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Phylogenetic Analysis of Black Bengal and Jamunapari Goats in Bangladesh Based on Partial Sequence of Cytochrome B Gene

S.M.Z.H. Chowdhury
Livestock Division, Bangladesh Agricultural Research Council, Farmgate, Dhaka, Bangladesh.

M.S. Mahmud
Livestock Division, Bangladesh Agricultural Research Council, Farmgate, Dhaka, Bangladesh.

M.R. Islam
Livestock Division, Bangladesh Agricultural Research Council, Farmgate, Dhaka, Bangladesh.

K.H.M.N.H. Nazir
Department of Microbiology and Hygiene, Bangladesh Agriculture University Mymensingh-2202, Bangladesh.

Abstract/ Executive Summary:

Goats, among the livestock species, are considered the most prolific ruminant especially under callous climatic conditions. The aim of the present study was to depict the current phylogenetic status and genetic diversities of Black Bengal (BBG) and Jamunapari goat of Bangladesh and the world. Cytochrome b (cytb) gene (1140 bp) of mitochondrial DNA of Black Bengal goats (Capra hircus) was amplified by Polymerase Chain Reaction (PCR) for the first time in Bangladesh. The sequence from BBG had no nucleotide (nt) difference and 100% homology with the BBG (C. hircus) of India and also the goats (C. hircus) from China (Yangtze River Delta White Goat), Thailand (Wild Cervidae), Japan (Bezoar goat) and South Africa (Domestic goat). The sequence had 1-5 nt differences and 99% homology with the goats (C. hircus) from China, Thailand and Japan (other goats), and also with the goats (C. hircus) from Malaysia, South Korea, France, Italy, Pakistan, Slovenia, Switzerland and USA. Phylogenetic tree constructed with Black Bengal Goat (BBG-K-2) and Jamunapari goats (SG-1) of Bangladesh with cytochrome b nucleotide sequences were closely related to China-HM7. China-YP xj46, Pakistan-Lineage C1, Pakistan-Lineage C2, Slovenia- ChSo1, Switzerland-ChTo2992 and shared 98.8% to 99% and 98.3% to 98.6% similarity, respectively and 1-1.2% and 1.4 to 1.7% genetic distance, respectively. Based on Ctb gene Sequence collected from Bangladeshi Black Bengal Goats (BBG-K-2) and Jamunapari goats (SG1) that were closely related and shared with the same genetic lineage of China HM18 and India-BBG-DQ073048, respectively, suggesting a common origin.

Keywords: Domestic Goats, Genetic Diversity, mtDNA, cytb Gene, Phylogenetic analysis

Location: Three different goat farms located in semi-urban area of Savar region of Dhaka and Khulna for Black Bengal goats, Gazipur area for Jamnapari goats in Bangladesh

Start Date: 00-00-2010

End Date: 00-00-2011

Program Area: Animal Health and Management

Commodity: Goat

Objectives:

The present study was investigated to current phylogenetic status and genetic diversities of Black Bengal and Jamnapari goat of Bangladesh and the world in order to understand the genetic basis of this breed.

Methodology:

Breed selection There were two different local breeds Black Bengal and Jamnapari goats of Bangladesh selected for this research study. Study area This study was conducted in three different goat farms located in semi-urban area of Savar region of Dhaka and Khulna for Black Bengal goats, Gazipur area for Jamnapari goats in Bangladesh during the period 2010 to 2011. Three goat farms are designated as farm code A, B, and C. The samples were collected from the three goats of selected farms and brought to the Department of Microbiology and Hygiene, Bangladesh Agricultural University, for laboratory analysis. Sample collection A total of 3 blood samples from individual goats of 2.5 years of age were collected from jugular vein each from three selected goat farms. Blood samples of Black Bengal goat were taken from Khulna (BBG-K-2), Dhaka and Jamunapari goats from Sardagonj of Gazipur (SG-1) area of Bangladesh. All blood samples (5ml in EDTA Containing tubes) were aseptically collected and stored at -20°C until used at Microbiology laboratory. The goat samples were unrelated genetically based on the information of the owners and local breeding data. Processing of blood samples was followed by Chowdhury et al. (2011). DNA extraction, amplification, and sequencing of cytb gene DNA was extracted from whole blood using the method as described by Chowdhury et al (2011) for sequence analysis Cyt b gene in mtDNA. All DNA samples were brought to the final concentration of 50 ng/µL and stored at -80°C. The forward primer (5-ATG ACC AAC ATC CGA AAG ACC C-3 (nt 1-22)) and reverse primer (5?-TCT TCA TTT TAG AAG GTT GTT TCC-3 (nt 1140-1117) that generated 1140 bp polymerase chain reaction (PCR) product were used to amplify 1140 bp of Cytb gene as described by Takada et al (1997) and Chowdhury et al (2011). Sequence Alignment and identification Partial sequences, obtained using forward and reverse primers of mtDNA Cyt b sequences were combined to full length sequences (420 bp for Black Bengal) via the SeqMan Genome Assembler (DNAstar, USA) and were compared to the Gene Bank database of the National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/GenBank) by means of the basic local alignment search tool (BLAST) to identify close phylogenetic relatives. The nucleotide sequences then were translated into amino acids form by mitochondrial vertebrate genetic code. All mtDNA Cyt b sequences were analyzed using Molecular Evolutionary Genetics Analysis 6 program (Tamura et al., 2013) and aligned by ClustalW. Partial cyt b gene sequence (N-terminal part) of mtDNA of Jamnapari goat from Gazipur was published. Based on the resulted partial cyt b gene sequence (N-terminal part) of mitochondrial DNA of Black Bengal goat (Bangladesh-BBG-K-2) of Khulna district, similar sized sequence was taken from that of Jamnapari goat (Bangladesh-Jamnapari-SG) and that of 42 other goats of different countries from Gene Bank Databases. Multiple alignment was carried out using Laser gene MgAlign program of DNASTAR Software (http://www.dnastar.com, Product Key: NXRAY-GQ8NJ-EKJW7). Sequence distances were obtained using MgAlign Distance ClustalW. Construction of Phylogenetic tree The multiple sequence alignment of the retrieved reference sequences from NCBI, EMBL or DDBJ and representative isolates’ sequences were performed with the ClustalW software. Aligned sequences were exported to the GeneDoc software for sequence trimming and conserved region identification. Refined sequences were further exported to the Molecular Evolutionary Genetic Analysis (MEGA) software for phylogenetic tree construction using the Neighbor joining algorithm and selecting 1000 bootstrap replication. Further analysis of the genes was carried out using the Distance and Pattern analysis tool in the MEGA software. The phylogenetic tree was inferred using the Neighbor-Joining method. A bootstrap consensus tree was inferred from 1000 replicates (Felsenstein, 1985). Nucleotide sequence accession numbers The partial mtDNA Cytochrome B gene sequences obtained in this study have been deposited in the GenBank database under the accession numbers MN066604 for Black Bengal goat (BBG-K-2) and MN066605 for Jamunapari goat (SG-1). Isolates name have been abbreviated using the following format: country/organization/location/isolate no. .

Source of Information: SAARC J. Agric., 17(1): 23-35 (2019)

Article Link (Online Journal): DOI: https://doi.org/10.3329/sja.v17i1.42759

Funding Source:

Budget:

Total Budget (Tk.) :

Achievement/Findings:

Black Bengal and Jamunapari goats of Bangladesh have a close genetic relationship to several local goats in Southeast Asia. We speculated that gene flow among goat populations facilitated by the traditional seasonal pastoralism and annual long distance migrations in history as well as trade would account for the pattern discerned in regional goat pools.

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