Phylogenetic Analysis of Cytochrome B of Mitochondrial Genome in some Iranian Goat Breeds

Document Type : Research Paper

Authors

1 Department of Animal Science, Faculty of Agriculture, Yasouj University, Yasouj, Iran

2 MSc Graduated, Department of Animal Science, Faculty of Agriculture, Yasouj University, Yasouj

3 Assistant Professor, Department of Animal Science, Faculty of Agriculture, Yasouj University, Yasouj

4 Assistant Professor, Department of Agriculture, Payame Noor University, Tehran, Iran.

5 Department of Animal Science, Faculty of Agriculture, University of Zabol, Zabol, Iran.

Abstract

Objective
Identifying the genetic diversity of native goat breeds of Iran can play an important role in the management and conservation of these breeds. The purpose of the current study was genetic and phylogenetic investigation of mitochondrial genome cytochrome b region in Lori, Pakistani, Zaboli and Adeni goats.
 
Materials and Methods
Blood samples were collected from 16 goats of each breed 4 blood samples. After extracting DNA, fragment 684 bp of cytochrome b region genome mitochondrial amplified by primers were designed and fragment amplified after purification was sequenced. Using the DNAsp software was determined in six different haplotypes.
 
Results
 The result of comparative analysis between goat breeds indicates that nucleotide diversity Pakistani and Zaboli breeds 0.35461 and 0.11199 respectively. Tajima D was obtaining 1.06945 that was significant. This confirmed the evolution by natural selection. Results from the analysis of molecular variance indicated that genetic variation was 80% of within and 20% was between populations that indicates high gene flow, migration among the studied populations or little sample size.
 
Conclusions
Based on a phylogenetic tree analysis, Lori and adni goat form a group with Capra hircus and Pakistani and Zabli goats form a separate group. This indicates the goat breeds have a common origin area.

Keywords


توحیدی نژاد فاطمه، محمدآبادی محمدرضا، اسمعیلی زاده کشکوئیه علی، نجمی نوری عذرا (1393) مقایسه سطوح مختلف بیان ژنRheb  در بافت های مختلف بز کرکی راینی. مجله بیوتکنولوژی کشاورزی 6(4)، 50-35.
عسکری ناهید، باقی زاده امین، محمدآبادی محمدرضا (1389) بررسی تنوع ژنتیکی در چهار جمعیت بز کرکی رایینی با استفاده از لوکوس های بین ریز ماهواره ای (ISSR). مجله ژنتیک نوین 5(2)، 49-56.
 عسکری ناهید، محمدآبادی محمدرضا، بیگی نصیری محمد تقی، باقی زاده امین ، فیاضی جمال (1387) مطالعه تنوع ژنتیکی بز کرکی راینی بر اساس نشانگرهای ریز ماهواره. مجله دانش کشاورزی و تولید پایدار 18(4)، 155-164.
علی‏نقی‎زاده روح الله ، محمدابادی محمدرضا، زکی زاده سونیا (1389) چند شکلی اگزون2 ژنBMP15  در بز سرخ جبال بارز. مجله بیوتکنولوژی کشاورزی 2(1)، 69-80
 نبی حسنی محمد، اسدی فوزی مسعود، علی اسمعیلی زاده، محمدآبادی محمدرضا (1389)  تجزیه ژنتیکی صفات رشد در بز کرکی رائینی با استفاده از مدل حیوانی چند متغیره. مجله علوم دامی ایران 41(4)، 323-329.
 
