Fine genetic structure of Brazilian white Morada Nova hair sheep breed from semi-arid region

Abstract

Due to the critical population status of the Morada Nova breed, this research aimed to carry out an additional study of fine genetic structure, using thousands of SNP markers, to support the development of ex situ and in situ conservation strategies for this breed. Blood samples were collected from seven herds located in the Northeast region of Brazil. DNA was extracted and samples were genotyped using Ovine SNP50 BeadChip. Raw genotyping data were imported and quality control filters were applied. The following measures of genetic variability were used to compare levels of heterogeneity within herds: Observed heterozygosity (HO), Expected heterozygosity (HE), Inbreeding coefficient (F) and Number of polymorphic SNPs with MAF > 0.05 (NSNP.) The pairwise fixation index (FST) and an analysis of molecular variance (AMOVA) were calculated to estimate the genetic differentiation between all pairs of herds studied. To assess the existence of significant genetic structure among the herds, a principal component analysis (PCA) was performed. The HO for populations B, E, F, and G were greater than He, and the F in all subpopulations was low (F < 0.05). Population pairs D-E (FST = 5.9%) and D-G (FST = 6.2%) showed higher values of genetic differentiation from each other, and the two closest population pairs were A-F (FST = 0.2%) and B-E (FST = 0.9%). PCA corroborates the low overall genetic divergence among the populations. The white Morada Nova subpopulations studied here have low genetic differentiation among themselves, with no differentiation by states, but have three main genetic groups. The Morada Nova breed may be a repository of alleles of economic interest for the sheep production chain. These findings may initiate other studies that will make it possible to crossbreeding between the herds by identifying the herds that are more genetically distant and increasing the genetic diversity of the population.