Identification of Disease Resistance Parents and Genome-Wide Association Mapping of Resistance in Spring Wheat

Abstract

The likelihood of success in developing modern cultivars depend on multiple factors, including the identification of suitable parents to initiate new crosses, and characterizations of genomic regions associated with target traits. The objectives of the present study were to (a) determine the best economic weights of four major wheat diseases (leaf spot, common bunt, leaf rust, and stripe rust) and grain yield for multi-trait restrictive linear phenotypic selection index (RLPSI), (b) select the top 10% cultivars and lines (hereafter referred as genotypes) with better resistance to combinations of the four diseases and acceptable grain yield as potential parents, and (c) map genomic regions associated with resistance to each disease using genome-wide association study (GWAS). A diversity panel of 196 spring wheat genotypes was evaluated for their reaction to stripe rust at eight environments, leaf rust at four environments, leaf spot at three environments, common bunt at two environments, and grain yield at five environments. The panel was genotyped with the Wheat 90K SNP array and a few KASP SNPs of which we used 23,342 markers for statistical analyses. The RLPSI analysis performed by restricting the expected genetic gain for yield displayed significant (p < 0.05) differences among the 3125 economic weights. Using the best four economic weights, a subset of 22 of the 196 genotypes were selected as potential parents with resistance to the four diseases and acceptable grain yield. GWAS identified 37 genomic regions, which included 12 for common bunt, 13 for leaf rust, 5 for stripe rust, and 7 for leaf spot. Each genomic region explained from 6.6 to 16.9% and together accounted for 39.4% of the stripe rust, 49.1% of the leaf spot, 94.0% of the leaf rust, and 97.9% of the common bunt phenotypic variance combined across all environments. Results from this study provide valuable information for wheat breeders selecting parental combinations for new crosses to develop improved germplasm with enhanced resistance to the four diseases as well as the physical positions of genomic regions that confer resistance, which facilitates direct comparisons for independent mapping studies in the future.

Identification and characterization of stripe rust, leaf rust, leaf spot, and common bunt resistance in spring wheat

“…Several studies reported genes ( Bt4 , Bt5 , and Bt6 ) and QTLs associated with Cbt resistance on chromosome 1B (Dumalasová et al., 2012; Ehn et al., 2022; Fofana et al., 2008; Iqbal et al., 2022; Mourad et al., 2018; Muellner et al., 2021; Scmidt et al., 1969; Singh et al., 2016; Wang et al., 2009), 2B (Chen et al., 2016; Ehn et al., 2022; Iqbal et al., 2022; Steffan et al., 2022), and 6D (Gordon et al., 2020; Iqbal et al., 2022; Singh et al., 2016). The positions of the Cbt resistance genes and QTLs on 1B varied across populations and includes 11.2 Mb near BS00032266_51 in a diversity panel of bread wheat accessions from the USDA National Small Grains Collection (Ehn et al., 2022), 4.4–38.9 Mb in two RIL populations derived from Blizzard/Rainer and Bonneville/Rainer (Muellner et al., 2021), and 645.2 Mb in Canadian spring wheat (Iqbal et al., 2022). The physical position of the QCbt.dms‐1B identified in the present study, therefore, overlapped with the QTLs reported in the USDA bread wheat accessions and the two RIL (Blizzard/Rainer and Bonneville/ Rainer) populations.…”

“…Recently, Iqbal et al. (2022) reported a Cbt resistance QTL at 7.4 Mb near D_contig17056_55 on chromosome 6D which accounted for 16.9% of the Cbt severity in Canadian spring wheat. Both Bt9 and Bt10 have been reported on the long and short arms of chromosome 6D, respectively (Menzies et al., 2006; Steffan et al., 2017).…”

“…We identified three QTLs associated with Cbt resistance in all combined environments at 244.0 Mb on chromosome 2B in Attila/CDC Go ( QCbt.dms‐2B ) and 21.4 Mb on 1B ( QCbt.dms‐1B ) and 7.6 Mb on 6D ( QCbt.dms‐6D ) in Peace/Carberry populations (Table 1). Several studies reported genes ( Bt4 , Bt5 , and Bt6 ) and QTLs associated with Cbt resistance on chromosome 1B (Dumalasová et al., 2012; Ehn et al., 2022; Fofana et al., 2008; Iqbal et al., 2022; Mourad et al., 2018; Muellner et al., 2021; Scmidt et al., 1969; Singh et al., 2016; Wang et al., 2009), 2B (Chen et al., 2016; Ehn et al., 2022; Iqbal et al., 2022; Steffan et al., 2022), and 6D (Gordon et al., 2020; Iqbal et al., 2022; Singh et al., 2016). The positions of the Cbt resistance genes and QTLs on 1B varied across populations and includes 11.2 Mb near BS00032266_51 in a diversity panel of bread wheat accessions from the USDA National Small Grains Collection (Ehn et al., 2022), 4.4–38.9 Mb in two RIL populations derived from Blizzard/Rainer and Bonneville/Rainer (Muellner et al., 2021), and 645.2 Mb in Canadian spring wheat (Iqbal et al., 2022).…”

“…The severity of each disease was rated either on a scale of 0 to 9 corresponding to resistant to highly susceptible, respectively, at some locations or 0 to 100% at other locations. For statistical analyses, the percent disease severity ratings were converted into the 0 to 9 scale as described in a previous study (Iqbal et al., 2022).…”

Genetics of Resistance to Leaf Rust in Wheat: An Overview in A Genome-Wide Level

“…A diversity panel of 196 spring wheat genotypes was phenotyped for the leaf rust resistance in the field. A GWAS approach using 90K SNP array revealed significant association of multiple SNPs on chromosomes 2B (QLr.dms-2B.2) and 2D (QLr.dms-2D) [90]. An AS gene LrNJ97 was identified from a Chines wheat line "Neijiang 977671" and linked with SSR markers on chromosome 2BL [91].…”