RecView: an interactive R application for viewing and locating recombination positions using pedigree data

Abstract

Recombination generates new haplotypes and disconnects linked genes thereby increasing the efficiency of selection and the adaptive potential. Quantifying the recombination landscape, i.e., the recombination rate variation along chromosomes, is important for understanding how evolutionary processes such as selection and drift are acting on genes and chromosomes. Here, we present RecView, an interactive R application, designed to view and locate recombination positions along chromosomes using whole-genome genotype data of a three-generation pedigree. RecView visualises the grandparent-of-origin of all informative alleles along each chromosome of the offspring in the pedigree. It also infers putative recombination positions with two algorithms, one based on change in the proportion of the alleles with specific grandparent-of-origin, and one on the degree of continuity of alleles with the same grandparent-of-origin, along the chromosome. Putative recombination positions are given in base pairs together with an estimated error based on the local density of informative alleles. We demonstrate the applicability of RecView using sequencing data of one 120 Mb-large chromosome of one offspring (and its four grandparents and two parents) of a passerine bird, the great reed warbler (Acrocephalus arundinaceus). On this chromosome, we detected five recombination events, three on the paternal chromosome and two on the maternal chromosome with both algorithms. To evaluate how sensitive the analysis is for SNP density, we downsampled our data to 10% of the original dataset. In conclusion, we provide an easy-to-use and highly effective application for viewing and locating recombination positions along chromosomes in small pedigrees. RecView and test data are available on GitHub (https://github.com/HKyleZhang/RecView.git).