Fine-scale population recombination rates, hotspots, and correlates of recombination in the Medicago truncatula genome.

Genome Biology and Evolution
Timothy PaapePeter Tiffin

Abstract

Recombination rates vary across the genome and in many species show significant relationships with several genomic features, including distance to the centromere, gene density, and GC content. Studies of fine-scale recombination rates have also revealed that in several species, there are recombination hotspots, that is, short regions with recombination rates 10-100 greater than those in surrounding regions. In this study, we analyzed whole-genome resequence data from 26 accessions of the model legume Medicago truncatula to gain insight into the genomic features that are related to high- and low-recombination rates and recombination hotspots at 1 kb scales. We found that high-recombination regions (1-kb windows among those in the highest 5% of the distribution) on all three chromosomes were significantly closer to the centromere, had higher gene density, and lower GC content than low-recombination windows. High-recombination windows are also significantly overrepresented among some gene functional categories-most strongly NB-ARC and LRR genes, both of which are important in plant defense against pathogens. Similar to high-recombination windows, recombination hotspots (1-kb windows with significantly higher recombination than the...Continue Reading

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Sep 21, 2013·Genome Biology·Eva BauerChris-Carolin Schön
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Methods Mentioned

BETA
genotyping
Illumina sequencing

Software Mentioned

sequenceLDhot
R
LDhat

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