Molecular Plant Letter to the Editor
A Sequencing-Based Linkage Map of Cucumber Dear Editor, Cucumber (Cucumis sativus L., 2n = 2x = 14) is an economically important vegetable worldwide and has served as a model system for plant vascular biology and sex determination studies. We reported the draft genome assembly of the North China type cucumber line 9930 in 2009 (Huang et al., 2009a) and constructed a single-base resolution map of cucumber genomic variation by resequencing of the genomes of 115 core germplasm lines (Qi et al., 2013), which enabled genome-wide association studies of important traits in cucumber (Shang et al., 2014). The genome sequences available for cucumber facilitated the development of PCR-based markers and the construction of the genetic linkage maps (Ren et al., 2009; Miao et al., 2011). However, the density and resolution of these linkage maps are insufficient for accurately mapping genes or quantitative trait loci (QTLs) of interest. The advent of the next-generation sequencing technology provides an alternative for marker discovery and genotyping, which has increased the marker density in genetic studies by several orders of magnitude. As a good example in rice, through sequencing 150 recombinant inbred lines (RILs) at 0.023 coverage, over 1 million single nucleotide polymorphisms (SNPs) were genotyped and a major QTL for plant height was delimited into a 100-kb interval (Huang et al., 2009b). In this study, we constructed an ultra-high-density cucumber genetic map using the RIL population derived from a gynoecious line 9110Gt from Europe and a monoecious line 9930 from North China, which was phenotyped over multiple seasons. We generated 73 Gb sequences by barcoded multiplexed sequencing of 147 RILs, equivalent to approximately 500 Mb per RIL, covering about 33% of the assembled 9930 genome for each RIL. Based on the previous resequencing data of 9110Gt (five-fold genome coverage), we identified 116 710 SNPs between the parental lines (Supplemental Figure 1 and Supplemental Table 1), adding 10 629 novel polymorphic sites into the cucumber genomic variation map (Qi et al., 2013). In the RILs, 99.3% (115 933) of the 116 710 parental SNPs were present and genotyped. All SNPs were imported into a hidden Markov model (HMM) to infer recombination events, and thus we detected 2084 recombination events (Figure 1A) with an average of 2.0 crossovers per chromosome. The crossovers were delimited into an average 207-kb interval, which was substantially refined compared with the current resolution of 788 kb based on SSR markers for the same population (Miao et al., 2011) (Supplemental Figure 2). By aligning the recombination maps of all RILs, we defined the block of the same genotype across the entire population as a raw bin (Figure 1B) and constructed a genetic linkage map spanning 1384.4 cM with bin markers. After lumping successive raw bins with identical genetic position, 759 unique bins were anchored on seven linkage groups corresponding to seven chromosomes (Supplemental Tables 1 and 3). These bins had an average physical length of 248.8 kb, ranging from 10.6 kb
to 1.6 Mb, representing more than 98% of the 9930 reference genome. We observed 13 segregation distortion regions (SDRs) on the whole genome involving 67 bins (Supplemental Figure 3 and Supplemental Table 4). Among them, 10 SDRs including the largest SDR comprising 41 bins on chromosome 6 displayed a preference for 9930 alleles. Based on SNP locations on the reference genome, the bin map was integrated with the physical map, and we found that 99% (748/759) of bins showed concordance between the genetic and physical positions (Figure 1C) indicating high accuracy of the map