Genomic architecture of insertion-deletion (indel) variants in beetal goats of India

Beetal goats, the second largest indigenous goat breed in India, are known for their superior growth and production traits. In this study, we performed a comprehensive genome-wide characterization of insertion-deletion (indel) variants in the Beetal goat genome using pooled whole-genome resequencing. Following stringent filtering criteria, a total of 373,084 high-confidence indels were identified in the Beetal goat genome. Chromosome-wise distribution revealed the highest number of variants on Capra hircus chromosome (CHI) 1 (26,590), while CHI 25 showed the lowest (4303). Insertion variants (57.82%) outnumbered deletion variants (42.12%), yielding a deletion-to-insertion ratio of 0.73:1, a pattern distinct from most other mammalian genomes. The identified indel variants were distributed across intergenic (63.07%) and genic (36.93%) regions of the genome. Functional annotation classified 99.88% of the variants as MODIFIER and 0.05% as HIGH-impact, which included frameshift (144), splice site (31), donor disruptions (8) and start codon (1) mutations. Notably, high-impact indel variants were identified in key genes associated with growth and body conformation-LEPR, LCORL and PLAG1-underscoring their potential as candidate markers for larger body size. Functional enrichment analysis of high-impact indel variants using DAVID revealed significant overrepresentation (p ≤ 0.05) of biological processes related to G protein-coupled receptor signalling, immune regulation and innate immunity; molecular functions such as olfactory receptor activity and metal ion binding and KEGG pathways including olfactory transduction and extracellular matrix (ECM)-receptor interaction. These findings provide valuable insights into the functional relevance of indel variants and establish a foundational resource for future genomic selection strategies in Beetal goats.