Fine mapping of a Phytophthora-resistance gene RpsWY in soybean (Glycine max L.) by high-throughput genome-wide sequencing

Abstract

Key messageUsing a combination of phenotypic screening, genetic and statistical analyses, and high-throughput genome-wide sequencing, we have finely mapped a dominant Phytophthora resistance gene in soybean cultivar Wayao.Abstract Phytophthora root rot (PRR) caused by Phytophthora sojae is one of the most important soil-borne diseases in many soybean-production regions in the world. Identification of resistant gene(s) and incorporating them into elite varieties are an effective way for breeding to prevent soybean from being harmed by this disease. Two soybean populations of 191 F2 individuals and 196 F7:8 recombinant inbred lines (RILs) were developed to map Rps gene by crossing a susceptible cultivar Huachun 2 with the resistant cultivar Wayao. Genetic analysis of the F2 population indicated that PRR resistance in Wayao was controlled by a single dominant gene, temporarily named RpsWY, which was mapped on chromosome 3. A high-density genetic linkage bin map was constructed using 3469 recombination bins of the RILs to explore the candidate genes by the high-throughput genome-wide sequencing. The results of genotypic analysis showed that the RpsWY gene was located in bin 401 between 4466230 and 4502773 bp on chromosome 3 through line 71 and 100 of the RILs. Four predicted genes (Glyma03g04350, Glyma03g04360, Glyma03g04370, and Glyma03g04380) were found at the narrowed region of 36.5 kb in bin 401. These results suggest that the high-throughput genome-wide resequencing is an effective method to fine map PRR candidate genes.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-017-2869-5) contains supplementary material, which is available to authorized users.

A major natural genetic variation associated with root system architecture and plasticity improves waterlogging tolerance and yield in soybean

“…The bars flank the candidate region of the QTL for each year and the arrows point at the peaks of the corresponding QTL for each year The nearest maker to the peak position of the LOD distribution in the QTL in the progeny population of NIL147-87 confirmed the qWT_Gm03-containing interval and excluded genomic region downstream of Gm03_3517250_A/C. Previously, a locus (Rps1) conferring resistance to Phytophthora root rot caused by Phytophthora sojae was mapped near the qWT_Gm03 region (Cheng et al, 2017;Gao & Bhattacharyya, 2008). Based on the fine-mapping results, this resistance locus is excluded from the candidate region of qWT_Gm03 (Figure 4).…”

Fine mapping of a Phytophthora-resistance locus RpsGZ in soybean using genotyping-by-sequencing

“…Previous studies have identified 17 known Rps genes (alleles) and mapped them to chromosome 3 before RpsGZ, including five alleles of Rps1 (Rps1a, 1b, 1c, 1d, 1 k) [23,24,38,57,58], Rps7 [23], Rps9 [29], RpsYu25 [25], an Rps gene in Waseshiroge [26], RpsYD29 [27], an Rps gene in E00003 soybean within the Rps1 k interval [30], RpsHC18 [10], RpsQ [13], RpsHN [14], RpsX [9], RpsWY [31], and RpsUN1 [28]. Nevertheless, the positional relationships of these Rps genes had not been confirmed, and some of the mapping intervals for these Rps genes overlapped.…”

“…RpsQ, RpsX and an unnamed Rps gene in Wascshiroge and E00003 soybean were mapped to chromosome 3 [7,9,10,13,14,[22][23][24][25][26][27][28][29][30][31]. Rps3 (including three alleles, Rps3a, Rps3b and Rps3c) and RpsSN10 were mapped to chromosome 13, which is linked with Rps8 [6,22,32,33].…”

“…NGS technologies have been widely utilized in soybean, wheat, sunflower and other crops to develop SNP markers and map genes/QTLs [11,[43][44][45][46][47]. The dominant soybean Phytophthora root rot resistance gene RpsWY was mapped using a high-density soybean genetic map comprising 3469 recombination bin markers using RAD-seq technology in 196 F 7:8 RILs [31].…”

Genome-wide association analyses of quantitative disease resistance in diverse sets of soybean [Glycine max (L.) Merr.] plant introductions

“…Genetic resistance is considered the most effective strategy for preventing or reducing the impact of Phytophthora diseases [4,7].Soybean-breeding programs have relied on resistance conferred by single, dominantly inherited Resistance to Phytophthora sojae (Rps)-genes. More than 30 Rps-genes/alleles have been mapped (S1 Table) [8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25]. The effectiveness of Rps-mediated resistance is limited as these genes only confer immunity towards specific races of P. sojae.…”