PDF(Pubmed)
Abstract：
Grain-related traits are pivotal in rice cultivation, influencing yield and consumer preference. The complex inheritance of these traits, involving multiple alleles contributing to their expression, poses challenges in breeding. To address these challenges, a multi-locus genome-wide association study (ML-GWAS) utilizing 35,286 high-quality single-nucleotide polymorphisms (SNPs) was conducted. Our study utilized an association panel comprising 483 rice genotypes sourced from a northeast core set and a landraces set collected from various regions in India. Forty quantitative trait nucleotides (QTNs) were identified, associated with four grain-related traits: grain length (GL), grain width (GW), grain aroma (Aro), and length-width ratio (LWR). Notably, 16 QTNs were simultaneously identified using two ML-GWAS methods, distributed across multiple chromosomes. Nearly 258 genes were found near the 16 significant QTNs. Gene annotation study revealed that sixty of these genes exhibited elevated expression levels in specific tissues and were implicated in pathways influencing grain quality. Gene ontology (GO), trait ontology (TO), and enrichment analysis pinpointed 60 candidate genes (CGs) enriched in relevant GO terms. Among them, LOC_Os05g06470, LOC_Os06g06080, LOC_Os08g43470, and LOC_Os03g53110 were confirmed as key contributors to GL, GW, Aro, and LWR. Insights from QTNs and CGs illuminate rice trait regulation and genetic connections, offering potential targets for future studies.
摘要：
籽粒相关性状在水稻种植中至关重要，影响产量和消费者偏好。这些特征的复杂遗传，涉及促成其表达的多个等位基因，对育种提出了挑战。为了应对这些挑战，我们利用35,286个高质量单核苷酸多态性(SNPs)进行了多基因座全基因组关联研究(ML-GWAS).我们的研究利用了一个关联小组，该小组包括来自东北核心组的483个水稻基因型和从印度各个地区收集的地方品种组。鉴定了40个数量性状核苷酸（QTNs），与四个籽粒相关性状相关：籽粒长度(GL)，晶粒宽度(GW)，谷物香气（阿罗），和长宽比（LWR）。值得注意的是,使用两种ML-GWAS方法同时鉴定了16种QTNs，分布在多个染色体上。在16个显著的QTNs附近发现了近258个基因。基因注释研究表明，这些基因中有60个在特定组织中表现出升高的表达水平，并且与影响谷物品质的途径有关。基因本体论(GO)，特质本体论(TO)，和富集分析确定了60个富含相关GO术语的候选基因(CGs)。其中,LOC_Os05g06470、LOC_Os06g06080、LOC_Os08g43470和LOC_Os03g53110被确认为GL的主要贡献者，GW,阿罗,和LWR。来自QTNs和CGs的见解阐明了水稻性状调控和遗传联系，为未来的研究提供潜在的目标。
