Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2010 Jun 8;107(23):10578-83.
doi: 10.1073/pnas.1005931107. Epub 2010 May 24.

Parent-independent Genotyping for Constructing an Ultrahigh-Density Linkage Map Based on Population Sequencing

Affiliations
Free PMC article

Parent-independent Genotyping for Constructing an Ultrahigh-Density Linkage Map Based on Population Sequencing

Weibo Xie et al. Proc Natl Acad Sci U S A. .
Free PMC article

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.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
An example of inferring parental genotypes based on the principle of maximum parsimony of recombination (MPR). Different background colors represent different genotypes in matrices C, E, and G, whereas crosses indicate the recombination breakpoints between different genotypes. See text for details.
Fig. 2.
Fig. 2.
The scheme for global inference of parental genotypes. (AC) Procedures for inferring the draft genotypes of the two parents P1 and P2 assisted by low-coverage parental sequences of one parent (see text for details). (DG) Refining the SNPs of the inferred parental genotypes, including: (D and E) inferring the parental genotypes using permutation by resampling of SNPs according to individual RILs (see text for details), and (F and G) validating the SNPs by posterior probabilities (Bayesian inference). The number of genotype calls for an SNP site resulting from the permutations was recorded (F), and the probability for the assignment of the draft genotype was calculated (G), whereby the genotype is assigned by the highest posterior probability of P1, PN, and P2 at the given SNP site. It is also seen that the posterior probability of PN of SNPs at the fourth site (in gray) is the highest, and thus this site is regarded as a low-quality SNP site. (H) Assembling genotype calls from different windows aided by low-coverage parental sequences.
Fig. 3.
Fig. 3.
RIL genotyping, bin map construction, and mapping of QTLs controlling grain width. (A) Procedures of RIL genotyping and bin map construction. The lower panel shows the bin map of 238 rice RILs on chromosome 5. (B) Probabilistic parameters of the hidden Markov model used to genotype RILs. (C) Mapping curve of QTLs controlling grain width on chromosome 5. A simple Student's t test was used to locate bins associated with grain width. The x axis is the position of bins along the chromosome and the rugs on the x axis represent the borders of bins. The y axis shows the log10-transformed P values resulting from the t test, which represents the degree of association between grain width and bins.

Similar articles

See all similar articles

Cited by 121 articles

See all "Cited by" articles

Publication types

LinkOut - more resources

Feedback