title: Genomic-assisted phylogenetic analysis and marker development for next generation soybean cyst nematode resistance breeding.
abstract: Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is a serious soybean pest. The use of resistant cultivars is an effective approach for preventing yield loss. In this study, 19,652 publicly available soybean accessions that were previously genotyped with the SoySNP50K iSelect BeadChip were used to evaluate the phylogenetic diversity of SCN resistance genes Rhg1 and Rhg4 in an attempt to identify novel sources of resistance. The sequence information of soybean lines was utilized to develop KASPar (KBioscience Competitive Allele-Specific PCR) assays from single nucleotide polymorphisms (SNPs) of Rhg1, Rhg4, and other novel quantitative trait loci (QTL). These markers were used to genotype a diverse set of 95 soybean germplasm lines and three recombinant inbred line (RIL) populations. SNP markers from the Rhg1 gene were able to differentiate copy number variation (CNV), such as resistant-high copy (PI 88788-type), low copy (Peking-type), and susceptible-single copy (Williams 82) numbers. Similarly, markers for the Rhg4 gene were able to detect Peking-type (resistance) genotypes. The phylogenetic information of SCN resistance loci from a large set of soybean accessions and the gene/QTL specific markers that were developed in this study will accelerate SCN resistance breeding programs.
authors.affiliation: Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO 65211, USA. Electronic address: kadamsu@missouri.edu.
authors.forename: Suhas
authors.initials: S
authors.lastname: Kadam
authors.affiliation: Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO 65211, USA. Electronic address: vuongt@missouri.edu.
authors.forename: Tri D
authors.initials: TD
authors.lastname: Vuong
authors.affiliation: Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO 65211, USA. Electronic address: qiud@missouri.edu.
authors.forename: Dan
authors.initials: D
authors.lastname: Qiu
authors.affiliation: Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO 65211, USA. Electronic address: meinhardtc@missouri.edu.
authors.forename: Clinton G
authors.initials: CG
authors.lastname: Meinhardt
authors.affiliation: Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO 65211, USA. Electronic address: songli@missouri.edu.
authors.forename: Li
authors.initials: L
authors.lastname: Song
authors.affiliation: Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO 65211, USA. Electronic address: deshmukhr@missouri.edu.
authors.forename: Rupesh
authors.initials: R
authors.lastname: Deshmukh
authors.affiliation: Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO 65211, USA. Electronic address: patilg@missouri.edu.
authors.forename: Gunvant
authors.initials: G
authors.lastname: Patil
authors.affiliation: Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO 65211, USA. Electronic address: wanj@missouri.edu.
authors.forename: Jinrong
authors.initials: J
authors.lastname: Wan
authors.affiliation: Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO 65211, USA. Electronic address: valliyodanb@missouri.edu.
authors.forename: Babu
authors.initials: B
authors.lastname: Valliyodan
authors.affiliation: Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO 65211, USA. Electronic address: scabooa@missouri.edu.
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Scaboo
authors.affiliation: Division of Plant Sciences and NCSB, University of Missouri, Portageville, MO 63873, USA. Electronic address: shannong@missouri.edu.
authors.forename: J Grover
authors.initials: JG
authors.lastname: Shannon
authors.affiliation: Division of Plant Sciences and National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO 65211, USA. Electronic address: nguyenhenry@missouri.edu.
authors.forename: Henry T
authors.initials: HT
authors.lastname: Nguyen
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D056915:DNA Copy Number Variations; D060467:Disease Resistance / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D023281:Genomics / Q000379:methods*; D005838:Genotype; D006790:Host-Parasite Interactions; D010802:Phylogeny; D000069600:Plant Breeding / Q000379:methods*; D010935:Plant Diseases / Q000235:genetics* / Q000469:parasitology; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000145:classification / Q000235:genetics* / Q000469:parasitology; D014431:Tylenchoidea / Q000502:physiology
chemical_list: D005819:Genetic Markers
keywords: Copy Number Variation; Digital-PCR assay; KASPar assay; Phylogenetic diversity; SCN resistance genes/QTL; SNP genotyping; Soybean