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Loci and candidate gene identification for resistance to Phytophthora sojae via association analysis in soybean [Glycine max (L.) Merr.]


Phytophthora sojae is an oomycete soil-borne plant pathogen that causes the serious disease Phytophthora root rot in soybean, leading to great loss of soybean production every year. Understanding the genetic basis of this plant–pathogen interaction is important to improve soybean disease resistance. To discover genes or QTLs underlying naturally occurring variations in soybean P.sojae resistance, we performed a genome-wide association study using 59,845 single-nucleotide polymorphisms identified from re-sequencing of 279 accessions from Yangtze-Huai soybean breeding germplasm. We used two models for association analysis. The same strong peak was detected by both two models on chromosome 13. Within the 500-kb flanking regions, three candidate genes (Glyma13g32980, Glyma13g33900, Glyma13g33512) had SNPs in their exon regions. Four other genes were located in this region, two of which contained a leucine-rich repeat domain, which is an important characteristic of R genes in plants. These candidate genes could be potentially useful for improving the resistance of cultivated soybean to P.sojae in future soybean breeding.

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This study was funded by Modern Agro-industry Technology Research System of China (Grant Number CARS-004-PS10), Genetically modified organisms breeding major projects (Grant Number 2015ZX08004), the key technologies R & D program of Jiangsu (Grant Number BE2013350), Program for Changjiang Scholars and Innovative Research Team in University (Grant Number PCSIRT13073), Jiangsu Collaborative Innovation Center for Modern Crop Production, National Hightech R&D Program of China (Grant Number 2012AA101106), the National Natural Science Foundation of China (Grant Number 31271750).

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Correspondence to Tuanjie Zhao or Han Xing.

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All authors, Lihong Li, Na Guo, Jingping Niu, Zili Wang, Xiaoxia Cui, Jutao Sun, Tuanjie Zhao and Han Xing declare that they have no conflict of interest.

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Communicated by B. Yang.

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Li, L., Guo, N., Niu, J. et al. Loci and candidate gene identification for resistance to Phytophthora sojae via association analysis in soybean [Glycine max (L.) Merr.]. Mol Genet Genomics 291, 1095–1103 (2016). https://doi.org/10.1007/s00438-015-1164-x

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  • Soybean
  • Phytophthora sojae
  • Single-nucleotide polymorphisms
  • Genome-wide association mapping