Open Journal Systems

Polymorphism in the Mitochondrial Cytochrome B of Crossbred Madura-Limousine Cattle

Rimayanti Rimayanti, Budi Utomo, Dilasdita Kartika Pradana, Indah Norma Triana, Adeyinka Oye Akintunde, Imam Mustofa

Abstract

Madura cattle breeders in rural Indonesia prefer to request artificial insemination services for their cows with Limousin bull's freeze-thawed semen. However, crossbred Madura-Limousin (Madrasin) bulls reported a high infertility rate. This study aimed to identify the mutation of cytochrome b (Cytb) mtDNA in Madura-Limousin crossbred cattle to develop a fundamental breeding approach that would promote animal protein production and preserve the genetics of purebred Madura cattle. Blood samples were collected from the two bulls of crossbred Madura-Limousin, purebred Madura, and Limousin bulls for DNA analysis. The polymerase chain reaction was used to amplify the Cytb mtDNA, which was then sequenced using the Sanger method. The MEGA 7.0 software was used with the neighbor-joining method to construct the phylogenetic tree. Compared to the purebred Madura cattle and purebred Limousin bulls, the crossbred Madura-Limousin bulls (also known as Madrasin) exhibited alterations in their nucleotide sequence as follows: Deletion of Adenine (number 37), mutation Guanine (66) to Cytosine, Thymine (73) to Cytosine, Guanine (78) to Adenine, Cytosine (84) to Guanine, Thymine (85) to Cytosine, Thymine (99) to Cytosine, Adenine (105) to Guanine, Adenine (114) to Guanine, Cytosine (126) to Thymine, Cytosine (141) to Thymine, and Adenine (144) to Cytosine, resulting in corresponding changes in the deletion of amino acid Isoleucine (position number 11) and mutation of Isoleucine (34) to Methionine. As observed in the resulting clades, the purebred Madura and Limousin cattle were grouped, while Madrasin crossbred cattle were separated. It could be concluded that Madrasin bulls exhibited alterations in their nucleotide and protein sequences of Cytb mtDNA, placing them in a distinct group from purebred Madura cattle and Limousin bulls.

Keywords

crossbreeding Madura-Limousin, cultivating food for producers, mutating amino acids, smallholder farmers

Full Text:

PDF

References

Agustine, R., S. Bintara, S. Andarwati, T.S.M. Widi. & A.R.S. Putra. (2019). Farmer’s decision in selecting the bull semen for artificial insemination in Central Java. IOP Conf. Series: Earth and Environmental Science. 260, 012048. https://doi.org/10.1088/1755-1315/260/1/012048

Andalib, S., Divani, A. A., Michel, T. M., Høilund-Carlsen, P. F., Vafaee, M. S., & Gjedde, A. (2017). Pandora's Box: mitochondrial defects in ischaemic heart disease and stroke. Expert reviews in molecular medicine, 19, e5. https://doi.org/10.1017/erm.2017.5

Bunmee, T., Chaiwang, N., Kaewkot, C., & Jaturasitha, S. (2018). Current situation and future prospects for beef production in Thailand - A review. Asian-Australasian journal of animal sciences, 31(7), 968–975. https://doi.org/10.5713/ajas.18.0201

Cañizares-Martínez, M.A., G.M. Parra-Bracamonte, J.C. Segura-Correa, & J.G. Magaña-Monforte. (2021). Effect of leptin, pituitary transcription factor and luteinizing hormone receptor genes polymorphisms on reproductive traits and milk yield in Holstein cattle. Braz Arch Biol Technol. 64, e21190643. https://doi.org/10.1590/1678-4324-2021190643

Çiftci, Y., O. Eroğlu, & Firidin Ş. (2013). Mitochondrial cytochrome b sequence variation in three Sturgeon species (A. stellatus Pallas, 1771, A. gueldenstaedtii Brandt, 1833, H. huso Linnaeus, 1758) from the black sea coasts of Turkey. Turk J Fish Aquat Sci. 13, 291-303. https://doi.org/10.4194/1303-2712-v13_2_11

