The Genetic and Phylogenetic Analysis of the D-Loop Region in Mitochondrial Genome of Najdi Goat

Document Type : Research Paper

Authors

1 M.S. graduate of Animal genetic and Breeding

2 Professor, Department of Animal Science, Faculty of Animal science and Food Technology, Agricultural Science and Natural Resources University of Khuzestan, Ahvaz, Iran

3 Assistant Professor, Department of Venomous Animals and Anti-venom Production, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Ahvaz, Iran.

Abstract

Objective
The analysis of mitochondrial DNA has been a potent tool in our understanding of evolution, owing to characteristics such as high copy number, apparent lack of recombination, high substitution rate and maternal mode of inheritance. This study aims to carry outgenetic and phylogenetic analysis on the D-Loop region of the mitochondrial genome in Najdi goats and to evaluate the relations between Najdi goats and other goat breeds available in Iran and around the world.
 
Materials and methods
12 blood samples from unrelated Najdi goats from various areas of Khuzestan Province were collected. After extraction of DNA, a 968 nucleotide fragment of the D-loop region of the mitochondrial genome was amplified and sequenced. Then, the fragments were compared to the other breeds submitted in NCBI database. Finally, a phylogenetic tree was constructed using MEGA6 software.
 
Results
The results showed that the Najdi goat breed classified into A Haplogroup and has the lowest genetic distance with the breeds of Chinese and Pakistani goats. The results of genetic variation led to the identification of 20 mutations with 5 Haplotypes in Najdi goat population. Moreover, the haplotype, nucleotide diversities and the average number of pairwise differences were estimated as 0.727, 0.009 and 0.540, respectively; which indicates a high diversity in the Nadji goat. The results obtained from Tajima's D show that in the population of the Najdi goat, a balanced natural selection is going on and the frequency of rare alleles in this population is very low.
 
Conclusions
The genetic diversity of Najdi goats has increased over the years, while the number of livestock in Khuzestan province has decreased. The increase in genetic diversity could be due to crossbreed of this breed with Pakistani breeds and so on. The result of these crossbreeding in the near future will be the extinction of Najdi goats, and this issue requires more attention from the authorities.

