Genetic identification and characterization of chromosomal intervals related to flag leaf size in common wheat

The flag leaf is a crucial component of the ideal plant architecture in wheat (Triticum aestivum L.), directly influencing photosynthetic efficiency and yield. This study utilized an F₆ recombinant inbred line (RIL) population derived from a cross between the natural mutant msf, which possesses elongated and broad flag leaves, and the cultivar Chuannong 16 (CN16). A genetic linkage map constructed using a 16 K SNP chip enabled the identification of 34 quantitative trait loci (QTL) for flag leaf length (FLL), flag leaf width (FLW), flag leaf area (FLA), and flag leaf length-to-width ratio (FLR). Notably, major QTL QFlw.sau-MC-1A for FLW and QFla.sau-MC-1A for FLA were co-localized on chromosome 1AS, explaining 9.26-19.47% and 9.70-17.53% of the phenotypic variation, respectively. The favorable alleles from the msf parent significantly increased FLL, FLW, and FLA. A Kompetitive Allele-Specific PCR (KASP) marker developed from a SNP within the QTL interval was used to successfully validate the major QTL in independent populations. Pleiotropic effects showed that this locus positively influenced spike length (SL) and seven spike-related traits, including fertile florets per spike (FFS), kernel weight per spike, total florets per spike, florets per spikelet, florets in the middle spikelet, fertile florets per spikelet, and kernel weight per spikelet, but negatively influenced effective tiller number (ETN), plant height (PH), and anthesis date (AD). Cell morphologic analysis indicated that the difference in flag leaf size between msf and CN16 may be attributable to combined differences in cell morphology and cell number. Based on these results, together with the functional annotation of candidate genes in the interval, three genes putatively controlling leaf development were predicted. These findings offer valuable insights for breeding wheat varieties with ideal plant architecture.