Loci and candidate gene identification for soybean resistance to Phytophthora root rot race 1 in combination with associ
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Loci and candidate gene identification for soybean resistance to Phytophthora root rot race 1 in combination with association and linkage mapping Xue Zhao & Dongfang Bao & Wei Wang & Chanjuan Zhang & Yan Jing & Haipeng Jiang & Lijuan Qiu & Wenbin Li & Yingpeng Han
Received: 27 August 2019 / Accepted: 30 September 2020 # Springer Nature B.V. 2020
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
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11032-020-01179-9) contains supplementary material, which is available to authorized users. X. Zhao : D. Bao : W. Wang : C. Zhang : Y. Jing : H. Jiang : W. Li (*) : Y. Han (*) Key Laboratory of Soybean Biology in Chinese Ministry of Education (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, 150030 Harbin, China e-mail: [email protected] e-mail: [email protected]
Sequencing (SLAF-seq) approach, and 28,722 singlenucleotide 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. Keywords Association analysis . Candidate genes . Linkage analysis . Phytophthora sojae resistance . Soybean
Introduction L. Qiu Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, 100081 Beijing, China
Phytophthora sojae (P. sojae), a soil-borne oomycete pathogen, causes Phytophthora root or stem-rot (PRR) of soybean
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