ≤ 1.0 mm Volume, diameter class 1.0 < d ≤ 1.5 mm Volume, diameter class 1.5 < d ≤ 2.0 mm Volume, diameter class 2.0 < d ≤ 2.5 mm Volume, diameter class 2.5 < d ≤ 3.0 mm Volume, diameter class 4.0 < d ≤ 4.5 mm Number of tips Number of tips, diameter class 0.0 < d ≤ 0.5 mm Number of tips, diameter class 0.5 < d ≤ 1.0 mm Number of tips, diameter class 1.5 < d ≤ 2.0 mm Number of tips, diameter class 2.0 < d ≤ 2.5 mm Number of tips, diameter class 2.5 < d ≤ 3.0 mm Number of tips, diameter class 3.0 < d ≤ 3.5 mm

3. Results 3.1. Evaluation of the Phenotypic Data. The analysis of the phenotypic data revealed that the two parents were clearly different in terms of the size of the shoot. “Molise Colli” was characterized by greater shoot height and dry weight, compared to “Simeto.” This was expected, as “Molise Colli” is derived from an accession of T. dicoccum, while “Simeto” is a modern durum wheat variety. This difference in growth between these two genotypes was also observed for the root structure. There was a significant difference between these parents for root dry weight (“Molise Colli,” 46.7 mg; “Simeto,” 33.9 mg). These data indicated that “Molise Colli”

Unit — — cm g g cm cm cm cm cm cm cm cm cm2 cm2 cm2 cm2 cm2 cm2 cm2 cm2 cm3 cm3 cm3 cm3 cm3 cm3 cm3 cm3 — — — — — — —

Abbreviation C Shoots PH SDW RDW L L1 L2 L3 L4 L5 L6 L9 SA SA1 SA2 SA3 SA4 SA5 SA6 SA9 V V1 V2 V3 V4 V5 V6 V9 T T1 T2 T4 T5 T6 T7

is characterized by superior growth with respect to “Simeto” for both the aerial and root parts, even if the differences observed for the root lengths, surface areas, diameters, volumes, and numbers of tips were not significantly different. For the segregating population, there was a large range of variation for all of the examined traits, with significant differences across the RILs (Table 2; Supplementary Tables S2 and S3). In the PCA, the first two principal components (PCs) explained about 65% of the total variation among the 138 genotypes evaluated for 50 morphological root traits (Figure 1). According to the factor loadings, PC1 was positively correlated with root volume, length, and surface area

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Table 2: Phenotypic variations among the parental lines and RILs from the “Simeto” × “Molise Colli” population for the shoot and root traits. Trait DAS PH Shoots SDW RDW L SA D F V T

Units Days cm N mg mg cm cm2 mm N cm3 N

“Molise Colli” 23.30 60.90 1.75 212.90 46.70 1317.20 135.40 0.33 4546.25 1.12 1860.30

“Simeto” 22.80 39.40 1.00 162.60 33.90 1096.20 108.10 0.31 3270.00 0.86 1513.80

Mean 24.70 53.40 1.58 221.70 51.50 1355.00 128.20 0.30 5352.22 0.99 1990.10

Min. 19.80 36.20 1.00 121.00 13.50 377.20 33.90 0.23 994.00 0.25 679.00

Max. 34.00 71.20 2.25 380.90 106.60 2439.40 234.00 0.38 12172.75 2.22 3303.80

Range 14.30 35.00 1.25 260.00 93.10 2062.10 200.20 0.15 11178.75 1.96 2624.80

±SD 2.70 8.10 0.38 56.50 18.30 395.40 40.30 0.03 2352.46 0.36 597.50

CV (%) 11.00 15.20 24.35 25.50 35.50 29.20 31.40 9.10 43.95 36.50 30.00

H 0.35 0.76 0.29 0.63 0.27 0.35 0.47 0.08 0.34 0.45 0.35

LSD0.05 4.22 6.09 0.66 0.06 0.03 616.70 52.30 0.07 3747.18 0.48 929.20

Min.: minimum value; max.: maximum value; SD: standard deviation; CV: coefficient of variation; H: broad sense heritability; LSD: least significant difference; DAS: days after sowing; PH: plant height; shoots: number of shoots per plant; SDW: shoot dry weight; RDW: root dry weight; L: length; SA: surface area; D: diameter; F: number of forks; V: volume; T: number of tips.

10

138

156 205 144 5

7

207

165

PC 2: 16.08%

43

0

−5

67 40 181 81211 209 193 83 54 63 72 37 59 5 203 188B170145 152 194 12 90 178 61 159 160 174 198 167 Simeto 92A 124 154 149 208 210 6 204 191 163 197 126 164 7949 148 89 190 172B 91 131 56 189 150 133 201 196 195 60 158 68 19 192 161 3532 151 4 177 32142 Molise 95 114 70182 9 74 1 206 50 128 99 57 139 113188B 20 8 48 31 13 166 96 52 10 55 26 12278185 8829 76 130 199 23 105 125 30 115 137B 106 14 153 22 121 27 38 117 172B

15

1180

187 137B

127

94 107

−10 −10

−5

0

5

10

15

20

25

PC 1: 48.45%

Figure 1: Principal component analysis score plot of the first two principal components of the parental lines and RILs from the durum wheat “Simeto” × “Molise Colli” population for the root traits.

in the root-diameter classes from 0.5 mm to 3.0 mm. PC2 was negatively associated with the number of crossings and the root length in the root-diameter classes from 0.0 mm to

0.5 mm. In particular, “Molise Colli” showed higher values for all root traits in the root-diameter classes 0.0 mm to 2.0 mm, for which the most significant differences were

6 observed in terms of total variability, while “Simeto” was phenotypically superior for root traits in the larger rootdiameter classes (Supplementary Table S2). These traits can be considered as key characteristics for the estimation of the genetic diversity in a durum wheat population. Due to the high phenotypic variation, the scatter diagram showed wide dispersion along both of the PC axes and evident and significant groups of genotypes with different root architectures (Figure 1). Moreover, correlation analysis was carried out considering the root traits evaluated in the present study and the traits related to seed size and morphology that were previously analyzed [57]. In particular, the means over 2 years of field evaluation were considered, and the most significant correlations were between 1000-kernel weight and seed area on the one hand and a number of root traits on the other (Supplementary Table S4). 3.2. QTL Mapping for Root Traits in the Durum Wheat “Simeto” × “Molise Colli” RIL Population. The linkage map used for the QTL analysis included SSR and SNP markers for a total of 9040 markers that covered 2879.3 cM [57]. A total of 61 QTL covering 17 chromosomal regions were identified in the present study, which were located on chromosomes 1B, 2A, 3A, 4B, 5B, 6A, 6B, and 7B (Table 3). Some of these QTL controlled the above-ground biomass (e.g., number of shoots, plant height, and shoot dry weight), and for all of these, the “Molise Colli” allele effect was positive, as indicated by the negative sign of the additive effects. The analysis with the markers BF-MR1 and BFMR2 allowed “Simeto” to be assigned by the Rht-B1b allele, while “Molise Colli” was characterized by the RhtB1a allele. The scoring of the markers across the segregating population led to locate this locus on the SMC genetic map (Figure 2). The region on chromosome 4B that corresponds to the Rht-B1 region was of particular interest; this controlled plant height, shoot dry weight, and a number of root morphological traits, most of which were in the smallest root-diameter classes. The LODs were very high for the shoot traits (12.1–21.6), with the explained variability between 52% for plant height and 34% for shoot dry weight. For the root traits controlled by this QTL, the LODs were between 3.1 for root volume class 3 and 7.4 for root surface area. The observed variability explained by this QTL was from 10% to 22%. The highest R2 values were observed for root surface area and volume in root-diameter class 1. All of the root traits explained by this QTL were in rootdiameter classes 1, 2, and 3, except for root volume and surface area, which were in class 6. As well as this region on chromosome 4B, other QTL involved in the control of shoot traits were identified: QTL6 for the number of shoots per plant and number of root tips in root-diameter class 2 was located on chromosome 2A and explained 17% of the observed variability, with a LOD of 5.4. The allele of “Molise Colli” was effective in increasing the trait. The same allelic effect was found for QTL7 on chromosome 3A and QTL13 on chromosome 6A, which controlled plant height (QTL7) and plant height and leaf dry weight (QTL13). The LODs were between 3.4 and 5.2 for these

International Journal of Genomics QTL, which explained from 11% to 17% of the observed phenotypic variability. All of the other QTL identified in the present study were specifically involved in the control of root traits. In some cases, these QTL controlled only a single trait, as for chromosome region 5 on chromosome 2A for root volume and chromosome region 2 on chromosome 1B for the number of root tips in root-diameter class 2. For the allelic effects, the effect of the “Molise Colli” allele was positive for QTL2, and the effect of the “Simeto” allele was positive for a QTL identified in chromosome region 5. Most of the QTL identified in the present study showed effects on many different root traits, but only for specific root-diameter classes. The QTL identified in chromosome regions 11, 14, and 15 on chromosomes 4B, 6A, and 6B, respectively, were involved in the control of various root traits and, in particular, for root-diameter class 1. The QTL mapped to chromosome region 10 were also on chromosome 4B, and as well as the number of forks, they controlled the root lengths, volumes, and surface area as in root-diameter class 2. A positive effect of the “Molise Colli” allele was observed for all of these QTL. QTL in chromosome region 16 on chromosome 6B explained 9% to 12% of the observed phenotypic variability for root length, volume, and surface area for root-diameter classes 4 to 6. In this case, the values of these traits were increased by the allele of “Simeto.” The same allelic effect was observed for QTL in region 17 on chromosome 7B, which explained 11% of the observed variability for length, surface area, and volume, but only for root-diameter class 9. 3.3. Meta-QTL Analysis. A number of studies have reported QTL for root traits in wheat based on reliable information, such as R2, confidence intervals, and common markers (see Supplementary Table S1). To compare the QTL regions in the SMC genetic map with those reported in the literature and to identify the precise consensus QTL, MQTL analysis was carried out. A very dense consensus map comprising the A and B genomes was used for this meta-analysis. This was composed of >40,000 markers and spanned a total map length of 2791 cM. More details about the final consensus map will be the aim of a future study, such as the number of markers per chromosome and the mean marker distances. Here, only the chromosomes involved with the QTL identified in the SMC genetic map are reported, along with the data on the MQTL (Figure 2). The meta-analysis was launched on 100 QTL for a number of traits linked to the growth and morphology of the root structure retrieved from the literature and the 17 QTL regions identified in the present study, which resulted in 34 MQTL. The MQTL merged from two to eight individual QTL. The MQTL are reported in Table 4, along with the AICs, confidence intervals, flanking markers, and number of initial QTL involved. Twenty-nine out of the initial 100 QTL remained as singletons, their numbers per chromosome ranged from 1 (3A, 5B, 7B) to 2 (1B), and some of these were found only in the SMC (Figure 2, Table 4). The 95% confidence intervals of the MQTL varied from 0.5 cM to 30.5 cM, with a mean of 5.6 cM. The MQTL were on chromosomes 1B, 2A, 3A, 4B, 5B, 6A, 6B, and 7B. All of the MQTL

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Table 3: QTL detected in the “Simeto” × “Molise Colli” RIL populations for the evaluated traits. Chromosome region 1 2 3 4 5 6 7 8 9

10

11

12 13 14

15 16

QTL qF-1B qC1B qT2-1B.1 qT2-1B.2 qT4-1B.1 qT2-2A.1 qShoots-2A.1 qPH-3A.1 qT2-3A.1 qV-4B.1 qL3-4B.1 qSA3-4B.1 qSA6-4B.1 qV3-4B.1 qV6-4B.1 qPH-4B.1 qSDW-4B.1 qRDW-4B.1 qSA-4B.1 qT-4B.1 qV1-4B.1 qT1-4B.1 qL-4B.1 qF-4B.1 qL1-4B.1 qSA1-4B.1 qV2-4B.1 qC-4B.1 qL2-4B.1 qSA2-4B.1 qV2-4B.2 qL2-4B.2 qSA2-4B.2 qF-4B.1 qL-4B.2 qSA-4B.2 qL1-4B.2 qSA1-4B.2 qV1-4B.2 qT7-5B.1 qPH-6A.1 qSDW-6A.1 qT-6A.1 qL1-6A.1 qSA1-6A.1 qT1-6A.1 qT-6B.1 qT1-6B.1 qL4-6B.1