References
Alinaghizadeh H, Mohammad Abadi MR, Zakizadeh S (2010) Exon 2 of BMP15 gene polymorphism in Jabal Barez Red Goat. Agric Biotechnol J 2(1), 69-80.
Askari N, Baghizadeh A, Mohammadabadi MR (2008) Analysis of the genetic structure of Iranian indigenous Raini Cashmere goat populations using microsatellite markers. Modern Genetics J 2, 1-4.
Askari N, Mohammadabadi MR, Beigi Nasiri MT, Bagizadeh A, Fayyazi J (2008) Study of genetic diversity of Raini cashmere goats based on micro satellite markers. J Agric Sci Sustainable Prod 18, 155-164.
Baghizadeh A, Bahaaddini M, Mohamadabadi MR. Askari N (2009) Allelic Variations in Exon 2 of Caprine MHC Class II DRB3 Gene in Raeini Cashmere Goat. Am Eurasian J Agric Environ Sci, 6, 454-459.
Barazandeh A, Moghbeli SM, Vatankhah M, Mohammadabadi MR (2012) Estimating non-genetic and genetic parameters of pre-weaning growth traits in Raini Cashmere goat. Trop Anim Health Pro 44, 811-817.
Barnett, RG. Larson (2012) A phenol-chloroform protocol for extracting DNA from ancient samples. Methods Mol Biol 840, 13-19.
Batubara A (2011) Phenotypic and genetic diversity study of some sub-populations of local goat Indonesia and sustainable use strategy. Vol. Ph.D Thesis. Bogor Agricultural University Indonesia.
Budisatria IGS, Udo HMJ, van der Zijpp AJ et al. (2008) Religious festivities and marketing of small ruminants in Central Java-Indonesia. Asian J Agri Dev 5, 57-73.
Chen S, Fan B, Liu B et al. (2006) Genetic variation of 13 indigenous Chinese goat breeds based on cytochrome b gene sequences. Biochem Genet 44, 87-97.
Ewing B, Green P (1998) Based-Calling of Automated Sequencer Traces Using Phred.II. Error Probabilities. Genome Res 8, 186-194.
Eyre-walker A, Awadalla P (2001) Does human mtDNA recombine. J Mol Evol 53, 430-435.
Galtier N, Nabholz B, Glémin S, Hurst G (2009) Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Mol Ecol 18, 4541-4550.
Gholizadeh M, Mianji G, Zadeh H (2008) Potential use of molecular markers in the genetic improvement of livestock. Asian J Anim Vet Adv 3, 120-128.
Hall, TA, Carlsbad C (2011) BioEdit: An important software for molecular biology. GERF Bull Biosci 2, 60-61.
Hedayat-Evrigh N, Vahedi V, Seyed Sharifi R, Boustan A (2016) Sequencing and identification of single nucleotide polymorphisms of Partial myostatin gene in dromedary and Bactrian camels. J Agric Biotech 8, 119-124.
Ishida N, Hasegawa T, Takeda K et al. (1994) Polymorphic sequence in the D-loop region of equine mitochondrial DNA. Animal genetic 25, 215-221.
Lalitha, S. (2000) Primer premier 5. Biotech Software & Internet Report The Computer Software J Sci 1, 270-272.
Larkin MA, Blackshields G, Brown N et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948.
Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451-1452.
Liu Y, Cao S, Chen S et al. (2009) Genetic diversity of Chinese domestic goat based on the mitochondrial DNA sequence variation. J Anim Breed Genet 126, 80-89.
Moghadaszadeh M, Mohammadabadi MR, Esmailizadeh Koshkoieh A (2015) Association of Exon 2 of BMP15 Gene with the Litter Size in the Raini Cashmere Goat. Genetics in the 3rd Millennium, 13, 4062-4067.
Mohammadabadi MR (2012) Relationships of IGFBP-3 gene polymorphism with cashmere traits in Raini Cashmere goat. Modern Gen J 7, 115-120 (In Persian).
Mohammadabadi MR, Askari N, Baghizadeh A, Esmailizadeh A (2009) A directed search around caprine candidate loci provided evidence for microsatellites linkage to growth and cashmere yield in Rayini goats. Small Rumin Res 81, 146-51.
Mohammadabadi MR, Esfandyarpoor E, Mousapour A (2017) Using Inter Simple Sequence Repeat Multi-Loci Markers for Studying Genetic Diversity in Kermani Sheep. J Res Dev 5, 154-157.
Molaei Moghbeli S, Barazandeh A, Vatankhah M, Mohammadabadi MR (2013) Genetics and non-genetics Parameters of body Weight for Post WEANING Traits in Raini Cashmere goats. Trop Anim Health Pro 45, 1519-24.
MacCarthy, C. 2005. Chromas. Technelysium Pty Ltd.
