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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Tao, Ye Pathan, Safiullah M. Boerma, Roger Noe, Jim Wan, Jinrong Nguyen, Henry T. Xu, Xiangyang Finnerty, Steve Zeng, Liang Shannon, J. Grover Vuong, Tri Li, Zenglu |
| Description | Author Affiliation: Xu X ( Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO 65211, USA. xiangyang.xu@ars.usda.gov); |
| 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. |
| ISSN | 00278424 |
| e-ISSN | 10916490 |
| Journal | Proceedings of the National Academy of Sciences of the United States of America |
| Issue Number | 33 |
| Volume Number | 110 |
| Language | English |
| Publisher | National Academy of Sciences |
| Publisher Date | 2013-08-01 |
| Publisher Place | United States |
| Access Restriction | Open |
| Subject Keyword | Disease Resistance Genetics Nematoda Plant Diseases Parasitology Polyploidy Quantitative Trait Loci Soybeans Animals Carboxylic Ester Hydrolases Antagonists & Inhibitors Chromosome Mapping Crosses, Genetic Gene Expression Profiling Genome, Plant Genotype High-Throughput Nucleotide Sequencing Molecular Sequence Data Polymorphism, Single Nucleotide Research Support, Non-U.S. Gov't Multidisciplinary |
| Content Type | Text |
| Resource Type | Article |
| Subject | Multidisciplinary |
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