Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

• DOI: 10.1038/ncomms6087
• Publication Date: 2014-10-08T13:04:39Z
• Authors: Wanneng Yang; Zilong Guo; Chenglong Huang; Lingfeng Duan; Guoxing Chen; Ni Jiang; Wei Fang; Hui Feng; Weibo Xie; Xingming Lian; Gongwei Wang; Qingming Luo; Qifa Zhang; Qian Liu; Lizhong Xiong
• Keywords: 2. Zero hunger; 0303 health sciences; Optical Imaging; Quantitative Trait Loci; Genetic Variation; Oryza; 15. Life on land; Article; High-Throughput Screening Assays; 03 medical and health sciences; Phenotype; Tomography, X-Ray Computed; Genome, Plant; Genome-Wide Association Study

AbstractEven as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gene, SD1. Based on a performance evaluation of the HRPF and GWAS results, we demonstrate that high-throughput phenotyping has the potential to replace traditional phenotyping techniques and can provide valuable gene identification information. The combination of the multifunctional phenotyping tools HRPF and GWAS provides deep insights into the genetic architecture of important traits.