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


RESULTS
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
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.
Istituto di Zootecnica, Laboratorio di Genetica Animale, Università Cattolica del Sacro Cuore di Piacenza, Piacenza, Italy ; BioDNA Research Center, Università Cattolica del Sacro Cuore di Piacenza, Piacenza, Italy.
Licia
L
Colli
Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
Stéphane
S
Joost
Istituto di Zootecnica, Laboratorio di Genetica Animale, Università Cattolica del Sacro Cuore di Piacenza, Piacenza, Italy ; Associazione Italiana Allevatori, Roma, Italy.
Riccardo
R
Negrini
Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università degli Studi di Milano, Milano, Italy.
Letizia
L
Nicoloso
Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università degli Studi di Milano, Milano, Italy.
Paola
P
Crepaldi
Istituto di Zootecnica, Laboratorio di Genetica Animale, Università Cattolica del Sacro Cuore di Piacenza, Piacenza, Italy ; BioDNA Research Center, Università Cattolica del Sacro Cuore di Piacenza, Piacenza, Italy.
Paolo
P
Ajmone-Marsan
D000222:Adaptation, Physiological / Q000235:genetics*; D054458:Amplified Fragment Length Polymorphism Analysis; D000818:Animals; D001211:Asia, Western; D001499:Bayes Theorem; D004777:Environment; D005060:Europe; D056726:Genetic Association Studies; D056426:Genetic Loci; D005819:Genetic Markers; D006041:Goats / Q000235:genetics*; D008957:Models, Genetic; D058974:Phylogeography
D005819:Genetic Markers