مقایسه روش های مختلف لایه بندی جمعیتی گاوهای سرابی و نجدی با استفاده از نشانگرهای ژنتیکی متراکم

منابع

بحرینی بهزادی محمدرضا، امینی علی، اسلمی­نژاد علی­اصغر ، طهمورث­پور مجتبی (1392) برآورد پارامترهای ژنتیکی صفات تولیدی گاوهای شیری هولشتاین ایران. تحقیقات دامداری توسعه روستایی 25(9)، 24-21.

توکلیان جواد (1377) ذخائر ژنتیکی دام و طیور بومی ایران ص 27-4.

خراتی­کوپایی حامد، محمدآبادی محمدرضا و همکاران (1390) تغییرات ژنتیکی ژن DGAT1 و ارتباط آن با تولید شیر در جمعیت گاو هولشتاین ایران. مجله علمی پژوهشی ایران 3(2)، 192-185 .

خراتی­کوپایی حامد، محمدآبادی محمدرضا، ترنگ علی­رضا و همکاران (1391) بررسی ارتباط بین تغییرات آلل ژن DGAT1 با ورم پستان در گاوهای هولشتاین ایران. مجله ژنتیک نوین 7(1)، 101-104.

رحمانی­نیا جواد، میرائی­آشتیانی سیدرضا، مرادی شهرباباک حسین (1394) تجزیه و تحلیل خوشه­ای بدون نظارت ساختار جمعیت و زیرجمعیت با استفاده از نشانگرهای SNP متراکم. مجله علوم دامی ایران 3(46)، 877-277.

رحمانی­نیا جواد، میرائی­آشتیانی سیدرضا، مرادی شهربابک حسین (1394) تنوع ژنتیکی و ساختار جمعیتی گاومیش­های ایران با استفاده از نشانگرهای متراکم SNP. رساله دکترا. ص 120-114.

علینقی­زاده روح­الله، محمدآبادی محمدرضا، زکی­زاده سونیا (1389) چند شکلی اگزون 2 ژن BMP15 در بز قرمز جبال بارز. مجله بیوتکنولوژی کشاورزی 2(1)،80-69.

محمدآبادی محمدرضا، محمدی اکرم (1389) بررسی ژنوتیپ­های بتا لاکتوگلوبولین در گاوهای بومی و هولشتاین استان کرمان. مجله تولیدات دامی 12(2)، 67-61 .

محمدی اکرم ، محمدآبادی محمدرضا، میرزایی حمیدرضا و همکاران (1389) بررسی ژن کاپاکازئین گاوهای شیری بومی و هولشتاین در استان کرمان با استفاده از روش PCR-RFLP . مجله علوم کشاورزی و منابع طبیعی 16(2)132-125.

واجدابراهیمی محمدتقی، محمدآبادی محمدرضا، اسمعیلی­زاده کشکوئیه علی (1396) تجزیه و تحلیل تنوع ژنتیکی در پنج گروه گوسفند ایرانی با استفاده از نشانگرهای ریزماهواره. مجله بیوتکنولوژی کشاورزی 7، 158-143.

هادی­زاده مرتضی، محمدآبادی محمدرضا، نیازی علی و همکاران (1392) استفاده از ابزارهای بیوانفورماتیک برای مطالعه اگزون 2 ژن GDF9 در بز های تالی و بی­تال. مجله ژنتیک نوین 8) 334(، 288-283.

هادی­زاده مرتضی، نیازی علی، محمدآبادی محمدرضا و همکاران (1392) تجزیه و تحلیل بیوانفورماتیک از اگزون 2 ژنBMP15 در بزهای تالی و بی­تال. ژنتیک نوین 9(1)،120-117.

References

Alexander DH, Lange K (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics 12, 246.

Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19, 1655-1664.

Alinaghizadeh H, Mohammadabadi MR, Zakizadeh S (2010) Exon 2 of BMP15 gene polymorphismin Jabal Barez Red Goat. Agric Biotechnol J 2, 69-80 (In Persian).

