Genome-wide study of an elite rice pedigree reveals a complex history of genetic architecture for breeding improvement.
Genome-wide study of an elite rice pedigree reveals a complex history of genetic architecture for breeding improvement.
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DOI：
10.1038/srep45685
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发表时间：
2017-04-04
影响因子：
4.6
通讯作者：
He H
中科院分区：
文献类型：
--
作者：
Chen S;Lin Z;Zhou D;Wang C;Li H;Yu R;Deng H;Tang X;Zhou S;Wang Deng X;He H
改良育种已广泛应用于作物育种中，有助于提高产量和品质，但目前很少有研究全面分析育种改良背后的遗传结构。在这里，我们收集了完整谱系中的 99 个品种的基因型和表型数据，其中包括黄花占，这是一种优良的优质常规籼稻，在中国南方种植面积超过 450 万公顷，并衍生出 20 多个优良品种。我们鉴定了 1,313 个选择性扫描（SSW），揭示了 65 年来与改良偏好相对应的四种阶段特异性选择模式，并且从不同供体引入并在超过 3 个育种代中保守的 1113 个保守的黄花站可追溯块（cHTB）是黄花站优异性能的核心基因组区域。基于谱系中 13 个改良性状的 151 个数量性状位点 (QTL)，我们在计算机中重现了它们的改良过程，强调改良育种对于由主效/主效 + 次要效应 QTL 控制的性状效果良好，但对于由具有复杂相互作用或解释低水平表型变异的 QTL 控制的性状则效率较低。这些结果表明，长期育种改良对于构建优良性能的优良遗传结构是有效的，而具有设计的 QTL 基因型的分子育种可以促进复杂的性状改良。
Improving breeding has been widely utilized in crop breeding and contributed to yield and quality improvement, yet few researches have been done to analyze genetic architecture underlying breeding improvement comprehensively. Here, we collected genotype and phenotype data of 99 cultivars from the complete pedigree including Huanghuazhan, an elite, high-quality, conventional indica rice that has been grown over 4.5 million hectares in southern China and from which more than 20 excellent cultivars have been derived. We identified 1,313 selective sweeps (SSWs) revealing four stage-specific selection patterns corresponding to improvement preference during 65 years, and 1113 conserved Huanghuazhan traceable blocks (cHTBs) introduced from different donors and conserved in >3 breeding generations were the core genomic regions for superior performance of Huanghuazhan. Based on 151 quantitative trait loci (QTLs) identified for 13 improved traits in the pedigree, we reproduced their improvement process in silico, highlighting improving breeding works well for traits controlled by major/major + minor effect QTLs, but was inefficient for traits controlled by QTLs with complex interactions or explaining low levels of phenotypic variation. These results indicate long-term breeding improvement is efficient to construct superior genetic architecture for elite performance, yet molecular breeding with designed genotype of QTLs can facilitate complex traits improvement.