Genetic Diversity of Native Buffalo Populations in Vietnam Based on Mitochondrial D-Loop Nucleotide Sequence
Genetic Diversity of Native Buffalo Populations in Vietnam Based on Mitochondrial D-Loop Nucleotide Sequence
Ngoc Tan Nguyen1*, Pham Kim Ngan Nguyen1, Thao Huong Phan1, Tan Loi Le1, Thi Khanh Ly Nguyen1, Tuan Thanh Hoang2, Cong Thieu Pham3, Cong Dinh Nguyen3, Nguyen Khang Duong4
ABSTRACT
This study aimed to better understand the genetic diversity of native buffalo populations in different regions of Vietnam based on nucleotide sequence in a displacement loop (D-loop) of mitochondrial DNA (mtDNA). Thirty-one blood samples that were collected from three native buffalo populations such as Bao Yen (BY: 7 samples), LangBiang (LB: 7 samples) and Thanh Chuong (TC: 7 samples) and two imported buffaloes from Thailand (T: 5 samples) and India (Murrah – M: 5 samples) were extracted for total DNA and amplified about 760 bp mtDNA fragment, with 576 bp in the D-loop region, followed by sequencing to analyze genetic diverse indices and genetic distance to construct a phylogenetic tree. Results showed that the fragment of 760 bp was successfully amplified. Variations of nucleotide sequence in 576 bp fragment length from 31 individual buffaloes were analyzed and revealed the nucleotide composition as Adenine (A) = 32.6%, Thymine (T) = 26.8 %, Guanine (G) = 14.7% and Cytosine (C) = 25.9%. A total of 108 nucleotide polymorphic sites and 26 haplotypes were observed. Nucleotide and haplotype diversity index (π and Hd) were 0.06267 and 0.987, respectively. Genetic distance among swamp buffalo populations was smaller (ranging 0.050-0.056) than between Murrah and the swamp buffalo populations (ranging 0.091-0.125). Among the three native Vietnamese buffalo groups, the genetic distance between Bao Yen and LangBiang (0.050) buffalo populations was smaller than between Thanh Chuong and Bao Yen (0.055) or LangBiang (0.056). The phylogenetic tree showed that domestic buffalo populations are separated into two clusters that could be distinguished from the Murrah population. In conclusion, the genetic variation on Vietnamese domestic buffaloes is higher than other Asian swamp buffaloes. Most of native buffalo populations cluster in one clade and have a genetic relationship closer to Thai and Philippine swamp buffaloes in maternal origin. Further insights regarding the genetic diversity of Vietnamese native buffaloes will require more in-depth studies.
Keywords | Bubalus bubalis, D-loop sequence, Genetic divergence, Mitochondrial DNA, Swamp buffalo
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