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PLoS Genet. 2016 Apr 1;12(4):e1005951. doi: 10.1371/journal.pgen.1005951. eCollection 2016 Apr.

The Genetic Architecture of Natural Variation in Recombination Rate in Drosophila melanogaster.

Hunter CM1,2, Huang W1,2,3, Mackay TF1,2, Singh ND1,2,4.

Author information

1
Program in Genetics, Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America.
2
W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina, United States of America.
3
Initiative in Biological Complexity, North Carolina State University, Raleigh, North Carolina, United States of America.
4
Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, United States of America.

Abstract

Meiotic recombination ensures proper chromosome segregation in many sexually reproducing organisms. Despite this crucial function, rates of recombination are highly variable within and between taxa, and the genetic basis of this variation remains poorly understood. Here, we exploit natural variation in the inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) to map genetic variants affecting recombination rate. We used a two-step crossing scheme and visible markers to measure rates of recombination in a 33 cM interval on the X chromosome and in a 20.4 cM interval on chromosome 3R for 205 DGRP lines. Though we cannot exclude that some biases exist due to viability effects associated with the visible markers used in this study, we find ~2-fold variation in recombination rate among lines. Interestingly, we further find that recombination rates are uncorrelated between the two chromosomal intervals. We performed a genome-wide association study to identify genetic variants associated with recombination rate in each of the two intervals surveyed. We refined our list of candidate variants and genes associated with recombination rate variation and selected twenty genes for functional assessment. We present strong evidence that five genes are likely to contribute to natural variation in recombination rate in D. melanogaster; these genes lie outside the canonical meiotic recombination pathway. We also find a weak effect of Wolbachia infection on recombination rate and we confirm the interchromosomal effect. Our results highlight the magnitude of population variation in recombination rate present in D. melanogaster and implicate new genetic factors mediating natural variation in this quantitative trait.

PMID:
27035832
PMCID:
PMC4817973
DOI:
10.1371/journal.pgen.1005951
[Indexed for MEDLINE]
Free PMC Article

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