Genome-wide Association Study Of Peduncle Vascular Bundles Related Traits In Rice

The vascular bundle especially in the peduncle is one of crucial limiting factors of rice yield,and it determines how plants efficiently transport photosynthetic products,mineral nutrients and water from leaf and root to panicle.However,the genetic base of rice vascular bundle related traits in the peduncle still remains unknown.In this study,we performed a GWAS to excavate the SNPs significant associations with eight vascular bundle related traits in the peduncle using 27K SNPs and the mean trait values of the 423 accessions generated from the 3K RGP.Gene-based association analysis and haplotype analysis were carried out to detect candidate genes for important QTL.The main results were as follows:1.The 423 panel showed substantial natural variations of peduncle vascular bundle.The number of large vascular bundle in peduncle of indica?averaged 21 in 2015 and 19.9 in 2016?was also significantly higher than those of japonica?averaged 16.1 in 2015 and 15.5 in 2016?,though there was no significant difference in the number of small vascular bundle between them.2.In total,20 quantitative trait loci/locus?QTL?affecting the eight traits were identified throughout the genome by applying a significance threshold of P<1.0�10^-4.Among them,12 QTL were commonly detected in two years.3.Combined determining linkage disequilibrium?LD?blocks associated with significant SNPs and haplotype analyses allowed us to shortlist six candidate genes for four important QTL regions affecting the peduncle vascular bundle traits,including one cloned gene?NAL1?and three newly identified QTL?qLVN6,qSVN7,and qSVA8.1?.Further the most likely candidate genes for each important QTL were also discussed based on functional annotation.4.Compared with Teqing,NIL-NAL1 had larger phloem area and total area of large vascular bundle.Genetic base on peduncle vascular bundle related traits in rice was systematically dissected,and most likely candidate genes of the known gene NAL1 and the three newly identified QTL?qLVN6,qSVN7,and qSVA8.1?were analyzed.The results provided valuable information for future functional characterization and rice breeding for high yield through optimizing transportation efficiency of photosynthetic products by marker-assisted selection.