Estimation of genomic inbreeding coefficient and effective population size in different goat breeds

The selection of animals by humans left detectable signatures on the genome of modern goat. The identification of these signals can help us to improve the genetic characteristics of economically important traits in goat. Over the last decade, interest in detection of genes or genomic regions that are targeted by selection has been growing. Identifying signatures of selection can provide valuable insights about the genes or genomic regions that are or have been under selection pressure, which in turn leads to a better understanding of genotype-phenotype relationships. A run of homozygosity (ROH) is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents. Run of homozygosity one of the most methods were used to detecting the genomic inbreeding. The locations of ROHs which are under positive selection, or laboring favorable allele in population, tend to be fixed in the genome and formation of ROH Island during long times. Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands. As detecting the ROH Islands, the genomic regions contain economic traits could be detectable.

In this research, the amount of genomic inbreeding and the effective size of the population were investigated using the information obtained from 879 goats of different breeds including Beetal, Daira Deen Panah, Nachi, Barbari, Teddi, Pahari, and Pothwari. In order to determine the genotype of the samples, Illumina caprine Bead Chip 50K were used. The genomic information of goat breeds was extracted from the figshare database. Quality control was conducted using the Plink software. The markers or individuals were excluded from the further study based on the following criteria: unknown chromosomal or physical location, call rate <0.95, missing genotype frequency >0.05, minor allele frequency (MAF) < 0.05, and a P-value for Hardy–Weinberg equilibrium test less than 10-3. After quality control, 36,861 SNPs from Goat SNP chip 50K on 827 goats were remained for the future analysis. Inbreeding coefficient was calculated using four methods including, genomic relationship matrix (FGRM), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI) using the GCTA 1.0 software and run of homozygosity (FROH) using the PLINK 1.9 software. The effective population size (Ne) was calculated from linkage disequilibrium data with SNeP software (version 1.1). GeneCards (http://www.genecards.org) and UniProtKB (http://www.uniprot.org) databases were also used to interpret the function of the obtained genes.

The lowest and highest inbreeding coefficient calculated by three methods (FGRM, FHOM, and FUNI) were related to Beetal and Barbari breed, respectively. The highest (0.159) and lowest (0.028) amount of FROH was estimated in the Barbari and Pothwari breeds, respectively. The average length of ROH ranged from 70.2 to 391.4 Mb, and the average number of ROH fragments varied between 8.19 and 48.65. Also, the highest and lowest number of ROH were observed on chromosome 2 and 29, respectively. The size of Ne in in the current generations (fifth generation) of the studied breeds was ranged from 35 to 365. The highest Ne was estimated in the Beetal breed (365 heads) and the lowest in the Barbari breed (35 heads). The average inbreeding coefficient in Beetal, Teddi, Pahari, Nachi, Barbari, Daira Deen Panah and Pothwari breeds was obtained 0.035, 0.081, 0.031, 0.052, 0.15, 0.11 and 0.02, respectively. In addition, the Ne of most of the studied populations has been decreased. The results of this study revealed that, the selection processes in different goat breeds for economic traits during several years, has led to the formation of many ROH islands in goat genome, therefore scanning these regions at the genome level can be an alternative strategy to identify genes and associated loci with economic traits.

our findings contribute to the understanding of genetic diversity and population demography, and help design and implement breeding and conservation strategies for study goat breeds. Therefore, it is necessary to economize production and planning a suitable mating scheme to control inbreeding and genetically conserve the remaining pure animals of these breeds.