Interval 10.4 7.2 14.1 11.8 10.2 11.4 7.2 7.3 10.1 8.7 11.6 11.8 11.6 11.9 11.8 2.3 3.6 6.7 5.4 8.9 5.7 8.9 5.6 7.1 7.3 6.1 6.9 6.5 6.5 6.5 9.1 17.1 16.6 17.9 9.7 7.8 12.5 8.1 8 12.2 11 7.4 10.4 13.3 14.1 10.4 10.7 10.7 13.2

Position (cM) 0 0 36 72 50 28 2 12 12 28 28 28 28 28 28 32 32 32 32 32 32 32 34 34 34 34 36 38 38 38 94 96 96 104 122 122 122 122 122 24 0 0 24 24 24 24 20 20 98

Peak marker Excalibur_c71158_117 Excalibur_c71158_117 RAC875_c195_499 BS00110148_51 CAP11_c6406_104 BS00067159_51 BS00062843_51 TA015264–0958 wsnp_BE426418A_Ta_2_1 Tdurum_contig51688_681 Tdurum_contig51688_681 Tdurum_contig51688_681 Tdurum_contig51688_681 Tdurum_contig51688_681 Tdurum_contig51688_681 Tdurum_contig51688_681 Tdurum_contig51688_681 Tdurum_contig51688_681 Tdurum_contig51688_681 Tdurum_contig51688_681 Tdurum_contig51688_681 Tdurum_contig51688_681 Tdurum_contig63153_343 Tdurum_contig63153_343 Tdurum_contig63153_343 Tdurum_contig63153_343 Tdurum_contig63153_343 Tdurum_contig63153_343 Tdurum_contig63153_343 Tdurum_contig63153_343 Tdurum_contig28920_296 Tdurum_contig4795_404 Tdurum_contig4795_404 Tdurum_contig29112_483 Tdurum_contig56458_594 Tdurum_contig56458_594 Tdurum_contig56458_594 Tdurum_contig56458_594 Tdurum_contig56458_594 Excalibur_c9969_98 TA001855–0472 TA001855–0472 Excalibur_rep_c103232_355 Excalibur_rep_c103232_355 Excalibur_rep_c103232_355 Excalibur_rep_c103232_355 Excalibur_c28771_400 Excalibur_c28771_400 Kukri_c5168_162

Chr. 1B-1 1B-1 1B-1 1B-1 1B-2 2A-1 2A-3 3A-2 3A-4 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 4B-1 5B-1 6A-2 6A-2 6A-2 6A-2 6A-2 6A-2 6B-2 6B-2 6B-2

Trait F C T2 T2 T4 V Shoots PH T2 V L3 SA3 SA6 V3 V6 PH SDW RDW SA T V1 T1 L F L1 SA1 V2 C L2 SA2 V2 L2 SA2 F L SA L1 SA1 V1 T7 PH SDW T L1 SA1 T1 T T1 L4

LOD 3.6 5.3 2.6 3.2 3.7 3.3 5.4 5.3 3.7 4.4 3.2 3.2 3.2 3.1 3.2 21.6 12.1 5.8 7.4 4.3 6.9 4.2 7.1 5.5 5.3 6.5 5.6 6 6 6 4.2 2.2 2.2 2.1 3.9 4.9 3 4.7 4.8 3.1 3.4 5.2 3.6 2.8 2.6 3.6 3.5 3.5 2.8

R2 0.12 0.17 0.09 0.1 0.12 0.11 0.17 0.17 0.12 0.14 0.1 0.1 0.1 0.1 0.1 0.52 0.34 0.18 0.22 0.13 0.21 0.13 0.22 0.17 0.17 0.2 0.17 0.18 0.18 0.19 0.13 0.07 0.07 0.07 0.12 0.15 0.1 0.15 0.15 0.1 0.11 0.16 0.12 0.09 0.09 0.12 0.11 0.11 0.09

Add. eff. 697.21 428.62 −1.21 −1.26 0.06 0.11 −0.14 −2.49 −1.41 −0.13 −2.59 −0.92 −0.08 −0.03 −0.01 −6.56 −0.04 −0.01 −20.5 −234.13 −0.05 −232.7 −200.86 −1064.59 −158.61 −9.58 −0.07 −478.32 −20.37 −4.05 −0.06 −29.3 −5.91 −532.67 −125.98 −14.14 −97.79 −7.07 −0.04 −0.02 −1.89 −0.02 −180.92 −94.13 −5.03 −180.09 −195.9 −194.99 0.55

8

International Journal of Genomics Table 3: Continued.

Chromosome region

17

QTL qSA4-6B.1 qSA6-6B.1 qV4-6B.1 qV6-6B.1 qL5-6B.1 qL6-6B.1 qSA5-6B.1 qV5-6B.1 qL9-7B.1 qSA9-7B.1 qV9-7B.1

Interval 13 13.3 13 13.5 10.2 13.5 10.2 10.1 11.3 11.3 11.1

Position (cM) 98 98 98 98 100 100 100 100 14 14 14

Peak marker Kukri_c5168_162 Kukri_c5168_162 Kukri_c5168_162 Kukri_c5168_162 CAP7_c3697_87 CAP7_c3697_87 CAP7_c3697_87 CAP7_c3697_87 RAC875_c23521_589 RAC875_c23521_589 RAC875_c23521_589

Chr. 6B-2 6B-2 6B-2 6B-2 6B-2 6B-2 6B-2 6B-2 7B-1 7B-1 7B-1

Trait SA4 SA6 V4 V6 L5 L6 SA5 V5 L9 SA9 V9

LOD 2.8 2.8 2.9 2.8 3.7 2.8 3.7 3.7 3.3 3.3 3.4

R2 0.09 0.09 0.09 0.09 0.12 0.09 0.12 0.12 0.11 0.11 0.11

Add. eff. 0.29 0.07 0.01 0.01 0.23 0.08 0.15 0.01 0.01 0.01 0.001

Chr.: chromosome; LOD: log10 odds ratio; Add. eff.: additive effects.

identified corresponded to chromosomal regions that are involved in the control of a number of root traits. In some cases, these resulted from individual QTL, each of which is involved in the control of a different trait. As an example, MQTL22 was mapped to chromosome 6A and merged three individual QTL for root numbers, lateral roots, and root dry weights. In the other cases, the MQTL merged two or more QTL that explained the same trait, for example, MQTL23 on chromosome 6A merged two individual QTL for root dry weight and one QTL for total root length, and one more that explained root length, surface area, volume, and tip number. Based on the molecular markers mapped to both chromosomes 6A and 6B, a homoeologous relationship can be established between MQTL26 (6A) and 30 (6B) and between MQTL27 (6A) and 31 (6B). In particular, MQTL27 and MQTL31 are both involved in the control of root length. Based on this MQTL analysis, three QTL identified in the SMC in the present study did not correspond to previously published QTL. Two QTL were mapped to chromosomes 3A and 5B and were related to the number of root tips, although in different root-diameter classes. The third QTL, on chromosome 7B, was involved in the control of root length, surface area, and volume, although only in the largest root-diameter class.

4. Discussion A number of methods have been described for phenotypic evaluation of root morphology under controlled conditions for numerous samples, as required for genetic analyses (e.g., [2–5, 35]). In the present study, a method in which the plants were grown in soil mixed with sand was used, to have more reliable data. The use of this growth substrate and the growth stage considered allowed us to carry out an evaluation of the root system that is independent of the effect of seed weight. For bread and durum wheat, linkage and association mapping studies have both been carried out to identify chromosome regions involved in the control of root traits. In most studies, elite and old cultivars were used, and although good phenotypic variability has been observed [31, 35, 37], it can be useful to consider more genetically diverse genotypes

to search for novel haplotypes that control root architecture. On this basis, a biparental population derived from a durum wheat elite cultivar and a T. dicoccum accession represents a valuable resource to identify novel loci of interest for root traits. The parents of this SMC, “Simeto” and “Molise Colli,” are very different in terms of plant morphology, for both the aerial and below-ground organs, and this can provide indications of the relationships between plant height and the development of the root system. Moreover, the two parents are also different in terms of seed size and morphology, and in a previous study, a genetic map with more than 9000 SNP markers was used to identify QTL for seed morphology [57]. When evaluated at Zadoks stage 15, the two parents were clearly different for plant height, shoot dry weight, and root dry weight, whereby “Molise Colli” showed greater growth with respect to “Simeto” for the whole plant. When specific root traits were considered, in all cases, “Molise Colli” had higher phenotypic expression compared to “Simeto,” although this difference did not reach significance. Significant differences were observed across the RIL population, with large and transgressive variations for all of the traits examined. This indicates that both genotypes have loci that contribute to the development of the root structure. The MQTL analysis was carried out to compare the genetic positions of the QTL identified in the present study with those of previously published QTL in wheat. An integrated map that contained different types of molecular markers was used to project the known QTL, which is of particular importance as the SMC genetic map which nearly contains only SNPs from the Infinium 90K wheat assay. Some of the QTL identified in the present study were seen for chromosome regions in which a MQTL was present, as for MQTL1 (chromosome 1B), MQTL2 (chromosome 2A), MQTL3 (chromosome 3A), MQTL9 (chromosome 6A), MQTL11 and MQTL12 (chromosome 6B), and MQTL13 (chromosome 7B). For MQTL2 and MQTL3, the QTL for the number of shoots per plant and for plant height, respectively, were coincident with the QTL previously reported for root traits. Closely linked genes or a single locus with pleiotropic effects might be responsible for these different traits. Considering the results of this MQTL analysis and the studies

International Journal of Genomics

9

SL_MC (Maccaferri2016)

MQTL7

RT6_CL (Maccaferri2016)

MQTL10

QMrl.2 (Guo2012)

RDW_CL (Maccaferri2016) TRN_MC (Maccaferri2016)

MQTL12

QRN (Ren2012)

SDW_CL (Maccaferri2016)

MQTL11

QPRE (Ren2012)

MQTL8

SLL,SLSA,SLV (Bai2013)

T5_B (CP) L5,S5,V5 (CP)

MQTL9

TRD,PRD_MC (Maccaferri2016) SH (SMC) TRD_CL (Maccaferri2016) TRN_CL (Maccaferri2016) QMrl.1 (Guo2012) QRV (Ibrahim2012)

