Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by re-sequencing Landsberg erecta and all four products of a single meiosis
- 1 The Penn State University;
- 2 the Pennsylvania State University;
- 3 Fudan University;
- 4 6Institute of Hydrobiology, Chinese Academy of Science
- ↵* Corresponding author; email: hxm16{at}psu.edu
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 2,315 large insertions/deletions (indels), with highly correlated genome-wide distributions of SNPs and small indels. 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, 6 of which had an associated GC event, and 4 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 re-distributed 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.
- Received June 16, 2011.
- Accepted November 17, 2011.
- Copyright © 2011, Cold Spring Harbor Laboratory Press