construction. However, we noticed that nine bins (C5B469–C5B477) covering 0–3.3 Mb on chromosome 5 were genetically placed between C5B468 and C5B478, which were physically located at 12.3–12.4 Mb on chromosome 5. The nine scaffolds within the C5B469–C5B477 region were anchored on the distal end of the short arm of chromosome 5 based on the previous SSR map (Ren et al., 2009), on which most markers in this region were clustered because of an inversion between the cultivated (Gy14) and wild (C. sativus var. hardwickii, PI 183967) parental lines used for that map construction. In addition, fluorescence in situ hybridization analysis highlighted that two of nine scaffolds were misplaced and should be placed in the interval from 11.1 to 13.5 Mb on chromosome 5 (Sun et al., 2013). Taken together, we concluded that the chromosome 5 0–3.3 Mb segments of the draft 9930 genome were previously misplaced and should be resettled between 12.3 and 12.4 Mb. We found that the recombination rate varies extensively from 0 to 25.2 cM/Mb on the genome with a mean of 7.2 cM/Mb. On chromosomes 3, 5, and 7 the recombination rate reduced at the pericentromeric region but such tendency was not clear on the other chromosomes (Supplemental Figure 4A). We identified 22 intervals scattering on seven chromosomes with a significantly elevated recombination rate (t test, P < 0.01) revealing the existence of recombination hotspots in cucumber (Supplemental Figure 4B). To assess the efficiency of the bin map for genetic mapping, we re-mapped qualitative genes that had been mapped with SSR markers (Miao et al., 2011). In all cases, the genes were localized into smaller intervals indicating improved precision of the bin map. Two linked genes, D for dull fruit skin and H for heavy fruit netting, were refined from the 8.3 Mb to 1.2 Mb region on chromosome 5 involving two bins C5B505 and C5B506. The locus for foliage bitterness was localized into a 543-kb interval on chromosome 6 containing the cloned cucurbitadienol synthase coding gene Bi (Shang et al., 2014) indicating the high quality of the bin map.
Published by the Molecular Plant Shanghai Editorial Office in association with Cell Press, an imprint of Elsevier Inc., on behalf of CSPB and IPPE, SIBS, CAS.
Molecular Plant 8, 961–963, June 2015 ª The Author 2015.
961
Molecular Plant
Letter to the Editor
Figure 1. High Density Genetic Map Construction and QTL Mapping. (A) Recombination map of 147 RILs. Blue, 9110Gt; gray, unknown; red, 9930. (B) Schematic representation defining the raw recombination bins. (C) Integration of physical (left) and genetic (right) maps. Red blocks show the physical interval of the bins; the yellow blocks are the gaps between the bins. Blue short lines represent the genetic positions of the bin markers. (D) QTL mapping for fruit wart size, uniform immature fruit color using the bin map. Phenotypic data were collected in the spring of 2006 (06S), autumn of 2006 (06A), autumn of 2007 (07A) and spring of 2009 (09S). The repeatable QTLs are marked near the peaks of the LOD value.
Scab, caused by Cladosporium cucumerinum, is a devastating fungal disease that attacks almost all cucurbit vegetables and causes heavy economic losses. The cucumber scab resistance gene Ccu confers stable resistance and has been a very valuable gene in cucumber breeding (Kang et al., 2011). By analyses of a segregating population of 1944 F2 plants, Ccu was mapped to a 180-kb genomic region that harbors four nucleotide binding site leucine-rich repeat (NBS-LRR) type resistance gene (Kang et al., 2011). Using the bin map, we delimited Ccu into bin C2B123, which spans 191 kb. Bin C2B123 and the 180-kb 962
Molecular Plant 8, 961–963, June 2015 ª The Author 2015.
