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 adaptivepotential 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 theidentification of genotypes better adapted to specific or extreme environmental conditions. Therefore we analyzed 101AFLP 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 naturalselection. MATSAM identified four loci possibly under natural selection – also confirmed by FST-outlier methods – andsignificantly associated with environmental variables such as diurnal temperature range, frequency of precipitation, relativehumidity and solar radiation.Conclusions/Significance: These results show that landscape genomics can provide useful information on theenvironmental factors affecting the adaptive potential of livestock living in specific climatic conditions. Besides addingconservation value to livestock genetic resources, this knowledge may lead to the development of novel molecular toolsuseful to preserve the adaptive potential of local breeds during genetic improvement programs, and to increase theadaptability of industrial breeds to changing environments.