Identification of genetic loci and a candidate gene related to flag leaf traits in common wheat by genome-wide association study and linkage mapping

Flag leaf traits influence wheat yield by affecting photosynthetic capacity and plant architecture. In this study, flag leaf traits over 4 years in Chinese common wheat were investigated for genome-wide association study (GWAS) analysis using the wheat 90 K SNP array. A total of 618 significant SNPs were identified in 9 environments and 36 of them are significant in at least three environments and BLUP (best linear unbiased prediction). Linkage mapping indicated that 23 QTL regulating flag leaf traits were detected in a bi-parental population with 5.8 to 28.7% phenotypic variation explained, respectively. Further analysis of multi-environmentally significant SNP revealed a candidate gene TaFLL-5B1 (TraesCS5B02G390300) related to flag leaf length (FLL). Sequencing results indicated that a 40-bp InDel (insertion/deletion) was identified in TaFLL-5B1 gene of different wheat cultivars. Association analysis showed that cultivars with TaFLL-5B1a (with a 40-bp InDel) showed significantly longer FLL than those with TaFLL-5B1b (without a 40-bp InDel). EMS-mutagenized tetraploid wheat line Kronos2282 with premature stop codon of TaFLL-5B1 gene showed significantly shorter FLL than wild type. It suggests that TaFLL-5B1 possibly plays a key role in modulating wheat flag leaf traits. This research increases our understanding of the genetic basis of flag leaf traits and provides genetic loci potentially useful in breeding programs focused on improving wheat architecture and yield.