A High-Resolution Map of Arabidopsis Recombinant Inbred Lines by Whole-Genome Exon Array Hybridization

Singer, Tatjana; Fan, Yiping; Chang, Hur-Song; Zhu, Tong; Hazen, Samuel P.; Briggs, Steven P.

doi:10.1371/journal.pgen.0020144

Cited by 104 publications

(103 citation statements)

References 69 publications

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“…We analyzed closely the relationship between SFP diversity and recombination rate variation using a recently generated very highdensity genetic linkage map that precisely defined 676 recombination events in 98 Col/Ler recombinant inbred lines (33). The number of recombination events in a 1-Mb region centered on a gene was calculated here for every gene and compared with the total SFP diversity within a 50-kb window centered on that gene.…”

Section: Resultsmentioning

confidence: 99%

Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana

Borevitz

Hazen

Michael

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

154

148

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We used hybridization to the ATH1 gene expression array to interrogate genomic DNA diversity in 23 wild strains (accessions) of Arabidopsis thaliana (arabidopsis), in comparison with the reference strain Columbia (Col). At <1% false discovery rate, we detected 77,420 single-feature polymorphisms (SFPs) with distinct patterns of variation across the genome. Total and pair-wise diversity was higher near the centromeres and the heterochromatic knob region, but overall diversity was positively correlated with recombination rate (R 2 ‫؍‬ 3.1%). The difference between total and pair-wise SFP diversity is a relative measure contrasting diversifying or frequency-dependent selection, similar to Tajima's D, and can be calibrated by the empirical genome-wide distribution. Each unique locus, centered on a gene, has a diversity and selection score that suggest a relative role in past evolutionary processes. Homologs of disease resistance (R) genes include members with especially high levels of diversity often showing frequencydependent selection and occasionally evidence of a past selective sweep. Receptor-like and S-locus proteins also contained members with elevated levels of diversity and signatures of selection, whereas other gene families, bHLH, F-box, and RING finger proteins, showed more typical levels of diversity. SFPs identified with the gene expression array also provide an empirical hybridization polymorphism background for studies of gene expression polymorphism and are available through the genome browser http:// signal.salk.edu/cgi-bin/AtSFP. evolutionary genomics ͉ gene array ͉ nucleotide diversity

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Section: Resultsmentioning

confidence: 99%

Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana

Borevitz

Hazen

Michael

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

154

148

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“…Because a plethora of new genome assemblies is available and various kinds of mapping populations have been constructed in many species, including plants (23,24) and animals (25)(26)(27), the method developed here will be generally applicable and cost-effective for genotyping of mapping populations.…”

Section: Discussionmentioning

confidence: 99%

Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing

Xie

Feng²,

Yu³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

292

258

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Bar-coded multiplexed sequencing approaches based on newgeneration 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 0.05× 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.genomics | maximum parsimony of recombination | Bayesian inference | hidden Markov model | rice G enetic maps provide the bases for a wide range of genetic and genomic studies and are pivotal for mapping and identifying genes associated with phenotypic performance, referred to as traits. The resolution of a genetic linkage map depends on the number of recombination events in the mapping population and the density of molecular markers. The number of recombination events depends on how the population is created, whereas the density of the markers can be improved continually with advances in molecular techniques. Traditional molecular markers that have been widely used in genotyping assays of populations, although laborious and time-consuming, have limitations in throughput and can provide information only for low-density maps, and thus are of low efficiency.Oligonucleotide microarrays, composed of millions of probes based on genome sequences, can capture large numbers of sequence variations between different samples by comparative genomic hybridization, which can be used for high-throughput marker discovery and genotyping (1-3). However, restrictions in microarray design and the number of probes on the microarrays limit the applications of this technology. In addition, it is cost-prohibitive for genotyping especially if the mapping population is large.New sequencing t...

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“…Genetic map positions for the haplomarkers were lacking. Therefore, the physical map position of the middle SNP of each haplomarker was linearly projected on to the genetic map (Singer et al, 2006), resulting in an average genetic map distance of B0.7 cM. The number of haplotypes per haplomarker ranged from two to nine with an average of five.…”

Section: Methodsmentioning

confidence: 99%

QTL detection power of multi-parental RIL populations in Arabidopsis thaliana

2012

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A major goal of today's biology is to understand the genetic basis of quantitative traits. This can be achieved by statistical methods that evaluate the association between molecular marker variation and phenotypic variation in different types of mapping populations. The objective of this work was to evaluate the statistical power of quantitative trait loci (QTL) detection of various multi-parental mating designs, as well as to assess the reasons for the observed differences. Our study was based on an empirical data of 20 Arabidopsis thaliana accessions, which have been selected to capture the maximum genetic diversity. The examined mating designs differed strongly with respect to the statistical power to detect QTL. We observed the highest power to detect QTL for the diallel cross with random mating design. The results of our study suggested that performing sibling mating within subpopulations of joint-linkage mapping populations has the potential to considerably increase the power for QTL detection. Our results, however, revealed that using designs in which more than two parental alleles segregate in each subpopulation increases the power even more.

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A High-Resolution Map of Arabidopsis Recombinant Inbred Lines by Whole-Genome Exon Array Hybridization

Cited by 104 publications

References 69 publications

Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana

Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana

Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing

QTL detection power of multi-parental RIL populations in Arabidopsis thaliana

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