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

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.

Great majority of recombination events in Arabidopsis are gene conversion events

“…To enable comparison with prior studies (8-10, 12, 13), we group these events into long (>500 kb) and short spans (10-500 kb). The average number of long blocks are limited (8.4 or 3.6 cM/Mb per genome; Table 1) and consistent with prior reports for which a 500-kb interval was about the limit of resolution (8)(9)(10)(11). The position of every long CO is unique (SI Appendix, Fig.…”

“…Investigations in Arabidopsis have resulted in highly consistent estimates as regards CO events with under 10 (3.74-8.3) per meiosis (8)(9)(10)(11). Similarly, the most recent report, using nextgeneration sequencing (NGS), revealed 9 COs per meiosis (9).…”

“…Similarly, the most recent report, using nextgeneration sequencing (NGS), revealed 9 COs per meiosis (9). According to the analyses in humans and yeast, meiotic gene conversion events typically have tract lengths less than 2 kb (12,13), commonly smaller (9).…”

“…Similarly, the most recent report, using nextgeneration sequencing (NGS), revealed 9 COs per meiosis (9). According to the analyses in humans and yeast, meiotic gene conversion events typically have tract lengths less than 2 kb (12,13), commonly smaller (9). The small size of gene conversions makes them all but impossible to be detected in nearly all of the prior recombinational analyses for our species, as markers were on average usually hundreds of kilobases or a few megabases apart.…”

“…NGS approaches can potentially be influential in this arena allowing markers every few hundred base pairs to be used. The one recent NGS analysis suggested there to be as many CO events as gene conversions (9), making Arabidopsis more like yeast. This direct estimate, however, disagrees with indirect inferences.…”