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

Colli, Licia, Joost, Stéphane, Negrini, Riccardo, Nicoloso, Letizia, Crepaldi, Paola, Ajmone-Marsan, Paolo, Bruford, Michael William, Juma, Gabriela Alexandra Pinto and Perez, Maria Trinidad 2014. Assessing the spatial dependence of adaptive loci in 43 European and Western Asian goat breeds using AFLP markers. PLoS ONE 9 (1) , e86668. 10.1371/journal.pone.0086668

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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.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Biosciences
Sustainable Places Research Institute (PLACES)
Subjects: Q Science > Q Science (General)
Uncontrolled Keywords: Amplified fragment length polymorphism; animal genomics; animal husbandry; genome analysis; goats; humidity; livestock; meteorology.
Additional Information: © 2014 Colli et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Publisher: Public Library of Science
ISSN: 1932-6203
Date of First Compliant Deposit: 30 March 2016
Date of Acceptance: 12 December 2013
Last Modified: 22 Feb 2019 14:21
URI: http://orca.cf.ac.uk/id/eprint/60336

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