Development and utilization of CAPS/dCAPS markers based on the SNPs lying in soybean cyst nematode resistant genes Rhg4

Xue Hui Shi, Ying Hui Li, Bai Shuang Yu, Yong Guo, Jia Jun Wang, Li Juan Qiu

Research output: Contribution to journalArticlepeer-review


Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most destructive diseases which largely suppressed soybean production worldwide. Rhg4 was one of two major resistant loci for SCN. In this study two nonsynonymous SNPs (Rhg4-389-G/C and Rhg4-1165-T/A) in GmSHMT were deduced to confer SCN resistance or susceptibility. One CAPS marker (Rhg4-389) and one dCAPS marker (Rhg4-1165) with the advantages of rapid, economic, simple and easy way to use were developed based on two nonsynonymous SNPs (Rhg4-389-G/C and Rhg4-1165-T/A), respectively. Then, a total of 193 soybean cultivars mainly from SCN-applied-core collection were genotyped by markers Rhg4-389 and Rhg4-1165. Linkage disequilibrium (LD) analysis indicated pairwise of Rhg4-389 and Rhg4-1165 was in significant LD (P-value = 0.0001) with r2 of 0.87. Among four haplotypes detected in this panel, Rhg4-389-G/Rhg4-1165-T and Rhg4-389-C/Rhg4-1165-A were predominant; while both Rhg4-389-G/Rhg4-1165-A and Rhg4-389-C/Rhg4-1165-T were rare, which only discovered in the resistant cultivars from China. Rhg4-389-G and Rhg4-1165-T alleles mainly occurred in resistant cultivars, and almost coincided with Rhg4-389-G/ Rhg4-1165-T haplotype. Of 101 resistant cultivars with Rhg4-389-G/Rhg4-1165-T haplotype, 94.1% (95) were resistant to SCN. In this study, we not only developed convenient CAPS/dCAPS markers for marker assisted selection (MAS) breeding, but also dissected the genetic architecture of Rhg4 locus among SCN-applied-core collection. Hopefully, this study will provide helpful information for improving the utilization efficiency of resistant resources in soybean breeding.

Original languageEnglish
Pages (from-to)1463-1471
Number of pages9
JournalActa Agronomica Sinica(China)
Issue number10
StatePublished - 2015
Externally publishedYes


  • CAPS/dCAPS marker
  • Haplotype
  • Marker assisted selection
  • Rhg4
  • Soybean cyst nematode

ASJC Scopus subject areas

  • Biotechnology
  • Agronomy and Crop Science
  • Plant Science


Dive into the research topics of 'Development and utilization of CAPS/dCAPS markers based on the SNPs lying in soybean cyst nematode resistant genes Rhg4'. Together they form a unique fingerprint.

Cite this