Malik Naveen, Dwivedi Nidhi, Singh Ashok K, Parida Swarup K, Agarwal Pinky, Thakur Jitendra K, Tyagi Akhilesh K
National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
Division of Genetics, Rice Section, Indian Agricultural Research Institute (IARI), New Delhi 110012, India.
Sci Rep. 2016 Mar 22;6:23253. doi: 10.1038/srep23253.
The present study deployed a Mediator (MED) genes-mediated integrated genomic strategy for understanding the complex genetic architecture of grain size/weight quantitative trait in rice. The targeted multiplex amplicon resequencing of 55 MED genes annotated from whole rice genome in 384 accessions discovered 3971 SNPs, which were structurally and functionally annotated in diverse coding and non-coding sequence-components of genes. Association analysis, using the genotyping information of 3971 SNPs in a structured population of 384 accessions (with 50-100 kb linkage disequilibrium decay), detected 10 MED gene-derived SNPs significantly associated (46% combined phenotypic variation explained) with grain length, width and weight in rice. Of these, one strong grain weight-associated non-synonymous SNP (G/A)-carrying OsMED4_2 gene was validated successfully in low- and high-grain weight parental accessions and homozygous individuals of a rice mapping population. The seed-specific expression, including differential up/down-regulation of three grain size/weight-associated MED genes (including OsMED4_2) in six low and high-grain weight rice accessions was evident. Altogether, combinatorial genomic approach involving haplotype-based association analysis delineated diverse functionally relevant natural SNP-allelic variants in 10 MED genes, including three potential novel SNP haplotypes in an OsMED4_2 gene governing grain size/weight differentiation in rice. These molecular tags have potential to accelerate genomics-assisted crop improvement in rice.
本研究采用中介体（MED）基因介导的综合基因组策略，以了解水稻粒长/粒重数量性状的复杂遗传结构。对384份材料的水稻全基因组注释的55个MED基因进行靶向多重扩增子重测序，发现了3971个单核苷酸多态性（SNP），这些SNP在基因的不同编码和非编码序列成分中进行了结构和功能注释。利用384份材料（连锁不平衡衰减为50-100 kb）结构化群体中3971个SNP的基因分型信息进行关联分析，检测到10个源自MED基因的SNP与水稻粒长、粒宽和粒重显著相关（解释了46%的组合表型变异）。其中，一个携带与粒重相关的强非同义SNP（G/A）的OsMED4_2基因在水稻作图群体的低粒重和高粒重亲本材料及纯合个体中得到了成功验证。在6个低粒重和高粒重水稻材料中，包括3个与粒长/粒重相关的MED基因（包括OsMED4_2）的差异上调/下调在内的种子特异性表达是明显的。总之，涉及基于单倍型关联分析的组合基因组方法在10个MED基因中描绘了多种功能相关的天然SNP等位变异，包括OsMED4_2基因中3个潜在的新型SNP单倍型，其控制着水稻粒长/粒重的分化。这些分子标记有潜力加速水稻基因组辅助作物改良。