D_GDEEGVY02FU4W8_119a CAP8_c1361_367a Tdurum_contig84762_258a CAP11_c7974_175a Xbarc57 Excalibur_c11079_101a Xwmc206c BobWhite_rep_c49374_348 wPt-3094 Excalibur_c60530_113 RAC875_rep_c77067_347 BS00048491_51 CAP12_c2940_354 RAC875_rep_c111243_125 BS00110922_51 Excalibur_rep_c109599_89 BS00073063_51 GENE-1989_800 BS00064422_51 wsnp_Ku_c7060_12212702 Kukri_c96747_274a RAC875_c371_251a BobWhite_c29706_369 Excalibur_rep_c80735_81 wsnp_Ra_c9738_16174002 Tdurum_contig75764_146 BobWhite_c48246_303 wsnp_Ex_c8409_14170476 wsnp_Ex_c55051_57706127 RAC875_c17393_553 wsnp_BE497169B_Ta_2_1a RAC875_c16583_1259 tplb0056l18_796 tplb0056l18_622 wsnp_JD_rep_c63739_40660910 BobWhite_c2448_96 Kukri_c63647_1522 wsnp_CAP12_c2692_1286812 BS00065382_51 CAP8_c1702_71 Ra_c31046_1652 Excalibur_c27972_654 Kukri_c32377_399 Excalibur_c34472_211 Tdurum_contig99640_243 Ku_c8627_745 RAC875_c10628_941 wsnp_Ex_c33765_42199371 RAC875_c14060_1935 Excalibur_c12446_155 RAC875_rep_c109701_76 Tdurum_contig45380_92 RAC875_c2292_402 wPt-7217 Tdurum_contig86206_149 RAC875_c50864_1921 wsnp_Ex_c57322_59084809 wPt-2813 Tdurum_contig14694_211 wsnp_Ku_c40218_48484410 Tdurum_contig44029_158 Tdurum_contig60631_336 Xgwm5b RAC875_rep_c100137_586 TA002997-0276 wsnp_Ex_c3478_6369892 wPt-7608 wsnp_Ex_c14420_22402673 Tdurum_contig28100_112 Kukri_rep_c71128_1811 wsnp_Ex_rep_c66865_65262612 wsnp_JD_c5699_6859527 Xwmc527b Excalibur_c11807_106 Tdurum_contig49981_703 Excalibur_c61765_220a wsnp_Ex_rep_c66685_65003254 Xbarc45 wPt-2698 Excalibur_rep_c107798_68 wPt-1596 Xwmc664 wPt-6891 wPt-4077 Xwmc505a Xgwm720 Xbarc356 Xcfd193a Xwmc489c Kukri_c60531_131 Kukri_rep_c111139_338 wsnp_Ex_c18223_27035083 Ra_c18366_203 Xwmc695a Xwmc269b wsnp_Ku_c18497_27803432 BS00074617_51 Tdurum_contig76296_461 Tdurum_contig42827_1693 Excalibur_c7544_288 wsnp_Ex_c4923_8767234 Excalibur_rep_c105978_544 BS00078669_51 BS00048355_51 Kukri_rep_c116421_403a Xwmc264a RAC875_c57977_121b Excalibur_c24402_471 Tdurum_contig9912_228 Xwmc169 Ra_c1619_432 Excalibur_c39508_88 tplb0046k04_484 wsnp_Ku_c8400_14280021 BS00084158_51 Tdurum_contig8584_354 BS00041339_51 F129 Tdurum_contig49518_1002 Xgwm494b wPt-5943a Kukri_c49798_300 wsnp_Ex_c1894_3575749 RAC875_c15003_377 wsnp_Ex_c12341_19693090 IAAV5984 KukBi_c10751_264 Tdurum_contig8365_319 Kukri_c15151_436 Xgwm751a RAC875_rep_c90531_283 RAC875_c15109_106 Xwmc96a Xbarc69 Ku_c1255_1107 Excalibur_c3429_652b Hu_c1255_862 wPt-4407 Xwmc153 wsnp_Ku_c10468_17301042a Ku_c6126_1140 Xwmc173a Excalibur_c640_464b Xwmc559 GENE-1918_152 Excalibur_c3969_1208 Xwmc215a RAC875_c52195_324 Kukri_c29993_593 Xgwm155 KukBi_c6645_570 Xcfa2076 BobWhite_c31562_95 Xgwm156c GENE-3665_61 Tdurum_contig55841_351a RAC875_c18230_901 Xbarc51 Xbarc19 wPt-1864 Kukri_c2596_146 wsnp_BE604885A_Ta_2_1 TduBum_contiA10544_92 Tdurum_contig28518_122 Excalibur_rep_c76177_243 Xgwm480 wPt-2659 wPt-3816 tPt-7492 BS00108976_51 RFL_Contig114_878 Xwmc206d BS00059618_51a RAC875_c3084_415 Excalibur_c77321_69 wPt-9422 wPt-9238 Excalibur_c361_1321 Excalibur_c77321_196a wPt-2492 Xbarc314 Tdurum_contig38751_317 wPt-3978 Tdurum_contig50577_620 TC77302 Excalibur_c90478_62 Excalibur_c71730_105a wsnp_Ex_rep_c66274_64426834 Tdurum_contig13646_292 wPt-2144 wsnp_Ex_c11229_18163892 wsnp_Ex_c28679_37784735 wsnp_Ra_c66411_64796843 Xgwm162a Kukri_rep_c70441_132 Excalibur_rep_c114569_56 RAC875_c46236_214 Tdurum_contig75336_518 Tdurum_contig51914_740 RAC875_c20905_383 Tdurum_contig16865_174 Tdurum_contig10022_413 GENE-1910_570

TRN,RT6_CL (Maccaferri2016)

MQTL6

TRV_MC (Maccaferri2016)

LRN_MC (Maccaferri2016)

Figure 2: Continued.

0.0 11.0 12.1 13.4 14.6 14.9 16.0 17.9 18.6 20.7 21.1 22.7 23.4 24.2 25.3 26.0 27.6 28.6 29.5 31.2 32.3 33.7 34.5 35.5 38.4 40.5 42.6 44.3 47.2 48.0 49.1 53.3 54.9 55.1 55.6 56.2 59.0 60.2 61.1 61.9 63.5 63.9 64.3 66.5 67.5 68.7 71.5 73.2 75.1 75.6 76.0 76.5 77.3 77.9 78.1 79.8 80.6 81.6 82.2 83.9 84.5 85.0 85.5 86.0 86.2 86.6 87.4 87.7 88.0 88.9 89.2 89.5 90.0 90.5 90.7 91.1 91.7 92.4 92.9 93.0 93.4 93.7 93.9 94.2 94.6 94.7 95.0 95.2 96.0 97.3 97.8 98.4 98.7 99.4 100.8 101.0 102.0 102.7 103.3 103.6 104.9 105.7 106.1 106.8 107.1 108.2 109.3 109.6 109.9 110.4 111.3 111.6 112.9 113.2 113.9 114.6 115.6 115.9 116.3 117.0 117.6 119.5 120.2 122.7 123.1 124.3 125.1 126.7 127.8 128.4 130.2 131.0 131.4 133.6 136.2 138.1 138.9 140.2 141.3 141.9 142.6 143.3 143.8 144.0 144.6 145.6 146.1 146.9 147.9 148.2 149.3 150.2 151.8 152.1 153.6 154.2 154.7 155.3 156.6 157.2 158.4 159.7 160.1 161.5 162.1 164.1 165.2 166.5 167.3 168.1 168.9 172.1 173.2 174.1 175.3 176.5 176.7 176.9 177.4 178.0 178.6 179.5 179.8 180.3 180.4 180.6 181.1 182.1 182.7 182.9 184.8 185.4 187.0 187.4 188.4 189.5 190.3 191.4 193.8 194.3 195.1 197.2 207.3

T2 (SMC)

MQTL5

Culms (SMC)

MQTL4

V (SMC) Frk,TRL,RV,SRA (Ibrahim2012) L,L2,L5,S,S1,S2,S5,T,T1,T2,V,V1,V2,V5 (CP)

RT6_MC (Maccaferri2016)

LRN_CL (Maccaferri2016)

3A wPt-8328 Xwmc382 Xwmc326c Excalibur_c59428_237 Xbarc212 BS00105593_51 CAP7_c4676_94 BS00080570_51 D_contig79877_194 wPt-2147 Tdurum_contig49144_321 D_contig71899_62 Jagger_c5341_126 Xwmc326b BS00014897_51 Tdurum_contig30824_197 Tdurum_contig55029_963 RAC875_c1968_103 wPt-8925 Excalibur_c12980_2392 RAC875_c8069_1874 RAC875_c57889_55 Xmag3807 wPt-4197 Ex_c12425_506 BobWhite_c10673_330 wPt-4984 wPt-9672 RAC875_c2300_1021 Xgwm512 BS00065192_51 Xwmc728 Tdurum_contig74742_224 BS00107263_51 Xwmc630b Excalibur_rep_c106338_424 Xwmc602 wPt-1368 Excalibur_c21663_145 BS00067159_51 Xwmc149 wPt-5839 BS00067684_51 BS00069752_51 RAC875_rep_c113106_56 Kukri_c63732_593 wPt-3896 CAP11_c2293_200 BobWhite_rep_c51499_280 BS00068139_51 BS00084333_51 BS00075855_51 BobWhite_c19433_329 BS00070797_51 RAC875_rep_c78744_228 BS00076693_51 BS00065276_51 Excalibur_c43811_527 Excalibur_rep_c102244_1103 D_GA8KES401BVP4P_43 BobWhite_c26374_339 Xwmc826 BobWhite_c30988_361 Tdurum_contig32692_271 wsnp_Ex_c5412_9564346 Tdurum_contig44316_486 Ra_c58279_684 Excalibur_c54892_188 wsnp_Ex_c30481_39394826 wPt-7285 Xgwm296 BS00044274_51 wPt-4201 Tdurum_contig62138_556 Xwmc453 Xwmc51d wPt-9320 Excalibur_c25235_1289 wPt-3037 wPt-2435 Xwmc522 Xwmc32 RAC875_c17787_274 BS00070693_51 Excalibur_rep_c103108_709 Xwmc474 TA004602-1630 Xwmc792 Tdurum_contig93115_517 BS00078612_51 Excalibur_c37649_125 Xgwm275 BS00055933_51 Xbcd855 Xbcd1709 Xgwm558 D_contig15270_478 Tdurum_contig10579_413 Xgwm95 GENE-1350_36 Xwmc632 Xwmc455 BS00062843_51 Xgwm372 Xbarc353 Xwmc819 BS00078116_51 BS00022301_51 Xcfa2263 Xbarc5 RFL_Contig4517_961 IAAV4464 BS00070004_51 Xgwm445 BS00000297_51 Excalibur_c40617_983 Xgwm817 BS00029332_51 wPt-5865 BobWhite_c2058_367 BAC875_c77816_365 BS00107804_51 Excalibur_c7282_285 Excalibur_c3171_416 BobWhite_c17403_635 BS00065865_51 RAC875_c9691_870 Tdurum_contig11678_289 BS00080751_51 Ku_c25175_1248 RAC875_c16333_340 Xwmc109 BS00079611_51 RAC875_rep_c107961_348 GENE-1908_331 wsnp_Ex_c14953_23104041 BS00024921_51 BS00067907_51 Kukri_c43875_671 BS00023048_51 RAC875_c104160_61 BS00065366_51 BS00001260_51 Excalibur_c33040_447 wPt-3244 Tdurum_contig93508_119 BS00077768_51 RAC875_c25848_122 wPt-7056 Excalibur_c44487_642 RFL_Contig785_1156 Excalibur_c8009_325 BS00022409_51 BobWhite_c17783_174 BS00110516_51 RAC875_c9523_328 RAC875_c1758_373 RAC875_c4609_1756 BS00108288_51 TA004785-1734 BS00096927_51 BS00102709_51 Excalibur_c7971_985 Excalibur_c21117_300 Tdurum_contig92425_1612 Excalibur_c63622_125 Xgwm356 Xgwm761 Xgwm526 RAC875_c1789_253 Kukri_c41234_126 BS00022252_51 Xwmc658 Xwmc198 Xcfd86 Xwmc181 Excalibur_c15671_87 wPt-669355 tPt-3136 Tdurum_contig92425_1324 wPt-9586 Excalibur_c21501_237 wPt-5850 Excalibur_c24213_314 Xgwm1067 wPt-1615 RFL_Contig5277_1283 BS00091763_51 Tdurum_contig92425_431 GENE-0762_808 Xbarc76 Ku_c105361_414 wPt-3728 Xgwm382 Excalibur_c12916_123 BS00095525_51 IAAV5706 Xgwm311 Tdurum_contig42013_538 BS00022510_51 RFL_Contig2972_2819 Tdurum_contig50720_204 Excalibur_c27531_86 Ku_c68139_836

QTRSA (Bai2013)

MQTL2

QRDW (Kubo2007)

L,L2,S2,V2 (CP)

T2 (SMC) MQTL3

QRdw.2 (Guo2012)

T2 (SMC)

QArn.1 (Guo2012)

QRN (Christopher2013)

MQTL1

F,C (SMC)

T_A, T_2A (CP)

TRL (Liu2013) TRS,TRV_MC (Maccaferri2016)

TRL,ARL_MC (Maccaferri2016) SL_CL (Maccaferri2016) T4 (SMC) QDRR1 (Hamada2011)