Elango, K., Kumaresan, A., Sharma, A., Nag, P., Prakash, M. A., Sinha, M. K., Manimaran, A., Peter, E. S. K. J., Jeyakumar, S., Selvaraju, S., Ramesha, K. P., & Datta, T. K. (2020). Sub-fertility in crossbred bulls: deciphering testicular level transcriptomic alterations between zebu (Bos indicus) and crossbred (Bos taurus x Bos indicus) bulls. BMC genomics, 21(1), 502. https://doi.org/10.1186/s12864-020-06907-1

Feuillie, C., Merheb, M. M., Gillet, B., Montagnac, G., Daniel, I., & Hänni, C. (2014). Detection of DNA sequences refractory to PCR amplification using a biophysical SERRS assay (Surface Enhanced Resonant Raman Spectroscopy). PloS one, 9(12), e114148. https://doi.org/10.1371/journal.pone.0114148

Freitas, P. H. F., Wang, Y., Yan, P., Oliveira, H. R., Schenkel, F. S., Zhang, Y., Xu, Q., & Brito, L. F. (2021). Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions. Frontiers in genetics, 12, 604823. https://doi.org/10.3389/fgene.2021.604823

Fu, L., Luo, Y. X., Liu, Y., Liu, H., Li, H. Z., & Yu, Y. (2021). Potential of Mitochondrial Genome Editing for Human Fertility Health. Frontiers in genetics, 12, 673951. https://doi.org/10.3389/fgene.2021.673951

Hartati, H. & W.P.B. Putra. (2021). Predicting the growth curve of body weight in Madura cattle. Kafkas Univ Vet Fak Derg, 27, 431-437. https://doi.org/10.9775/kvfd.2021.25448

Hartatik, T., D. A. Mahardika, , T. S. M. Widi, & C. Baliarti. (2009). Characteristic and performance of Madura-Limousin grade and Madura cows in Sumenep and Pamekasan Regencies. Bul Anim Sci. 33, 143-147. https://doi.org/10.21059/buletinpeternak.v33i3.109

Hartatik, T., D. Maharani, J.H.P. Sidadolog, A. Fathoni, & S. Sumadi. (2018). Haplotype diversity of partial cytochrome b gene in Kebumen Ongole Grade cattle. Trop Anim Sci J. 41, 8-14. https://doi.org/10.5398/tasj.2018.41.1.8

Hartatik, T., D.N.H. Hariyono, & Y. Adinata. (2019). Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences. Biodiversitas 20, 17-22. https://doi.org/10.13057/biodiv/d200103

Hartatik, T., S.M. Widi, S.D. Volkandari, D. Maharani, & S. Sumadi. (2014). Analysis of DNA Polymorphism in SRY Gene of Madura Cattle Populations. Procedia Environ. Sci. 20, 365-369. https://doi.org/10.1016/j.proenv.2014.03.046

Hartatik, T., W.B.P. Putra, S.D. Volkandari, & S. Sumadi. (2015). Polymorphism of mtDNA cytochrome b gene of local cattle in Indonesia. J-SustaiN. 3, 21-24. https://repository.ugm.ac.id/136064/1/2015_Tety%20el%20al_SustaiN_Vol3_No1_21-24_FA-018-04151.pdf

Jiang, M., Kauppila, T. E. S., Motori, E., Li, X., Atanassov, I., Folz-Donahue, K., Bonekamp, N. A., Albarran-Gutierrez, S., Stewart, J. B., & Larsson, N. G. (2017). Increased Total mtDNA Copy Number Cures Male Infertility Despite Unaltered mtDNA Mutation Load. Cell metabolism, 26(2), 429–436.e4. https://doi.org/10.1016/j.cmet.2017.07.003

Kastelic, J. P., Rizzoto, G., & Thundathil, J. (2018). Review: Testicular vascular cone development and its association with scrotal thermoregulation, semen quality and sperm production in bulls. Animal: an international journal of animal bioscience, 12(s1), s133–s141. https://doi.org/10.1017/S1751731118001167

Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Molecular biology and evolution, 33(7), 1870–1874. https://doi.org/10.1093/molbev/msw054

Kumaresan, A., Elango, K., Datta, T. K., & Morrell, J. M. (2021). Cellular and Molecular Insights Into the Etiology of Subfertility/Infertility in Crossbred Bulls (Bos taurus × Bos indicus): A Review. Frontiers in cell and developmental biology, 9, 696637. https://doi.org/10.3389/fcell.2021.696637

Kutsiyah, K., S. Sholeh, M. Zali, & Y. Heryadi. (2018). The development analysis the crossing of madura x limousin cattle implementation in Madura island. JITP 6, 6-12. https://doi.org/10.20956/jitp.v6i1.6285

Larrea-Sarmiento, A., Alvarez, A. M., Stack, J. P., & Arif, M. (2019). Synergetic effect of non-complementary 5' AT-rich sequences on the development of a multiplex TaqMan real-time PCR for specific and robust detection of Clavibacter michiganensis and C. michiganensis subsp. nebraskensis. PloS one, 14(7), e0218530. https://doi.org/10.1371/journal.pone.0218530

Li, J. L., Lin, T. Y., Chen, P. L., Guo, T. N., Huang, S. Y., Chen, C. H., Lin, C. H., & Chan, C. C. (2021). Mitochondrial Function and Parkinson's Disease: From the Perspective of the Electron Transport Chain. Frontiers in molecular neuroscience, 14, 797833. https://doi.org/10.3389/fnmol.2021.797833

Lorenz T. C. (2012). Polymerase chain reaction: basic protocol plus troubleshooting and optimization strategies. Journal of visualized experiments : JoVE, (63), e3998. https://doi.org/10.3791/3998

Marques, P., Skorupskaite, K., Rozario, K. S., Anderson, R. A., & George, J. T. (2022). Physiology of GnRH and Gonadotropin Secretion. In K. R. Feingold (Eds.) et. al., Endotext. MDText.com, Inc.

Marshall K. (2014). Optimizing the use of breed types in developing country livestock production systems: a neglected research area. Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie, 131(5), 329–340. https://doi.org/10.1111/jbg.12080

MCGA (Meteorological, Climatological, and Geophysical Agency). 2022. https://www.bmkg.go.id/CUACA/prakiraan-cuaca.bmkg?AreaID=501272&Prov=12〈=EN (January 05, 2022).

Meher, B. R., Dixit, A., Bousfield, G. R., & Lushington, G. H. (2015). Glycosylation Effects on FSH-FSHR Interaction Dynamics: A Case Study of Different FSH Glycoforms by Molecular Dynamics Simulations. PloS one, 10(9), e0137897. https://doi.org/10.1371/journal.pone.0137897

Meles, D. K., Mustofa, I., Hariadi, M., Wurlina, W., Susilowati, S., Amaliya, A., Suparto, S., & Rimayanti, R. (2022). The enriched Y-bearing sperm combined with delayed fixed-time artificial insemination for obtaining male Simmental crossbred offspring. Veterinary world, 15(1), 102–109. https://doi.org/10.14202/vetworld.2022.102-109

Mendonça, F. S., MacNeil, M. D., Leal, W. S., Azambuja, R. C. C., Rodrigues, P. F., & Cardoso, F. F. (2019). Crossbreeding effects on growth and efficiency in beef cow-calf systems: evaluation of Angus, Caracu, Hereford and Nelore breed direct, maternal and heterosis effects. Translational animal science, 3(4), 1286–1295. https://doi.org/10.1093/tas/txz096

Merheb, M., Matar, R., Hodeify, R., Siddiqui, S. S., Vazhappilly, C. G., Marton, J., Azharuddin, S., & Al Zouabi, H. (2019). Mitochondrial DNA, a Powerful Tool to Decipher Ancient Human Civilization from Domestication to Music, and to Uncover Historical Murder Cases. Cells, 8(5), 433. https://doi.org/10.3390/cells8050433