region overlapped at an interval of 88 kb, where only one NBSLRR gene, Csa2G021710, is present, which seems to be a strong candidate gene for Ccu. Using the bin map, we also detected 28 QTLs above the permutated LOD thresholds for 10 quantitatively inherited traits (multiple fruit epidermal features were showed in Supplemental Figure 5). Among them, 15 were reproducible in more than two experiments (Supplemental Table 2) and 15 were newly detected that would provide fresh loci and haplotypes for
Molecular Plant
Letter to the Editor molecular marker-assisted selection in cucumber breeding (Supplemental Tables 2 and 4). The major-effect QTL for fruit wart size, fws5, was resolved into a single bin C5B506 in all four trials (Figure 1D); it was 520 kb in length and harbored the cloned fruit wart gene Tu (Yang et al., 2014). The major QTL for uniform immature fruit color u5 was also mapped to the bin C5B506 in all three trials (Figure 1D); it contained the 313.2-kb interval previously determined using 800 segregants (Yang et al., 2013). Major QTLs for fruit ribbing, fr5, and for mature fruit color, mfc5, were mapped at the neighboring region C5B496–C5B505. The clustering of fruitassociated trait QTLs fws5, u5, fr5, mfc5 and the two Mendelian genes D and H suggested the region of C5B496–C5B506, located at 17.5–20.4 Mb on chromosome 5, played an important role in cucumber fruit development. The cucumber genomic variation map revealed two selective sweeps, DS078 and DS079, within this region (Qi et al., 2013), supporting the vital role of this region during cucumber domestication. Within this region, 320 genes are predicted and 185 of them are expressed in fruits (Supplemental Table 5). We detected 1490 parental SNPs in this region and 39 of them are non-synonymous resulting in missense or nonsense mutations in 25 genes. Among 25 genes, 13 genes are expressed in fruits (Supplemental Table 5), thus providing candidates for these fruit-associated traits. Discovery of this genomic region, key to cucumber fruit external quality, will pave the way for gene cloning and fruit quality improvement in breeding. Overall, we generated an ultra-high-density genetic map with high resolution and accuracy by multiplexed sequencing of an RIL population. Using this map, we identified a strong candidate for the Ccu gene conferring scab resistance and revealed a genomic region conferring multiple fruit epidermal features. This should be a valuable tool for molecular breeding and facilitate our understanding of cucumber biology.
SUPPLEMENTAL INFORMATION Supplemental Information is available at Molecular Plant Online.
FUNDING This work was supported by funding from the National Natural Science Foundation of China (NSFC: 31272161, 31322047, 31225025), the earmarked fund for Modern Agro-industry Technology Research System (CARS-25), the National Program on Key Basic Research Projects in China (the 973 Program: 2012CB113900), and the Chinese Ministry of Finance (1251610601001).
ACKNOWLEDGMENTS No conflict of interest declared. Received: January 9, 2015 Revised: March 7, 2015 Accepted: March 10, 2015 Published: March 17, 2015
Qian Zhou1,2,4, Han Miao1,4, Shuai Li1,4, Shengping Zhang1, Ye Wang1, Yiqun Weng3, Zhonghua Zhang1,*, Sanwen Huang1,2,* and Xingfang Gu1,* 1 Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10081, China 2 Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China 3 Vegetable Crops Research Unit, Department of Horticulture, United States Department of Agriculture (USDA), ARS, University of Wisconsin, Madison, WI 53706, USA 4 These authors contributed equally to this article. *Correspondence: Sanwen Huang ([email protected]), Xingfang Gu ([email protected]), Zhonghua Zhang ([email protected]) http://dx.doi.org/10.1016/j.molp.2015.03.008
