Genomic Exploration of Selection Signatures Linked to Reproductive Traits in Locally Adapted Indicine, Taurine and Crossbred Cattle of India

Abstract

This study aims to comprehensively explore genome-wide selective processes influencing reproductive traits across six cattle breeds by employing different statistical methods. Reproductive efficiency is crucial for livestock productivity, as it directly influences the number of offspring and, consequently, the availability of animals for production. Early reproductive development and high fertility in herds boost selection intensity, driving faster genetic gains. This efficiency underpins the sustainability and profitability of livestock systems. To identify genomic signatures related to these traits, this study utilises genotyping technologies, including the Illumina BovineSNP50 Bead Chip and GGP Bos indicus 70k array. For this work, we used four summary statistics, including two intra-population statistics (Tajima's D and iHS), and two inter-population statistics (Rsb and XP-EHH). After identifying the key locations for selection, the NCBI database and the Cattle QTL database were utilised for annotation. The genes CACNA1H, KCNIP4, GDF9, SLC4A4, DHX57, EIF2AK3 and ME3 have been demonstrated to be under positive selection in Gir cattle. These are associated with characteristics such as udder cleft, age at puberty, sperm counts, sperm motility, sperm acrosome integrity rate, sperm motility per conception, sperm counts, conception rate, etc. Two genes, ENTHD1 and PRDM16 found on chromosomes 5 and 16, respectively, have been shared by Tharparkar and Gir which were undergoing positive selection. The ENTHD1 gene is linked to reproductive traits such as calving ease and stillbirth. Meanwhile, the PRDM16 gene is associated with characteristics like udder cleft, udder attachment, udder depth and udder height. The genes RXFP2, FRY, ENTHD1, SREBF2, RNF10, NYAP2, VWF, PPP1R8, EYA3, BBX, and TRPM3 were consistently identified across multiple selection signature methods, highlighting them as strong candidates under intense selection pressure. This approach offers valuable insights into the genetic basis of variations in reproductive traits, facilitating informed selection processes and enhancing our understanding of evolutionary and domestication in diverse cattle breeds.

Keywords: adaptation; cattle; evolution; reproduction; selection signature.