title: Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice.
abstract: Even 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.
authors.affiliation: 1] Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China [2] National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China [3] MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China [4] College of Engineering, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Wanneng
authors.initials: W
authors.lastname: Yang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Zilong
authors.initials: Z
authors.lastname: Guo
authors.affiliation: 1] Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China [2] MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Chenglong
authors.initials: C
authors.lastname: Huang
authors.affiliation: 1] Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China [2] MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China [3] College of Engineering, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Lingfeng
authors.initials: L
authors.lastname: Duan
authors.affiliation: MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Guoxing
authors.initials: G
authors.lastname: Chen
authors.affiliation: 1] Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China [2] MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Ni
authors.initials: N
authors.lastname: Jiang
authors.affiliation: 1] Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China [2] MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Fang
authors.affiliation: 1] Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China [2] MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Feng
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Weibo
authors.initials: W
authors.lastname: Xie
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Xingming
authors.initials: X
authors.lastname: Lian
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Gongwei
authors.initials: G
authors.lastname: Wang
authors.affiliation: 1] Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China [2] MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Qingming
authors.initials: Q
authors.lastname: Luo
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Qifa
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: 1] Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China [2] MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Liu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Lizhong
authors.initials: L
authors.lastname: Xiong
mesh_terms: D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D055106:Genome-Wide Association Study; D057166:High-Throughput Screening Assays / Q000379:methods*; D061848:Optical Imaging; D012275:Oryza / Q000235:genetics* / Q000502:physiology; D010641:Phenotype; D040641:Quantitative Trait Loci / Q000235:genetics; D014057:Tomography, X-Ray Computed