Genome-wide Association Study Of The Flag Leaf Vascular Bundles Related Traits In Rice

The photosynthesis of rice is influenced by the vascular system of the leaves.In this process,the cell differentiation pattern plays an important role in maintaining leaf photosynthesis.The total area of vascular bundles and mesophyll cells in leaf is associated with rice yield.However,the genetic analysis of vascular bundle-related traits in rice leaf still remains unclear.Here,we identified quantitative trait loci(QTL)associated with 13 vascular bundle-related traits in the flag leaf of rice by GWAS analysis using 386 diverse accessions under the whole,indica,and japonica populations in the two years.Based on haplotype analysis and bioinformatics analysis,candidate genes of important QTL were speculated.The main results were as follows:1.The 386 rice panel used in the study exhibited substantial natural variations of 13 leaf vascular bundle related traits.The 13 vascular bundle related traits showed significant differences between indica and japonica.The area of vascular bundle and mesophyll area between vascular bundles showed significantly positive phenotypic correlations.2.Using 4.8M SNP markers from 3K RGP rice resequencing database,71,50,and 44 QTL influencing the 13 vascular bundle related traits in flag leaf were identified in the whole,indica,and japonica populations,respectively.Of these,70 QTL were consistently identified for the same traits in two years;5 QTL were commonly detected in the whole and indica populations;and 26 QTL were commonly detected in the whole and japonica populations.3.A total of 25 QTL regions were simultaneously detected for the two or more vascular bundles related traits in the same year,explaining the genetic bases of significant correlations of the vascular bundles related traits.4.We screened 50 candidate genes for the 22 consistent QTL identified in the two populations and two years by performing haplotype analysis.Among them,LOC_Os01g10840?LOC_Os01g43650?LOC_Os03g08480?LOC_Os04g27960?LOC_Os04g52479?LOC_Os04g54790?LOC_Os06g50060?LOC_Os08g42540?LOC_Os10g31330?LOC_Os10g39440 were considered as the most likely candidate gene based on functional annotations.The results provide useful information for improving rice yield through deploying the favorable alleles underlying vascular bundle-related traits by marker-assisted selection.And,it laid a solid foundation for the cloning of vascular bundle related genes in rice leaves.