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. 2019 Mar 25;20(1):37.
doi: 10.1186/s12863-019-0741-0.

Karyotypic and mtDNA based characterization of Malaysian water buffalo

Nor ' Ammar Liyana Shaari  1 , Marilyn Jaoi-Edward  2 , Shu San Loo  2 , Mohd Shahrom Salisi  1 , Rosnina Yusoff  3 , Nurul Izza Ab Ghani  4 , Mohd Zamri Saad  5 , Hafandi Ahmad  6
Affiliations

Karyotypic and mtDNA based characterization of Malaysian water buffalo

Nor ' Ammar Liyana Shaari et al. BMC Genet. .

Abstract

Background: In Malaysia, the domestic water buffaloes (Bubalus bubalis) are classified into the swamp and the murrah buffaloes. Identification of these buffaloes is usually made via their phenotypic appearances. This study characterizes the subspecies of water buffaloes using karyotype, molecular and phylogenetic analyses. Blood of 105 buffaloes, phenotypically identified as swamp, murrah and crossbred buffaloes were cultured, terminated and harvested using conventional karyotype protocol to determine the number of chromosomes. Then, the D-loop of mitochondrial DNA of 10 swamp, 6 crossbred and 4 murrah buffaloes which were identified earlier by karyotyping were used to construct a phylogenetic tree was constructed.

Results: Karyotypic analysis confirmed that all 93 animals phenotypically identified as swamp buffaloes with 48 chromosomes, all 7 as crossbreds with 49 chromosomes, and all 5 as murrah buffaloes with 50 chromosomes. The D-loop of mitochondrial DNA analysis showed that 10 haplotypes were observed with haplotype diversity of 0.8000 ± 0.089. Sequence characterization revealed 72 variables sites in which 67 were parsimony informative sites with sequence diversity of 0.01906. The swamp and murrah buffaloes clearly formed 2 different clades in the phylogenetic tree, indicating clear maternal divergence from each other. The crossbreds were grouped within the swamp buffalo clade, indicating the dominant maternal swamp buffalo gene in the crossbreds.

Conclusion: Thus, the karyotyping could be used to differentiate the water buffaloes while genotypic analysis could be used to characterize the water buffaloes and their crossbreds.

Keywords: Karyotyping; Mitochondrial DNA; Phylogenetic; Water buffaloes.

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Conflict of interest statement

Ethics approval and consent to participate

All testing related to animal care and handling was approved by the Institutional Animal Care and Use Committee (IACUC) of the Faculty of Veterinary Medicine, Universiti Putra Malaysia, Malaysia (UPM/IACUC/AUP-U017/2018, 8 January 2018). The blood samples were collected from the farm by qualified veterinarians and with the permission of the owners of the animals.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
a Metaphase field exhibits 48 chromosomes showing female swamp buffalo (2n=48) by using giemsa staining method under 1000 magnification. b Metaphase field exhibits 49 chromosomes showing female crossbreed buffalo (2n=49) using giemsa staining method under 1000 magnification. c Metaphase field exhibits 50 chromosomes showing female murrah buffalo (2n=50) by using giemsa staining method under 1000 magnification
Fig. 2
Fig. 2
a Purified PCR product of primer H15773F and L16371R for swamp, crossbreed and murrah samples. The size is estimated around 500 bp. M represent 1 kb marker (Promega). b Purified PCR product of primer H16231F and L421R for murrah and crossbreed samples. The size is estimated around 500 bp. M represent 1 kb marker (Promega). c Purified PCR product of primer H16231F and L421R for swamp samples. The size is estimated around 500 bp. M represent 1 kb marker (Promega)
Fig. 3
Fig. 3
The maximum likelihood phylogram reconstructed by MEGA 7 from 10 swamp, 4 murrah and 6 crossbreed buffaloes of the mitochondrial D-loop region, rooted by Bos taurus
See this image and copyright information in PMC

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