Genome-wide scan for selection signatures for litter size in goat breeds of Kerala

Genome-wide search to detect selection signatures harbouring candidate prolificacy genes was carried out in low prolific Attappady Black and high prolific Malabari goat breeds of Kerala. Selective sweep regions were identified by analysing the genotypic data generated by Illumina Goat SNP 50 Bead Chip sequencing of 48 animals (24 each of two breeds) using Out FLANK statistical method based on FST outlier approach. There were 2844 outlier SNPs at genome-wide significance level of P<0.01 and 595 protein coding genes linked to these outlier SNPs. Further analysis showed 16 candidate prolificacy genes inclusive of BMPR, PRLR, INHBB, ESR1, GHR, IGF1, LHCGR, LEPR, SMAD4, BMP2, NR5A2, MTNR1A, GRIA2, MEF2A and MFGE8 located in selection signals. Gene enrichment analysis showed significantly (P<0.05) over-represented 37 gene ontology (GO) biological processes, 14 GO molecular functions and 7 KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathways. The information concerning candidate genes could be further utilised for association analysis for onward utilisation in the genetic improvement of litter size in goats.