Genetic Diversity Relationship Between Grain Quality and Appearance in Rice

Hua Zhong; Shuai Liu; Gangqing Zhao; Chenhao Zhang; Zhaohua Peng; Zhaohai Wang; Jing Yang; Yangsheng Li

doi:10.3389/fpls.2021.708996

Genetic Diversity Relationship Between Grain Quality and Appearance in Rice

Front Plant Sci. 2021 Aug 2:12:708996. doi: 10.3389/fpls.2021.708996. eCollection 2021.

Authors

Hua Zhong¹, Shuai Liu², Gangqing Zhao¹, Chenhao Zhang¹, Zhaohua Peng², Zhaohai Wang³, Jing Yang⁴, Yangsheng Li¹

Affiliations

¹ State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan University, Wuhan, China.
² Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS, United States.
³ Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, China.
⁴ College of Life Sciences, Nanchang University, Nanchang, China.

Abstract

Grain quality is an important breeding objective in rice, and the appearance of the grain also affects its commercial value in the market. The aim of this study was to decode the rice grain qualities and appearances, such as gelatinization temperature (GT), amylose content (AC), grain protein content (GPC), pericarp color (PC), length/width ratio (LWR), and grain volume (GV) at phenotypic and genetic levels, as well as the relationships among them. A genome-wide association study (GWAS) was used to identify the quantitative trait locus (QTLs) associated with the target traits using mixed linear model (MLM) and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) methods. In general, AC was negatively correlated with GPC and GV, while it was positively correlated with LWR and PC. GPC was positively correlated with LWR. Using the rice diversity panel 1 (RDP1) population, we identified 11, 6, 2, 7, 11, and 6 QTLs associated with GT, AC, GPC, PC, LWR, and GV, respectively. Five germplasm lines, superior in grain qualities and appearances for basic breeding materials or improvement, were identified. Notably, an F-box gene OsFbox394 was located in the linkage disequilibrium (LD) block of qLWR7-2, which specifically expresses in endosperm and seed tissues, suggesting that this gene may regulate the seed development in rice grain. Besides, different haplotypes of OsHyPRP45 showed significant differences in AC, indicating that this gene may be related to AC in rice grain.

Keywords: GWAS; Oryza sativa L.; amylose content; gelatinization temperature; grain protein content; grain volume; length-width ratio; pericarp color.