Barazandeh A, Mohammadabadi MR, Ghaderi M, Nezamabadipour H (2016) Predicting CpG Islands and Their Relationship with Genomic Feature in Cattle by Hidden Markov Model Algorithm. Iran J Appl Anim Sci 6, 571-579.

Behzadi Behzadi MR, Amini A, Slaminejad A, Tahmoorespour M (2013) Estimation of genetic parameters for production traits of Iranian Holstein dairy cattle. Livest Res Rural Develop 25, 21-24 (In Persian).

Bowden R, MacFie TS, Myers S et al. (2012) Genomic tools for evolution and conservation in thechimpanzee: Pan troglodytesellioti is a genetically distinct population. PLOS Genet 8, e1002504.

Brohée S, Faust K, Lima-Mendez G et al. (2008) NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways. Nucleic Acids Res 36, W444-W451.

Decker JE, Pires JC, Conant GC et al. (2009) Resolving the evolution of extant andextinct ruminants with high-throughput phylogenomics. Proceedings of the National Academy of Sciences 106, 18644-18649.

Domany E (2003) Cluster analysis of gene expression data. J Statistical Physics 110, 1117-1139.

Ebrahimi Z, Mohammadabadi MR, Esmailizadeh AK et al. (2015a). Association of PIT1 gene with milk fat percentage in Holstein cattle. Iran J Appl Anim Sci 5, 575-582.

Ebrahimi Z, Mohammadabadi MR, Esmailizadeh AK et al. (2015b) Association of PIT1 gene and milk protein percentage in Holstein cattle. J Livest Sci Technol 3, 41-49.

Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14, 2611-2620.

Faraji-Arough H, Aslaminejad A, Tahmoorespur M et al. (2015) Bayesian Inference of (Co) Variance Components and Genetic Parameters for Economic Traits in Iranian Holsteins via Gibbs Sampling. Iran J Appl Anim Sci 5, 51-60.

Fernández ME, Goszczynski DE, Lirón JP et al. (2013) Comparison of the effectiveness of microsatellites and SNP panels for genetic identification, traceability and assessment of parentage in an inbred Angus herd. Genet Mol Biol 36, 185-191.

Gao X, Starmer J (2007) Human population structure detection via multilocus genotype clustering. BMC Genet 8, 34.

Gautier M, Laloë D, Moazami-Goudarzi K (2010) Insights into the genetic history of French cattle from dense SNP data on 47 worldwide breeds. PloS One 5, e13038.

Getz G, Gal H, Kela I, Notterman DA et al. (2003) Coupled two-way clustering analysis of breast cancer and colon cancer gene expression data. Bioinformatics 19, 1079-1089.

Getz G, Levine E, Domany E (2000a) Coupled two-way clustering analysis of gene microarray data. Proceedings of the National Academy of Sciences 97, 12079-12084.

Getz G, Levine E, Domany E et al. (2000b) Super-paramagnetic clustering of yeast gene expression profiles. Physica A: Statistic Mechanic Appl 279, 457-464.

Ghasemi M, Baghizadeh A, Abadi MRM (2010) Determination of genetic polymorphism in Kerman Holstein and Jersey cattle population using ISSR markers. Australian J Basic Appl Sci 4, 5758-5760

Hadizadeh M, Mohammadabadi MR, Niazi A et al. (2013) Use of bioinformatics tools to study exon 2 of GDF9 gene in Tali and Beetal goats. Modern Genet J 8, 283-288 (In Persian).

Hadizadeh M, Niazi A, Mohammadabadi MR et al. (2014) Bioinformatics analysis of the BMP15 exon 2 in Tali and Beetal goats. Modern Genet J 9, 117-120 (In Persian).

Heaton MP, Keen JE, Clawson ML et al. (2005) Use of bovine single nucleotide polymorphism markers to verify sample tracking in beef processing. J Am Vet Med Assoc 226, 1311-1314.