Nabi Hassani M, Asadi Fozi M, Esmailizadeh AK and Mohammadabadi MR (2010) A genetic analysis of growth traits in Raieni Cashmere goat using multivariate animal model. Iranian J Anim Sci 41, 323-329.
Naderi S, Rezaei HR, Taberlet P et al. (2007) Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. Plos One 2, 1-12.
Nei M, Kumar S (2000) Molecular Evolution and Phylogenetics. Oxford University Press, New York.
Pakpahan S, Artama WT, Suparta IG (2016a) Genetic characteristics and relationship in different goat populations of Indonesia based on Cytochrome B gene sequences. Asian J Anim Sci 10, 29-38.
Pakpahan S, Artama WT, Widayanti R, Budisatria IGS (2016b) Molecular phylogenetic of Hutan Sumatera goat (Sumatran Serow) and Domestic goat (Capra hircus) in Indonesia based on analysis mitochondrial cytochrome b gene. Asian J Anim Vet Adv 11, 331-340.
Pakpahan S, Artama WT, Widayanti R, Suparta IG (2015) Genetic variations and the origin of native indonesian goat breeds based on mtDNA D-loop sequences. Asian J Anim Sci 9, 341-350.
Pariset L, Joost S, Gargani M, Valentini A (2012) Landscape genomics in livestock. In analysis of genetic variation in animals. (No BOOK_CHAP, p. 360) Intech.
Rahman A, Ramli A, Wan Embong W (2008) A review of reproductive biotechnologies and their application in goat. Biotechnology 7(2), 371-384.
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic tree. Mol Biol Evol 4, 406-425.
Sawaimul A, Sahare M, Ali S et al. (2014) Assessment of genetic variability among Indian sheep breeds using mitochondrial DNA cytochrome-b region. Vet World 7, 852-855.
Sayers EW, Barrett T, Benson DA et al. (2011) Database resources of the national center for biotechnology information. Nucleic Acids Res 39, 38-51.
Shamsalddini S, Mohammadabadi MR, Esmailizadeh AK (2016). Polymorphism of the prolactin gene and its effect on fiber traits in goat. Russ J Genet 52(4), 461-465.
Shojaei M, Mohammad Abadi MR, Asadi Fozi M et al. (2010). Association of growth trait and Leptin gene polymorphism in Kermani sheep. J Cell Mol Res 2, 67-73.
Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690.
Sultana S, Mannen H, Tsuji S (2003) Mitochondrial DNA diversity of Pakistani goats. Anim Genet 34, 417-421.
Takada T, Kikkawa Y, Yonekawa H et al. (1997) Benzor (C . aegagrus) is a matriarchal candidate for ancestor of domestic goat (C. hircus): evidence from the mitochondrial DNA diversity. Biochem Genet 35, 315-326.
Tamura K, Stecher G, Peterson D et al. (2013) MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30, 2725-2729.
 Tobe S, Linacre A (2008) A multiplex assay to identify 18 European mammal species from mixtures using the mitochondrial cytochrome b gene. Electrophoresis 29, 340-347.
Tohidi nezhad F, Mohammadabadi MR, Esmailizadeh AK, Najmi Noori A (2015) Comparison of different levels of Rheb gene expression in different tissues of Raini Cashmir goat. Agric Biotechnol J 6, 37-50.
Vajed Ebrahimi MT, Mohammad Abadi MR, Esmailizadeh AK (2016). Analysis of genetic diversity in five Iranian sheep population using microsatellites markers. Agric Biotechnol J 7, 143-158 (In Persian).
Vajed Ebrahimi MT, Mohammad Abadi MR, Esmailizadeh AK (2017). Using microsatellite markers to analyze genetic diversity in 14 sheep types in Iran. Archiv fuer Tierzucht (Arch. Anim. Breed) 60, 183-189
Widayanti R, Agustianti T, Kunda RM, Pakpahan S (2016) Phylogenetic relationship of cuscuses  (Marsupialia: Phalangeridae) from  papua  and maluku based on mitochondrial sequences of  NADH dehydrogenase sub-unit 1 gene. Biotechnology 15, 17-25.
Zamani P, Akhondi M, Mohammadabadi MR (2015) Associations of Inter-Simple Sequence Repeat loci with predicted breeding values of body weight in sheep. Small Rumin Res 132, 123-127.
Zewdu E, Hailu D, Sang-Wook K et al. (2013) Genetic diversity, population structure and relationships in indigenous cattle populations of Ethiopia and Korean Hanwoo breeds using SNP markers. Front Genet 4, 35.
Zhao Y, Zhang J, Zhao E et al. (2011) Mitochondrial DNA diversity and origins of domestic goats in Southwest China (excluding Tibet). Small Ruminant Res 95, 40-47.