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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.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-6005-6) contains supplementary material, which is available to authorized users.

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