Muhammad Aslam, M. K., Kumaresan, A., Rajak, S. K., Tajmul, M., Datta, T. K., Mohanty, T. K., Srinivasan, A., & Yadav, S. (2015). Comparative proteomic analysis of Taurine, Indicine, and crossbred (Bos taurus × Bos indicus) bull spermatozoa for identification of proteins related to sperm malfunctions and subfertility in crossbred bulls. Theriogenology, 84(4), 624–633. https://doi.org/10.1016/j.theriogenology.2015.04.020

Mustofa, I., Susilowati, S., Wurlina, W., Hernawati, T., & Oktanella, Y. (2021). Green tea extract increases the quality and reduced DNA mutation of post-thawed Kacang buck sperm. Heliyon, 7(3), e06372. https://doi.org/10.1016/j.heliyon.2021.e06372

Pérez Sirkin, D. I., Lafont, A. G., Kamech, N., Somoza, G. M., Vissio, P. G., & Dufour, S. (2017). Conservation of Three-Dimensional Helix-Loop-Helix Structure through the Vertebrate Lineage Reopens the Cold Case of Gonadotropin-Releasing Hormone-Associated Peptide. Frontiers in endocrinology, 8, 207. https://doi.org/10.3389/fendo.2017.00207

Prakash, M. A., Kumaresan, A., Ebenezer Samuel King, J. P., Nag, P., Sharma, A., Sinha, M. K., Kamaraj, E., & Datta, T. K. (2021). Comparative Transcriptomic Analysis of Spermatozoa From High- and Low-Fertile Crossbred Bulls: Implications for Fertility Prediction. Frontiers in cell and developmental biology, 9, 647717. https://doi.org/10.3389/fcell.2021.647717

Prakash, M. A., Kumaresan, A., Sinha, M. K., Kamaraj, E., Mohanty, T. K., Datta, T. K., & Morrell, J. M. (2020). RNA-Seq analysis reveals functionally relevant coding and non-coding RNAs in crossbred bull spermatozoa. Animal reproduction science, 222, 106621. https://doi.org/10.1016/j.anireprosci.2020.106621

Prihandini, PW., A. Primasari, M. Luthfi, J. Efendy, & D. Pamungkas. (2020). Genetic diversity of mitochondrial DNA cytochrome b in Indonesian native and local cattle populations. JITV 25, 39-47. https://doi.org/10.14334/jitv.v25i2.2496

Putra, W.P.B., W. Kurniati, & M. Setyarini. (2020). Early selection in limousine and simmental candidate bulls based on the preweaning growth curve of body weight. J Bahri Dagdas Anim Res. 9, 1-6. https://dergipark.org.tr/en/download/article-file/1303261

Rahmatullaili, S., D. Fatmawati, C. Nisa, A. Winaya, L. Chamisijatin, & I. Hindun. (2019). Genetic diversity of Bali cattle: Cytochrome b sequence variation. IOP Conf. Series: Earth and Environmental Science 276, 012048. https://doi.org/10.1088/1755-1315/276/1/012048

Romaino, S. M., Fazly-Ann, Z. A., Loo, S. S., Hafiz, M. M., Hafiz, M. D., Iswadi, M. I., Kashiani, P., Rosli, M. K., Syed-Shabthar, S. M., Md-Zain, B. M., & Abas-Mazni, O. (2014). Species identification of Malayan Gaur, Kedah-Kelantan and Bali cattle using polymerase chain reaction-restricted fragment length polymorphism. Genetics and molecular research : GMR, 13(1), 406–414. https://doi.org/10.4238/2014.January.21.8

Saraf, K. K., Kumaresan, A., Sinha, M. K., & Datta, T. K. (2021). Spermatozoal transcripts associated with oxidative stress and mitochondrial membrane potential differ between high- and low-fertile crossbred bulls. Andrologia, 53(5), e14029. https://doi.org/10.1111/and.14029

Schierenbeck K. A. (2017). Population-level genetic variation and climate change in a biodiversity hotspot. Annals of botany, 119(2), 215–228. https://doi.org/10.1093/aob/mcw214

