Genetic Divergence of Local Goats in Ninh Thuan Province Vietnam
Genetic Divergence of Local Goats in Ninh Thuan Province Vietnam
Ngoc Tan Nguyen1*, Minh Thanh Tram1, Thi Thu Pham1, Tan Loi Le1, Thi Khanh Ly Nguyen1, Tuan Thanh Hoang2, Cong Thieu Pham3, Nguyen Khang Duong4
ABSTRACT
The hypervariable region (D-loop) of mtDNA (mitochondrial DNA) of local goat breeds in Ninh Thuan Province, Vietnam was studied to provide useful information on their origin. Blood samples were taken from two local goat breeds in Ninh Thuan (De Co = CO and Bach Thao = BT, 10 samples each) and three other exotic goats including Saanen (SA; 10 samples), Red Boer (RB; 10 samples) and White Boer (WB; 9 samples) raised at An Phu Dairy Company in Cu Chi District, Ho Chi Minh City. Extracted mtDNA was used to amplify the fragment of 687 bp in the D-loop by polymerase chain reaction (PCR) followed by sequencing to analyze nucleotide polymorphism, haplotype diversity and genetic distance to construct a phylogram. Results showed that the fragment of 687 bp was successfully amplified. Examination of 49 sequence variants in 599 bp of the control region revealed the nucleotide composition was Adenine (A) = 32.55%, Thymine (T) = 28.33%, Guanine (G) = 14.67%, Cytosine (C) = 24.87% and G+C content was 39.12%. Out of a total of 50 nucleotide polymorphic sites, 48 were transition and 2 were transversion, with 21 haplotypes observed. Nucleotide and haplotype diversity indices (π and Hd) were 0.03005 and 0.889, respectively. The genetic diversity of Saanen goats was highest at (π) = 0.03031 and (Hd) = 0.987, while the lowest genetic diversity was found in Bach Thao goats (π = 0.00089 and Hd = 0.533). Genetic distance between WB and CO or BT was higher (0.058) than between RB and CO or BT (0.056 or 0.055). The lowest genetic distance was found between CO and BT goats (0.001). Most local goat breeds were grouped in one clade, with exotic goat breeds concentrated in other clade, indicating clear maternal divergence between local and exotic goat breeds. D-loop mtDNA diversity within the two local goat breeds in Ninh Thuan Province of Vietnam was low, indicating a close genetic relationship with Indochina goats (Laos), separated into a sub-lineage from maternal lineage B. Further insights regarding the genetic diversity of Vietnamese local goats require detailed in-depth studies.
Keywords | Local goat, D-loop, Mitochondrial DNA, Genetic divergence, Phylogeny
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