REFERENCES Huang, S., Li, R., Zhang, Z., Li, L., Gu, X., Fan, W., Lucas, W.J., Wang, X., Xie, B., Ni, P., et al. (2009a). The genome of the cucumber, Cucumis sativus L. Nat. Genet. 41:1275–1281. Huang, X., Feng, Q., Qian, Q., Zhao, Q., Wang, L., Wang, A., Guan, J., Fan, D., Weng, Q., Huang, T., et al. (2009b). High-throughput genotyping by whole-genome resequencing. Genome Res. 19:1068– 1076. Kang, H., Weng, Y., Yang, Y., Zhang, Z., Zhang, S., Mao, Z., Cheng, G., Gu, X., Huang, S., and Xie, B. (2011). Fine genetic mapping localizes cucumber scab resistance gene Ccu into an R gene cluster. Theor. Appl. Genet. 122:795–803. Miao, H., Zhang, S., Wang, X., Zhang, Z., Li, M., Mu, S., Cheng, Z., Zhang, R., Huang, S., Xie, B., et al. (2011). A linkage map of cultivated cucumber (Cucumis sativus L.) with 248 microsatellite marker loci and seven genes for horticulturally important traits. Euphytica 182:167–176. Qi, J., Liu, X., Shen, D., Miao, H., Xie, B., Li, X., Zeng, P., Wang, S., Shang, Y., Gu, X., et al. (2013). A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat. Genet. 45:1510–1515. Ren, Y., Zhang, Z., Liu, J., Staub, J.E., Han, Y., Cheng, Z., Li, X., Lu, J., Miao, H., Kang, H., et al. (2009). An integrated genetic and cytogenetic map of the cucumber genome. PLoS One 4:e5795. Shang, Y., Ma, Y., Zhou, Y., Zhang, H., Duan, L., Chen, H., Zeng, J., Zhou, Q., Wang, S., Gu, W., et al. (2014). Biosynthesis, regulation, and domestication of bitterness in cucumber. Science 346:1084–1088. Sun, J., Zhang, Z., Zong, X., Huang, S., Li, Z., and Han, Y. (2013). A highresolution cucumber cytogenetic map integrated with the genome assembly. BMC Genomics 14:461. Yang, X., Li, Y., Zhang, W., He, H., Pan, J., and Cai, R. (2013). Fine mapping of the uniform immature fruit color gene u in cucumber (Cucumis sativus L.). Euphytica 196:341–348. Yang, X., Zhang, W., He, H., Nie, J., Bie, B., Zhao, J., Ren, G., Li, Y., Zhang, D., Pan, J., et al. (2014). Tuberculate fruit gene Tu encodes a C2 H2 zinc finger protein that is required for the warty fruit phenotype in cucumber (Cucumis sativus L.). Plant J. 78:1034–1046.
Molecular Plant 8, 961–963, June 2015 ª The Author 2015.
963
A Sequencing-Based Linkage Map of Cucumber Dear Editor, Cucumber (Cucumis sativus L., 2n = 2x = 14) is an economically important vegetable worldwide and has served as a model system for plant vascular biology and sex determination studies. We reported the draft genome assembly of the North China type cucumber line 9930 in 2009 (Huang et al., 2009a) and constructed a single-base resolution map of cucumber genomic variation by resequencing of the genomes of 115 core germplasm lines (Qi et al., 2013), which enabled genome-wide association studies of important traits in cucumber (Shang et al., 2014). The genome sequences available for cucumber facilitated the development of PCR-based markers and the construction of the genetic linkage maps (Ren et al., 2009; Miao et al., 2011). However, the density and resolution of these linkage maps are insufficient for accurately mapping genes or quantitative trait loci (QTLs) of interest. The advent of the next-generation sequencing technology provides an alternative for marker discovery and genotyping, which has increased the marker density in genetic studies by several orders of magnitude. As a good example in rice, through sequencing 150 recombinant inbred lines (RILs) at 0.023 coverage, over 1 million single nucleotide polymorphisms (SNPs) were genotyped and a major QTL for plant height was delimited into a 100-kb interval (Huang et al., 2009b). In this study, we constructed an ultra-high-density cucumber genetic map using the RIL population derived from a gynoecious line 9110Gt from Europe and a monoecious line 9930 from North China, which was phenotyped over multiple seasons. We generated 73 Gb sequences by barcoded multiplexed sequencing of 147 RILs, equivalent to approximately 500 Mb per RIL, covering about 33% of the assembled 9930 genome for each RIL. Based on the previous resequencing data of 9110Gt (five-fold genome coverage), we identified 116 710 SNPs between the parental lines (Supplemental Figure 1 and Supplemental Table 