Molecular genetic architecture analysis of Nellore sheep (Ovis aries) revealed through short tandem repeat markers
Author(s): Jeyakumar M and Ramachandran A
Abstract: The objective of the present investigation is to employ the Nellore Sheep population's genetic analysis at the molecular level to create sustainable advancements, conservation, and utilization of the breed, all of which are capable of improving the quality of life for all involved. The Food and Agricultural Organization, Rome, Italy, recommended the use of 25 short tandem repeat markers for the genetic characterization and bottleneck analysis of Nellore Sheep. This was achieved by isolating genomic DNA from blood samples of 65 unrelated Nellore Sheep with typical phenotypic features collected from various villages in the breeding tract. Bioinformatics software has been employed to calculate the fundamental measures of genetic variation. Three tests were conducted under three different mutation models—the infinite allele model (IAM), the stepwise mutation model (SMM), and the two-phase model (TPM)—in order to assess the Nellore Sheep for mutation drift equilibrium. Additionally, the expected equilibrium gene diversity (Heq) and observed gene diversity (He) were estimated under various microsatellite evolution models. The analysis showed that there were 162 alleles overall, with a mean of 6.48±1.75 alleles across loci, and that the observed number of alleles varied from 3 (SRCRPS5) to 11(OarJMP29). High genetic diversity was indicated by the total observed heterozygosity, expected heterozygosity, inbreeding estimate, and polymorphism information content values which were 0.6580±0.2065, 0.7591±0.099, 0.233±0.044, and 0.7105±0.023 respectively. In accordance to the IAM, TPM, and SMM models, there were 18, 07, and 12 locations that have been shown to exhibit an excess of gene diversity, respectively. Under the IAM and TPM models, there was a substantial deviation of sheep from the mutation-drift equilibrium as revealed by all three statistical tests (sign test, standardized differences test, and Wilcoxon sign rank test); under the SMM model, there was a non-significant deviation. The results under SMM showing the absence of the genetic bottleneck in sheep in the recent past have been verified by the qualitative test of mode shift analysis.
