title: Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing.
abstract: 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.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Weibo
authors.initials: W
authors.lastname: Xie
authors.forename: Qi
authors.initials: Q
authors.lastname: Feng
authors.forename: Huihui
authors.initials: H
authors.lastname: Yu
authors.forename: Xuehui
authors.initials: X
authors.lastname: Huang
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhao
authors.forename: Yongzhong
authors.initials: Y
authors.lastname: Xing
authors.forename: Sibin
authors.initials: S
authors.lastname: Yu
authors.forename: Bin
authors.initials: B
authors.lastname: Han
authors.forename: Qifa
authors.initials: Q
authors.lastname: Zhang
mesh_terms: D008040:Genetic Linkage; D005838:Genotype; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*