Population structure, runs of homozygosity analysis and construction of single nucleotide polymorphism fingerprinting database of Longnan goat population

The Longnan goat (LN) is a local breed discovered during the third census of China's livestock and poultry genetic resources. In order to thoroughly comprehend the population traits, this research examined a total of 70 animals from three different goat populations, namely the LN goat, Nanjiang Brown goat (NJ), and Boer goat (Boer). Specific-Locus Amplified Fragment Sequencing was employed to analyze genetic diversity, population structure, and selective sweep patterns. Additionally, individual DNA fingerprints were generated to provide detailed genetic profiles for each subject. A total of 643,868 single nucleotide polymorphisms (SNPs) were detected, with a majority located in intergenic and intronic regions. Genetic diversity analysis uncovered lower diversity within the LN population compared to the other two populations. The analysis of population structure unveiled significant genetic distance between LN and both NJ and Boer populations, with distinct clustering patterns observed. Moreover, genetic differentiation coefficients (F_ST) of 0.1019 and 0.0854 were determined between LN and Boer, as well as LN and NJ, respectively, indicating substantial genetic differentiation. Selective sweep analysis, combining F_ST and π ratio, identified several genes associated with growth and development, reproduction, hair color, and immunity that may serve as valuable candidates for marker-assisted breeding. Furthermore, identification of 47,541 runs of homozygosity (ROHs) revealed non-uniform distribution across chromosomes, with the highest frequency on chromosome 1 and the lowest on chromosome 27. Correlations between different inbreeding coefficients varied, with the highest observed between F_HOM and F_GRM, and the lowest between F_{ROH >1.5Mb} and F_{ROH <500kb}. A total of 46 candidate genes were annotated within high-frequency ROH islands, primarily associated with biological processes such as reproduction, growth and development, and immunity. Finally, a DNA fingerprint, consisting of 371 highly polymorphic SNPs, was generated and presented in the form of a two-dimensional code for convenient access. Based on the population structure analysis, LN goats have been found to have a distant genetic distance and a higher degree of differentiation from both the Boer and NJ populations. Evaluation of genetic diversity parameters and ROH analysis indicates that the LN population exhibits lower genetic diversity and shows signs of inbreeding. Our findings offer theoretical support for the identification of genetic resources within this population.