Ullah Zaid Imdad, Tang Weijie, He Jianbo, Ullah Khan Sana, Hong Delin
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.
Key Laboratory of Agricultural Water Resources, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 286 Huaizhong Rd, Shijiazhuang, China.
AoB Plants. 2018 Dec 18;11(1):ply077. doi: 10.1093/aobpla/ply077. eCollection 2019 Feb.
Association analysis between constructed single nucleotide polymorphism linkage disequilibrium blocks (SNPLDBs) and general combining ability (GCA) effects is a novel approach to uncover the genetic basis of GCA within the sequence genomes of parents of hybrid rice. Here, we calculated the GCA effect values of 33 parents of hybrid rice and sequenced them to identify genome-wide single nucleotide polymorphisms (SNPs). In total, 64.6 % of the uniquely mapped paired-end short reads revealed a final total of 291 959 SNPs between the 33 parental genomes and the Nipponbare reference genome. The identified SNPs were non-randomly distributed among all chromosomes of rice, whereas one-fourth of the SNPs were situated in the exonic regions with 16 % being non-synonymous. Further, the identified SNPs were merged and optimized for construction of 2612 SNPLDB markers, using linkage disequilibrium information. The single-factor analysis of variance-based association method between the constructed SNPLDB markers and GCA effects values detected 99 significant SNPLDBs for GCA of 11 yield-related traits. The associated SNPLDB markers explained 26.4 % of phenotypic variations with traits, on average. We mined 50 favourable GCA alleles at the associated SNPLDBs regions, distributed across the 33 parental genomes. The parental genomes possessed a small number of favourable GCA alleles for studied traits, with the exception of days to heading and plant height. Our results suggest that the identified GCA alleles could be used to improve the GCA performance of parents of hybrid rice through optimal crossing design. Moreover, favourable GCA alleles should be incorporated in the parental genomes through marker-assisted selection experiments, and the parental lines carrying more alleles could be utilized in breeding as superior parents for developing rice hybrids of desirable characteristics.
构建的单核苷酸多态性连锁不平衡块（SNPLDBs）与一般配合力（GCA）效应之间的关联分析是一种在杂交水稻亲本序列基因组中揭示GCA遗传基础的新方法。在此，我们计算了33个杂交水稻亲本的GCA效应值，并对其进行测序以鉴定全基因组单核苷酸多态性（SNP）。总共，64.6%的唯一映射双端短读段揭示了33个亲本基因组与日本晴参考基因组之间最终共有291959个SNP。鉴定出的SNP在水稻的所有染色体上非随机分布，其中四分之一的SNP位于外显子区域，16%为非同义突变。此外，利用连锁不平衡信息对鉴定出的SNP进行合并和优化，构建了2612个SNPLDB标记。基于单因素方差分析的构建的SNPLDB标记与GCA效应值之间的关联方法检测到11个产量相关性状的GCA有99个显著的SNPLDB。相关的SNPLDB标记平均解释了26.4%的性状表型变异。我们在相关的SNPLDB区域挖掘了50个有利的GCA等位基因，分布在33个亲本基因组中。除抽穗天数和株高外，亲本基因组对所研究性状的有利GCA等位基因数量较少。我们的结果表明，鉴定出的GCA等位基因可通过优化杂交设计用于提高杂交水稻亲本的GCA表现。此外，应通过标记辅助选择实验将有利的GCA等位基因整合到亲本基因组中，携带更多等位基因的亲本系可作为培育具有理想特性水稻杂交种的优良亲本用于育种。
