Dataset Information

Genetic Diversity Relationship Between Grain Quality and Appearance in Rice.

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.

SUBMITTER: Zhong H

PROVIDER: S-EPMC8365354 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Genetic Diversity Relationship Between Grain Quality and Appearance in Rice.

Zhong Hua H Liu Shuai S Zhao Gangqing G Zhang Chenhao C Peng Zhaohua Z Wang Zhaohai Z Yang Jing J Li Yangsheng Y

Frontiers in plant science 20210802

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 ...[more]

PMID: 34408762

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Project description:Long grain geng/japonica rice has a higher market preference due its excellent appearance quality. The dense and erect-panicle 1 (dep1) gene has been widely used in the breeding of high-yielding geng/japonica rice cultivars in China. However, this gene causes short and round grain shape thus making it less attractive in global rice markets. Therefore, breeding of high-yielding long-grain geng/japonica rice cultivars by incorporating dep1 with major-effect grain shape gene is of high priority in rice industry. Up to now, multiple grain shape genes' effect mechanism has been clearly elaborated, however, under the background of erect-panicle geng/japonica rice, the effect of major grain shape genes on the appearance quality need to be further clarified, as detailed reports are limited. Utilizing CRISPR/Cas9 technology, a series of near-isogenic lines (NILs) (YF47dep1-gw8, YF47dep1-gs3, YF47dep1-gl7, YF47dep1-qgl3 and YF47dep1-tgw6) in Yanfeng 47(YF47dep1) background were created. Grain appearance and yield components analysis showed that: (1) All NILs' grain length to width ratio was significantly increased compared to that of YF47dep1, excepted YF47dep1-gs3, (2) The chalkiness degree was significantly reduced in all of the NILs, (3) In all of the NILs, YF47dep1-gw8 grains exhibited the greatest length to width ratio and the lowest chalkiness degree, (4) The composition of glume cells and filling characteristics of the endosperm were two key factors contributing grain shape and grain chalk variations, respectively, and v) Owning to a substantial increase in the thousand grain weight, the yields of YF47dep1-gs3 and YF47dep1-tgw6 were significantly higher than that of YF47dep1, whereas YF47dep1-qgl3 exhibited the lowest yield because of a dramatic decrease in the effective panicle number and thousand grain weight. All the results revealed that pyramiding dep1 with major-effect grain shape alleles was an effective approach to improving the appearance quality of erect-panicle geng/japonica rice, owning to both of the appearance quality and yield improvement, GS3 and TGW6 alleles can be applied directly for breeding long-grain shape geng/japonica rice, and editing GW8 resulted in excellent appearance quality but low yield, therefore, this gene would be difficult to use directly but can be considered as the core germplasm resource.

Project description:High temperature significantly impacts grain appearance quality, yet few studies have focused on identifying new quantitative trait loci (QTLs)/genes related to these traits under heat stress during the flowering stage in rice. In this study, a natural population of 525 rice accessions was used to identify QTLs and candidate genes associated with grain appearance quality using a Genome-Wide Association Study under heat stress. We identified 25 QTLs associated with grain length (GL), grain width (GW), and grain chalkiness (GC) under heat stress across 10 chromosomes in the three rice populations (full, indica, and japonica). Notably, three sets of overlapping QTLs were identified (set 1: qHTT-L3 and qHTT-XL3; set 2: qHTT-C5 and qHTT-XC5; set 3: qHTT-L11.1 and qHTT-GL11), located on chromosomes 3, 5, and 11, respectively. Haplotype analysis indicated that Hap1 is the superior haplotype, and pyramiding more than two superior alleles improved rice grain appearance quality (longer GL, wider GW, and lower GC) in high-temperature environments. Based on RNA-seq, qRT-PCR and functional annotations analysis, LOC_Os05g06920, LOC_Os05g06970, and LOC_Os11g28104 were highly expressed, identifying them as the high-priority candidate genes for QTLs linked to grain appearance quality (GL, GW, and GC) under heat stress. Expression analysis revealed that LOC_Os05g06920, which encodes a relA-SpoT-like protein RSH4, and LOC_Os11g28104, which encodes a protein kinase with a DUF26 domain, were highly expressed in seeds, leaves, and shoots. And LOC_Os05g06970, encoding a peroxidase precursor, exhibited high expression levels in roots. Compared to the wild-type (WT) plants, the mutants of LOC_Os05g06920, LOC_Os05g06970, and LOC_Os11g28104 exhibited increased GL and grain length-to-width ratio, but reduced GW under both natural and heat stress conditions, while the LOC_Os05g06970 and LOC_Os11g28104 mutants significantly increased the chalky grain rate and grain chalkiness degree under natural conditions. Furthermore, the LOC_Os05g06920, LOC_Os05g06970, and LOC_Os11g28104 mutants showed a lower decline in grain appearance quality traits than the WT after high-temperature treatment. These findings suggest that LOC_Os05g06920, LOC_Os05g06970, and LOC_Os11g28104 play crucial roles in regulating both grain development and heat tolerance under heat stress at anthesis, thus affecting grain appearance quality in rice. Our results provide a promising genetic resource for improving rice grain appearance quality under heat stress.

Dataset Information

Genetic Diversity Relationship Between Grain Quality and Appearance in Rice.

Publications

Genetic Diversity Relationship Between Grain Quality and Appearance in Rice.

Similar Datasets

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