Genomic-assisted phylogenetic analysis and marker development for next generation soybean cyst nematode resistance breeding

Suhas Kadam, Tri D. Vuong, Dan Qiu, Clinton G. Meinhardt, Li Song, Rupesh Deshmukh, Gunvant Patil, Jinrong Wan, Babu Valliyodan, Andrew M. Scaboo, J. Grover Shannon, Henry T. Nguyen

Research output: Contribution to journalArticlepeer-review

73 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)342-350
Number of pages9
JournalPlant Science
Volume242
DOIs
StatePublished - Jun 2 2015

Bibliographical note

Funding Information:
This research was supported by the United Soybean Board and the Missouri Soybean Merchandising Council . The authors acknowledge Adama Tukuli and Theresa Musket, Division of Plant Sciences, University of Missouri, for their technical assistance. The authors would like to thank Drs. Perry B. Cregan and Qijian Song, Soybean Genomics and Improvement Lab, USDA-ARS, Beltsville, MD 20705 for the of SoySNP50K iSelect BeadChip used in this study.

Publisher Copyright:
© 2015 The Authors.

Copyright:
Copyright 2015 Elsevier B.V., All rights reserved.

Keywords

  • Copy Number Variation
  • Digital-PCR assay
  • KASPar assay
  • Phylogenetic diversity
  • SCN resistance genes/QTL
  • SNP genotyping
  • Soybean

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