REDUCED PANEL OF SINGLE-NUCLEOTIDE POLYMORPHISMS FOR BIODIVERSITY STUDIES IN BOVINES
Keywords:
Bioinformatics, biotechnology, molecular markers, livestock.Abstract
The aim of this work was to evaluate a reduced panel of 200 single-nucleotide polymorphisms markers recommended by International Society of Animal Genetics and the International Committee for Animal Recording, using Next Gen Sequencing sequencing. Parameters such as number of usable loci, loci polymorphism, observed heterozygosis (Hob) and expected (He), average molecular diversity per loci (DML), distance between populations, fixation index that estimates the coefficient of inbreeding (Fis) and genetic differentiation value between populations (Fst). Of the total loci used, an average of 186 usable alleles were observed: maximum of 187 in the Guabala breed and a minimum of 183 in the Brahman. An average of 174 polymorphic loci with a maximum of 184 in crossed genotypes and a minimum of 149 in the Guabala breed. The values of Hob, He and DML were 0,378, 0,439 and 0,438, respectively. The molecular Analysis of Variance (AMOVA) showed a percentage of variation between populations of 19,25 and Fst index of 0,19. The percentage of variation and Fst between the Panamanian Creole and Zebu breeds were 5,22% and 0,22, respectively and the percentage of variation between Creole and Taurine breeds was 1,82% with genetic differentiation value (Fst) of 0,163, respectively. The Fis values ranged from 0,00302 (Guaymi) to 0,04333 (Holstein); negative values of Fis were observed for Senepol and Guabala breeds, so a Wahlund effect is presumed. The tree of circular distances showed a similar behavior to those reported in a previous work carried out with microsatellites, as was observed in the AMOVA and Fst in the populations. Preliminary results suggest that the single nucleotide polymorphism markers used have potential for genetic diversity studies and it is recommended to extend the study to more breeds and numbers of animals.
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