Fine Mapping and Identification of a Novel Phytophthora Root Rot Resistance Locus RpsZS18 on Chromosome 2 in Soybean.

Chao Zhong,Junjie Ding,Liangliang Yao,Suli Sun,Zhendong Zhu,Canxing Duan

doi:10.3389/fpls.2018.00044

Abstract

Phytophthora root rot (PRR) caused by Phytophthora sojae is a major soybean disease that causes severe economic losses worldwide. Using soybean cultivars carrying a Rps resistance gene is the most effective strategy for controlling this disease. We previously detected a novel Phytophthora resistance gene, RpsZS18, on chromosome 2 of the soybean cultivar Zaoshu18. The aim of the present study was to identify and finely map RpsZS18. We used 232 F2:3 families generated from a cross between Zaoshu18 (resistant) and Williams (susceptible) as the mapping population. Simple sequence repeat (SSR) markers distributed on chromosome 2 were used to map RpsZS18. First, 12 SSR markers linked with RpsZS18 were identified by linkage analyses, including two newly developed SSR markers, ZCSSR33 and ZCSSR46, that flanked the gene at distances of 0.9 and 0.5 cM, respectively. Second, PCR-based InDel markers were developed based on sequence differences between the two parents and used to further narrow down the mapping region of RpsZS18 to 71.3 kb. Third, haplotype analyses were carried out in the RpsZS18 region using 14 soybean genotypes with whole-genome resequencing. We detected six genes with unique haplotype sequences in Zaoshu18. Finally, quantitative real-time PCR assays of the six genes revealed an EF-hand calcium-binding domain containing protein encoding gene (Glyma.02g245700), a pfkB carbohydrate kinase encoding gene (Glyma.02g245800), and a gene with no functional annotation (Glyma.02g246300), are putative candidate PRR resistance genes. This study provides useful information for breeding P. sojae-resistant soybean cultivars.

Highlights

Phytophthora root rot (PRR), caused by the soil-borne oomycete Phytophthora sojae (Kanfman and Gerdemann), is a devastating disease in most soybean-growing regions
The best method to control PRR involves growing soybean cultivars with complete resistance because partial resistance to P. sojae is ineffective under conditions of high disease pressure (Schmitthenner, 1999; Dorrance et al, 2003b)
A total of 17 reaction types among the 25 soybean cultivars were formed in response to the 14 P. sojae isolates, and Zaoshu18 showed a distinct reaction type

Summary

Introduction

Phytophthora root rot (PRR), caused by the soil-borne oomycete Phytophthora sojae (Kanfman and Gerdemann), is a devastating disease in most soybean-growing regions. Two types of resistance to P. sojae have been identified in soybean, namely complete and partial resistance (Sugimoto et al, 2012). The best method to control PRR involves growing soybean cultivars with complete resistance because partial resistance to P. sojae is ineffective under conditions of high disease pressure (Schmitthenner, 1999; Dorrance et al, 2003b). Some soybean cultivars and lines carrying Rps genes, including Rps1a, Rps1c, and Rps1k, have been used widely in commercial breeding programs to reduce yield losses caused by PRR (Dorrance and Schmitthenner, 2000; Sugimoto et al, 2012). The exact physical location of Rps1k remains unknown in the soybean Williams 82 (carries Rps1k) reference genome (Lin et al, 2013; Sun et al, 2014; Li et al, 2016), and this has hindered studies of the mechanism of soybean resistance to P. sojae

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Methods

Results