Genome-Wide Association Study for Leaf Photosynthesis Using High-Throughput Gas Exchange System in Rice

Abstract

Abstract Enhancing leaf photosynthetic capacity is essential for improving yield of rice (Oryza sativa L.). The exploitation of natural genetic variation is a promising approach to enhance photosynthetic capacity, as well as molecular engineering approaches. However, genetic resources have yet to be efficiently used in breeding programs, partially due to the low-throughput of photosynthetic measurements. Here we examined the diversity of photosynthetic rates among 168 temperate japonica rice varieties at the vegetative stage for three years with the newly developed rapid closed-gas exchange system, MIC-100. The data showed a large genetic variation in net CO2 assimilation rate (A) between the varieties. The modern varieties exhibited higher A relative to the landraces, while there was no significant relationship between the released year and A among the modern varieties. Genome-wide association study (GWAS) revealed two major peaks located on chromosomes 4 and 8 which were repeatedly detected in different experiments and in the generalized linear modeling approach. We suggest that the high-throughput gas exchange measurement combined with GWAS is a reliable approach for understanding genetic mechanisms in photosynthetic diversities in crop species.