1), adding 10 629 novel polymorphic sites into the cucumber genomic variation map (Qi et al., 2013). In the RILs, 99.3% (115 933) of the 116 710 parental SNPs were present and genotyped. All SNPs were imported into a hidden Markov model (HMM) to infer recombination events, and thus we detected 2084 recombination events (Figure 1A) with an average of 2.0 crossovers per chromosome. The crossovers were delimited into an average 207-kb interval, which was substantially refined compared with the current resolution of 788 kb based on SSR markers for the same population (Miao et al., 2011) (Supplemental Figure 2). By aligning the recombination maps of all RILs, we defined the block of the same genotype across the entire population as a raw bin (Figure 1B) and constructed a genetic linkage map spanning 1384.4 cM with bin markers. After lumping successive raw bins with identical genetic position, 759 unique bins were anchored on seven linkage groups corresponding to seven chromosomes (Supplemental Tables 1 and 3). These bins had an average physical length of 248.8 kb, ranging from 10.6 kb
to 1.6 Mb, representing more than 98% of the 9930 reference genome. We observed 13 segregation distortion regions (SDRs) on the whole genome involving 67 bins (Supplemental Figure 3 and Supplemental Table 4). Among them, 10 SDRs including the largest SDR comprising 41 bins on chromosome 6 displayed a preference for 9930 alleles. Based on SNP locations on the reference genome, the bin map was integrated with the physical map, and we found that 99% (748/759) of bins showed concordance between the genetic and physical positions (Figure 1C) indicating high accuracy of the map construction. However, we noticed that nine bins (C5B469–C5B477) covering 0–3.3 Mb on chromosome 5 were genetically placed between C5B468 and C5B478, which were physically located at 12.3–12.4 Mb on chromosome 5. The nine scaffolds within the C5B469–C5B477 region were anchored on the distal end of the short arm of chromosome 5 based on the previous SSR map (Ren et al., 2009), on which most markers in this region were clustered because of an inversion between the cultivated (Gy14) and wild (C. sativus var. hardwickii, PI 183967) parental lines used for that map construction. In addition, fluorescence in situ hybridization analysis highlighted that two of nine scaffolds were misplaced and should be placed in the interval from 11.1 to 13.5 Mb on chromosome 5 (Sun et al., 2013). Taken together, we concluded that the chromosome 5 0–3.3 Mb segments of the draft 9930 genome were previously misplaced and should be resettled between 12.3 and 12.4 Mb. We found that the recombination rate varies extensively from 0 to 25.2 cM/Mb on the genome with a mean of 7.2 cM/Mb. On chromosomes 3, 5, and 7 the recombination rate reduced at the pericentromeric region but such tendency was not clear on the other chromosomes (Supplemental Figure 4A). We identified 22 intervals scattering on seven chromosomes with a significantly elevated recombination rate (t test, P < 0.01) revealing the existence of recombination hotspots in cucumber (Supplemental Figure 4B). To assess the efficiency of the bin map for genetic mapping, we re-mapped qualitative genes that had been mapped with SSR markers (Miao et al., 2011). In all cases, the genes were localized into smaller intervals indicating improved precision of the bin map. Two linked genes, D for dull fruit skin and H for heavy fruit netting, were refined from the 8.3 Mb to 1.2 Mb region on chromosome 5 involving two bins C5B505 and C5B506. The locus for foliage bitterness was localized into a 543-kb interval on chromosome 6 containing the cloned cucurbitadienol synthase coding gene Bi (Shang et al., 2014) indicating the high quality of the bin map.
Published by the Molecular Plant Shanghai Editorial Office in association with Cell Press, an imprint of Elsevier Inc., on behalf of CSPB and IPPE, SIBS, CAS.
Molecular Plant 8, 961–963, June 2015 ª The Author 2015.
