Soybean is one of the most important crops in China. There are a large number of soybean accessions in China, of which many PRR resistance cultivars/lines were identified in previous study [10, 13, 14, 52–56]. In the present study, Guizao1 was a PRR-resistance cultivar to P. sojae PNJ4 and PNJ1, and distinct from that of other soybean cultivars tested (Table 1). Genetic analyses of the resistance to P. sojae PNJ4 in Guizao1 was controlled by a single locus.
To more fine map the PRR-resistance locus, RpsGZ was mapped in a population based on genotyping through resequencing, resulting in the integration of 54,002 SNPs into 3748 recombination bin units. These markers were then employed to construct a high-density bin linkage map with an average distance of 0.81 cM between adjacent markers. The map had well-distributed linkage distances and higher resolution than did the conventional map, and gene/QTL mapping was thus more accurate and reliable. The position of RpsGZ was refined through fine mapping to a 460,702 bp interval between 4,022,530 - 4,483,231 bp on chromosome 3, which was the rich regions of Rps gene.
Previous studies showed that 16 known Rps genes were identified and mapped to chromosome 3 before RpsGZ, including five alleles of Rps1 (Rps1a, 1b, 1c, 1d, 1k) [23, 24, 39, 57, 58], Rps7 [23], RpsYu25 [25], Rps9 [29], an Rps gene in Waseshiroge [26], RpsYD29 [27], RpsUN1 [59], an Rps gene in soybean E00003 within the Rps1k interval [30], RpsWY [49], RpsHN14], RpsQ [13], and RpsHC18 [10]. Nevertheless, the positional relationships of these Rps genes had not been confirmed, and a part of the mapping intervals for these Rps genes overlapped. Therefore, whether these genes were allelic or at a new locus need to be confirmed.
In the present study, RpsGZ was a distinct gene from the Rps1 alleles because five differentials carrying Rps1 (1a, 1b, 1c, 1d and 1k) were PRR-susceptible to P. sojae PNJ4, though the candidate region of RpsGZ partly overlaps with the regions of the Rps1 andRps1k. Cultivar Wayao (RpsWY) was susceptible to P. sojae PNJ4 and Guizao1 was resistant to P. sojae PNJ4 [49], and these two mapping parents had different resistance reaction, suggesting that RpsGZ may be different from RpsWY. When compared with the nucleotide position of Rps genes mapped to chromosome 3 (Table 4) according to the Glyma1.0 soybean gene annotation database (http://soybase.org/), the position information of RpsGZ suggests that RpsGZ is distinct from Rps1a, Rps1b, Rps1c, Rps1d, Rps9, RpsQ, RpsYu25 and RpsHC18.
In addition, Rps7 was mapped to a 15,457.9 kb genomic region (3,910,260–19,368,212 bp) flanked by SSR markers Satt009 and Satt125 [23]. The Rps gene in Waseshiroge was located between Satt009 and T003044871 and may reside in the nucleotide region between 3,910,260 and 4,486,048 bp of Williams 82 genome [26]. The Rps gene in cv. E00003 was positioned within interval 4,475,877 to 4,563,799 bp [30]. RpsHN was mapped to a 278.7 kb genomic region flanked by SSR markers SSRSOYN–25 and SSRSOYN–44 and may reside at the nucleotide position 4,227,863 and 4,506,526 bp [14]. RpsUN1 was defined to the region at 4,001,862 - 4,362,217 bp flanked by the two SSR markers BARCSOYSSR_03_0233 and BARCSOYSSR_03_0246 [28]. RpsGZ and the Rps7, RpsHN, RpsUN1, and Rps gene from Waseshiroge or E00003 may be tightly linked genes, different alleles of the same gene, or identical alleles of the same gene. However, further confirmation is needed. Moreover, if the sources of resistance mentioned above carry different resistance genes, a pyramiding effect of different resistance genes may increase the resistance of soybean cultivars to P. sojae.
NBS-LRR genes are the vast family of plant disease resistance genes [60], and local tandem duplication of NBS genes has created many homogenous clustered loci identified in each legume genome studied [61]. Meziadi et al. suggested that NBS-LRR proteins were encoded by one of the largest and most variable multigene families and were often organized into complex clusters of tightly linked genes in plants [62]. In soybean, 319 putative NBS-LRR genes and 175 disease-resistance QTLs were found, with 36 NBS-LRR genes clustered on chromosome 3, and most of the NBS-LRR genes were located at the front end of chromosome 3 [63]. The 16 identified Rps genes were all mapped to the regions between 2,916,450 - 9,758,181 bp on chromosome 3. Among the 20 genes in the region close to RpsGZ detected in this study, 8 tightly linked candidate resistance genes contain a NBS-LRR domain. Most of the R-like genes had the same functional description, including iapoptosis, signal transduction, ADP binding, defense response, systemic acquired resistance, salicylic acid biosynthetic process and other biological and metabolic processes, suggesting that these 8 R-like genes may be involved in defence mechanisms against this disease.