0.0 1.3 4.0 5.2 5.6 6.4 7.8 9.8 10.6 11.3 12.8 13.2 15.7 16.0 16.7 16.9 17.4 18.3 19.1 20.0 20.5 21.6 22.5 23.0 25.4 26.4 27.4 28.3 29.3 30.2 30.8 32.0 34.0 35.2 37.5 39.7 41.1 42.1 43.9 44.0 45.7 46.6 47.6 48.5 50.6 52.4 53.7 54.0 61.7 62.9 63.2 64.4 65.4 66.0 67.1 67.9 68.3 69.3 70.9 73.8 74.3 75.0 76.0 76.6 77.3 77.9 78.4 79.0 79.7 80.2 81.3 82.3 83.2 84.1 84.8 85.6 86.1 88.0 88.5 89.3 90.1 91.4 92.0 92.7 93.9 94.1 94.8 95.4 96.1 97.9 98.8 99.4 100.0 100.5 101.8 102.1 102.8 103.5 104.2 104.5 105.4 106.2 106.6 107.1 107.9 108.2 108.8 109.0 109.6 110.1 111.5 112.5 113.7 114.6 115.8 116.4 117.1 117.6 118.8 120.3 121.6 122.3 122.9 123.4 124.0 124.9 125.8 126.8 127.4 127.8 128.0 129.0 129.3 130.8 131.8 132.4 132.8 133.1 133.8 134.0 135.1 135.7 136.0 139.0 139.6 139.9 140.2 140.7 141.2 141.8 142.0 142.7 143.0 143.6 144.0 144.5 146.8 148.4 149.2 149.9 150.0 150.5 150.7 151.4 152.0 152.7 153.1 153.5 153.9 154.0 155.0 155.4 156.9 157.3 157.7 159.4 160.1 160.7 161.5 162.0 163.6 164.6 165.1 165.5 165.8 166.2 166.7 167.0 168.0 168.3 171.9 173.1 174.9 175.3 176.9 177.3 178.0 179.2 179.5 180.1 180.5 182.2 184.2 185.8

TRN_MC (Maccaferri2016)

2A BS00071333_51 RFL_Contig293_498 Excalibur_c10065_411 RAC875_c18591_175a Excalibur_c71158_117 Kukri_c18951_853b Kukri_c18951_493 RAC875_c24163_155 Tdurum_contig28703_293 Excalibur_c51033_173 Kukri_c5384_86 BS00023084_51a Excalibur_rep_c107678_98 Tdurum_contig403_122 GENE-1322_33 D_GB5Y7FA01C2ERV_339 BS00015608_51b wPt-0308 D_GDRF1KQ01EEUZ7_267 Excalibur_c28255_482 Excalibur_c23212_125 ExcalibuB_c71158_117 Ku_c36151_691 BS00038243_51b wPt-304810 Kukri_c24615_823 BobWhite_c17559_105 BS00022101_51 BS00022429_51 BS00064829_51 BobWhiBe_c28295_256 BS00062122_51 wPt-1912 wsnp_Ku_c7822_13408189 wsnp_Ex_rep_c67665_66326492b TduBum_contiA50555_944 Tdurum_contig50667_409 BobWhite_c28295_256 wPt-4811 wPt-4434 Xbarc128a wPt-3177 Xgwm24 wPt-7529 wPt-5164 Xbarc119b Tdurum_contig83093_443 BS00066682_51 Xgwm413 wPt-7242 BobWhite_c3335_1438a wPt-6777 wPt-3889 wsnp_Ex_c14273_22230844 Tdurum_contig44861_581 Xgwm133a wPt-1399 BS00067043_51 Excalibur_c6726_357 Tdurum_contig9811_127 Tdurum_contig61410_467 Tdurum_contig42446_1999 Tdurum_contig60037_528 RAC875_c16247_107a Tdurum_contig11004_688 TA005995-0488 Tdurum_contig17609_117 BobWhite_c33976_317 P4133-170 Kukri_c5861_360 RAC875_c195_499 Tdurum_contig24287_300 BS00067586_51 TA001559-0515 RAC875_c14049_376 RAC875_c25692_343 Excalibur_c56657_282 BS00065117_51 Excalibur_rep_c108957_173 RAC875_c4377_524 RAC875_c1914_942 RAC875_rep_c70022_1648 Excalibur_c2181_927 BobWhite_c4126_442 BS00031023_51 wsnp_Hu_c30982_40765254 Xgwm498 wsnp_Ku_c12464_20125626a Xcfd59b BS00012051_51 BS00022133_51 RAC875_c46646_549 wsnp_Ex_c31567_40338517 Xbarc120 RAC875_c8878_232 Tdurum_contig98080_171 Xbarc240b BS00022343_51 wsnp_Ex_c1600_3051075 Tdurum_contig29363_461 BS00085546_51 BS00022742_51 IACX9510 Excalibur_c48379_116 RAC875_rep_c111001_187 Ra_c62804_1641 RAC875_c22886_261 RFL_Contig4576_702 wsnp_Ex_rep_c69766_68723140 Xbarc181 wsnp_Ex_rep_c66389_64588992 CAP8_c4697_108a Tdurum_contig57101_505 wPt-3579 BS00081396_51 Tdurum_contig47550_699 Tdurum_contig30517_578 wsnp_Ex_c9577_15857465 Tdurum_contig13117_1316 RAC875_rep_c106876_558 wsnp_Ex_c9063_15093396a CA651264 Ku_c1932_1583 wsnp_Ex_rep_c67299_65845319 Ku_c17871_1360 Ku_c9909_1766 BS00072289_51 Excalibur_c94658_59 BS00012029_51 Tdurum_contig85180_99 wsnp_Ku_c56140_59771244 Xbarc81 RFL_Contig2826_548 RFL_Contig5937_1677 RAC875_c291_2201 wsnp_JD_c1544_2179305 Tdurum_contig67656_58 Tdurum_contig67368_157 wPt-2257 Excalibur_c33470_175 Tdurum_contig65853_534 BS00022249_51 BS00072791_51 KukBi_c32448_268 Tdurum_contig11077_122 BS00011596_51 Excalibur_c65152_572 ExcalibuB_c35755_110 Ra_c7324_527 BobWhite_c2027_350 Xgwm124 Kukri_c21276_1056 wsnp_Ex_c27176_36393952 IAAV7428 BS00063721_51 wsnp_Ex_c48677_53513032 RFL_Contig4352_926 BS00002484_51 CAP11_c599_115 Tdurum_contig8580_1285 BS00077498_51 BS00035267_51 Tdurum_contig8840_540 Excalibur_c12875_1643a F109 Tdurum_contig11046_318 Excalibur_c98553_61 AENE-0163_949 Xwmc44 BS00015519_51 Tdurum_contig57153_1439 Tdurum_contig10475_87 IACX8074 IACX2234 tplb0034g09_1257 Tdurum_contig29059_185 Xwmc728 Tdurum_contig4904_2923 Xbarc80 wPt-5253 wPt-5721 Xgwm659 Excalibur_c14706_421 BS00066052_51 Wsnp_Ex_c750_1474300 wsnp_Ex_c11461_18489681 Tdurum_contig94450_255 BS00065694_51 tplb0049h18_765 RAC875_rep_c111993_160 Tdurum_contig8669_296 BS00103710_51a RAC875_c14613_112a Tdurum_contig13879_352a BS00011892_51 BobWhiBe_c20073_382 RAC875_rep_c112737_766 Kukri_c59535_427 Excalibur_c35345_476 Tdurum_contig44851_593a Excalibur_rep_c102616_317 Kukri_c94613_316a Wsnp_Ex_c750_1474351a Tdurum_contig4851_653 Kukri_rep_c111174_132 Excalibur_c14806_1091a

TRL,TRV_CL (Maccaferri2016)

1B 0.0 0.7 2.1 4.1 5.0 6.0 6.6 9.1 10.1 11.0 11.5 14.9 16.7 17.7 18.3 19.4 20.5 21.7 22.2 22.9 23.4 24.7 25.2 26.5 27.2 28.7 29.5 30.4 31.0 31.6 32.4 32.8 37.5 39.2 40.2 40.7 41.1 41.6 41.8 42.0 42.6 43.0 43.2 43.7 44.1 44.5 44.8 45.0 45.2 46.0 46.3 46.7 47.1 47.9 48.3 50.5 51.3 51.8 53.2 53.8 54.1 56.1 56.7 57.1 57.8 58.0 58.5 58.7 59.3 60.2 60.7 61.1 61.3 62.0 62.3 63.1 63.5 63.7 64.0 64.4 64.6 65.0 65.4 66.0 66.5 67.3 67.6 68.0 68.9 69.5 70.0 70.8 71.3 71.5 72.0 72.7 74.0 74.3 74.7 75.0 75.4 76.0 76.5 76.8 77.2 77.6 78.1 78.9 79.7 80.2 80.5 81.5 82.4 82.6 83.0 84.2 85.1 86.1 86.8 87.4 87.8 89.3 90.0 90.3 90.7 91.3 93.9 95.1 95.7 96.0 97.1 97.5 98.3 99.8 100.1 100.9 101.5 103.1 103.4 104.3 105.1 105.4 106.5 106.9 107.8 108.0 109.1 109.9 110.4 111.2 111.8 113.1 114.5 115.3 115.9 116.6 118.5 119.6 120.2 121.0 122.4 123.1 123.5 125.8 126.1 127.2 129.4 130.5 132.4 133.3 133.8 134.9 135.1 135.9 136.7 137.7 139.4 140.2 141.7 142.4 143.1 144.0 145.6 146.5 147.1 148.7 152.1 153.0 154.6 155.3 156.0 157.0 158.4 159.3 160.9 161.1 162.8 164.9 165.2 166.7 168.4 169.5 171.3 172.0 173.4 174.8

10

International Journal of Genomics

Figure 2: Continued.

MQTL27

TRL_MC (Maccaferri2016)

MQTL25 QPVRN (Kubo2007)

RGA_MC (Maccaferri2016)

PRL_MC (Maccaferri2016)

MQTL28

SL_CL (Maccaferri2016)

MQTL26 TRS,PRV_MC (Maccaferri2016)

PRS_MC (Maccaferri2016)

MQTL23

MQTL22 TRL (Bai2013)

L,L1,L2,S,S1,S2,V1,V2,T,T1 (CP)

RDW_MC (Maccaferri2016)

TRL (Ren2012) RDW (Guo2012)

QRN (Christopher2013)

RDW (Yu2013) MQTL24

SLV (Bai2013)

SAL (Bai2013)

RT6_MC (Maccaferri2016)

LRL (Ren2012) RDW (Guo2012)

SH,LDW (SMC) T,L1,SA1,T1 (SMC)

