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.
Highlights
Rice (Oryza sativa L.) is one of the most widely cultivated cereal crops all over the world and provides the staple food for over half of the world population (Mbanjo et al, 2020)
Six traits that were widely used to characterize rice grain quality and apparent traits were studied in this study, such as grain amylose content (AC), alkali spreading value (ASV), grain protein content (GPC), grain length/width ratio (LWR), grain volume (GV), and pericarp color (PC)
Based on the principal component analysis (PCA), we divided the varieties into six subgroups [i.e., IND, AUS, temperate japonica (TEJ), tropical japonica (TRJ), aromatic subgroups (ARO), and ADM (Admixture)]
Summary
Rice (Oryza sativa L.) is one of the most widely cultivated cereal crops all over the world and provides the staple food for over half of the world population (Mbanjo et al, 2020). With modern technology advancement and improvement of the quality of life, people are seeking food with high nutritional and appearance qualities. Eating and cooking qualities (ECQs) and grain protein content (GPC) are the main factors that determine rice grain quality. ECQ could be further dissected into amylose content (AC), gel consistency (GC), and gelatinization temperature (GT). The AC could be divided into five groups, namely, waxy (0–2%), very low (3–9%), low (10–19%), intermediate (20–25%), and high (>25%). Rice grains with an AC of 16–20% are the most popular type in markets and meet the demand of ECQ from customers (Song et al, 2019).
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