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PMID: 22106370 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis.

Genome research ·Vol. 22 ·No. 3 ·2012-03-00 ·Pages 508-18

Lu P, Han X, Qi J, Yang J, Wijeratne AJ, Li T, Ma H

Abstract

Meiotic recombination, including crossovers (COs) and gene conversions (GCs), impacts natural variation and is an important evolutionary force. COs increase genetic diversity by redistributing existing variation, whereas GCs can alter allelic frequency. Here, we sequenced Arabidopsis Landsberg erecta (Ler) and two sets of all four meiotic products from a Columbia (Col)/Ler hybrid to investigate genome-wide variation and meiotic recombination at nucleotide resolution. Comparing Ler and Col sequences uncovered 349,171 Single Nucleotide Polymorphisms (SNPs), 58,085 small and 2315 large insertions/deletions (indels), with highly correlated genome-wide distributions of SNPs, and small indels. A total of 443 genes have at least 10 nonsynonymous substitutions in protein-coding regions, with enrichment for disease-resistance genes. Another 316 genes are affected by large indels, including 130 genes with complete deletion of coding regions in Ler. Using the Arabidopsis qrt1 mutant, two sets of four meiotic products were generated and analyzed by sequencing for meiotic recombination, representing the first tetrad analysis with whole-genome sequencing in a nonfungal species. We detected 18 COs, six of which had an associated GC event, and four GCs without COs (NCOs), and revealed that Arabidopsis GCs are likely fewer and with shorter tracts than those in yeast. Meiotic recombination and chromosome assortment events dramatically redistributed genome variation in meiotic products, contributing to population diversity. In particular, meiosis provides a rapid mechanism to generate copy-number variation (CNV) of sequences that have different chromosomal positions in Col and Ler.

MeSH Terms
Arabidopsis/genetics Crossing Over, Genetic DNA Copy Number Variations Gene Conversion Genetic Variation Genome, Plant Genome-Wide Association Study Meiosis Mutagenesis, Insertional Polymorphism, Single Nucleotide Recombination, Genetic Sequence Analysis, DNA Sequence Deletion
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Lu Pingli
Department of Biology and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, PA 16802, USA.
Han Xinwei
Qi Ji
Yang Jiange
Wijeratne Asela J
Li Tao
Ma Hong
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1549-5469
DOI
10.1101/gr.127522.111
Published
2012-03-00
Epub
2011-00-21
Pages
508-18
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC3290786
Subset
IM
External Links
PubMed source DOI: 10.1101/gr.127522.111 PMC Full Text View journal details
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