Holmström E, Bock N, Brännlund J (2009) Modularity density of network community divisions. Physica D: Nonlinear Phenomena 238, 1161-1167.

Karimi K, Strucken Eva M, Moghaddar N et al. (2016) Local and global patterns of admixture and population structure in Iranian native cattle. BMC Genet 17, 108.

Karimi K, Beigi Nassiri MT, Mirzadeh Kh et al. (2009) Polymorphism of the β-lactoglobulin gene and its association with milk production traits in Iranian Najdi cattle. Iran J Biotchnol 7, 82-85.

Khansefid SM (2009) An introduction to Sarabi cow breed a vernacular cow breed of Iran. Nolan Special Magazine on Dairy cows. No3/Jan-Mar.

Kharrati Koopaei H, Mohammadabadi MR, Ansari.Mahyari S et al. (2012a) Effect of DGAT1 variants on milk composition traits in Iranian Holstein cattle population. Anim Sci Paper Report 30, 231-240

Kharrati Koopaei H, Mohammadabadi MR, Ansari Mehyari S et al. (2011) Genetic Variation of DGAT1 Gene and its Association with Milk Production in Iranian Holstein Cattle Breed Population. Iran J Anim Sci Res 3, 185-192 (In Persian).

Kharrati Koopaei H, Mohammadabadi MR, Tarang A et al. (2012b) Study of the association between the allelic variations in DGAT1 gene with mastitis in Iranian Holstein cattle. Modern Genet J 7, 101-104 (In Persian).

Kijas JW, Lenstra JA, Hayes B et al. (2012) Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection. Plos-Biol 10, 331.

Kijas JW, Townley D, Dalrymple BP et al. (2009) A genome wide survey of SNP variation reveals the genetic structure of sheep breeds. PloS One 4, e4668.

Lee C, Abdool A, Huang CH (2009) PCA-based population structure inference with generic clustering algorithms. BMC Bioinformatics 10, S73.

Levy M, Feingold J (2000) Estimating prevalence in single-gene kidney diseases progressing to renal failure. Kidney International 58, 925-943.

Li Q, Yu K (2008) Improved correction for population stratification in genome‐wide association studies by identifying hidden population structures. Genet Epidemiol 32, 215-226.

Lirón J, Ripoli M, De Luca J et al. (2002) Analysis of genetic diversity and population structure in Argentine and Bolivian Creole cattle using five loci related to milk production. Genet Mol Biol 25, 413-419.

Markovtsova L, Marjoram P, Tavaré S (2000) The age of a unique event polymorphism. Genet 156, 401-409.

Marquitti FMD, Guimarães PR, Pires MM, Bittencourt LF (2014) MODULAR: software for the autonomous computation of modularity in large network sets. Ecography 37, 221-224.

Meuwissen T, Solberg TR, Shepherd R, Woolliams JA (2009) A fast algorithm for BayesB type of prediction of genome-wide estimates of genetic value. Genet Sel Evol 41, Doi: 10.1186/1297-9686-41-2.

Mohammadabadi MR, Mohammadi A (2010) Study of beta-lactoglobulin genotypes in native and Holstein cattle of Kerman province. J Anim Prod 12, 61-67 (In Persian).

Mohammadabadi MR (2017) Role of clostridium perfringens in pathogenicity of some domestic animals. Journal Adv Agric 7, 1117-1121.

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 A, Mohammadabadi MR, Mirzaei H et al. (2009) Study of Kappa Casein gene of local and Holstein dairy cattle in Kerman province using PCR-RFLP method. J Agric Sci Natural Resources 16, 125-132 (In Persian).

Morin PA, Luikart G, Wayne RK (2004) SNPs in ecology, evolution and conservation. Trends Ecol Evol 19, 208-216.

