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Edited* by Qifa Zhang, Huazhong Agricultural University, Wuhan, China, and approved June 4, 2013 (received for review January 16, 2013)
Abstract
The objective of this study was to use next-generation sequencing technologies to dissect quantitative trait loci (QTL) for southern root-knot nematode (RKN) resistance into individual genes in soybean. Two hundred forty-six recombinant inbred lines (RIL) derived from a cross between Magellan (susceptible) and PI 438489B (resistant) were evaluated for RKN resistance in a greenhouse and sequenced at an average of 0.19× depth. A sequence analysis pipeline was developed to identify and validate single-nucleotide polymorphisms (SNPs), infer the parental source of each SNP allele, and genotype the RIL population. Based on 109,273 phased SNPs, recombination events in RILs were identified, and a total of 3,509 bins and 3,489 recombination intervals were defined. About 50.8% of bins contain 1 to 10 genes. A linkage map was subsequently constructed by using bins as molecular markers. Three QTL for RKN resistance were identified. Of these, one major QTL was mapped to bin 10 of chromosome 10, which is 29.7 kb in size and harbors three true genes and two pseudogenes. Based on sequence variations and gene-expression analysis, the candidate genes underlying the major QTL for RKN resistance were pinpointed. They are Glyma10g02150 and Glyma10g02160, encoding a pectin methylesterase inhibitor and a pectin methylesterase inhibitor -pectin methylesterase, respectively. This QTL mapping approach not only combines SNP discovery, SNP validation, and genotyping, but also solves the issues caused by genome duplication and repetitive sequences. Hence, it can be widely used in crops with a reference genome to enhance QTL mapping accuracy.
Footnotes
- ↵1To whom correspondence may be addressed. E-mail: nguyenhenry{at}missouri.edu or xiangyang.xu{at}ars.usda.gov.
Author contributions: X.X. and H.T.N. designed research; X.X., T.V., J.W., R.B., J.N., Z.L., and S.F. performed research; S.M.P., J.G.S., and H.T.N. developed and maintained genetic resources; X.X., L.Z., and Y.T. analyzed data; X.X. wrote the paper; and H.T.N oversaw the project.
The authors declare no conflict of interest.
↵*This Direct Submission article had a prearranged editor.
Data deposition: The sequences reported in this paper have been deposited in Soykb, http://soykb.org/public_data.php.
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1222368110/-/DCSupplemental.
Freely available online through the PNAS open access option.
- Xiangyang Xua,b,1,
- Liang Zengc,d,
- Ye Taoc,
- Tri Vuonga,
- Jinrong Wana,
- Roger Boermae,
- Jim Noef,
- Zenglu Lie,
- Steve Finnertye,f,
- Safiullah M. Pathana,
- J. Grover Shannona, and
- Henry T. Nguyena,1
- aDivision of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO 65211;
- bWheat, Peanut, and Other Field Crop Research, US Department of Agriculture–Agricultural Research Service, Stillwater, OK 74075;
- cBeijing Genome Institute, Shenzhen 518083, China;
- dShanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, 200032, China;
- eCenter for Applied Genetic Technologies and Department of Crop and Soil Sciences, and
- fDepartment of Plant Pathology, University of Georgia, Athens, GA 30602
Edited* by Qifa Zhang, Huazhong Agricultural University, Wuhan, China, and approved June 4, 2013 (received for review January 16, 2013)
Abstract
The objective of this study was to use next-generation sequencing technologies to dissect quantitative trait loci (QTL) for southern root-knot nematode (RKN) resistance into individual genes in soybean. Two hundred forty-six recombinant inbred lines (RIL) derived from a cross between Magellan (susceptible) and PI 438489B (resistant) were evaluated for RKN resistance in a greenhouse and sequenced at an average of 0.19× depth. A sequence analysis pipeline was developed to identify and validate single-nucleotide polymorphisms (SNPs), infer the parental source of each SNP allele, and genotype the RIL population. Based on 109,273 phased SNPs, recombination events in RILs were identified, and a total of 3,509 bins and 3,489 recombination intervals were defined. About 50.8% of bins contain 1 to 10 genes. A linkage map was subsequently constructed by using bins as molecular markers. Three QTL for RKN resistance were identified. Of these, one major QTL was mapped to bin 10 of chromosome 10, which is 29.7 kb in size and harbors three true genes and two pseudogenes. Based on sequence variations and gene-expression analysis, the candidate genes underlying the major QTL for RKN resistance were pinpointed. They are Glyma10g02150 and Glyma10g02160, encoding a pectin methylesterase inhibitor and a pectin methylesterase inhibitor -pectin methylesterase, respectively. This QTL mapping approach not only combines SNP discovery, SNP validation, and genotyping, but also solves the issues caused by genome duplication and repetitive sequences. Hence, it can be widely used in crops with a reference genome to enhance QTL mapping accuracy.
- high throughput genotyping
- high resolution linkage map
Footnotes
- ↵1To whom correspondence may be addressed. E-mail: nguyenhenry{at}missouri.edu or xiangyang.xu{at}ars.usda.gov.
Author contributions: X.X. and H.T.N. designed research; X.X., T.V., J.W., R.B., J.N., Z.L., and S.F. performed research; S.M.P., J.G.S., and H.T.N. developed and maintained genetic resources; X.X., L.Z., and Y.T. analyzed data; X.X. wrote the paper; and H.T.N oversaw the project.
The authors declare no conflict of interest.
↵*This Direct Submission article had a prearranged editor.
Data deposition: The sequences reported in this paper have been deposited in Soykb, http://soykb.org/public_data.php.
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1222368110/-/DCSupplemental.
Freely available online through the PNAS open access option.
Soybean root-knot nematode resistance gene
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