Kukri_c3009_1822 BS00003772_51 RAC875_c16610_470 RAC875_c13610_822 GENE-1756_564 Tdurum_contig55193_347 Xpsr899 BobWhite_c704_596 Kukri_c3827_337b Tdurum_contig12045_327 Ku_c17678_1161 RFL_Contig5170_1904 BS00077635_51 wPt-1377 wPt-1664 BS00082191_51 wPt-9382 RAC875_c106584_747 wPt-0562a BobWhite_c15802_720 Kukri_c49017_404 wPt-9679 wPt-7565 wPt-2153 wPt-0495 wPt-8266 BobWhite_c5092_422 BS00022032_51a tPt-0877 Kukri_c34219_355 wPt-3468 Xgwm334 Ex_c68796_2057 wsnp_Ku_c20866_30535489 Excalibur_rep_c68175_305 Xgwm1040 Excalibur_c5442_1691 wPt-7663 Ku_c10377_335 BS00059475_51b Excalibur_rep_c102994_1689 RAC875_c21158_99a BS00110963_51 tplb0039m17_2125 wPt-2822 BobWhite_c36070_89 wsnp_Ex_c19873_28889970 wPt-9692 RAC875_c38494_52 BS00065496_51 BobWhite_c13839_111 wsnp_Ex_c1011_1931797 wPt-7623 Excalibur_c62661_195 RAC875_c53520_103 Xgwm825 Excalibur_c14693_724b Excalibur_c14222_179 wsnp_Ex_c31149_39975724 BS00066452_51 Xbarc23a tplb0048b19_119 IAAV4117 wsnp_Ex_c31149_39976066 wPt-9829 wPt-10645 RAC875_c5395_564 BS00063990_51 BS00023627_51 Jagger_c2853_75 Tdurum_contig50698_601 wsnp_BE490604A_Ta_2_1 Xpsr312b wsnp_Ex_c14692_22766127 CAP7_c11100_94 Ku_c11950_931 IAAV5188 RAC875_c64560_111a TA004097-0977 Kukri_c16868_1062 Xgwm82 Xwmc243b BS00036878_51 Xgwm356b Xwmc807 BS00064548_51 wsnp_Ex_c341_667884 Xwmc335a Xwmc684 Tdurum_contig43974_219 Xpsr142 Xgwm907b Excalibur_c2287_1327 Xbarc113 tPt-4209 Xwmc553 wPt-7063 Xwmc179b Xwmc163 wsnp_Ra_c12086_19452422 BobWhite_c13845_195 BS00040166_51 Tdurum_contig82427_252 Kukri_c4458_1060 Tdurum_contig75814_655 Excalibur_c8784_1005 wsnp_Ex_c26147_35395259 Tdurum_contig54796_1427 CAP7_rep_c11162_75 Excalibur_c25898_434 CAP11_rep_c6864_291a Kukri_c9763_115 wsnp_Hu_c1075_2160065 BobWhite_c14304_687b BS00065700_51 Tdurum_contig7464_1168 Excalibur_c5868_1486 Ku_c604_705 wsnp_Ex_rep_c68010_66754171 Ex_c5868_1113 CAP7_c9578_263 IAAV3609 BQ838884 Tdurum_contig97355_136 Tdurum_contig62188_108 TA001855-0472 Tdurum_contig14676_637 Tdurum_contig92441_354 Xgwm169 Tdurum_contig43566_822 Tdurum_contig29357_338 Tdurum_contig43566_801 Kukri_rep_c70063_663 wPt-11612 Xwmc417a wsnp_Ra_c5346_9501281 wsnp_Ex_c8510_14306239 wsnp_Ex_c20457_29526403 Xcdo1091a RAC875_c103443_475 Tdurum_contig28802_213 Xwmc580 Kukri_rep_c95718_868 wPt-8373 wPt-11668 wPt-2877 Xgwm427 BobWhite_c232_563 tPt-6661 Xgwm617b wsnp_Ku_c1318_2624758 BobWhite_c5872_589 RAC875_c2090_219 wsnp_JD_c26552_21868492 wPt-7390 wPt-1375 Xcdo836 Excalibur_rep_c103232_355 Xpsr546a RAC875_c26158_376 RAC875_c10648_86a RFL_Contig2765_1148a Tdurum_contig51627_1211 Excalibur_c79991_552 Tdurum_contig43308_465 F133 wPt-2975 wPt-9976 wPt-2632 BS00062776_51a Xbarc28b Excalibur_c64804_348 wPt-6829 D_contig37522_188a Xgwm999 Tdurum_contig27971_183a CAP8_c950_198a Ra_c74397_248 BS00064970_51a Xwmc621 BS00086174_51 Tdurum_contig17378_299 Excalibur_c35871_596 GENE-3993_694a wsnp_JG_c5646_2148296a BobWhite_s67399_107 TA005679-0546b Kukri_c67474_466a BS00064558_51a Tdurum_contig10729_118a Ex_c10413_1606a Excalibur_c37062_65a Excalibur_c62474_82 Swes123 Xwmc254c

TRL,RGA,ARL_CL (Maccaferri2016)

0.0 2.9 3.8 4.7 6.4 7.0 10.6 11.9 12.1 13.5 14.9 15.7 16.0 17.0 18.1 19.3 20.4 21.1 21.4 22.2 23.2 24.0 24.9 25.5 26.2 27.0 27.5 28.0 28.5 29.0 29.5 30.2 30.8 31.4 33.1 34.7 35.7 36.9 37.6 38.1 39.8 40.1 42.8 43.3 44.5 45.2 45.6 45.8 46.6 47.4 47.7 48.3 48.6 49.0 49.7 50.2 51.5 52.2 52.7 53.0 53.6 54.1 55.1 55.5 55.9 56.7 57.2 57.9 58.7 59.2 59.7 60.1 60.9 61.2 62.2 62.5 63.1 64.2 64.8 65.0 65.5 65.6 66.0 66.4 67.0 67.7 67.9 68.6 69.4 69.6 70.0 70.4 71.5 72.7 73.0 74.0 74.5 76.0 76.5 76.8 77.4 78.6 79.4 80.0 80.7 81.5 82.0 84.0 84.4 85.0 85.4 85.8 86.0 86.3 86.6 89.2 89.6 90.0 90.7 91.1 91.9 93.6 95.7 96.6 97.0 98.1 100.2 102.0 102.9 103.9 104.3 105.2 105.9 106.6 107.4 108.0 108.8 110.0 110.8 111.9 112.4 112.8 113.4 113.9 114.3 114.8 115.1 115.6 116.8 117.2 117.4 118.3 118.8 119.2 120.1 120.8 121.7 122.2 122.9 123.2 123.9 124.2 125.1 125.5 125.7 126.0 126.6 127.1 128.3 129.1 129.8 130.5 131.0 131.6 132.8 133.2 134.9 136.7 138.9 141.2 143.3 147.5 148.2 149.1 150.4 152.0 158.5 162.2 163.1 165.7 167.7 168.6 170.9 172.4 181.5

RDW (Guo2012)

MQTL19 MQTL20

RGA_MC (Maccaferri2016)

ARL_MC (Maccaferri2016)

SDW_MC (Maccaferri2016) MQTL21

TRL,PRA,RSA (Liu2013)

TTRL,SLL,SLSA,SLV (Bai2013)

QRN (Zhang2013)

6A tplb0060p09_735 Kukri_c14683_65b Xwmc728b BobWhite_rep_c63710_181 Xgwm234 wPt-1302 wPt-9800b wPt-0033 Xgwm443b wsnp_Ex_c33932_42333941 RAC875_c103396_446 RAC875_rep_c106241_304b wPt-0819 Tdurum_contig9291_553b BS00064042_51 wPt-8604 wsnp_Ex_rep_c110196_92676847 wsnp_Ku_c5308_9450093 BS00015136_51 RAC875_c18322_670 Excalibur_c40676_447a Excalibur_c3730_546 wsnp_Hu_c568_1187615 Ku_c3398_941 wsnp_Ku_c35090_44349446 Xwmc149b Ra_c19173_1010 Tdurum_contig16267_354 Kukri_rep_c106411_137 Xwmc274b BS00063769_51 Xgwm544a Xgwm66c BobWhite_c43220_84 RAC875_c60836_741a JD_c4730_663 wsnp_Ex_c2571_4784380 wsnp_Ex_c13468_21202450 wsnp_RFL_Contig4574_5416228 wPt-5914 wPt-6348 Xwmc386 wsnp_Ex_rep_c68119_66884852 RAC875_c4219_1340 wsnp_BE497820B_Ta_2_3 Xbarc216 tPt-0228 IAAV1835 Xgwm335 Kukri_c22967_1272 Excalibur_c8082_478 Xwmc616 Xbarc74 BS00064578_51 Xbarc89 Xbarc176a Tdurum_contig42092_947 Xgwm564b BS00031411_51 Xgwm213a GENE-3211_372 Xwmc435a wsnp_Ex_c974_1864971 IAAV5974 wsnp_Ra_c15297_23684845 wsnp_Ra_c26091_35652620 Tdurum_contig10172_176 Xwmc745 Kukri_rep_c69515_183 Xgwm777 wPt-0935 Xgwm371 wsnp_Ex_c2727_5053747 Xwmc415a wsnp_Ex_c28687_37791888 RFL_Contig2304_1569 BS00015205_51 BobWhite_c6633_240 wPt-4936 Xgwm639b wPt-7167 Xwmc405a Kukri_c3541_185 Xwmc759 wPt-3661 IAAV2509 Kukri_c6424_810 wPt-3457 wPt-1250a wPt-3503a Kukri_rep_c102132_410b wPt-9613 Kukri_c1137_1421 Kukri_c18158_354 BS00009335_51 Excalibur_c80450_75b Xwmc537a Xpsr911b BS00022582_51b wPt-6135 Tdurum_contig97342_274 wsnp_Ex_c13485_21225504 Tdurum_contig29319_256 Xgwm554a Tdurum_contig44181_730 Tdurum_contig27797_654 Ra_c69621_237 BS00009443_51 RAC875_rep_c102342_470 Excalibur_c32708_225 IACX5702 RFL_Contig5461_683 wPt-9454 Excalibur_c5329_1335 wsnp_Ex_rep_c68600_67448893 RFL_Contig539_1789 Kukri_c59540_137 tplb0053c01_1628 Kukri_c2955_281 Kukri_c57954_369 Ra_c2216_1442 Excalibur_c100531_251 Excalibur_rep_c113786_110 Tdurum_contig29967_456 BS00064593_51 Tdurum_contig10793_127 Tdurum_contig47491_258 wsnp_Ex_c12152_19431363 Tdurum_contig70554_1006 wPt-6989 Xwmc289a Kukri_c10508_253 wPt-1482b tPt-1253 Xwmc500f Tdurum_contig42069_208 Xwmc160 Xbarc232b Xwmc326d Kukri_rep_c113552_119 Tdurum_contig97407_196 BS00037023_51 Xcfd86b Xwmc28 Tdurum_contig32091_165 Xwmc235 BS00012140_51 Excalibur_c17489_804 Xwmc118 Ra_c6374_1984 Xwmc508 Tdurum_contig58293_755 Excalibur_c53149_153 Excalibur_c4699_147 Kukri_c27433_2333 BS00062618_51 GENE-4868_140 wsnp_Ra_c38873_46699852 RAC875_c88582_131b Tdurum_contig81337_335 wsnp_Ex_c2870_5296539 IACX751 wPt-8418a wPt-7561 Xwmc640b Excalibur_c9543_1268 BS00069417_51 wsnp_Ku_c38713_47298856 BS00033182_51 Tdurum_contig45588_730 Gs-41a wsnp_JD_rep_c50403_34392266 wPt-1348 wPt-1179 Kukri_c1214_2316 Xwmc430e Xbarc59a Excalibur_c2618_1412 BobWhite_c7818_278 BS00022876_51a BS00031338_51 CAP11_c2765_78 wPt-0566 Tdurum_contig13965_1223 BAC875_Bep_c106941_417 Xwmc783 Tdurum_contig5522_455 BobWhite_c15406_510 BS00024829_51 Y4c TC88560 Tdurum_contig51669_668 RAC875_c14078_202a Xgwm497d Tdurum_contig13489_292b Excalibur_c9969_98 Kukri_c84307_76 Excalibur_c34579_263 wPt-7665 Tdurum_contig42257_3252 Kukri_c7546_1739 wsnp_Ex_c24031_33277293 wPt-9116 Kukri_c5318_380 Tdurum_contig43552_666a wPt-1500 wPt-5373 wPt-5168 TC86533 wPt-0484

SL_MC (Maccaferri2016)

0.0 2.3 3.1 3.9 4.4 5.1 8.0 10.0 12.2 13.6 14.6 15.6 17.6 18.1 18.7 19.7 20.2 21.4 22.6 23.4 25.0 26.5 27.4 28.3 29.6 30.1 32.1 33.0 34.3 34.8 35.0 35.4 36.2 37.0 38.3 38.9 39.4 40.4 41.3 42.1 43.1 43.5 45.4 46.5 47.0 48.2 48.9 49.4 50.4 51.0 51.5 52.1 53.5 53.9 54.1 55.1 55.5 56.0 56.6 57.3 58.7 59.3 60.0 60.3 60.6 61.7 62.5 63.2 64.3 64.6 65.0 67.1 68.3 68.6 69.5 70.8 71.1 71.9 72.3 73.9 74.0 75.6 76.9 77.3 78.0 78.4 79.0 81.2 82.8 83.6 85.6 87.5 88.7 89.5 90.9 91.2 92.4 93.0 94.2 95.1 96.6 97.3 98.0 99.3 99.8 101.0 103.2 104.2 105.5 106.6 107.2 108.3 109.6 110.2 111.0 112.4 114.5 115.7 116.1 117.2 118.0 119.0 119.5 120.9 121.2 122.0 123.0 124.6 125.1 126.1 128.0 129.0 130.1 130.9 131.7 132.7 133.6 134.9 135.8 136.8 137.1 138.7 139.2 140.9 141.7 142.9 143.2 144.9 145.2 146.1 147.5 148.6 149.2 150.2 151.3 152.1 153.0 154.1 157.1 158.6 159.6 160.3 161.2 162.2 164.5 165.4 167.3 168.1 170.5 171.4 172.8 174.0 175.6 176.8 177.6 178.1 178.9 179.3 179.6 180.1 181.1 182.1 183.2 183.9 184.3 185.3 186.2 188.3 189.5 190.5 194.5 198.3 199.8 200.8 202.6 204.0 205.3 206.1 208.8 209.6 211.5 212.4 213.3 215.7 217.0 217.3 218.9 219.7 222.0 223.9

