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

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

doi:10.1038/ncomms6087

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

Nat Commun. 2014 Oct 8:5:5087. doi: 10.1038/ncomms6087.

Authors

Wanneng Yang¹, Zilong Guo², Chenglong Huang³, Lingfeng Duan⁴, Guoxing Chen⁵, Ni Jiang³, Wei Fang³, Hui Feng³, Weibo Xie², Xingming Lian², Gongwei Wang², Qingming Luo³, Qifa Zhang², Qian Liu³, Lizhong Xiong²

Affiliations

¹ 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.
² National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
³ 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.
⁴ 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.
⁵ MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan 430070, China.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genetic Variation*
Genome, Plant / genetics*
Genome-Wide Association Study
High-Throughput Screening Assays / methods*
Optical Imaging*
Oryza / genetics*
Oryza / physiology
Phenotype*
Quantitative Trait Loci / genetics
Tomography, X-Ray Computed*