Abstract
Artificial selection is one of the major forces modifying the genetic composition of livestock populations. Identifying genes under selection could be useful to elucidate their impact on phenotypic variation. We aimed to identify genomic regions targeted by selection for dairy and pigmentation traits in Murciano-Granadina goats. Performance of a selection scan based on the integrated haplotype score test in a population of 1183 Murciano-Granadina goats resulted in the identification of 77 candidate genomic regions/SNPs. The most significant selective sweeps mapped to chromosomes 1 (69.86Mb), 4 (41.80-49.95Mb), 11 (65.74Mb), 12 (31.24 and 52.51Mb), 17 (34.76-37.67Mb), 22 (31.75Mb), and 26 (26.69-31.05Mb). By using previously generated RNA-Seq data, we built a catalogue of 6414 genes that are differentially expressed across goat lactation (i.e. 78days post-partum, early lactation; 216days post-partum, late lactation; 285days post-partum, dry period). Interestingly, 183 of these genes mapped to selective sweeps and several of them display functions related with lipid, protein, and carbohydrate metabolism, insulin signaling, cell proliferation, as well as mammary development and involution. Of particular interest are the CSN3 and CSN1S2 genes, which encode two major milk proteins. Additionally, we found three pigmentation genes (GLI3, MC1R, and MITF) co-localizing with selective sweeps. Performance of a genome-wide association study and Sanger sequencing and TaqMan genotyping experiments revealed that the c.801C>G (p.Cys267Trp) polymorphism in the melanocortin 1 receptor (MC1R) gene is the main determinant of the black (GG or GC genotypes) and brown (CC genotypes) colorations of Murciano-Granadina goats.
Highlights
Selection for production and morphological traits has strongly modified the genetic composition of livestock populations (Saravanan et al 2020)
Identification of putative selective sweeps in a population of MG goats By making a selection scan based on the integrated haplotype score (iHS) score algorithm, we identified 77 genomic regions/single nucleotide polymorphisms (SNPs) that reached the threshold of significance (Fig. 1, Tables 1 & S3)
The most significant SNP lies close to the zinc finger protein 804B (ZNF804B) gene, and there are several genes related with metabolism, such as adenylyl cyclase type 1 (ADCY1), insulin-like growth factor-binding proteins 1 (IGFBP1) and 3 (IGFBP3)
Summary
Selection for production and morphological traits has strongly modified the genetic composition of livestock populations (Saravanan et al 2020). John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics The main aim of the current work was to identify genomic signatures produced by artificial selection for dairy and pigmentation traits in MG goats. To achieve this goal, we have genotyped a population of MG goats with the Goat SNP50 BeadChip and subsequently, we have investigated the footprint of selection by integrating several sources of information
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