T7 (SMC)

MQTL17

F,SA2,V2,L2 (SMC)

RT6_CL (Maccaferri2016)

TRL_MC (Maccaferri2016)

MQTL15

MQTL13

LRN_MC (Maccaferri2016)

SL_MC (Maccaferri2016) PRL,PRS_CL (Maccaferri2016)

PRV_MC (Maccaferri2016)

RDW,RSR_CL (Maccaferri2016) TRN_CL (Maccaferri2016)

LRL,TRL,RN (Ren2012) RGA_MC (Maccaferri2016) MQTL18

TRS_MC (Maccaferri2016)

V,L,SA,T,SH,LDW,RDW,F,C (SMC)

MQTL14 TRN_MC (Maccaferri2016)

TRV_MC (Maccaferri2016)

L,L1,SA,SA1,V1 (SMC)

LRN_MC (Maccaferri2016) MQTL16

RT6_CL (Maccaferri2016)

RGA_CL (Maccaferri2016)

SDW_MC (Maccaferri2016)

5B RAC875_c86104_111 Excalibur_c14401_743 RFL_Contig4708_1477 RAC875_c78248_193 RAC875_c215_329b wsnp_Ku_c12399_20037334 tplb0025f09_1853 BS00064403_51 wsnp_Ex_c31121_39955117 Tdurum_contig49608_1323 RAC875_rep_c106667_302 wPt-1708 Kukri_rep_c117247_191 Xbarc10b wsnp_Ex_c17561_26284693 wPt-0608 tplb0050b23_546 Excalibur_c55463_232 Xbarc68b wsnp_Ex_c29500_38529808 Xwmc679b Xwmc652 Tdurum_contig29961_68 GENE-2384_84 Tdurum_contig97386_207 tplb0045c06_1675 Xbarc163 Tdurum_contig31139_143 Xwmc310 Excalibur_c31953_382 tplb0024a16_411 Xbarc193 Xwmc692 tPt-5519 Kukri_c4078_3176 Tdurum_contig74720_539 Tdurum_contig31514_449 Tdurum_contig17416_577 wsnp_Ku_c8075_13785546 Tdurum_contig93615_735 Tdurum_contig93615_540 RAC875_c65971_127 Xgwm149 TC67416 BS00081631_51 BS00022431_51 Xwmc617a RAC875_c2226_933 Tdurum_contig28671_295 Tdurum_contig51688_681 Tdurum_contig81905_502 Tdurum_contig42038_2826 Xgwm1278 Tdurum_contig42528_936 Excalibur_c23248_148 BS00033614_51 Tdurum_contig33737_277 Xgwm193a BS00065688_51 Xgwm368 Xwmc206b Xwmc48b Xgwm856 Kukri_c8973_1986 Tdurum_contig2859_70 Xgwm513 Xgwm925 RAC875_c75075_313 Xgwm112a Tdurum_contig42307_2647 tplb0043l14_1189 CA663888 Tdurum_contig92997_676 Excalibur_c1043_667 BS00022177_51b tplb0034b12_591 BS00010940_51 Xgwm251 BobWhite_c12067_311 BS00106144_51 wsnp_Ra_c3790_6990678 Xgwm375 Kukri_c36207_91 BS00063008_51 RAC875_c1357_860 RAC875_c52774_135 Tdurum_contig29112_483 wPt-3255 Tdurum_contig97308_88 Excalibur_rep_c109675_738 Kukri_c6388_1030 Tdurum_contig10466_78 Tdurum_contig45927_677 Excalibur_c27139_396 Tdurum_contig82603_67 tplb0036a20_1295 Tdurum_contig50783_285 BS00023035_51 RAC875_c36213_352 Tdurum_contig46788_529 Excalibur_c49297_159a tplb0056i06_856 CAP12_c4704_232 Tdurum_contig920_126 Ex_c45493_761 wsnp_Ex_c5187_9195120 Tdurum_contig76671_435a BobWhite_c8115_648 Tdurum_contig60051_169a Kukri_rep_c103450_1504 Kukri_c2639_290 wsnp_Ex_c38704_46166494 GENE-2826_325 Kukri_c44559_429 BS00004727_51 Tdurum_contig9893_571 Kukri_rep_c78644_408 Tdurum_contig51521_90 Kukri_c93922_68 Kukri_c93922_206 wPt-0391 IAAV5564 BobWhite_c27801_429 BobWhite_c4818_173 D_F5XZDLF01C3B2R_358 Ra_c19259_1799 Excalibur_c29255_366 wsnp_BG604404B_Ta_2_1 BS00022366_51 RAC875_c10029_341 IAAV7394 IAAV8499 Tdurum_contig56887_501 wPt-5564 Tdurum_contig56887_322 BobWhite_c11977_428 BobWhite_c47144_153 wPt-8292 wPt-3804 wPt-5996 Tdurum_contig52336_160 Tdurum_contig56887_256 RAC875_rep_c117991_66 JG_c3271_440 Tdurum_contig9168_2214 BS00034148_51 BS00034147_51 BobWhite_c15529_288 RAC875_rep_c82932_428 RAC875_c17026_714 JD_c48945_490 IAAV3549 Xdupw43 BS00004012_51 BS00065222_51 BS00014101_51 Tdurum_contig42695_410 RFL_Contig3368_209 Tdurum_contig9118_1078 RFL_ConBiA3368_209 RAC875_c6026_963 Kukri_rep_c86966_239

TRD_MC (Maccaferri2016)

4B 0.0 1.9 2.5 4.5 6.0 6.8 8.5 11.1 12.0 15.5 18.0 20.1 21.9 22.3 23.7 24.4 25.1 26.0 26.5 27.4 28.1 29.6 31.4 32.7 33.4 34.1 35.2 35.8 36.7 37.7 38.1 38.8 39.0 39.7 40.2 41.5 42.9 43.6 44.9 45.5 46.2 47.3 47.9 48.7 49.4 50.1 51.0 52.7 53.0 Rht-1B 54.3 54.8 55.2 55.8 56.2 56.9 57.9 58.2 58.9 59.4 60.4 61.0 61.4 61.7 62.2 62.5 63.1 63.5 64.0 64.7 65.6 66.6 68.0 68.9 69.4 70.3 70.9 71.5 71.8 72.5 72.9 73.5 74.0 74.6 74.9 75.2 75.6 76.0 76.7 77.2 78.0 78.4 79.0 79.4 79.7 80.6 80.9 81.3 81.7 83.1 83.5 84.0 84.8 85.0 85.8 86.6 87.0 88.5 89.3 89.6 90.1 90.6 91.2 92.1 92.7 94.0 95.0 95.6 96.1 97.0 97.7 98.3 98.7 100.3 101.3 102.3 103.1 103.7 104.0 104.8 105.0 105.7 108.2 108.7 108.8 109.1 109.2 109.5 110.3 110.5 110.8 111.6 112.0 112.1 112.7 113.7 114.3 114.9 115.5 116.5 116.7 117.4 117.7 117.9 118.8 118.9 119.3 119.4 120.9 121.3 122.9 123.2

International Journal of Genomics

11

MRL,PRE (Ren2012)

MQTL32

SDW_CL (Maccaferri2016) MQTL34

PRS,PRL_MC (Maccaferri2016)

MRL (Ren2012)

MQTL33

RT6_MC (Maccaferri2016)

L9,S9,SA9 (SMC)

Tdurum_contig11531_522 Xgwm255 wPt-0276 Jagger_c9100_76 Xwmc606a Xwmc323 wPt-3147 Xgwm569 Tdurum_contig16244_335 Excalibur_c50044_1221 Kukri_c50501_299b Tdurum_contig100306_98 BS00062990_51 Tdurum_contig30677_55 BJ239878 wsnp_CAP8_c334_304253 RAC875_c23521_589 wPt-2278 Xwmc338 wPt-4309 BobWhite_c41356_62 Kukri_c67849_109 Xwmc597f BS00081132_51 Excalibur_c29698_76 IAAV5530 BobWhite_c44404_312 Kukri_c109962_396 Excalibur_c108159_334 wPt-2883 Excalibur_c41298_459 wsnp_Ex_c2103_3947695a Xgwm46b Xgwm601a wsnp_Ex_c23755_32994701 Xgwm951 GENE-0293_65 wPt-8283 Xgwm68b RAC875_c5683_136 Xwmc546a Tdurum_contig68347_605 RAC875_c1638_165 RAC875_c56878_518 Xbarc85 Xpsr103 wPt-4230 wPt-9630 wsnp_Ex_c10251_16815792b Xgwm963b Xbarc65 Xwmc653b Xgwm213b wPt-3873 Kukri_c2796_1436 TC69176 Kukri_rep_c69312_647 wPt-3833 BobWhite_c27679_112 BobWhite_rep_c64772_309 wPt-4025 wPt-0920 BobWhite_c3541_152 wPt-8919 Kukri_rep_c71173_2043 RAC875_c28901_836 Tdurum_contig9966_724 Tdurum_contig9966_646 Xgwm1036 wPt-6180 wPt-4323 Xwmc723 Tdurum_contig49861_368 wPt-8069 Xdupw403 wsnp_Ex_c758_1488368 Xdupw145 BS00063208_51 Excalibur_c11857_1196 RAC875_c21537_368 BS00029286_51 tplb0033d17_389 Xbarc1181 Tdurum_contig81911_179 Excalibur_c33549_95 wPt-2273 Xwmc517 tplb0062h23_1362 Excalibur_c93217_61 tplb0021f14_1700 Xwmc537b BS00080621_51 Xbarc272 Tdurum_contig14821_751 Excalibur_c33267_263 BS00064871_51 Kukri_c15912_1189 BS00009995_51 Ku_c31231_285 wPt-5922 wPt-1826 wPt-4258 RFL_Contig4842_579 wPt-7887 Excalibur_rep_c74778_252 Xwmc792b Excalibur_rep_c104090_439 RAC875_c41903_122 Xdupw398 wPt-5341 tPt-7362 Xwmc311 rPt-3887 wPt-5343 wsnp_Ex_rep_c68762_67626384 Excalibur_c12644_58b Kukri_c10430_1138 Xgwm420 BobWhite_c12048_145 IAAV9045 wPt-4297 wsnp_Ex_c323_629461 Excalibur_c19471_197b wPt-2356 wPt-4814 RAC875_c31791_559 BobWhite_c26534_532 Ra_c3092_741 Xgwm611 wPt-0600 Tdurum_contig8402_638 wPt-3939 wPt-5138 RAC875_c49954_1172 Xgwm577 Xbarc1073 wPt-7219b Excalibur_s103240_100 wPt-2677 RAC875_c10372_671 Tdurum_contig11832_272 Xwmc500b Tdurum_contig28598_245 wPt-4902 Kukri_c7284_1859 Xbarc182 BS00066342_51 Xcfa2040c wPt-9877 Xbarc32 Xmag1933 wsnp_BE445506B_Ta_2_1 wPt-7891 Xwmc557 wPt-0504 Tdurum_contig45280_451 wsnp_Ex_c12556_19991329 Xwmc10 CAP7_c12398_110 tplb0040b02_465 Excalibur_rep_c110429_536 Xwmc526 RAC875_c525_941 Tdurum_contig30909_76 wPt-8650c Xwmc70 wPt-6865 RAC875_c9543_99b wPt-0465 wPt-1069 Xgwm344c wPt-7387 wsnp_Ex_c53387_56639949b Ex_c29172_877b Tdurum_contig13459_543a Excalibur_c1750_188 GENE-3073_258 RAC875_c1329_488 wPt-9488b

PRL (Ren2012)

