气候变化领域集成服务门户(CCPortal): Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing

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DOI	10.1073/pnas.1005931107
	Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing
	Xie, Weibo; Feng, Qi; Yu, Huihui; Huang, Xuehui; Zhao, Qiang; Xing, Yongzhong; Yu, Sibin; Han, Bin; Zhang, Qifa
发表日期	2010
ISSN	0027-8424
卷号	107 期号:23
英文摘要	Bar-coded multiplexed sequencing approaches based on new-generation sequencing technologies provide capacity to sequence a mapping population in a single sequencing run. However, such approaches usually generate low-coverage and error-prone sequences for each line in a population. Thus, it is a significant challenge to genotype individual lines in a population for linkage map construction based on low-coverage sequences without the availability of high-quality genotype data of the parental lines. In this paper, we report a method for constructing ultrahigh-density linkage maps composed of high-quality single-nucleotide polymorphisms (SNPs) based on low-coverage sequences of recombinant inbred lines. First, all potential SNPs were identified to obtain drafts of parental genotypes using a maximum parsimonious inference of recombination, making maximum use of SNP information found in the entire population. Second, high-quality SNPs were identified by filtering out low-quality ones by permutations involving resampling of windows of SNPs followed by Bayesian inference. Third, lines in the mapping population were genotyped using the high-quality SNPs assisted by a hidden Markov model. With 0.05x genome sequence per line, an ultrahigh-density linkage map composed of bins of high-quality SNPs using 238 recombinant inbred lines derived from a cross between two rice varieties was constructed. Using this map, a quantitative trait locus for grain width (GW5) was localized to its presumed genomic region in a bin of 200 kb, confirming the accuracy and quality of the map. This method is generally applicable in genetic map construction with low-coverage sequence data.
关键词	genomics maximum parsimony of recombination Bayesian inference hidden Markov model rice
学科领域	Science & Technology - Other Topics
语种	英语
WOS研究方向	Multidisciplinary Sciences
来源期刊	PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
来源机构	中国科学院西北生态环境资源研究院
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/111602
作者单位	Huazhong Agr Univ, Natl Ctr Plant Gene Res Wuhan, Natl Key Lab Crop Genet Improvement, Wuhan 430070, Peoples R China
推荐引用方式 GB/T 7714	Xie, Weibo,Feng, Qi,Yu, Huihui,et al. Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing[J]. 中国科学院西北生态环境资源研究院,2010,107(23).
APA	Xie, Weibo.,Feng, Qi.,Yu, Huihui.,Huang, Xuehui.,Zhao, Qiang.,...&Zhang, Qifa.(2010).Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,107(23).
MLA	Xie, Weibo,et al."Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing".PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 107.23(2010).