Association mapping of resistance to emerging stem rust pathogen races in spring wheat using genotyping‐by‐sequencing

Abstract

The identification and characterization of resistance genes should outpace the rapid emergence of new P. graminis f. sp. tritici races, such as TTRTF and TTKTT, to mitigate stem rust damage to wheat. The objective of the current study was to identify and characterize P. graminis f. sp. tritici race resistance association signals. A total of 250 North American spring wheat lines were evaluated at the seedling stage with a total of seven isolates including TKKTP, TKTTF, TKTTF, TRTTF, TTRTF, TTKSK, and TTKTT. The lines were genotyped by a GBS platform and 9,042 SNPs were used for identification of chromosome regions associated with resistance against the seven isolates. Strong association signals were detected on chromosomes 6BL (Sr11 gene region) and 4AL, likely Sr7a, for resistance against both TKKTP and TKTTF. Similarly, association signals were also detected on chromosomes 4AL (race TTRTF resistance) and 4BS (race TTKSK and TTKTT resistance). Association analysis based on mean phenotypic differences between closely related isolates identified QTL that were not elucidated by direct association mapping of the responses, individually. Overall, with the exception of race TRTTF, each race shared at least one association signal with another race. However, the number of race-specific association signals are larger than that of association signals common among races suggesting the need for identifying and characterizing QTL/genes for newly emerging stem rust pathogen races. There was also high concordance between PCA-based GWAS association signals and association signals from that of both single and multilocus mixed models.

Genome‐wide association mapping of seedling and adult plant response to stem rust in a durum wheat panel

“…A QTL at the 651-Mb region associated with seedling resistance against race TTKSK maps a region close to a QTL flanking marker (wPt5857, 1 Mb away) reported by Yu et al (2012) and a region associated with barc78 (4 Mb away) reported by Letta et al (2014) (Figure 3; Supplemental Table S1). A region at 718 Mb (718944322 bp) associated with seedling resistance to race TKTTF collocates with several markers reported by Bajgain et al (2015b) including IWB34733, IWB3569, and IWB61312 (809 kb away) for seedling resistance of spring wheat collections against TKTTF, marker IAAV3545 (809 kb) reported by Edae et al (2018) for seedling resistance of spring wheat against race RCRSC, several markers reported by Edae and Rouse (2020) for resistance of spring wheat against races TKTTF isolate from Ethiopia, (TKKTF-ETH, the closest marker is 5.6 Mb away) and TTRTF (2 Mb away), marker IWA4651 (324 kb) linked to Sr7a reported by Gao et al (2017) for seedling resistance of spring wheat against race TTTTF (Figure 4; Supplemental Table S2). Olivera et al (2015) and Bajgain et al (2015b) reported that Sr7a is effective against race TKTTF isolate from Ethiopia but not against the isolate from Germany (Olivera Firpo et al, 2017).…”

“…Chromosome 6A harbored six QTL represented by single and multiple markers Figures 3,4,7,and 9). A QTL at 5 Mb (5,058,172 bp) region associated with field resistance in TKTTF_MS18 is very close to QTL tagging markers IWA7913 (138 kb) and IWB23519 (146 kb) reported by Bajgain et al (2015b), IWB72958 (138 kb) reported by Nirmala et al (2017) as a predictive marker for Sr8155B1, markers IWA7913 (138 kb), and S6A_PART1_3015737/S6A_PART1_3206675 (2 Mb away) The Plant Genome associated with Sr8a reported by Guerrero-Chavez et al (2015) and Edae and Rouse (2020), respectively. Sr8155B1 is effective against several races but not TTKSK and JRCQC at the seedling stage (Nirmala et al, 2017) and Sr8a is ineffective against race TKTTF (Olivera et al, 2015).…”

“…(2017) ( IWA4897 , 11 Mb away) (Figure 9; Supplemental Table S4). On chromosome 1B, an MTA at 11 Mb for seedling resistance to race TKTTF and field resistance in JRCQC_OS20 is close to (4.5 Mb away) the Sr31 locus (Edae & Rouse, 2020). Sr31 is located on the short arm of chromosome 1B and transferred from rye ( Secale cereale L.) to hexaploid wheat.…”

“…A QTL at 683 Mb (not in LD with 681-Mb marker) associated with field resistance in TKTTF_MS19 and JRCQC_MS19 may represent the same regions as a QTL identified by markers wPt1715, wPt4298, and wPt7191 (3 Mb away) reported by Letta et al (2013) (Figure 7; Supplemental Table S3). A QTL flanking marker (wpt8007) reported by Yu et al (2014) (2.6 Mb away) and a locus associated with resistance of spring wheat against race TKTTF-ETH reported by Edae and Rouse (2020) may map the same region as the 721-Mb locus identified in TKTTF_MS19 (Supplemental Table S4). We were unable to determine the position of nine significant MTAs that were identified on unaligned contigs.…”

“…On chromosome 1A, a QTL at 566 Mb for field resistance in TKTTF_MS18 may tag a region close to regions reported by Edae et al (2018) (IWB45411, 9 Mb away) and Mihalyov et al (2017) (IWA4897, 11 Mb away) (Figure 9; Supplemental Table S4). On chromosome 1B, an MTA at 11 Mb for seedling resistance to race TKTTF and field resistance in JRCQC_OS20 is close to (4.5 Mb away) the Sr31 locus (Edae & Rouse, 2020). Sr31 is located on the short arm of chromosome 1B and transferred from rye (Secale cereale L.) to hexaploid wheat.…”