Nanjing Agricultural University, Nanjing, 210095, China.
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
BMC Genomics. 2020 Jan 9;21(1):31. doi: 10.1186/s12864-019-6428-0.
The general combining ability (GCA) of parents in hybrid rice affects not only heterotic level of grain yield and other important agronomic traits, but also performance of grain quality traits of F bulk population which is the commodity consumed by humans. In order to make GCA improvement for quality traits in parents of hybrid rice by molecular marker assisted selection feasible, genome-wide GCA loci for quality traits in parents were detected through association analysis between the effects of GCA and constructed single nucleotide polymorphism linkage disequilibrium blocks (SNPLDBs), by using unhusked rice grains harvested from F plants of 48 crosses of Indica rice and 78 crosses of Japonica rice. GCA-SNPLDBs association analysis.
Among the 8 CMS and 6 restorer lines of indica rice subspecies, CMS lines Zhenpin A, Zhenshan97 A, and 257A, and restorers Kanghui98, Minghui63 and Yanhui559 were recognized as good general combiners based on their GCA effect values for the 9 quality traits (brown rice rate, milled rice rate, head rice rate, percentage of chalky grains, chalky area size, chalkiness degree, gelatinization temperature, gel consistency and amylose content). Among the 13 CMS and 6 restorer lines of japonica rice subspecies, CMS 863A, 6427A and Xu 2A, and restorers C418, Ninghui8hao and Yunhui4hao showed elite GCA effect values for the 9 traits. GCA-SNPLDB association analysis revealed 39 significant SNPLDB loci associated with the GCA of the 9 quality-related traits, and the numbers of SNPLDB loci located on chromosome 1, 2, 3, 4, 5, 8, 9, 11 and 12 were 1, 4, 3, 9, 6, 5, 5, 4 and 2, respectively. Number of superior GCA alleles for the 9 traits among the 33 parents ranged from 1 to 26.
Thirty-nine significant SNPLDBs loci were identified associated with the GCA of 9 quality-related traits, and the superior SNPLDB alleles could be used to improve the GCA of parents for the traits in the future by molecular marker assisted selection. The genetic basis of trait GCA in parents is different from that of trait itself.
杂交水稻亲本的一般配合力（GCA）不仅影响籽粒产量和其他重要农艺性状的杂种优势水平，而且还影响 F 群体的籽粒品质性状表现，而 F 群体是人类消费的商品。为了使杂交水稻亲本的 GCA 对品质性状的改良通过 GCA 与构建的单核苷酸多态性连锁不平衡块（SNPLDBs）效应之间的关联分析成为可能，利用来自 48 个籼稻和 78 个粳稻杂种 F 植株收获的未去壳稻谷，对亲本的 8 个 CMS 和 6 个恢复系进行了全基因组 GCA 位点与质量性状的关联分析。结果：在籼稻亚种的 8 个 CMS 和 6 个恢复系中，CMS 系珍品 A、珍山 97A 和 257A 以及恢复系康辉 98、明辉 63 和艳辉 559，根据其对 9 个品质性状（糙米率、精米率、整精米率、垩白粒率、垩白粒面积、垩白度、胶稠度、凝胶化温度和直链淀粉含量）的 GCA 效应值，被认为是良好的一般配合力。在粳稻亚种的 13 个 CMS 和 6 个恢复系中，CMS 863A、6427A 和徐 2A 以及恢复系 C418、宁惠 8 号和云惠 4 号对 9 个性状具有优异的 GCA 效应值。GCA-SNPLDB 关联分析共发现 39 个与 9 个与品质相关性状的 GCA 显著相关的 SNPLDB 位点，位于染色体 1、2、3、4、5、8、9、11 和 12 上的 SNPLDB 位点数量分别为 1、4、3、9、6、5、5、4 和 2。33 个亲本中 9 个性状的 GCA 优势等位基因数量为 1-26 个。结论：共鉴定到 39 个与 9 个与品质相关性状的 GCA 显著相关的 SNPLDB 位点，通过分子标记辅助选择，可以利用优异的 SNPLDB 等位基因来改良亲本的 GCA 对这些性状的影响。亲本性状 GCA 的遗传基础与性状本身的遗传基础不同。
