Identification of 21-bp indel polymorphism in the LLGL1 gene in several Turkish native goat populations

Being one of the fundamental economically important traits, reproduction efficiency such as litter size plays a key role in determining profitability for livestock enterprises focusing on meat production. Numerous candidate genes identified to be associated with litter size have been subjected to Marker-Assisted Selection (MAS) studies to improve classical breeding approaches. Of these candidate genes, Scribble Cell Polarity Complex Component (LLGL1) was confirmed to carry 21 base pair (bp) insertion-deletion (InDel) variation which was directly related to multiple births in goats. This study aims to determine the polymorphisms caused by the 21 bp indel variation in the LLGL1 gene in Hair (HAI), Honamlı (HNM), and Kabakulak (KBK) goats reared in Türkiye. At the end of the PCR process, all populations were found to be polymorphic. I allele frequency was higher than D allele frequency across three populations while the highest frequency of ID (0.50) II genotypes (0.47) was observed in the HAI breed. The observed heterozygosity (Ho) values for HNM, HAI, and KBK populations were 0.63, 0.50, and 0.63, respectively, while the expected heterozygosity (He) values were 0.50, 0.59, and 0.51, respectively. All populations were found to be in Hardy-Weinberg equilibrium. This study confirms that the LLGL1 gene is promising to increase reproduction traits in three Anatolian goat populations due to conserving sufficient genetic variability. However, before proceeding with MAS studies, it is crucial to analyze the relationship between phenotypic data and the genotypes obtained for this gene region.