Reduced meiotic recombination in rhesus macaques and the origin of the human recombination landscape.

Cheng Xue,Muthuswamy Raveendran,Navin Rustagi,Manjunath Gorentla Venkata,Jeffrey Rogers,Xiaoming Liu,R Alan Harris,Fuli Yu,Karol Sestak

doi:10.1371/journal.pone.0236285

Abstract

Characterizing meiotic recombination rates across the genomes of nonhuman primates is important for understanding the genetics of primate populations, performing genetic analyses of phenotypic variation and reconstructing the evolution of human recombination. Rhesus macaques (Macaca mulatta) are the most widely used nonhuman primates in biomedical research. We constructed a high-resolution genetic map of the rhesus genome based on whole genome sequence data from Indian-origin rhesus macaques. The genetic markers used were approximately 18 million SNPs, with marker density 6.93 per kb across the autosomes. We report that the genome-wide recombination rate in rhesus macaques is significantly lower than rates observed in apes or humans, while the distribution of recombination across the macaque genome is more uniform. These observations provide new comparative information regarding the evolution of recombination in primates.

Highlights

Meiotic recombination is a fundamental genetic process that serves essential cellular functions [1, 2]
Single nucleotide polymorphism (SNP) genotypes were generated by first mapping the quality-filtered sequence reads to the rheMac2 rhesus macaque reference assembly using BWA [18], and using SNPtools [19] to identify high quality variants
We estimated autosomal recombination rates across 123 Indian-origin rhesus macaques using LDhat version 2.1 [20, 22] and phased genotypes obtained from whole genome sequencing

Summary

Introduction

Meiotic recombination is a fundamental genetic process that serves essential cellular functions [1, 2]. The frequency and distribution of recombination events shape the structure of haplotypes within a population, and influence population-level response to positive selection. This affects the distribution of phenotypic variation across environments [3, 4]. The structure of recombination maps and patterns of linkage disequilibrium in humans and other organisms are critical parameters in efforts to map genes that affect disease or reconstruct population genetic processes that shape the genomic and phenotypic diversity within species [5, 6]. Researchers have quantified recombination through linkage mapping in large pedigrees [7, 8], and generated fine-scale recombination maps using single nucleotide

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Results

Conclusion