Keywords

References

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، 50-35.
جوانروح علی آبادی علی، اسماعیل خانیان سعید، دین پرست نوید، واعظ ترشیزی رسول (1383) تنوع ژنتیکی شش توده بز بومی ایران با استفاده از نشانگرهای RAPD. پژوهش و سازندگی 64 ، 17-12.
روحی پور مرضیه، نظری محمود، بیگی نصیری محمدتقی (1398) تجزیه و تحلیل ژنتیکی و فیلوژنتیکی بز عدنی بر اساس ژن سیتوکروم b. پژوهشهای تولیدات دامی 10، 89-84.
عسکری ناهید، محمدآبادی محمدرضا، بیگی نصیری محمدتقی، باقی زاده امین، فیاضی جمال (1387) مطالعه تنوع ژنتیکی بز کرکی رائینی بر اساس نشانگرهای ریزماهواره. مجله دانش کشاورزی 18، 161-155.
عسکری ناهید، باقی زاده امین، محمدآبادی محمدرضا (1389) بررسی تنوع ژنتیکی در چهار جمعیت بز کرکی رائینی با استفاده از لوکوس های بین ریزماهواره(ISSR). فصلنامه ژنتیک نوین 5، 56-49.
علی نقی زاده روح الله، محمدآبادی محمدرضا، زکی زاده سونیا (1389) چند شکلی اگزون 2 ژن BMP15 در بز سرخ جبال بارز. مجله بیوتکنولوژی کشاورزی 2، 80-69.
کریمی عوری وحیده، هدایت ایوریق نعمت، سیدشریفی رضا، نیک بین سعید (1396) بررسی ساختار ژنتیکی و تجزیه فیلوژنتیکی جمعیت بز خلخالی با استفاده از ژنوم میتوکندری. فصلنامه ژنتیک نوین 12، 227-217.
محمدی پسته بیگ فاطمه، پیرانی نصرالله، شجاع جلیل، محمد هاشمی آرزو (1390) تعیین توالی بخش HVS-I از ناحیه D-Loop ژنوم میتوکندری جمعیتی از مرغ بومی مرندی و ترسیم رابطه فیلوژنی آن با سایر مرغان اهلی. فصلنامه پژوهش های علوم دامی 21، 9-1.
محمدی غزال، نظری محمود، محمدآبادی محمد، حیدری راضیه (1398) آنالیز ژنتیکی و فیلوژنتیکی ناحیه HVR1 میتوکندری در سه نژاد گوسفند ایرانی. فصلنامه ژنتیک نوین 14، 217-209.   
محمدآبادی محمدرضا (1391) ارتباط چند شکلی ژن 3IGFBP  با مقدار تولید کرک در بز کرکی راینی. فصلنامه ژنتیک نوین 7، 120-115.
مقدس زاده محبوبه، محمدآبادی محمد، اسمعیلی زاده کشکوئیه علی (1395) چند شکلی اگزون 2 ژن BMP15 و ارتباط آن با چندقلوزایی در بز کرکی راینی. مجله ژنتیک در هزاره سوم 13، 4067-4062.
نبی حسنی محمد، اسدی فوزی مسعود، اسمعیلی زاده علی، محمدآبادی محمدرضا (1389) تجزیه ژنتیکی صفات رشد در بز کرکی رائینی با استفاده از مدل حیوانی چند متغیره. مجله علوم دامی ایران 41، 329-323.
References
Alinaghizadeh R, Mohammad Abadi MR, Zakizadeh S (2010) Exon 2 of BMP15 gene polymorphismin Jabal Barez Red Goat. Agric Biotec J 2, 69-80 (In Farsi).
Askari N, Mohammadabadi MR, Beygi Nassiry MT, Baghizadeh A and Fayazi J (2009) Study of Genetic Diversity of Raeini Cashmere Goat Based on Microsatellite Markers. J. Agric. Sci 18, 155-161 (In Farsi).
Askari N, Baghizadeh A and Mohammadabadi MR (2010) Study of genetic diversity in four populations of Raeini Cashmere goat using ISSR markers. Mod Gene J 5, 49-56 (In Farsi).
Askari N, Mohammadabadi MR and Baghizadeh A (2011) ISSR markers for assessing DNA polymorphism and genetic characterization of cattle, goat and sheep populations. Iranian J. Biotec 9, 222-229.
Baca M, Molak M (2008) Research on ancient DNA in the Near East. Bioarc Near East 39-61.
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. American-Eurasian J. Agric Envir Sci 6, 454-459.
Barazandeh A, Moghbeli SM, Vatankhah M and Mohammadabadi MR (2012) Estimating non-genetic and genetic parameters of pre-weaning growth traits in Raini Cashmere goat. Trop Anim Hfalth Pro 44, 811-817.
Colli L, Lancioni H, Cardinali I, Olivieri A, Capodiferro MR,  Pellecchia M, Rzepus M, Zamani W, Naderi S, Gandini F, Vahidi SM, Agha S, Randi E, Battaglia V, Sardina MT, Portolano B, Rezaei HR, Lymberakis P, Boyer F, Coissac E, Pompanon F, Taberlet P, Ajmone Marsan P and Achilli A (2014). Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability. BMC Gen 16, 1115
Chen SY, Su YH, Wu SF et al. (2005) Mitochondrial diversity and phylogeographic structure of Chinese domestic goats. Mole Phylogen Evol 37, 804–814.
Chen S, Fan B, Liu B, Yu M et al. (2006) Genetic variations of 13 indigenous Chinese goat breed based on cytochrome b gene sequences. Biochem Genet 44, 87-97.
Colombo F, Marchisio E, Pizzini A, Cantoni C (2002) Identification of the goose species (Anser ancer) in Italian mortara salami by DNA sequencing and a polymerase chain reaction with an original primer pair. Meat Sci 61, 261-294.
Doro MG, Piras D, Leoni GG et al. (2014) Phylogeny and patterns of diversity of goat mtDNA haplogroup A revealed by resequencing complete mitogenomes. PLoS One 9, e95969.
Fernandez H, Taber let P, Mashkour M et al. (2005) Assessing the origin and diffusion of domestic goats using ancient DNA. Paper presented at the first steps of animal domestication: new archaezoological approaches. Proceedings of the 9th conference of the international council of Archaeozoology, Durham, August 2005.
Gorkhali N (2014) Mitochondrial DNA diversity in Npalese goats. 10th World congress on Genetic Applied to livestock Production 14, 940-945.
