Genome-wide selective sweeps providing classic evidence of emotional and behavioural control in Bos indicus cattle breeds

Diverse genomic selection signatures were identified from whole genome sequencing data of five cattle breeds of Tamil Nadu viz.Alambadi, Bargur, Kangayam, Pulikulam and Umblachery.Two complementary approaches were utilized to detect most recent (CLR) and distant past (FST) selective sweep regions from a total of 13,90,449 filtered SNPs.A total of 7,250 and 806 genomic regions were found to contain selective sweeps in 1,238 and 101 candidate genes using these methods respectively and were found mostly related to production (PAIPI, NNT, OCIAD1), coat colour (MC1R, KIT, KDR, PDGFRA), Disease resistance (TCF25, CDH15, SPIRE2) and adaptation (SLC22A31, SPG7) of indigenous breeds to tropical climatic conditions and disease resistance (SPIRE2, CHAMP1A).Of the total candidate genes, 12 were identified by both CLR and FST methods (e.g.GABRG1, GABRA4, CBFA2T3, GAS8, USP46, RASL11B, SCFD2, FIP1L1, LNX1, FRYL, LOC109560438 and NNT) and are related to production, disease resistance and emotional and behavioural control of these cattle.KEGG pathway analysis showed significance (P<0.05) in GABRG1 and GABRA4 genes that are responsible for aggressive behaviour in Alambadi and Pulikulam cattle showing their importance in Jallikattu sport.The knowledge about signatures of selection and candidate genes affecting aggressive behaviour in these cattle would facilitate in formulating the selection index and genome-assisted breeding that help in conservation of these native cattle.