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

doi:10.1111/pbi.12409

CORC > 北京大学 > 生命科学学院

	Pedigree-based analysis of derivation of genome segments of an elite rice reveals key regions during its breeding
	Zhou, Degui ; Chen, Wei ; Lin, Zechuan ; Chen, Haodong ; Wang, Chongrong ; Li, Hong ; Yu, Renbo ; Zhang, Fengyun ; Zhen, Gang ; Yi, Junliang ; Li, Kanghuo ; Liu, Yaoguang ; Terzaghi, William ; Tang, Xiaoyan ; He, Hang ; Zhou, Shaochuan ; Deng, Xing Wang
刊名	PLANT BIOTECHNOLOGY JOURNAL
	2016
关键词	genetic improvement resequencing single nucleotide polymorphisms pedigree artificial selection breeding BLAST-RESISTANCE GENE ORYZA-SATIVA L. MARKER-ASSISTED SELECTION DISEASE RESISTANCE NUCLEOTIDE-BINDING NATURAL VARIATION DNA POLYMORPHISM DRAFT SEQUENCE HYBRID RICE GRAIN-SIZE
DOI	10.1111/pbi.12409
英文摘要	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.; National High Technology Research and Development Program of China (863 Program) [2012AA10A304, 2014AA10A602]; National Program on Key Basic Research Project of China (973 Program) [2011CB100101]; National Natural Science Foundation of China [U1031001, 31201277]; Ministry of Agriculture of China (948 Program) [2011-G2B, 2012-G2]; SCI(E); PubMed; ARTICLE; hehang@pku.edu.cn; xxs123@163.com; deng@pku.edu.cn; 2; 638-648; 14
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/419217]
专题	生命科学学院
推荐引用方式 GB/T 7714	Zhou, Degui,Chen, Wei,Lin, Zechuan,et al. Pedigree-based analysis of derivation of genome segments of an elite rice reveals key regions during its breeding[J]. PLANT BIOTECHNOLOGY JOURNAL,2016.
APA	Zhou, Degui.,Chen, Wei.,Lin, Zechuan.,Chen, Haodong.,Wang, Chongrong.,...&Deng, Xing Wang.(2016).Pedigree-based analysis of derivation of genome segments of an elite rice reveals key regions during its breeding.PLANT BIOTECHNOLOGY JOURNAL.
MLA	Zhou, Degui,et al."Pedigree-based analysis of derivation of genome segments of an elite rice reveals key regions during its breeding".PLANT BIOTECHNOLOGY JOURNAL (2016).