Novel genomic markers and genes related to reproduction in prolific Chios dairy sheep: a genome-wide association study

Genetic architecture of sheep reproduction is increasingly gaining scientific interest due to the major impact on sheep production systems. In the present study, we conducted pedigree-based analyses and genome-wide association studies using the Illumina Ovine SNP50K BeadChip to explore the genetic mechanisms underlying the reproduction of the highly prolific Chios dairy sheep. First lambing age, total prolificacy and maternal lamb survival were selected as representative reproductive traits and estimated as significantly heritable (h2 = 0.07–0.21) with no evident genetic antagonism among traits. We identified novel genome-wide and suggestive significant single-nucleotide polymorphisms (SNPs) on chromosomes 2 and 12 associated with age at first lambing. The new variants detected on chromosome 2 span a region of 357.79 kb with high pairwise linkage disequilibrium estimates (r2 = 0.8–0.9). Functional annotation analysis revealed candidate genes, such as the collagen-type genes and the Myostatin gene, that participate in osteogenesis, myogenesis, skeletal and muscle mass development resembling the functionality of major genes affecting the ovulation rate and prolificacy. Additional functional enrichment analysis associated the collagen-type genes with multiple uterine-related disfunctions, such as cervical insufficiency, uterine prolapse and abnormalities of the uterine cervix. Several genes (e.g., KAZN, PRDM2, PDPN, LRRC28) localised close to the SNP marker on chromosome 12 were grouped in annotation enrichment clusters majorly involved in developmental and biosynthetic pathways, apoptosis, and nucleic acid-templated transcription. Our findings may further contribute to unravel the genomic regions that are important for sheep reproduction and could be incorporated into future selective breeding programmes.