Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study

• Published in: 分子植物：英文版 2015, Vol.8 (1), p.946-957
• Main Author: Quanxiu Wang Weibo Xie Hongkun Xing Ju Yan Xiangzhou Meng Xinglei Li Xiangkui Fu Jiuyue Xu Xingming Lian Sibin Yu Yongzhong Xing Gongwei Wang
• Format: Article
• Language: English
• Subjects: 全基因组; 单核苷酸多态性; 叶片光合作用; 叶绿素含量; 水稻育种; 生物合成基因; 自然变异; 遗传结构
• ISSN: 1674-2052; 1752-9867

Chlorophyll content is one of the most important physiological traits as it is closely related to leaf photosynthesis and crop yield potential. So far, few genes have been reported to be involved in natural variation of chlorophyll content in rice （Oryza sativa） and the extent of variations explored is very limited. We conducted a genome-wide association study （GWAS） using a diverse worldwide collection of 529 O. sativa accessions. A total of 46 significant association loci were identified. Three F2 mapping populations with parents selected from the association panel were tested for validation of GWAS signals. We clearly demonstrated that Grain number, plant height, and heading date7 （Ghd7） was a major locus for natural variation of chlorophyll content at the heading stage by combining evidence from near-isogenic lines and transgenic plants. The enhanced expression of Ghd7 decreased the chlorophyll content, mainly through downregulating the expression of genes involved in the biosynthesis of chlorophyll and chloroplast. In addition, Narrow leaf1 （NAL1） corresponded to one significant association region repeatedly detected over two years. We revealed a high degree of polymorphism in the 5＇ UTR and four non-synonymous SNPs in the coding region of NAL1, and observed diverse effects of the major haplotypes. The loci or candidate genes identified would help to fine-tune and optimize the antenna size of canopies in rice breeding.