Schliep, K., A.J. Potts, D.A. Morrison, & G.W. Grimm. (2017). Intertwining phylogenetic trees and networks. Methods Ecol. Evol. 8, 1212-1220. https://doi.org/10.1111/2041-210X.12760

Straube, D., & Juen, A. (2013). Storage and shipping of tissue samples for DNA analyses: A case study on earthworms. European journal of soil biology, 57, 13–18. https://doi.org/10.1016/j.ejsobi.2013.04.001

Sutarno Setyawan, AD. (2016). Review: The diversity of local cattle in Indonesia and the efforts to develop superior indigenous cattle breeds. Biodiversitas. 17, 273-295. https://doi.org/10.13057/biodiv/d170139

Sweett, H., Fonseca, P. A. S., Suárez-Vega, A., Livernois, A., Miglior, F., & Cánovas, A. (2020). Genome-wide association study to identify genomic regions and positional candidate genes associated with male fertility in beef cattle. Scientific reports, 10(1), 20102. https://doi.org/10.1038/s41598-020-75758-3

Syakalima, M., M. Munyeme, & J. Yasuda. (2016). Cytochrome c oxidase sequences of zambian wildlife helps to identify species of origin of meat. Int J Zool. 5, 1808912. https://doi.org/10.1155/2016/1808912

Tarekegn, G. M., Ji, X. Y., Bai, X., Liu, B., Zhang, W., Birungi, J., Djikeng, A., & Tesfaye, K. (2018). Variations in mitochondrial cytochrome b region among Ethiopian indigenous cattle populations assert Bos taurus maternal origin and historical dynamics. Asian-Australasian journal of animal sciences, 31(9), 1393–1400. https://doi.org/10.5713/ajas.17.0596

Taylor, J. F., Schnabel, R. D., & Sutovsky, P. (2018). Identification of genomic variants causing sperm abnormalities and reduced male fertility. Animal reproduction science, 194, 57–62. https://doi.org/10.1016/j.anireprosci.2018.02.007

Vlasova, I., I. Ventsova, A. Vostroilov, V. Safonov, & A. Golubtsov. (2020). Beef productivity of limousine cattle at stable keeping. Am J Anim Vet Sci. 15, 266-274. https://doi.org/10.3844/ajavsp.2020.266.274

Wang, S., Veller, C., Sun, F., Ruiz-Herrera, A., Shang, Y., Liu, H., Zickler, D., Chen, Z., Kleckner, N., & Zhang, L. (2019). Per-Nucleus Crossover Covariation and Implications for Evolution. Cell, 177(2), 326–338.e16. https://doi.org/10.1016/j.cell.2019.02.021

Widi, T.S.M., H.M.J. Udo, K. Oldenbroek, I.G.S. Budisatria, E. Baliarti, & A.J. van der Zijpp. (2014). Unique cultural values of Madura cattle: Is crossbreeding a threat? Anim Genet Resour. 54, 141-152. https://doi.org/10.1017/S2078633613000349

Widi, T.S.M., H.M.J. Udo, K. Oldenbroek, I.G.S. Budisatria, E. Baliarti, & A.J. van der Zijpp. (2015). Is crossbreeding of cattle beneficial for mixed farming systems in Central Java? Anim Genet Resour. 56, 127-144. https://doi.org/10.1017/S2078633615000028

Saleh Jaweesh, M., Hammadeh, M. E., Dahadhah, F. W., Al Zoubi, M. S., & Amor, H. (2022). Association between the single nucleotide variants of the mitochondrial cytochrome B gene (MT-CYB) and the male infertility. Molecular biology reports, 49(5), 3609–3616. https://doi.org/10.1007/s11033-022-07200-y

Yan, L., She, Y., Elzo, M. A., Zhang, C., Fang, X., & Chen, H. (2019). Exploring genetic diversity and phylogenic relationships of Chinese cattle using gene mtDNA 16S rRNA. Archives animal breeding, 62(1), 325–333. https://doi.org/10.5194/aab-62-325-2019

DOI: http://dx.doi.org/10.5380/avs.v28i4.91501