Dataset Information

Assessing the spatial dependence of adaptive loci in 43 European and Western Asian goat breeds using AFLP markers.

ABSTRACT:

Background

During the past decades, neutral DNA markers have been extensively employed to study demography, population genetics and structure in livestock, but less interest has been devoted to the evaluation of livestock adaptive potential through the identification of genomic regions likely to be under natural selection.

Methodology/principal findings

Landscape genomics can greatly benefit the entire livestock system through the identification of genotypes better adapted to specific or extreme environmental conditions. Therefore we analyzed 101 AFLP markers in 43 European and Western Asian goat breeds both with Matsam software, based on a correlative approach (SAM), and with Mcheza and Bayescan, two FST based software able to detect markers carrying signatures of natural selection. Matsam identified four loci possibly under natural selection--also confirmed by FST-outlier methods--and significantly associated with environmental variables such as diurnal temperature range, frequency of precipitation, relative humidity and solar radiation.

Conclusions/significance

These results show that landscape genomics can provide useful information on the environmental factors affecting the adaptive potential of livestock living in specific climatic conditions. Besides adding conservation value to livestock genetic resources, this knowledge may lead to the development of novel molecular tools useful to preserve the adaptive potential of local breeds during genetic improvement programs, and to increase the adaptability of industrial breeds to changing environments.

SUBMITTER: Colli L

PROVIDER: S-EPMC3907386 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Publications

Assessing the spatial dependence of adaptive loci in 43 European and Western Asian goat breeds using AFLP markers.

Colli Licia L Joost Stéphane S Negrini Riccardo R Nicoloso Letizia L Crepaldi Paola P Ajmone-Marsan Paolo P

PloS one 20140130 1

<h4>Background</h4>During the past decades, neutral DNA markers have been extensively employed to study demography, population genetics and structure in livestock, but less interest has been devoted to the evaluation of livestock adaptive potential through the identification of genomic regions likely to be under natural selection.<h4>Methodology/principal findings</h4>Landscape genomics can greatly benefit the entire livestock system through the identification of genotypes better adapted to spec ...[more]

PMID: 24497965

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Project description:Native domestic breeds represent important cultural heritage and genetic diversity relevant for production traits, environmental adaptation and food security. However, risks associated with low effective population size, such as inbreeding and genetic drift, have elevated concerns over whether unique within-breed lineages should be kept separate or managed as one population. As a conservation genomic case study of the genetic diversity represented by native breeds, we examined native and commercial cattle (Bos taurus) breeds including the threatened Danish Jutland cattle. We examined population structure and genetic diversity within breeds and lineages genotyped across 770K single nucleotide polymorphism loci to determine (a) the amount and distribution of genetic diversity in native breeds, and (b) the role of genetic drift versus selection. We further investigated the presence of outlier loci to detect (c) signatures of environmental selection in native versus commercial breeds, and (d) native breed adaptation to various landscapes. Moreover, we included older cryopreserved samples to determine (e) whether cryopreservation allows (re)introduction of original genetic diversity. We investigated a final set of 195 individuals and 677K autosomal loci for genetic diversity within and among breeds, examined population structure with principal component analyses and a maximum-likelihood approach and searched for outlier loci suggesting artificial or natural selection. Our findings demonstrate the potential of genomics for identifying the uniqueness of native domestic breeds, and for maintaining their genetic diversity and long-term evolutionary potential through conservation plans balancing inbreeding with carefully designed outcrossing. One promising opportunity is the use of cryopreserved samples, which can provide important genetic diversity for populations with few individuals, while helping to preserve their traditional genetic characteristics. Outlier tests for native versus commercial breeds identified genes associated with climate adaptation, immunity and metabolism, and native breeds may carry genetic variation important for animal health and robustness in a changing climate.

Dataset Information

Assessing the spatial dependence of adaptive loci in 43 European and Western Asian goat breeds using AFLP markers.

Background

Methodology/principal findings

Conclusions/significance

Publications

Assessing the spatial dependence of adaptive loci in 43 European and Western Asian goat breeds using AFLP markers.

Similar Datasets

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