961
Molecular Plant
Letter to the Editor
Figure 1. High Density Genetic Map Construction and QTL Mapping. (A) Recombination map of 147 RILs. Blue, 9110Gt; gray, unknown; red, 9930. (B) Schematic representation defining the raw recombination bins. (C) Integration of physical (left) and genetic (right) maps. Red blocks show the physical interval of the bins; the yellow blocks are the gaps between the bins. Blue short lines represent the genetic positions of the bin markers. (D) QTL mapping for fruit wart size, uniform immature fruit color using the bin map. Phenotypic data were collected in the spring of 2006 (06S), autumn of 2006 (06A), autumn of 2007 (07A) and spring of 2009 (09S). The repeatable QTLs are marked near the peaks of the LOD value.
Scab, caused by Cladosporium cucumerinum, is a devastating fungal disease that attacks almost all cucurbit vegetables and causes heavy economic losses. The cucumber scab resistance gene Ccu confers stable resistance and has been a very valuable gene in cucumber breeding (Kang et al., 2011). By analyses of a segregating population of 1944 F2 plants, Ccu was mapped to a 180-kb genomic region that harbors four nucleotide binding site leucine-rich repeat (NBS-LRR) type resistance gene (Kang et al., 2011). Using the bin map, we delimited Ccu into bin C2B123, which spans 191 kb. Bin C2B123 and the 180-kb 962
Molecular Plant 8, 961–963, June 2015 ª The Author 2015.
region overlapped at an interval of 88 kb, where only one NBSLRR gene, Csa2G021710, is present, which seems to be a strong candidate gene for Ccu. Using the bin map, we also detected 28 QTLs above the permutated LOD thresholds for 10 quantitatively inherited traits (multiple fruit epidermal features were showed in Supplemental Figure 5). Among them, 15 were reproducible in more than two experiments (Supplemental Table 2) and 15 were newly detected that would provide fresh loci and haplotypes for
Molecular Plant
Letter to the Editor molecular marker-assisted selection in cucumber breeding (Supplemental Tables 2 and 4). The major-effect QTL for fruit wart size, fws5, was resolved into a single bin C5B506 in all four trials (Figure 1D); it was 520 kb in length and harbored the cloned fruit wart gene Tu (Yang et al., 2014). The major QTL for uniform immature fruit color u5 was also mapped to the bin C5B506 in all three trials (Figure 1D); it contained the 313.2-kb interval previously determined using 800 segregants (Yang et al., 2013). Major QTLs for fruit ribbing, fr5, and for mature fruit color, mfc5, were mapped at the neighboring region C5B496–C5B505. The clustering of fruitassociated trait QTLs fws5, u5, fr5, mfc5 and the two Mendelian genes D and H suggested the region of C5B496–C5B506, located at 17.5–20.4 Mb on chromosome 5, played an important role in cucumber fruit development. The cucumber genomic variation map revealed two selective sweeps, DS078 and DS079, within this region (Qi et al., 2013), supporting the vital role of this region during cucumber domestication. Within this region, 320 genes are predicted and 185 of them are expressed in fruits (Supplemental Table 5). We detected 1490 parental SNPs in this region and 39 of them are non-synonymous resulting in missense or nonsense mutations in 25 genes. Among 25 genes, 13 genes are expressed in fruits (Supplemental Table 5), thus providing candidates for these fruit-associated traits. Discovery of this genomic region, key to cucumber fruit external quality, will pave the way for gene cloning and fruit quality improvement in breeding. Overall, we generated an ultra-high-density genetic map with high resolution and accuracy by multiplexed sequencing of an RIL population. Using this map, we identified a strong candidate for the Ccu gene conferring scab resistance and revealed a genomic region conferring multiple fruit epidermal features. This should be a valuable tool for molecular breeding and facilitate our understanding of cucumber biology.
SUPPLEMENTAL INFORMATION Supplemental Information is available at Molecular Plant Online.
FUNDING This work was supported by funding from the National Natural Science Foundation of China (NSFC: 31272161, 31322047, 31225025), the earmarked fund for Modern Agro-industry Technology Research System (CARS-25), the National Program on Key Basic Research Projects in China (the 973 Program: 2012CB113900), and the Chinese Ministry of Finance (1251610601001).
