Genome-Wide Association Analysis of Rice Leaf Traits

Yield-related traits have always been a research hotspot in rice breeding, and functional leaves directly affect the photosynthetic efficiency and yield of rice. Therefore, it is of great significance to explore the genes related to rice leaf size and shape to improve rice leaf morphology, photosynthesis efficiency, and yield. This study detected the quantitative trait loci (QTLs) for the length, width, length–width ratio, and area of rice flag leaf and second leaf in 393 accessions from the 3000 Rice Genome Project (3KRGP) by high-density single-nucleotide polymorphism genotyping. As a result, 91 QTLs were detected, among which 5 candidate genes (LOC_Os03g29170, LOC_Os06g17285, LOC_Os04g35060, LOC_Os03g27450, and LOC_Os09g16280) were identified. In addition, the epistatic interactions affecting leaf-related traits were also investigated, resulting in the identification of 134 significant QQIs (QTL by QTL interactions) pairs. The results of this study provide an important genetic basis for mining genes associated with rice leaf shape and valuable genetic information for rice breeding.