Loci and candidate gene identification for soybean resistance to Phytophthora root rot race 1 in combination with association and linkage mapping

Abstract

As the second most destructive disease in soybean (Glycine max (L.) Merr), Phytophthora root or stem-rot (PRR) of soybean, which was caused by Phytophthora sojae (P. sojae), could lead to a 10–40% or complete yield loss annually. Researches were needed to perform to identify the P. sojae-resistant germplasm and to better understand the genetic basis of P. sojae resistance in soybean. A total of 225 diverse soybean cultivars and 109 recombinant inbred lines (RILs) derived from crossing ‘DongnongL-28’ (resistant to P. sojae race 1) and ‘Hefeng 25’ (susceptible to P. sojae race 1) were used to evaluate P. sojae race 1 resistance. These 225 soybean cultivars were sequenced using the Specific Locus Amplified Fragment Sequencing (SLAF-seq) approach, and 28,722 single-nucleotide polymorphisms (SNPs) were obtained from the mapping of resistant loci through genome-wide association. Eight quantitative trait nucleotides (QTNs) were associated with resistance to P. sojae race 1. The QTN on Chr.03 was colocalised according to linkage mapping of the RILs. A total of 18 candidate genes were predicted in the flanking region of the colocalised locus on Chr.03. There were stress response-related motifs, such as cis-acting regulatory elements involved in salicylic acid or MeJA responsiveness, in the 1-kb upstream region of sixteen genes. Quantitative RT-PCR showed that the Glyma.03G033700 was induced by P. sojae race 1. Association analysis for Rps loci showed that Glyma.03G033700 and Glyma.03G033800 were the candidates near peak SNP. The identified loci along with the candidate genes could be valuable for studying the molecular mechanisms underlying soybean resistance to P. sojae race 1 and breeding resistant varieties.

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Acknowledgements

This study was financially supported by the Heilongjiang Provincial Project (GJ2018GJ0098, GX17B002, JC2018007 and C2018016), the Chinese National Natural Science Foundation (31671717, 31471517), the National Key R & D Project (2016YFD0100304, 2017YFD0101302, and 2017YFD0101306-05), the National Project (2014BAD22B01, 2016ZX08004001-007), the Youth Leading Talent Project of the Ministry of Science and Technology in China (2015RA228), the National Ten-thousand Talents Program, Postdoctoral Fund in Heilongjiang Province (LBH-Z15017, LBH-Q17015), the national project (CARS-04-PS04), the ‘Youth Innovation Talent’ Project of the general undergraduate universities in Heilongjiang province (UNPYSCT-2016145), and the ‘Academic Backbone’ Project of Northeast Agricultural University (17XG22).

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XZ, DFB and WW conceived the study and contributed to population development. CJZ and YJ contributed to genotyping. HPJ contributed to phenotypic evaluation. LJQ, YPH and WBL contributed to the experimental design and writing of the paper. All authors contributed to and approved the final manuscript.

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Correspondence to Wenbin Li or Yingpeng Han.

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Zhao, X., Bao, D., Wang, W. et al. Loci and candidate gene identification for soybean resistance to Phytophthora root rot race 1 in combination with association and linkage mapping. Mol Breeding 40, 100 (2020). https://doi.org/10.1007/s11032-020-01179-9

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Keywords

  • Association analysis
  • Candidate genes
  • Linkage analysis
  • Phytophthora sojae resistance
  • Soybean