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Prospecting of oligonucleotide primers for Mitochondrial DNA and amplification in faecal samples of pampas deer (Ozotoceros bezoarticus)

Grant number: 17/26529-9
Support type:Scholarships in Brazil - Scientific Initiation
Effective date (Start): March 01, 2018
Effective date (End): February 28, 2019
Field of knowledge:Biological Sciences - Genetics
Principal Investigator:José Maurício Barbanti Duarte
Grantee:Shamira de Fátima Sallum Leandro
Home Institution: Faculdade de Ciências Agrárias e Veterinárias (FCAV). Universidade Estadual Paulista (UNESP). Campus de Jaboticabal. Jaboticabal , SP, Brazil

Abstract

The Pampas deer (Ozotoceros bezoarticus), a species of endangered neotropical deer, is found in Brazil in two subspecies (O. b. bezoarticus and O. b. leucogaster), with a wide geographic distribution. However, little known about its current genetic and evolutionary structure, which is fundamental for the definition of conservation strategy for free-living populations. Faced with this, we propose to explore the mitochondrial DNA, the species with the use of fecal samples. Thus, primer oligonucleotides (primers) were constructed from existing mitochondrial DNA sequences (control region, Cytochrome-b and ND5) without database (NCBI) and tested for amplification in 20 fecal samples from two populations of stag beetle: Pantanal (MT) and Emas National Park (GO).The oligos will be chosen according to some criteria, such as sites with minimal insertions or deletions, small sizes (17 to 22bp), amplicon generators between 150 and 200bp, composition of 45 to 55% of ATG and informative sites between codons within the fragments. The samples are already available in the sample database of the Center for Research and Conservation of Cervidae (Nupecce). The oligos will be further developed directly in sequences of the O. bezoarticus genome, increasing the specificity of DNA amplifications. With these results, the sampling area, through noninvasive approaches, combined with molecular investigations, can be amplified and immediate and timely actions for conservation can be facilitated. (AU)