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PubMed2025

Combining QTL mapping and RNA-Seq reveals candidate genes controlling flag leaf width in foxtail millet.

BACKGROUND: The flag leaf, a crucial component of plant architecture, significantly influences final grain yield in crops, including foxtail millet (Setaria italica L.). Optimizing flag leaf size is considered an effective strategy for enhancing grain yield potential under higher planting densities. However, the genetic mechanism underlying flag leaf size, particularly flag leaf width (FLW), remains largely unknown under varying planting densities in foxtail millet. RESULTS: An FLW phenotype variation analysis was conducted across multiple planting densities using a recombinant inbred line (RIL) population derived from Heizhigu (narrow leaf) and Changnong 35 (wide leaf). Based on a high-density genetic map with 3795 Bin markers, 11 flag leaf width (FLW) QTLs were identified on chromosomes 3, 5, and 6, explaining 2.35%-36.06%. Among these, qFLW5-2 was a major QTL, detected consistently across 3 environments and explaining a large proportion of FLW variation. The QTL was further validated with 9 InDel markers with its candidate region across different planting densities. Moreover, RNA-seq revealed 2,293 and 2,338 differentially expressed genes (DEGs) between biparents at heading stage and grain filling stage, respectively. There were 11 and 9 DEGs within the location range of qFLW5-2 among 2 comparison groups (HZG-H_vs_CN35-H and HZG-G_vs_CN35-G). Combining QTL mapping and RNA-seq, we speculated that Seita.5g134600 (encoding an auxin responsive protein Aux/IAA) and Seita.5G123900 (encoding a cytochrome P450 family protein) as key candidate genes for qFLW5-2. Furthermore, variation analysis confirmed that the lines or germplasm with Seita.5G1346005UTR277+ allele, both within the RIL population and natural populations, exhibited significantly wider leaves than those with Seita.5G1346005UTR277- allele. These findings advance our understanding of the genetic and molecular regulatory mechanisms governing flag leaf growth. CONCLUSIONS: This study elucidates genetic and molecular mechanism regulating flag leaf growth and development in foxtail millet. The results provide a theoretical foundation for improving plant architecture and facilitating molecular marker-assisted breeding in this crop.

Quantitative Trait Loci↗
PubMed2025

Exploring genomic regions and genes modulating plant height and flag leaf morphology in rice.

Plant height and flag leaf morphology critically affect plant yield because they determine above-ground plant biomass and photosynthate production. However, few genetic basis analyses and gene mining studies on plant height, flag leaf length, and flag leaf width have been performed, and there is little available information about the evolution and utilization of the underlying natural alleles. This study conducted a genome-wide association study (GWAS) using 689 rice accessions collected from diverse regions across the globe. The GWAS identified 73, 159, and 158 significant loci associated with plant height, flag leaf length, and flag leaf width, respectively. SD1HAP1 and NAL1A were also identified as superior alleles that could be used to improve plant architecture by reducing plant height and increasing flag leaf width, respectively. LEAF1 and its elite allele LEAF1G, which simultaneously modulated plant height and flag leaf morphology, were isolated, and the LEAF1 knockout lines showed reduced flag leaf length and plant height, whereas LEAF1G-complementary lines in the LEAF1A background had the opposite phenotypes. The results also showed that LEAF1G and SD1HAP1 evolved directly from wild rice and were mainly found in the Xian subgroup, whereas NAL1A might have originated from de novo mutation during domestication and was mainly found in the Geng subgroup. A joint haplotype analysis revealed that pyramiding SD1HAP1, NAL1A, and LEAF1G in Type I accessions optimized plant architecture, reduced plant height, and enlarged the flag leaves. In addition, genomic regions and genes that had been convergently selected for these traits were identified by combining a population genetics analysis with a GWAS. These findings provide valuable genetic targets for molecular breeding that will improve plant height and flag leaf morphology in rice.

Oryza↗