Mining and identification of solitary long terminal repeat (Solo-LTR) presence polymorphisms in the sheep genomes

Abstract

The analysis of 51 sheep genomes led to the identification of 3624 high-confidence Solitary Long Terminal Repeats (Solo-LTRs), remnants of Long Terminal Repeat retrotransposons (LTR-RTns). These elements, comprising 3308 absence-type and 316 presence-type sites, are integrated into functional regions of the genome, where they can influence gene structures and regulation. Approximately 4.39% of protein-coding genes and 0.54% of long noncoding RNA genes contain sequences derived from these Solo-LTRs. Analysis across 12 diverse sheep breeds revealed that 83.63% of the tested Solo-LTR sites were polymorphic, demonstrating substantial genetic diversity and highlighting their utility as genetic markers. Furthermore, these elements were linked to key genes governing economically important traits such as growth, immunity, and milk production. Notable genes identified include PAG3, ANXA5, KCNJ6, MX2, and XKR4. The findings confirm that Solo-LTRs are major contributors to genomic diversity and breed-specific adaptation in sheep, providing essential insights for future genetic research and breeding programs.