title: Pinpointing genes underlying the quantitative trait loci for root-knot nematode resistance in palaeopolyploid soybean by whole genome resequencing.
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.
authors.affiliation: Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO 65211, USA. xiangyang.xu@ars.usda.gov
authors.forename: Xiangyang
authors.initials: X
authors.lastname: Xu
authors.forename: Liang
authors.initials: L
authors.lastname: Zeng
authors.forename: Ye
authors.initials: Y
authors.lastname: Tao
authors.forename: Tri
authors.initials: T
authors.lastname: Vuong
authors.forename: Jinrong
authors.initials: J
authors.lastname: Wan
authors.forename: Roger
authors.initials: R
authors.lastname: Boerma
authors.forename: Jim
authors.initials: J
authors.lastname: Noe
authors.forename: Zenglu
authors.initials: Z
authors.lastname: Li
authors.forename: Steve
authors.initials: S
authors.lastname: Finnerty
authors.forename: Safiullah M
authors.initials: SM
authors.lastname: Pathan
authors.forename: J Grover
authors.initials: JG
authors.lastname: Shannon
authors.forename: Henry T
authors.initials: HT
authors.lastname: Nguyen
mesh_terms: D000818:Animals; D001483:Base Sequence; D002265:Carboxylic Ester Hydrolases / Q000037:antagonists & inhibitors; D002874:Chromosome Mapping; D003433:Crosses, Genetic; D060467:Disease Resistance / Q000235:genetics*; D020869:Gene Expression Profiling; D018745:Genome, Plant / Q000235:genetics; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D009348:Nematoda; D010935:Plant Diseases / Q000469:parasitology*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011123:Polyploidy; D040641:Quantitative Trait Loci / Q000235:genetics*; D013025:Glycine max / Q000235:genetics* / Q000469:parasitology
chemical_list: D002265:Carboxylic Ester Hydrolases; C022323:pectinesterase
keywords: high resolution linkage map; high throughput genotyping
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