Genome-wide association mapping for resistance to leaf rust, stripe rust and tan spot in wheat reveals potential candidate genes

Abstract

Key messageGenome-wide association mapping in conjunction with population sequencing map and Ensembl plants was used to identify markers/candidate genes linked to leaf rust, stripe rust and tan spot resistance in wheat.AbstractLeaf rust (LR), stripe rust (YR) and tan spot (TS) are some of the important foliar diseases in wheat (Triticum aestivum L.). To identify candidate resistance genes for these diseases in CIMMYT’s (International Maize and Wheat Improvement Center) International bread wheat screening nurseries, we used genome-wide association studies (GWAS) in conjunction with information from the population sequencing map and Ensembl plants. Wheat entries were genotyped using genotyping-by-sequencing and phenotyped in replicated trials. Using a mixed linear model, we observed that seedling resistance to LR was associated with 12 markers on chromosomes 1DS, 2AS, 2BL, 3B, 4AL, 6AS and 6AL, and seedling resistance to TS was associated with 14 markers on chromosomes 1AS, 2AL, 2BL, 3AS, 3AL, 3B, 6AS and 6AL. Seedling and adult plant resistance (APR) to YR were associated with several markers at the distal end of chromosome 2AS. In addition, YR APR was also associated with markers on chromosomes 2DL, 3B and 7DS. The potential candidate genes for these diseases included several resistance genes, receptor-like serine/threonine-protein kinases and defense-related enzymes. However, extensive LD in wheat that decays at about 5 × 107 bps, poses a huge challenge for delineating candidate gene intervals and candidates should be further mapped, functionally characterized and validated. We also explored a segment on chromosome 2AS associated with multiple disease resistance and identified seventeen disease resistance linked genes. We conclude that identifying candidate genes linked to significant markers in GWAS is feasible in wheat, thus creating opportunities for accelerating molecular breeding.Electronic supplementary materialThe online version of this article (10.1007/s00122-018-3086-6) contains supplementary material, which is available to authorized users.

The potential of hybrid breeding to enhance leaf rust and stripe rust resistance in wheat

“…Chromosome 4A appears to be an important genome region with a high potential for leaf rust resistance in wheat. Correspondingly, promising loci were previously detected in association studies observing adult plant resistance in a set of American spring wheat (Gao et al 2016) and in a diverse core set including winter and spring wheat (Li et al 2016) or considering seedling resistance in a wheat collection of CIMMYT (Juliana et al 2018). The detected single nucleotide polymorphism (SNP) BobWhite_c47168_289 (SNP332) was also found as significantly associated with leaf rust resistance on wheat chromosome 4A by Gao et al (2016).…”

“…Table 4). The importance of chromosome 2A for seedling and adult plant resistance in wheat was also shown by Juliana et al (2018) considering CIMMYT´s bread wheat pool. Positions of detected loci on 2A are in coincidence with previous detected NBS-LRR genes (IWGSC 2018).…”

Comparison of array‐ and sequencing‐based markers for genome‐wide association mapping and genomic prediction in spring wheat

“…Juliana et al. () reported that the lines in CIMMYT breeding populations had a complex structure, which was difficult to define due to the intensive breeding history including a large number of sister lines and closely related lines along with introgressions of unrelated materials. The different population structure from I9K was likely due to the lack of markers in some important regions determining the subtle population differentiation.…”

“…To dissect the genetic basis of traits through GWAS, several studies were conducted using array-based platforms (Liu, Pinto, Cossani, Sukumaran, & Reynolds, 2019;Lopes, Dreisigacker, Pena, Sukumaran, & Reynolds, 2015;Sukumaran, Dreisigacker, Lopes, Chavez, & Reynolds, 2015, 2018bValluru, Reynolds, Davies, & Sukumaran, 2017) in spring wheat and sequencing-based platforms (Sukumaran, Reynolds, & Sansaloni, 2018c) in durum wheat (Triticum durum Desf.). Genomic prediction studies were also conducted using the I90K and DArTseq platforms (Christy et al, 2018;Crossa et al, 2014Crossa et al, , 2016aCrossa et al, , 2016bCrossa et al, , 2017Juliana et al, 2018Juliana et al, , 2019Rutkoski et al, 2016;Sukumaran, Crossa, Jarquin, Lopes, & Reynolds, 2017a, 2017b.…”

Genome-wide association mapping revealed syntenic loci QFhb-4AL and QFhb-5DL for Fusarium head blight resistance in common wheat (Triticum aestivum L.)

“…One hundred-twenty consistent loci were detected using SNP-GWAS and Haplotype-GWAS, and 78 were potentially new [28]. The recently released reference genome sequence of Chinese Spring [29] provides an elit platform for detecting genes significantly associated with linked markers with known physical positions in the genome and promoting the molecular breeding process [30]. In this study, we report a GWAS analysis of FHB resistance using a set of 171 common wheat cultivars with 90 K SNP genotyping and 2 year's phenotyping data.…”