ACKNOWLEDGMENTS No conflict of interest declared. Received: January 9, 2015 Revised: March 7, 2015 Accepted: March 10, 2015 Published: March 17, 2015
Qian Zhou1,2,4, Han Miao1,4, Shuai Li1,4, Shengping Zhang1, Ye Wang1, Yiqun Weng3, Zhonghua Zhang1,*, Sanwen Huang1,2,* and Xingfang Gu1,* 1 Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10081, China 2 Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China 3 Vegetable Crops Research Unit, Department of Horticulture, United States Department of Agriculture (USDA), ARS, University of Wisconsin, Madison, WI 53706, USA 4 These authors contributed equally to this article. *Correspondence: Sanwen Huang ([email protected]), Xingfang Gu ([email protected]), Zhonghua Zhang ([email protected]) http://dx.doi.org/10.1016/j.molp.2015.03.008
REFERENCES Huang, S., Li, R., Zhang, Z., Li, L., Gu, X., Fan, W., Lucas, W.J., Wang, X., Xie, B., Ni, P., et al. (2009a). The genome of the cucumber, Cucumis sativus L. Nat. Genet. 41:1275–1281. Huang, X., Feng, Q., Qian, Q., Zhao, Q., Wang, L., Wang, A., Guan, J., Fan, D., Weng, Q., Huang, T., et al. (2009b). High-throughput genotyping by whole-genome resequencing. Genome Res. 19:1068– 1076. Kang, H., Weng, Y., Yang, Y., Zhang, Z., Zhang, S., Mao, Z., Cheng, G., Gu, X., Huang, S., and Xie, B. (2011). Fine genetic mapping localizes cucumber scab resistance gene Ccu into an R gene cluster. Theor. Appl. Genet. 122:795–803. Miao, H., Zhang, S., Wang, X., Zhang, Z., Li, M., Mu, S., Cheng, Z., Zhang, R., Huang, S., Xie, B., et al. (2011). A linkage map of cultivated cucumber (Cucumis sativus L.) with 248 microsatellite marker loci and seven genes for horticulturally important traits. Euphytica 182:167–176. Qi, J., Liu, X., Shen, D., Miao, H., Xie, B., Li, X., Zeng, P., Wang, S., Shang, Y., Gu, X., et al. (2013). A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat. Genet. 45:1510–1515. Ren, Y., Zhang, Z., Liu, J., Staub, J.E., Han, Y., Cheng, Z., Li, X., Lu, J., Miao, H., Kang, H., et al. (2009). An integrated genetic and cytogenetic map of the cucumber genome. PLoS One 4:e5795. Shang, Y., Ma, Y., Zhou, Y., Zhang, H., Duan, L., Chen, H., Zeng, J., Zhou, Q., Wang, S., Gu, W., et al. (2014). Biosynthesis, regulation, and domestication of bitterness in cucumber. Science 346:1084–1088. Sun, J., Zhang, Z., Zong, X., Huang, S., Li, Z., and Han, Y. (2013). A highresolution cucumber cytogenetic map integrated with the genome assembly. BMC Genomics 14:461. Yang, X., Li, Y., Zhang, W., He, H., Pan, J., and Cai, R. (2013). Fine mapping of the uniform immature fruit color gene u in cucumber (Cucumis sativus L.). Euphytica 196:341–348. Yang, X., Zhang, W., He, H., Nie, J., Bie, B., Zhao, J., Ren, G., Li, Y., Zhang, D., Pan, J., et al. (2014). Tuberculate fruit gene Tu encodes a C2 H2 zinc finger protein that is required for the warty fruit phenotype in cucumber (Cucumis sativus L.). Plant J. 78:1034–1046.
Molecular Plant 8, 961–963, June 2015 ª The Author 2015.
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