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PMID: 17044735 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

A high-resolution map of Arabidopsis recombinant inbred lines by whole-genome exon array hybridization.

PLoS genetics ·Vol. 2 ·No. 9 ·2006-09-15 ·Pages e144

Singer T, Fan Y, Chang HS, Zhu T, Hazen SP, Briggs SP

Abstract

Recombinant populations were the basis for Mendel's first genetic experiments and continue to be key to the study of genes, heredity, and genetic variation today. Genotyping several hundred thousand loci in a single assay by hybridizing genomic DNA to oligonucleotide arrays provides a powerful technique to improve precision linkage mapping. The genotypes of two accessions of Arabidopsis were compared by using a 400,000 feature exon-specific oligonucleotide array. Around 16,000 single feature polymorphisms (SFPs) were detected in approximately 8,000 of the approximately 26,000 genes represented on the array. Allelic variation at these loci was measured in a recombinant inbred line population, which defined the location of 815 recombination breakpoints. The genetic linkage map had a total length of 422.5 cM, with 676 informative SFP markers representing intervals of approximately 0.6 cM. One hundred fifteen single gene intervals were identified. Recombination rate, SFP distribution, and segregation in this population are not uniform. Many genomic regions show a clustering of recombination events including significant hot spots. The precise haplotype structure of the recombinant population was defined with unprecedented accuracy and resolution. The resulting linkage map allows further refinement of the hundreds of quantitative trait loci identified in this well-studied population. Highly variable recombination rates along each chromosome and extensive segregation distortion were observed in the population.

MeSH Terms
Arabidopsis/genetics Chromosome Segregation/genetics Chromosomes, Plant/genetics Exons/genetics Gene Dosage Genome, Plant/genetics Nucleic Acid Hybridization/methods Physical Chromosome Mapping/methods Polymorphism, Genetic Recombination, Genetic
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Singer Tatjana
Torrey Mesa Research Institute, Syngenta Research and Technology, San Diego, California, United States of America. [email protected]
Fan Yiping
Chang Hur-Song
Zhu Tong
Hazen Samuel P
Briggs Steven P
Conflict of Interest

Competing interests. The authors have declared that no competing interests exist.

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Article Info
Journal
PLoS genetics
Abbr.
PLoS Genet
ISSN
1553-7404
DOI
10.1371/journal.pgen.0020144
Email
[email protected]
Published
2006-09-15
Epub
2006-00-27
Pages
e144
Language
English
Region
United States
NLM ID
101239074
PMCID
PMC1564425
Subset
IM
Databases
RefSeq
NP_001031240, NP_178282, NP_196532
External Links
PubMed source DOI: 10.1371/journal.pgen.0020144 PMC Full Text View journal details
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