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Genetic Diversity of Red Chittagong Cattle of Bangladesh Using Microsatellite Markers

M. S. A. Bhuiyan
Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh, Bangladesh

O. Hanotte
Senior Scientist and Project Leader
Animal Genetic Resources, International Livestock Research Institute, Nairobi 00100, Kenya

A. K. F. H. Bhuiyan
Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh, Bangladesh

Abstract/ Executive Summary:

The genetic diversity and relationship of indigenous Red Chittagong cattle (Bas indicus) population of Bangladesh were evaluated using 9 micro satellite markers. Thirty-two unrelated DNA samples were genotyped to estimate within population genetic diversity. The estimated mean no. of alleles per locus was 6.22 ± 1.09, with a total of 56 alleles. Allele frequency varied from 1.61 to 75.93% across all loci. The average observed and expected heterozygosities for the population were 0.594 ± 0.032 and 0.649 ± 0.045 respectively. The average gene diversity and inbreeding co-efficient values were 0.649 and 0.085 respectively. One microsatellite locus (11.11%) deviated significantly form Hardy-Weinberg equilibrium. The neighbor-joining based dendogram tree showed 2 distinct clusters in Red Chittagong cattle population examined.

Keywords: Red Chittagong, Microsatellite, Genetic diversity, Cattle

Location: Anowara and Patia upazilla of Chittagong district and BAU dairy farm, Mymensingh, Bangladesh

Start Date:

End Date:

Program Area: Conservation and Biodiversity

Commodity: Cattle

Objectives:

Objective of the study was to assess/estimate the level of genetic diversity within RC cattle and to establish genetic relationships among the individuals of the said cattle population using a set of bovine specific microsatellite markers.

Methodology:

Blood samples and DNA isolation: Blood samples were collected from 32 (twenty-seven samples from Anowara and Patia upazilla of Chittagong district and five samples from BAU dairy farm) genetically unrelated RC cattle. The blood samples were transferred immediately in FTA filter paper (Whatman= Bioscience) and air-dried, packed well in polythene bag with silica gel, and transported to International Livestock Research Institute, Nairobi, Kenya. Genomic DNA was extracted using the DNA extraction kit QIAGEN, according to the manufacturer's instruction. Microsatellite loci, PCR amplification and genotyping: A total of 9 bovine microsatellite markers (Applied Biosystems, UK) were used in this study for DNA amplification. The characteristics and polymerase chain reaction (PCR) running conditions of nine markers. PCR reactions were carried out in 10 µl volumes comprising 30 ng of genomic DNA, 2ng of each primer, 0.5 units of Taq DNA polymerase (Promega, Madison, WI, USA), 0.125 mM dNTPs, 1.5 mM MgCl₂, triple distilled water and 1x PCR buffer containing 50 mM KCL, 10 mM Tris - HCL (pH 9.0 at 25°C) and 1.0% Tritol X-100. PCR amplifications were performed by CeneAmp PCR system 9700 (Applied Biosystems) programmable thermocycler. The cycling conditions were as follows: initial denaturation step at 94⁰C for 4 minutes following by 35 cycles of 94⁰C for 30 sec., 30 sec. at an annealing temperature and 30 sec at 72⁰C, and final extension step at 72⁰C for 10 minutes. All forward primers were end-labeled with an ABI compatible phosphoramidite dye (6-FAM, NED, VIC and PET). PCR products were electrophoresed using 3730 automatic DNA analyzer (Applied Biosystems). CeneScan 500 LIZ size standard (Applied Biosystems) was used as an internal lane size standard. The data were collected from the automatic DNA analyzer using GeneMapper software version 3.7 (Applied Biosystems). Data processing and allele sizes of microsatellite loci were also determined with GeneMapper software version 3.7 (Applied Biosystems). Statistical analyses: Genetic variation in RC cattle population was determined by mean number of alleles per locus (MNA), average observed heterozygosity and expected heterozygosity. MNA, observed and expected heterozygosity, and locus wise allele frequencies were calculated using the program EXCEL MICROSATELLITE TOOLKIT version 3.1 (Park, 2001). Gene diversity and inbreeding coefficient per locus were estimated using Weir and Cockerham's F_IS estimator (Weir and Cockerham, 1984) and the calculation was performed in the computer program FSTAT version 2.9.3 (Goudet, 2001). Hardy-Weinberg equilibrium tests was done in the computer program GENEPOP version 3.4 (Raymond and Rousset, 1995). A computer program, MICROSAT version 1.5d (Minch et al., 1995) was used to estimate distance matrices among the RC individuals. The distance matrices from MICROSAT program used as an input file for another computer program PHYLIP version 3.6 (Felsenstein, 2001) to construct a dendogram showing putative relationship between individuals. The tree was then visualized using TREEVIEW version 1.6.6 program.

Source of Information: Progress. Agric. 16(1): 141-148,2005, ISSN 1017-8139

Article Link (Online Journal):

Funding Source:

Budget:

Total Budget (Tk.) :

Achievement/Findings:

Decline in animal number and directional selection are the major causes of loss of genetic diversity. By investigating in the genetic structure of RC cattle, it is evident that still they maintain wider genetic variability even though they have some inbreeding effect. Within population pure breeding with selected superior animals may be done with discrimination to preserve this important farm animal genetic resource and to maintain genetic uniqueness of the cattle breed as an improved indigenous cattle type ot Bangladesh.

Knowledge Management: Journal