Abstract
Simple SummaryGenetic variability among native cattle breeds can disclose the important features that make a population adapted to harsh environments. The Aosta cattle breeds have been raised and selected for centuries to be farmed in a mountain environment, characterized by a semi-intensive system, i.e., summer pasture with winter recovery on the farms. To disclose the genomic variation and its association with known genes, it is important to genetically characterize these breeds.The Aosta Red Pied (Valdostana Pezzata Rossa (VRP)), the Aosta Black Pied (Valdostana Pezzata Nera (VBP)) and the Aosta Chestnut (Valdostana Castana (CAS)) are dual-purpose cattle breeds (meat and milk), very well adapted to the harsh environmental conditions of alpine territories: their farming is in fact characterized by summer pasture at very high altitude. A total of 728 individuals were genotyped with the GeenSeek Genomic Profiler® (GGP) Bovine 150K Illumina SNP chip as a part of the DUALBREEDING-PSRN Italian-funded research project. The genetic diversity among populations showed that the three breeds are distinct populations based on the FST values, ADMIXTURE and Principal Component Analysis (PCA) results. Runs of Homozygosity (ROH) were obtained for the three populations to disclose recent autozygosity. The genomic inbreeding based on the ROH was calculated and coupled with information derived from the F (inbreeding coefficient) and FST parameters. The mean FROH values were low: CAS = 0.06, VBP = 0.05 and VRP = 0.07, while the average F values were −0.003, −0.01 and −0.003, respectively. The annotation and enrichment analysis, performed in the identified most frequent ROH (TOP_ROH), showed genes that can be linked to the resilience capacity of these populations to harsh environmental farming conditions, and to the peculiar characteristics searched for by farmers in each breed.
Highlights
Animal genetic resources play an important role in local economies and in maintenance of territories and landscapes [1]
The innate instinct for the territoriality and hierarchical dominance of the cows translates first into a non-ferocious ritual of combat, where dominance of a cow over the other is expressed in knock-out battles, leading to the awarding of the title of Queen of the Valley in a final contest held in Aosta at the “Arena Croix Noir”
Chestnut) on a large number of individuals and on a medium density SNP chip (150K), is indicating that farmers in their mating decisions still prioritized adaptation to the environment and the farming system envisaging summer pasture, a practice that have characterized these breeds for centuries
Summary
Animal genetic resources play an important role in local economies and in maintenance of territories and landscapes [1]. Among the large number of autochthonous cattle populations in Italy, the Aosta breeds play an important role for the Aosta valley, located in the northwest Alpine territories of Italy [2] In addition to their milk and meat production, their economic value is related to the farming activity itself, closely linked to the use of local territories: farming activity, allows to Animals 2020, 10, 2385; doi:10.3390/ani10122385 www.mdpi.com/journal/animals. All three are dual-purpose cattle breeds and possess a considerable milk production (2019 average production per lactation: 3000 kg of milk for CAS and VBP and 4000 for VRP) in proportion to their body size (average adult live weight of 550 kg for males and 400 kg for females) Even if their production selection goal includes milk and meat, their capacity to adapt to the harsh alpine environment, i.e., their functionality, has been strongly pursued by farmers for decades [3].
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