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

TLDR

Plant genomics advances rapidly with high‑throughput sequencing, yet traditional phenotyping remains slow. The study develops a high‑throughput rice phenotyping facility to monitor 15 agronomic traits throughout the growth period. The authors constructed the HRPF to track 13 traditional and 2 newly defined traits across rice development. GWAS of these traits identified 141 loci, including 25 with known genes such as SD1, showing that high‑throughput phenotyping can replace traditional methods and provides deep insights into trait genetics.

Abstract

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.