Genome‐wide association mapping identifies the genetic basis of discrete and quantitative variation in sexual weaponry in a wild sheep population

Abstract

Understanding the genetic architecture of phenotypic variation in natural populations is a fundamental goal of evolutionary genetics. Wild Soay sheep (Ovis aries) have an inherited polymorphism for horn morphology in both sexes, controlled by a single autosomal locus, Horns. The majority of males have large normal horns, but a small number have vestigial, deformed horns, known as scurs; females have either normal horns, scurs or no horns (polled). Given that scurred males and polled females have reduced fitness within each sex, it is counterintuitive that the polymorphism persists within the population. Therefore, identifying the genetic basis of horn type will provide a vital foundation for understanding why the different morphs are maintained in the face of natural selection. We conducted a genome-wide association study using ∼36000 single nucleotide polymorphisms (SNPs) and determined the main candidate for Horns as RXFP2, an autosomal gene with a known involvement in determining primary sex characters in humans and mice. Evidence from additional SNPs in and around RXFP2 supports a new model of horn-type inheritance in Soay sheep, and for the first time, sheep with the same horn phenotype but different underlying genotypes can be identified. In addition, RXFP2 was shown to be an additive quantitative trait locus (QTL) for horn size in normal-horned males, accounting for up to 76% of additive genetic variation in this trait. This finding contrasts markedly from genome-wide association studies of quantitative traits in humans and some model species, where it is often observed that mapped loci only explain a modest proportion of the overall genetic variation.

Ecological characteristics andin situgenetic associations for yield-component traits of wildMiscanthusfrom eastern Russia

“…Analyses of phenotypic, ecological and genetic data were conducted with the following objectives: (1) to identify potential geographic, climatic, ecological and anthropogenic influences on the ranges of M. sinensis and M. sacchariflorus; (2) to quantify phenotypic variation for biomass traits; (3) to understand population structure of Russian M. sinensis and M. sacchariflorus in order to identify genetic groups for germplasm conservation, association analysis and potential sources of heterosis; (4) to compare genetic diversity of Russian Miscanthus with previously characterized Miscanthus populations in order to assess its relative utility for breeding; and (5) to investigate the potential to identify quantitative trait loci (QTLs) for traits of agronomic interest via GWAS of in situ phenotypic data obtained during germplasm collection. Although it is currently unusual to perform GWAS for crop germplasm without phenotypic data from replicated field trials, there are previous examples of successful association studies using phenotypic data from natural populations, particularly in forestry (Parchman et al, 2012;Budde et al, 2014) and animal ecology (Johnston et al, 2011(Johnston et al, , 2014Narum et al, 2013). Here we demonstrate that value can be added to a crop germplasm collection by combining in situ phenotype data and inexpensive genotyping data in a GWAS.…”

Genetic testing for phenotype-causing variants in sheep and goats

“…A genome wide association study using the ovine SNP50 beadchip gave also strong evidence that the relaxin/ insulin-like family peptide receptor 2 gene (RXFP2) is involved in the control of the horned/polled status of Soay sheep. However, the causative sequence variant was not identified in this study [15]. Very recently, a nucleotide substitution highly predictive for the polled genotype was also identified close to RXFP2 after genotyping sheep from two independent Australian Merino populations with the SNP50 beadchip [16].…”

Linkage mapping of a polymorphic plumage locus associated with intermorph incompatibility in the Gouldian finch (Erythrura gouldiae)

“…In the GF it is also likely to be difficult to obtain enough samples that include adequate phenotypic information, because informative crosses between heterozygous red males and black females produce offspring of low viability in this captive population (Pryke and Griffith, 2009a, b). Therefore, it would be difficult to obtain finer resolution than the currently identified candidate region from linkage mapping; a genomewide association study using many more markers and wild population samples that have small LD is required to help narrow down the candidate region (Johnston et al, 2011).…”