Since the time of their domestication, goats (Capra hircus) have evolved in a large variety of locally adapted populations in response to different human and environmental pressures. In the present era, many indigenous populations are threatened with extinction due to their substitution by cosmopolitan breeds, while they might represent highly valuable genomic resources. It is thus crucial to characterize the neutral and adaptive genetic diversity of indigenous populations. A fine characterization of whole genome variation in farm animals is now possible by using new sequencing technologies. We sequenced the complete genome at 12× coverage of 44 goats geographically representative of the three phenotypically distinct indigenous populations in Morocco. The study of mitochondrial genomes showed a high diversity exclusively restricted to the haplogroup A. The 44 nuclear genomes showed a very high diversity (24 million variants) associated with low linkage disequilibrium. The overall genetic diversity was weakly structured according to geography and phenotypes. When looking for signals of positive selection in each population we identified many candidate genes, several of which gave insights into the metabolic pathways or biological processes involved in the adaptation to local conditions (e.g., panting in warm/desert conditions). This study highlights the interest of WGS data to characterize livestock genomic diversity. It illustrates the valuable genetic richness present in indigenous populations that have to be sustainably managed and may represent valuable genetic resources for the long-term preservation of the species.

Mediterranean forest rangelands offer an important feed source for goats. Concerns about grazing strategies and management schemes in order to ensure the rangeland sustainability of Southern Mediterranean forest have revived interest in the foraging behavior of goats. This study was conducted to investigate the seasonal changes of feeding behavior of grazing goats in the Southern Mediterranean forest rangeland of Northern Morocco during two consecutive years beginning in 2016. The direct observation method was used to compare diet composition, intake rate, and diet selectivity of goats during three seasons (spring, summer, and fall). Bite mass of each plant species selected by goats was estimated using hand-plucked simulation. The optimal foraging theory was used as a tool to explain the goats foraging decisions. Bite mass range was extremely wide and varied seasonally. The goats’ diet was largely composed of Cistus spp., Lavandula stoechas, Quercus spp., and Myrtus communis. The result shows that the smaller the bite mass, the higher the biting rate, leading to increased short term intake rates. The selection of various plant species during fall and summer enlarged the diet diversity of goats. As expected, goats preferred trees and some shrubs despite their low availability. Consequently, the most available species is not necessarily the most positively selected. Particular high and positive selection of Quercus suber was observed over seasons. The outcomes confirm the high adaptability and ability of goats to select a woody species across seasons. Knowledge about forage availability and the feeding behavior of goats could be used as the first guide for rangeland managers to ensure herd and forest sustainability.

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Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low‐coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high‐density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low‐density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.

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