Lu Fu-Hao, Park Yong-Jin
Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 340-802, Republic of Korea.
Genet Res (Camb). 2012 Aug;94(4):179-89. doi: 10.1017/S0016672312000390.
Sequence-based variations in starch synthesis-related genes (SSRGs) exert a basic influence on the determination of eating quality in rice (Oryza sativa L.). This study aimed to investigate the relationship between the sequence variations from parts of 10 SSRGs and the amylose content (AC) plus rapid viscosity analysis (RVA) profiles in a heuristic rice core set by association mapping (AM). In total, 86 sequence variations were found in 10 sequenced amplicons, including 79 single-nucleotide polymorphisms (SNPs), six insertion-deletions (InDels) and one polymorphic simple sequence repeat (SSR). Among them, 61 variations were exon-based, of which 41 should lead to amino acid changes. Four subpopulations were revealed by population structure analysis based on 170 genome-wide SSR genotypes. The final AM showed a sum of four significant associations between three phenotypic indices and three sequence variations. An ADP-glucose pyrophosphorylase small unit 1 (OsAGPS1) SNP (A-G) was significantly associated with increased AC (P<0·001, R(2)=15·6%), while a 12-bp deletion of AGPase large unit 4 (OsAGPL4) was significantly related to the decreased breakdown viscosity (BDV) (P<0·001, R(2)=16·6%) in both general linear model (GLM) and mixed linear model (MLM). This study provides a new perspective of allele mining for breeding strategies based on marker-assisted selection.
基于序列的淀粉合成相关基因（SSRGs）变异对水稻（Oryza sativa L.）食味品质的决定具有基础性影响。本研究旨在通过关联分析（AM）探究启发式水稻核心种质中10个SSRGs部分序列变异与直链淀粉含量（AC）及快速粘度分析（RVA）谱之间的关系。在10个测序扩增子中共发现86个序列变异，包括79个单核苷酸多态性（SNP）、6个插入缺失（InDel）和1个多态性简单序列重复（SSR）。其中，61个变异基于外显子，其中41个会导致氨基酸变化。基于170个全基因组SSR基因型的群体结构分析揭示了四个亚群。最终的关联分析显示，三个表型指标与三个序列变异之间共有四个显著关联。在一般线性模型（GLM）和混合线性模型（MLM）中，ADP - 葡萄糖焦磷酸化酶小亚基1（OsAGPS1）的一个SNP（A - G）与AC增加显著相关（P<0·001，R(2)=15·6%），而AGPase大亚基4（OsAGPL4）的12 bp缺失与崩解粘度（BDV）降低显著相关（P<0·001，R(2)=16·6%）。本研究为基于标记辅助选择的育种策略的等位基因挖掘提供了新视角。
