Genome-wide association study reveals new loci for yield-related traits in Sichuan wheat germplasm under stripe rust stress

BACKGROUND

As one of the most important food crops in the world, increasing wheat (Triticum aestivum L.) yield is an urgent task for global food security under the continuous threat of stripe rust (caused by Puccinia striiformis f. sp. tritici) in many regions of the world. Molecular marker-assisted breeding is one of the most efficient ways to increase yield. Here, we identified loci associated to multi-environmental yield-related traits under stripe rust stress in 244 wheat accessions from Sichuan Province through genome-wide association study (GWAS) using 44,059 polymorphic markers from the 55 K single nucleotide polymorphism (SNP) chip.

RESULTS

A total of 13 stable quantitative trait loci (QTLs) were found to be highly associating to yield-related traits, including 6 for spike length (SL), 3 for thousand-kernel weight (TKW), 2 for kernel weight per spike (KWPS), and 2 for both TKW and KWPS, in at least two test environments under stripe rust stress conditions. Of them, ten QTLs were overlapped or very close to the reported QTLs, three QTLs, QSL.sicau-1AL, QTKW.sicau-4AL, and QKWPS.sicau-4AL.1, were potentially novel through the physical location comparison with previous QTLs. Further, 21 candidate genes within three potentially novel QTLs were identified, they were mainly involved in the regulation of phytohormone, cell division and proliferation, meristem development, plant or organ development, and carbohydrate transport.

CONCLUSIONS

QTLs and candidate genes detected in our study for yield-related traits under stripe rust stress will facilitate elucidating genetic basis of yield-related trait and could be used in marker-assisted selection in wheat yield breeding.

Genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in Sichuan wheat

BACKGROUND

Stripe rust (also called yellow rust) is a common and serious fungal disease of wheat (Triticum aestivum L.) caused by Puccinia striiformis f. sp. tritici. The narrow genetic basis of modern wheat cultivars and rapid evolution of the rust pathogen have been responsible for periodic and devastating epidemics of wheat rust diseases. In this study, we conducted a genome-wide association study with 44,059 single nucleotide polymorphism markers to identify loci associated with resistance to stripe rust in 244 Sichuan wheat accessions, including 79 landraces and 165 cultivars, in six environments.

RESULTS

In all the field assessments, 24 accessions displayed stable high resistance to stripe rust. Significant correlations among environments were observed for both infection (IT) and disease severity (DS), and high heritability levels were found for both IT and DS. Using mixed linear models, 12 quantitative trait loci (QTLs) significantly associated with IT and/or DS were identified. Two QTLs were mapped on chromosomes 5AS and 5AL and were distant from previously identified stripe rust resistance genes or QTL regions, indicating that they may be novel resistance loci.

CONCLUSIONS

Our results revealed that resistance alleles to stripe rust were accumulated in Sichuan wheat germplasm, implying direct or indirect selection for improved stripe rust resistance in elite wheat breeding programs. The identified stable QTLs or favorable alleles could be important chromosome regions in Sichuan wheat that controlled the resistance to stripe rust. These markers can be used molecular marker-assisted breeding of Sichuan wheat cultivars, and will be useful in the ongoing effort to develop new wheat cultivars with strong resistance to stripe rust.