Intra-population SNP analysis identifies signatures for grazing stress tolerance in Egyptian local goats

Abstract

The need to support agricultural industries and human livelihoods in dryland environments using adapted livestock is becoming an unavoidable priority as prospects of global warming become even more evident. Here, using the integrated haplotype score (iHS) approach, we analysed genotype data generated using the caprine 50K Illumina SNP BeadChip from 366 individuals of four local Egyptian desert goat populations to investigate the genetic basis of tolerance to grazing stress. The analysis identified 13 selection sweep regions that spanned 68 genes across eight chromosomes. The strongest selection sweeps were observed on chromosomes 6 and 12 which, spanned 21 and 17 genes, respectively. Though a majority of the identified genes were associated with multiple functions, functional analysis of the 38 genes found in the two strongest candidate regions, revealed the three most significant gene ontology functional term clusters were associated with biological processes of kidney function and development, cellular response to oxidative stress and intra-cellular calcium homeostasis. This suggests that water and mineral homeostasis and the proper maintenance of cellular responses to external stimuli and processes that modulate calcium homeostasis and other signal transduction pathways are key functions in tolerance to grazing stress. Our results could prove useful in genomic selection and identification of genes involved in desert grazing stress tolerance. Key words: adaptation, caprine, genotyping, SNP, selection sweeps,