BobWhite_c20735_255

8.6 10.6 11.8 12.6 13.7 14.8 16.2 18.3 19.2 21.9 22.4 23.0 24.5 27.3 28.5 29.5 31.9 32.5 34.7 35.4 36.1 38.2 39.0 40.3 42.4 43.7 44.3 46.2 47.6 48.6 49.4 50.4 51.8 52.9 53.8 55.0 57.1 58.3 59.8 62.5 63.3 64.6 65.4 67.0 68.9 69.6 70.5 71.4 71.7 72.2 73.4 74.7 75.5 76.1 77.0 78.0 78.7 79.1 79.8 80.2 80.9 81.3 82.0 82.9 83.8 84.5 85.3 86.1 86.6 87.1 88.2 88.6 89.1 89.9 90.8 91.0 91.6 92.0 92.4 93.2 94.8 95.7 98.0 98.7 99.3 99.7 100.3 101.2 102.4 103.2 104.8 105.4 106.6 107.5 109.1 111.1 112.4 113.9 114.8 115.2 116.5 117.0 117.6 118.0 118.7 120.1 120.8 121.6 122.7 123.9 126.1 127.3 128.6 129.0 129.8 130.7 131.1 132.0 133.2 134.1 135.0 136.0 137.3 138.5 139.1 140.1 140.9 142.7 143.5 144.4 144.8 145.0 146.2 147.0 147.5 148.5 149.2 149.9 150.2 150.6 151.2 151.8 152.4 152.9 153.4 154.0 154.8 155.2 156.4 157.2 158.1 159.4 160.2 160.8 161.9 162.2 163.0 163.8 164.2 165.0 166.2 166.8 167.3 168.0 168.7 169.8 170.6 171.6 172.9 174.1 175.7 176.1 177.1 178.9 180.7 181.9 183.1 188.6 197.3

QMRL (Liu2013)

RFL_Contig6075_1128

3.0

TRS,TRL_CL (Maccaferri2016)

0.0

ARL_CL (Maccaferri2016)

MQTL29 MQTL30 MQTL31

QMRL (Guo2012) PRS,PRL_MC (Maccaferri2016)

T,T1 (SMC)

RT6,ARL_MC (Maccaferri2016)

TRD_CL (Maccaferri2016) T_A (CP)

TL4,L5,L6,V4,V5,V6,SA4,SA5,SA6 (SMC)

QMRL (Ren2012)

PRL,TRL _MC (Maccaferri2016)

SL_CL (Maccaferri2016)

QLRL (Ren2012)

QRN (Ren2012)

7B BS00016587_51b Xwmc430d Excalibur_c28854_1580 BS00093063_51a Xgwm1051 wsnp_Ex_rep_c101133_86572194 BS00029434_51 Tdurum_contig43538_1582 wPt-8641 Xdupw217 wPt-0151 RAC875_c841_1329 wPt-4720 wPt-2714 wPt-3304 wPt-7777 tPt-0910 RAC875_c63707_140 wPt-6988 wPt-1474 wPt-8015 RAC875_c12259_1892 RFL_Contig5885_435 Kukri_rep_c111561_377 wPt-4233 wPt-4706 Tdurum_contig10149_284 Kukri_c67545_299 wPt-7954 wPt-1437 Kukri_c41439_313 wsnp_Ra_c30621_39857295 GENE-1970_158b wsnp_Ex_c14481_22485922 wPt-2095 BS00033629_51 GENE-1999_98 wPt-0259b BS00035056_51 Xwmc419c wPt-3376 Xwmc486 wsnp_Ku_c15011_23496657 Tdurum_contig50121_249 Kukri_c60727_356 wPt-5256 wPt-1241 BS00067133_51 wPt-3605b wPt-2786 wPt-2175 Xwmc487 Kukri_c46237_140 wPt-4858 TA004917-1090 Tdurum_contig11641_1008 Xwmc597d Xgwm508 wPt-2479 wPt-0470 JD_c63404_542 wPt-5333 wPt-3163 Excalibur_c55800_202 wPt-2218 Kukri_c21995_1652 wPt-8721 TC85037 wPt-7489 RAC875_rep_c111705_629 XksuD17 Xwmc494 IAAV8375 GENE-4142_601 Xgwm518 RAC875_c23812_187 Xbarc68c Xgdm113 BobWhite_rep_c65142_111 CAP8_rep_c9477_231 wsnp_Ex_c6057_10611952 Xbarc101 wsnp_CAP7_c1839_907899b Xbarc1169 BS00046966_51 Tdurum_contig62040_1253 wsnp_BE488206B_Ta_2_1 Ra_c19002_569 IAAV7767 wsnp_Ex_c18382_27210656 Tdurum_contig21737_203 RAC875_c20889_913 Xwmc398b RAC875_c30027_381 Xwmc265c Xgwm193b wPt-0446 BobWhite_c686_387 wsnp_Ex_c5058_8981554 Kukri_c25589_772 BS00067644_51 Excalibur_rep_c101274_113 wsnp_Ra_c11942_19247669 tplb0059j12_800 wPt-9124 Xgwm88 Xgwm644 Xbarc198 Xgwm887 Tdurum_contig69600_415 Kukri_c45250_289 wPt-0397 Excalibur_rep_c94584_98 Tdurum_contig93283_513 Xgpw3241 wsnp_Ku_c16522_25425455 wPt-9241 TA005272-0214 Xwmc152 Tdurum_contig47269_241 wsnp_CAP11_c1432_806102 Xbarc79 wPt-8554 wPt-1730 CAP7_c7065_166 wPt-1287 RAC875_c6649_642 BobWhite_c30500_527a Xwmc539 Excalibur_c11817_1125 Xdupw216 GENE-4221_313 BobWhite_rep_c53133_385 BS00037784_51 Xbarc178 Kukri_c49331_77 Xgwm219 RAC875_c4891_99 wPt-9930 wsnp_Ex_c18632_27501724 Xwmc417b wsnp_Ku_c11846_19263340 tplb0021a17_853 RFL_Contig2785_708 Kukri_c5168_162 BS00067129_51 Xgwm768 BS00063595_51 Kukri_c40428_72 wPt-7830a tPt-9948a wPt-6184 Excalibur_c47675_176 wPt-5092 wsnp_RFL_Contig3708_3946935a BobWhite_c3514_717 Tdurum_contig71517_158 wPt-7274 wPt-9481 wPt-2178 Xgwm735 RAC875_c16691_90 BS00068815_51 IACX2322 wPt-9952 RAC875_c3455_171 wPt-1325 BS00088277_51 JD_c7044_1403 BS00068166_51 RFL_Contig6086_1186b Excalibur_rep_c105053_313 BS00049082_51b RAC875_c17224_741 IAAV5595 GENE-3988_631 BobWhite_rep_c63427_478 Excalibur_c27139_516 Tdurum_contig7986_704 tplb0046e21_69 RAC875_c22494_231 Xwmc388 wsnp_Ex_c293_567035 RAC875_c55445_92 BobWhite_c27364_124 Excalibur_c14451_1137 wsnp_Ex_c791_1557333 wsnp_CAP7_c1735_859744 Excalibur_rep_c69865_157 BS00022278_51 RAC875_rep_c108385_407a IACX7844 BobWhite_c10171_323a Excalibur_c6108_262 TA002907-0816 Kukri_c36312_591 tplb0045b09_1555 Tdurum_contig42191_4367 wPt-6329 wPt-0171 wPt-5885 wPt-5480 wPt-5176 wPt-1541

LRN_MC (Maccaferri2016)

6B 0.0 1.0 2.0 2.6 3.7 4.0 5.3 6.0 6.5 6.9 7.0 8.1 8.4 9.2 10.0 11.0 11.8 12.3 13.4 14.0 15.7 17.4 18.3 18.9 19.8 20.9 21.3 22.2 23.2 23.9 24.3 25.5 26.4 27.2 27.8 29.6 30.4 31.0 32.0 33.0 33.5 33.9 34.5 35.0 35.5 35.9 36.8 37.1 38.0 38.9 39.8 40.5 40.8 41.3 42.0 42.8 43.1 43.8 44.0 44.5 44.7 45.1 45.4 46.4 46.8 47.0 48.1 48.7 49.6 50.2 50.5 51.0 52.0 52.9 53.4 53.7 54.0 54.3 57.1 58.1 59.0 59.9 60.3 60.8 61.7 62.0 62.5 63.0 63.8 64.2 64.7 65.1 65.7 66.3 67.2 68.7 69.0 69.4 70.2 71.2 71.8 72.1 73.0 74.0 74.5 74.9 75.3 76.0 76.7 77.2 77.8 78.7 79.1 79.7 80.2 80.6 81.1 81.3 81.6 82.1 82.9 83.1 83.6 83.9 84.6 85.2 85.7 86.2 86.7 87.1 87.7 89.1 90.1 92.4 92.9 93.0 93.7 95.0 95.7 96.7 98.4 99.2 100.2 100.8 101.2 101.6 102.0 103.3 104.7 105.1 106.0 106.6 107.2 107.5 107.9 108.7 109.2 109.7 110.8 111.6 112.2 113.1 114.8 115.9 116.2 117.0 118.4 119.4 121.9 123.0 123.6 124.6 125.1 125.8 126.3 126.7 127.0 128.2 128.6 129.2 130.0 130.9 131.4 132.2 133.4 133.9 134.6 135.0 135.9 136.6 137.1 138.7 138.8 139.0 139.3 139.8 143.9 144.4 157.7 161.5 162.8 166.4 167.9 170.4

Figure 2: Integrated map in wheat for the QTL and the MQTL identified through the meta-analysis for the root morphological traits. QTL from literature are not indicated with the QTL name reported in the correspondent study but with a nomenclature in which the trait and the reference are reported, as indicated in Table S1, for clarity. The same for the QTL identified in the present study, which are reported with the acronym “SMC” (i.e., “Simeto” × “Molise Colli” population). The genetic position of the Rht-B1 locus on chromosome 4B is also reported. Vertical lines on the right of the chromosomes indicate the confidence intervals, and horizontal lines indicate the peak marker positions, where the length represents the percentage of variability explained by the QTL. The MQTL are in bold, while the single QTL are in gray. The names of the QTL grouped in the same MQTL are in the same color.

12

International Journal of Genomics Table 4: Characteristics of the MQTL (in bold) and single QTL (in italics) identified in the meta-analysis in the present study.

Chr. 1B

2A

3A

4B

5B

6A

MQTL/single QTL TRL, TRV (Maccaferri et al. 2016) F,C (SMC) MQTL1 MQTL2 TRL, ARL (Maccaferri et al. 2016) QArn.1 (Guo et al. 2012) SL (Maccaferri et al. 2016) MTQL3 T4 (SMC) qDRR1 (Hamada et al. 2012) MTQL4 MTQL5 qTRSA (Bai and Hawkesford 2013) MTQL6 TRD, PRD (Maccaferri et al. 2016) MTQL7 MTQL8 MTQL9 QMrl.1 (Guo et al. 2012) MTQL10 MTQL11 MTQL12 T2 (SMC) QTrn.ubo (Maccaferri et al. 2016) QTrd.ubo (Maccaferri et al. 2016) MTQL13 MTQL14 LRL, TRL, RN (Ren et al. 2012) MTQL15 MTQL16 MTQL17 MTQL18 MTQL19 MTQL20 TRL, SLL, SLSA, SLV (Bai and Hawkesford 2013) MTQL21 T7 (SMC) MTQL22 MTQL23

AIC

Position (cM)

Mean MQTL/single initial QTL CI (cM) CI (cM)

4.66

39.72

20.14

12.8

BS00071333_51-BS00023084_51a

16.7 1.4 4.8

Excalibur_c71158_117-BobWhite_c28295_256 wPt-7529-Xgwm413 P4133–170-RAC875_c4377_524

68.2

1.5

wsnp_Hu_c30982_40765254-Xcfd59b

79.9

2.6

RFL_Contig4576_702-CAP8_c4697_108a

87.7

7

wPt-3579-Ku_c1932_1583

4.4 7.8

BS00072289_51-RFL_Contig2826_548 BS00072791_51-wsnp_Ex_c27176_36393952

1.6

Tdurum_contig29059_185-Xwmc728

11.7 0.5

Tdurum_contig74742_224-wPt-5839 Xwmc455-Xgwm372

44.8

Xgwm445-Xwmc181

9.7

RAC875_c1789_253-Excalibur_c21501_237

1.5

CAP11_c7974_175a-Excalibur_c11079_101a

6.9 1.6 4.5

CAP8_c1702_71-RAC875_c10628_941 wPt-6891-Xwmc489c wsnp_Ex_c4923_8767234-Excalibur_c24402_471

