Improved Litter Size in Thin-Tailed Indonesian Sheep Through Analysis of TGIF1 Gene Polymorphisms

Reproductive traits, particularly the litter size, are crucial for sheep husbandry. Molecular genetic selection methods, including single-nucleotide polymorphism (SNP) analyses, offer potential avenues for enhancing these traits. This study investigated the association between TGIF1 SNPs and litter size in thin-tailed Indonesian sheep. A total of 47 sheep were sampled, and their genomic DNA was analyzed. Bioinformatics, sequencing, and statistical analyses were conducted to identify SNPs, assess genetic parameters, and examine their association with litter size. Nine SNPs, including nonsynonymous variants, were successfully identified through targeted sequencing and Sanger sequencing within exon 3 of TGIF1. Noteworthy polymorphisms at g. 42725867 G>A, g. 42725886 G>A, g. 42725932 A>C, g. 42725950 A>G, g. 42726009 G>A, g.42726036 C>T, g.42726042 A>C, g. 42726051 A>G, and g. 42726059 G>A were revealed. Genetic parameter assessments indicated moderate diversity although no significant association was observed between the TGIF1 SNPs and litter size. This lack of association highlights the potential influence of environmental factors, polygenic effects, or the need for larger sample sizes in future studies. In addition, linkage disequilibrium analysis highlighted strong interconnectivity among six of the nine TGIF1 SNPs, designating them as potential Tag SNPs. Data analysis further demonstrated that the haplotype combination of H3 and Hap 6 within the identified blocks exhibited the highest litter size. This study unveils novel TGIF1 SNPs in thin-tailed Indonesian sheep, prompting the need for additional research to unravel their functional implications and potential impacts on reproductive traits. While no significant associations were found, these findings contribute to the growing body of knowledge on genetic factors influencing litter size and underscore the need for broader investigations, including whole-genome sequencing and validation in larger populations. This investigation provides valuable insights into the genetic factors that influence litter size in this breed and lays the foundation for future genetic improvement strategies.