Pedigree-based analysis of derivation of genome segments of an elite rice reveals key regions during its breeding

文献类型： 外文期刊

第一作者： Zhou, Degui

作者： Zhou, Degui;Wang, Chongrong;Li, Hong;Li, Kanghuo;Zhou, Shaochuan;Chen, Wei;Lin, Zechuan;Chen, Haodong;Yu, Renbo;Zhen, Gang;He, Hang;Deng, Xing Wang;Chen, Wei;Lin, Zechuan;Chen, Haodong;Yu, Renbo;Zhen, Gang;He, Hang;Deng, Xing Wang;Chen, Wei;Chen, Haodong;Yu, Renbo;Zhen, Gang;Tang, Xiaoyan;He, Hang;Deng, Xing Wang;Zhang, Fengyun;Yi, Junliang;Zhou, Shaochuan;Liu, Yaoguang;Terzaghi, William;He, Hang;Deng, Xing Wang

作者机构：

关键词： genetic improvement;resequencing;single nucleotide polymorphisms;pedigree;artificial selection;breeding

期刊名称：PLANT BIOTECHNOLOGY JOURNAL （ 影响因子：9.803； 五年影响因子：9.555 ）

ISSN：

年卷期：

页码：

收录情况： SCI

摘要： Analyses of genome variations with high-throughput assays have improved our understanding of genetic basis of crop domestication and identified the selected genome regions, but little is known about that of modern breeding, which has limited the usefulness of massive elite cultivars in further breeding. Here we deploy pedigree-based analysis of an elite rice, Huanghuazhan, to exploit key genome regions during its breeding. The cultivars in the pedigree were resequenced with 7.6x depth on average, and 2.1 million high-quality single nucleotide polymorphisms (SNPs) were obtained. Tracing the derivation of genome blocks with pedigree and information on SNPs revealed the chromosomal recombination during breeding, which showed that 26.22% of Huanghuazhan genome are strictly conserved key regions. These major effect regions were further supported by a QTL mapping of 260 recombinant inbred lines derived from the cross of Huanghuazhan and a very dissimilar cultivar, Shuanggui 36, and by the genome profile of eight cultivars and 36 elite lines derived from Huanghuazhan. Hitting these regions with the cloned genes revealed they include numbers of key genes, which were then applied to demonstrate how Huanghuazhan were bred after 30 years of effort and to dissect the deficiency of artificial selection. We concluded the regions are helpful to the further breeding based on this pedigree and performing breeding by design. Our study provides genetic dissection of modern rice breeding and sheds new light on how to perform genomewide breeding by design.

分类号： Q7

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