Hall TA (1999) BioEdit: A user friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl Acids Symp Ser 41, 95-98.
Haji Seyyed Javadi SMM, Javadi MA, Abazi M, Ehbali M (2009) Atlas of sheeps and goats breeds of the Iran and World. Sarva Publishers. Tehran. Iran. 152P.
Javanrouh Aliabad A, Esmaeilkhanian S, Dinparast N and Vaez Tarshizi R (2004) Genetic variation among six Iranian goat breeds using RAPD markers. Pajouhesh Sazandegi 64, 12-17 (In Farsi).
Joshi MB, Rout PK, Mandal AK et al. (2004) Phylogeography and origin of Indian domestic goats. Mol Bio Evo 21, 454-462.
Karimi V, Hedayat Evrigh N, Seyed Sharifi R, Nikbin S (2017) Investigation of genetic structure of Khalkhali goat using mitochondrial genome. Mod Gen J 12, 217-227 (In Farsi).
Kim KH, Lee JH (2002) Phylogenic relationships of Asian and European pig breed determined by mitochondrial DNA D-loop sequence polymorphism. Anim Gen 33, 19-25.
Luikart G, Gielly L, Excoffier L et al. (2001) Multiple maternal origins and weak phylogeographic structure in domestic goats. Proceedings of the National Academy of Sciences 98, 5927-5932.
Lu G, and Moriyama E (2004) "Vector NTI, a balanced all-in-one sequence analysis suite". Brief. Bioinformatics 5, 378–388.
Mazdarani F, Akbari M, fard R et al. (2014) Molecular identification of Capra hircus in east China Sabz, an Iranian pre-pottery Neolithic site, central Zagros, based on mtDNA. J Anim Plant sci 24, 945-950.
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 (In Farsi).
Mohammadabadi MR (2012) Relationships of IGFBP-3 gene polymorphism with cashmere traits in Raini Cashmere goat. Mod Gen J 7, 115-120 (In Farsi).
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.
Mohammadi G, Nazari M, Mohammadabadi MR, Heidari R (2020) Genetic and phylogenetic analysis of mitochondrial HVR1 region in three breeds of Iranian sheep. Mod Gen J 14, 209-217.
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, 1519-1524.
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 (In Farsi).
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, e 1012.
Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford university press.
Odahara S, Chung H, Choi S et al. (2006) Mitochondrial DNA diversity of Korean native goats. Asian Australian J Anim Sci 19, 482-485.
Porter v (1996). Goats of the world, farming press, Ipswich, UK. 12
Reicher S, Seroussi E, Weller JI et al. (2012) Ovine mitochondrial DNA sequence variation and its association with production and reproduction traits within an Afec-Assaf flock. J Anim 90, 2084-2091.
Rohipoor M, Nazari M ,Beigi Nassiri M.T (2020). Genetic and Phylogenetic Analysis of Adani Goat Population Based on Cytochrome B Gene. Res Anim Pro 10, 84-89 (In Farsi).
Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC et al. (2017) DnaSP 6: DNA Sequence Polymorphism Analysis of Large Datasets. Molr Bio Evo 34, 3299-3302.
Seyedabadi HR, Pahlevan Afshari, K, Abdolmaleki M (2016) The genetic characteristics of Marghos goat based on Cytochrome B gene. Iran. J. Appl. Anim. Sci 6, 679-684.
Shamsalddini S, Mohammadabadi MR , Esmailizadeh AK (2016) Polymorphism of the prolactin gene and its effect on fiber traits in goat. Russ J Genet 52, 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.
Sultana S, Mannen H, Tsuji S (2003) Mitochondrial DNA diversity of Pakistani goats. Anim Genet 34, 417–421.
Tamura K, Stecher G, Peterson D et al. (2013) MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Bio Evo 30, 2725-2729.
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. Biocatal. Agric. Biotechnol 6, 35-50 (In Farsi).
Vahidi SM, Tarang AR, Naqvi A et al. (2014). Investigation of the genetic diversity of domestic Capra hircus breeds reared within an early goat domestication area in Iran Genet Selec Evo 46, 27
Vajed Ebrahimi MT, Mohammad Abadi MR, Esmailizadeh AK (2016) Analysis of genetic diversity in five Iranian sheep population using microsatellites markers. J Agric Biotechnol 7, 143-158.
Vajed Ebrahimi MT, Mohammad Abadi MR, Esmailizadeh AK (2017) Using microsatellite markers to analyze genetic diversity in 14 sheep types in Iran. Arch Anim Breed 60, 183-189.
Wallce DC (1992). Mitochondrial genetics: a paradigm for aging and degenerative diseases. Sci 256, 628-632.
Xingbo Z, Mingxing C, Ning L, Changxin W (2000) Parternal inheritance of mitochondrial DNA in the sheep. Sci China 44, 321-326.
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.
Agricultural Biotechnology Journal
Volume 12, Issue 3
November 2020
Pages 45-66

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