5.2

wsnp_Ex_c1894_3575749-Tdurum_contig8365_319

2.8 2 3.9 5.4

Excalibur_c3429_652b-wsnp_Ku_c10468_17301042a Xwmc215a-KukBi_c6645_570 Tdurum_contig55841_351a-Kukri_c2596_146 Xgwm480-Xwmc206d

192

25.7

BS00108976_51-Tdurum_contig51914_740

9

18.4

RAC875_c215_329b-tplb0050b23_546

2.6 7.7

Tdurum_contig93615_540-BS00081631_51 Xwmc617a-BS00065688_51

0.9

Xgwm368-wPt-5497

3.1 1.1 1.2 9.2 9.6 3.3

kukri_c8973_1986-Tdurum_contig42307_2647 Tdurum_contig92997_676-BS00022177_51b BobWhite_c12067_311-Xgwm375 Tdurum_contig46788_529-BS00004727_51 tplb0060p09_735-wPt-0033 Xwmc274b-RAC875_c60836_741a

3.8

Xbarc74-Xgwm213a

9 13.6 11.2 2.8

Tdurum_contig29967_456-wPt-1482b BS00024829_51-Excalibur_c9969_98 BS00082191_51-Ex_c68796_2057 IAAV4117-BS00063990_51

24.7 44.5 62

96.1 111

6.3 11.3

8

139.4 75.22

40.5 106.6

27.2 25.8

114.6 20.4

159.6

17.2

13.6 9.39 31.94

65.8 94.9 107.3

9.9 12.5 10.9

123

52.31

40.73

140.3 147.8 156.5 168.5

48.1 55.4

5.9 7.4 11.3

16.1 12.5

60.4

84.94

11.44 12.43

63.7 69.6 73.2 88.3 3.9 36.5

5.8 3.9 7.2 17.5 16.2 10.7

53.5 9.94 96 64.09

Flanking markers

123.8 202.8 24.9 56.5

13.7 27.7 7.7

Number of involved QTL

3 4

2

4 3

2

2 4 2

2 3 2

3 2

2 2 8 2 2 2

2 3 4

International Journal of Genomics

13 Table 4: Continued.

Chr.

6B

MQTL/single QTL

Position (cM)

MTQL24 MTQL25

62.5 69.8

LRL (Ren et al. 2012)

76.8

MTQL26 MTQL27 74.71 MTQL28 QRga.ubo (Maccaferri et al. 2016) QRdw.3 (Guo et al. 2012) LRN (Maccaferri et al. 2016) qRN (Ren et al. 2012) qLRL (Ren et al. 2012) MTQL29 20.69 SL (Maccaferri et al. 2016) MTQL30

7B

AIC

PRL, TRN (Maccaferri et al. 2016) MTQL31 qMRL (Ren et al. 2012) MRL2, MRL3, PRE (Ren et al. 2012) L9, S9, SA9 (SMC) MTQL32 MTQL33 QMRL (Liu et al. 2013) PRS, PRL (Maccaferri et al. 2016) MTQL34

6.79

Mean MQTL/single initial QTL CI (cM) CI (cM) 7.7 2.9 7.1 5

7.9 7.6 4

Xpsr312b-RAC875_c64560_111a Xwmc807-Xbarc113 wsnp_Ra_c12086_19452422Tdurum_contig75814_655 CAP7_c9578_263-Tdurum_contig92441_354 wsnp_Ex_c20457_29526403-BobWhite_c5872_589 Xpsr546a-wPt-9976

132.9

11.3

BS00062776_51a-Xwmc621

162.2

9.6

TA005679-0546b-Excalibur_c62474_82

23.9

15.2

wPt-4233-Tdurum_contig50121_249

33.6 59.9 69.5 78.3

17.9 18.2 4.1 0.7

wPt-0259b-wPt-7489 XksuD17-wPt-0446 Xwmc265c-BS00067644_51 kukri_c45250_289-wPt-0397 Excalibur_rep_c94584_98Tdurum_contig47269_241

97.1 114.2 125.1

80.6

3.8 11.2 16.2 12

7.8

4

93.7 15.79

100.3 118.2

8.8

18.4

27.69

33 73.7 93.3 128.6

13.5 43.3

143.6 25.49

Flanking markers

162.2

11.5

2.7 12.2

Xdupw216-tplb0021a17_853

6 8.7

wsnp_Ex_c18632_27501724-BS00063595_51 RAC875_c3455_171_BobWhite_rep_c63427_478

11.5

Xgwm569-RAC875_c23521_589

14.1 8 30.5 5.5

BS00062990_51-Xwmc597f Xpsr103-GENE-4888_150 TC69176-Excalibur_c33267_263 rPt-3887-IAAV9045

13.4

Excalibur_c12644_58b-wPt-0600

8

Xmag1933-Excalibur_rep_c110429_536

Number of involved QTL 2 2

2 2 5

3

2

2

2 2

2

Chr.: chromosome; AIC: Akaike information criterion; CI: confidence interval; cM: centimorgan; SMC: “Simeto” × “Molise Colli” population.

previously published on association mapping for root traits in durum wheat [35, 37], to the best of our knowledge, three QTL represent novel loci for the control of root morphological traits, and these are located on chromosomes 3A, 5B, and 7B (Figure 2). Two of these are involved in the control of the number of tips, in different root-diameter classes (chromosomes 3A and 5B). The QTL on the short arm of chromosome 7B is of particular interest, whereby it is involved in the control of root length, volume, and surface area, but only for the largest root-diameter class. Similarly, in a previous study, a QTL that controlled root length, volume, and surface area only in a specific root-diameter class was identified in the “Creso” × “Pedroso” segregating population [67]. This finding indicates that specific loci can act in shaping the morphology of the root apparatus only in particular growth phases. QTL9 (on chromosome 4B) represents a strong QTL for the control of root traits in the SMC, which explains root volume, length, surface area, number of tips, plant height,

shoot dry weight, root dry weight, number of forks and crossing number. This is of interest not only for the number of traits but also for the high LOD and R2 (Table 3). This is involved in the control of both root and shoot traits, and the sign of the additive effect is negative for all of these traits, which indicates that the allele of “Molise Colli” increases the development of both the shoot and root systems in this segregating population. This region is coincident with that of the RhtB1 locus, which is the main locus involved in the control of plant height in durum wheat. Indeed, this QTL explains 52% and 34% of the observed variability for plant height and shoot dry weight, respectively, in the population in the present study. Moreover, this QTL shows high R2 also for the traits of the root system, for root surface area (22%), surface area in root class 1 (20%), and dry weight (18%). Although this QTL appears not to be useful in any breeding programs for the improvement of root growth, it clearly indicates a positive correlation between plant height and root traits in this SMC.

14 The relationships between plant height and root system development are a controversial topic that has not been completely defined at present. There have been diverse indications from a number of previous studies, which are probably due to the different conditions and growth stages in which the root traits were evaluated and to the different Rht alleles that were considered. Most recent studies have indicated that different sets of genetic loci control shoot and root growth [21, 49–51]. In some cases, there has been evidence of negative correlations. Very recently, Kabir et al. [36] defined a negative correlation between root traits and plant height in two bread-wheat segregating populations. In both of these populations, the plant height was mainly dependent on the Rht-D1 locus on chromosome 4D, which appears to be separate from the QTL for root traits that has been identified on the same chromosome. The role of the Rht-B1 locus on chromosome 4B was investigated by Bai et al. [31] who analyzed a set of near introgression lines for a number of Rht loci/alleles and showed clear effects of the Rht-B1c allele but not of the Rht-B1b allele in the reduction of the development of the root system, as well as that of the shoot. Bai et al. [31] also evaluated an “Avalon” × “Cadenza” bread-wheat population and reported on an important region on chromosome 4D (RhtD1) that controls both shoot and root traits. In light of their data, we can argue that not only the evaluation of root traits but also of the Rht alleles and the genetic backgrounds of the genotypes analyzed support these contrasting scenarios. As well as this region on chromosome 4B, in the present study, we identified QTL that were independent of loci for plant height, and some of these explained around 17% of the phenotypic variability observed. Recent studies have indicated correlations between loci for root traits and those involved in grain yield and other traits of agronomic importance. Canè et al. [35] used association mapping to identify loci for root morphology in a panel of durum wheat cultivars, and they showed that out of the 48 QTL detected for the rootsystem architecture, 15 overlapped with QTL for agronomic traits measured in the same panel for two or more environments. Bai et al. [31] reported coincidence between some QTL for root morphology and seed characteristics, including 1000-grain weight. Indeed, seed size can have an impact on early seedling root growth [68, 69]. Using linkage and association mapping, Maccaferri et al. [37] identified clusters of QTL with major effects on the morphology of the root system in durum wheat. Here, the QTL mapped to chromosome regions 10 and 11 identified in the SMC were included in MQTL17 and MQTL18, respectively, on the long arm of chromosome 4B, in a region in which the root system architecture RSA_QTLcluster_12# was identified by Maccaferri et al. [37]. Similarly, the SMC QTL14 that was mapped to the long arm of chromosome 6A fell within the region of RSA_QTLcluster_16#. Both of these regions are of interest, as they are strongly associated with grain yield and 1000kernel weight, as reported by Maccaferri et al. [37], and therefore, they appear valuable for breeding purposes. The SMC was previously used to investigate the genetic basis of some traits related to seed morphology in durum wheat [57]; therefore, it is possible to investigate eventual correspondences between root and seed traits. First of all,

International Journal of Genomics correlation analysis was carried out considering the root traits evaluated here and the traits related to seed size and morphology that were previously analyzed [57]. The most significant correlations here were between 1000-kernel weight and seed area on the one hand and, number of root traits on the other. As a confirmation of this, the region that corresponds to MQTL1 (on chromosome 1B), in which the SMC qT2-1B.2 is found, corresponds to the QTL for traits related to seed length, perimeter, and roundness that were identified by Russo et al. [57]. Another correspondence was found between the QTL on chromosome region 9 (4B) for plant height and various root traits and the QTL for 1000kernel weight, seed surface area, and seed width. Very interestingly, the direction of the effect was the same for root and seed morphology QTL: the SMC qT2-1B.2 and the QTL for traits related to seed length, perimeter, and roundness that were identified by Russo et al. [57] showed negative additive effects, which indicates that the allele of “Molise Colli” is effective in increasing both trait types. The same was observed for the QTL on chromosome region 9 (4B) for plant height and various root traits and the QTL for 1000-kernel weight, seed surface area, and seed width.

5. Conclusions In the present study, we carried out an analysis of the genetic basis of morphological root traits in wheat. MQTL analysis was used to compare the QTL identified in the SMC with those described in previous studies in wheat, where three QTL were novel. The use of a population derived from an elite durum wheat cultivar and a cultivar of T. dicoccum was useful for the exploitation of the larger variability with respect to previous studies. There are controversial indications in the literature for the relationships between shoot and root growth. As the Rht-B1a and Rht-B1b alleles are segregated in the SMC, the present study allows us to conclude that in this specific case, this locus has an effect on the promotion of growth of both aerial and below-ground parts of the plant. The integration of the knowledge from the present and previously published studies is a suitable means to identify regions that have effects on root traits and traits of agronomic importance, such as grain yield and 1000-kernel weight, and traits that are related to the size and shape of the grain. The phenotyping for root traits is very complex as it is influenced by the phenology of the plants and by the growth conditions. Therefore, further studies will be helpful to validate these regions as targets for breeding programs for optimization of root function for field performance.

Conflicts of Interest The authors declare that they have no conflicts of interest.

Acknowledgments This study was supported by the Ministry of Education, Universities and Research (MIUR), Italy, with a special

International Journal of Genomics

15

ISCOCEM grant. The authors are grateful to Dr. Christopher Berrie for scientific English language and editorial assistance. [16]

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