Widely distributed hot and cold spots in meiotic recombination as shown by the sequencing of rice F₂ plants

Abstract

Summary Numerous studies have argued that environmental variations may contribute to evolution through the generation of novel heritable variations via meiotic recombination, which plays a crucial role in crop domestication and improvement. Rice is one of the most important staple crops, but no direct estimate of recombination events has yet been made at a fine scale. Here, we address this limitation by sequencing 41 rice individuals with high sequencing coverage and c. 900 000 accurate markers. An average of 33.9 crossover (c. 4.53 cM Mb−1) and 2.47 non‐crossover events were detected per F2 plant, which is similar to the values in Arabidopsis. Although not all samples in the stress treatment group showed an increased number of crossover events, environmental stress increased the recombination rate in c. 28.5% of samples. Interestingly, the crossovers showed a highly uneven distribution among and along chromosomes, with c. 13.9% of the entire genome devoid of crossovers, including 11 of the 12 centromere regions, and c. 0.72% of the genome containing large numbers of crossovers (> 50 cM Mb−1). The gene ontology (GO) categories showed that genes clustered within the recombination hot spot regions primarily tended to be involved in responses to environmental stimuli, suggesting that recombination plays an important role for adaptive evolution in rapidly changing environments.

Understanding and Manipulating Meiotic Recombination in Plants

“…In accordance with this latter supposition, analyses in rice, maize, and wheat at the level of megabase genomic windows suggest that CO hotspots identified from maize microscopes and F2 populations (Saintenac et al, 2011;Rodgers-Melnick et al, 2015;Si et al, 2015) have low DNA methylation and transposons but are enriched in regions with high gene density. At a smaller physical scale (kilobase windows), hotspots are polarized toward the 59 and 39 ends of genes (Xu et al, 1995;Li et al, 2015).…”

“…Interestingly, recent fine-scale mapping of COs in rice showed that genes located at recombination hotspots are involved in responses to environmental stimuli. That study also showed that heat stress and pathogen infection increased the recombination rate for some individuals (Si et al, 2015).…”

“…Genome structure and CO distribution differ between Arabidopsis, rice, and maize. Arabidopsis (Stroud et al, 2013;Wijnker et al, 2013) and rice (Chodavarapu et al, 2012;Si et al, 2015) have low DNA methylation and transposon content along chromosome arms. Both factors are high in the recombinationrepressed heterochromatic regions close to centromeres.…”

Mutation rate analysis via parent–progeny sequencing of the perennial peach. II. No evidence for recombination-associated mutation

“…The CO rate of 2.6 cM Mbp −1 per meiosis per sample in peach is markedly lower than that in annual rice (4.53 cM Mbp −1 ) and Arabidopsis (4.0 cM Mbp −1 ) [45,46]. This result is consistent with previous reports of low recombination rates (0.63–2.5 cM Mbp −1 ) in other woody perennials, such as apple, pear, grape, oak and walnut, suggesting that low recombination rates may be part of the reproductive strategy of woody perennials [5].…”

Genomic characterization of African cultivated and wild Oryza species

“…The clustering of majority of the candidate markers in a genomic region of about 2.1Mbp could be as a result of linkage dragBased on a mean conversion rate of 200kbp/cM as the average physical distance per centimorgan (Orjuela et al 2010), the 2.1Mbp region corresponds to about 10cM. Recombination in rice is expected to occur at a frequency of between 0.39-0.45cM per 100kbp (Si et al 2015;Wu et al 2003) and so no recombination would be expected in the linkage interval. Linkage causes markers surrounding the causal loci to show deviations from the 50% inheritance pattern expected of parental alleles, though they may not be linked to the trait .…”