Neuditschko M, Khatkar MS, Raadsma HW (2012) NetView: A High-Definition Network-Visualization Approach to Detect Fine-Scale Population Structures from Genome-Wide Patterns of Variation. PloS One 7, e48375.

Newman ME, Girvan M (2004) Finding and evaluating community structure in networks. Phys Rev 69, 026113.

Ojango J, Pollott G (2001) Genetics of milk yield and fertility traits in Holstein-Friesian cattle on large-scale Kenyan farms. J Anim Sci 79, 1742-1750.

Pasandideh M, Mohammadabadi MR, Esmailizadeh AK, Tarang A (2015) Association of bovine PPARGC1A and OPN genes with milk production and composition in Holstein cattle. Czech J Anim Sci 60, 97-104.

Paschou P, Ziv E, Burchard EG, Choudhry S et al. (2007) PCA-correlated SNPs for structure identification in worldwide human populations. PLoS Genet 3, e160.

Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genet 155, 945-959.

Purcell S, Neale B, Todd-Brown K et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81, 559-575.

Radjiman & Sugiarto (2005) Super Paramagnetic Clustering of DNA Sequences. Master of Science dissertation. National University of Singapore.

Rahmanienia J, Miri Ashtiani SR, Moradi Shahrbabak H (2015a) Unsupervised clustering analysis of population and subpopulation structure using dense SNP markers. Iran J Anim Sci 46, 287-277 (In Persian).

Rahmanienia J, Miriya Ashtiani R, Moradi Shahrbabak H (2015b) Genetic diversity and demographic structure of Iranian buffaloes using dense SNP markers. Ph.D. thesis p. 120-114 (In Persian).

Sargolzaei M, Schenkel FS (2009) QMSim: a large-scale genome simulator for livestock. Bioinform 25, 680-681.

Seo TK, Thorne JL, Hasegawa M, Kishino H (2002) Estimation of effective population size of HIV-1 within a host: a pseudomaximum-likelihood approach. Genet 160, 1283-1293.

Serre D, Montpetit A, Paré G et al. (2008) Correction of population stratification in large multi-ethnic association studies. PloS One 3, e1382.

Shannon P, Markiel A, Ozier O et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13, 2498-2504.

Tang H, Peng J, Wang P, Risch NJ (2005) Estimation of individual admixture: analytical and study design considerations. Genet Epidemiol 28, 289-301.

Tavakkolian J (2000) Genetic Resources of Native Farm Animals in Iran. P. 4-27 (In Persian).

Tetko IV, Facius A, Ruepp A, Mewes HW (2005) Super paramagnetic clustering of protein sequences. BMC Bioinform 6, 82.

Troy CS, MacHugh DE, Bailey JF et al. (2001) Genetic evidence for Near-Eastern origins of European cattle. Nature 410, 1088-1091.

Tsafrir D, Tsafrir I, Ein-Dor L et al. (2005) Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices. Bioinform 21, 2301-2308.

Tsepilov YA, Ried JS, Strauch K et al. (2013) Development and application of genomic control methods for genome-wide association studies using non-additive models. Plos One 8, e81431.

Uzzaman MR, Edea Z, Bhuiyan MSA et al. (2014) Genome-wide Single Nucleotide Polymorphism Analyses Reveal Genetic Diversity and Structure of Wild and Domestic Cattle in Bangladesh. Asian-Australas J Anim Sci 27, 1381.

Vahidi SM, Tarang AR, Naqvi AU et al. (2014) Investigation of the genetic diversity of domestic Capra hircus breeds reared within an early goat domestication area in Iran. Genet Sel Evol 46, 27.

Vajed Ebrahimi MT, Mohammadabadi 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, Mohammadabadi MR, Esmailizadeh AK (2017) Using microsatellite markers to analyze genetic diversity in 14 sheep types in Iran. Archiv fuer Tierzucht (Archives Anim Breed) 60, 183-189.

Verdu P, Pemberton TJ, Laurent R et al. (2014) Patterns of admixture and population structure in native populations of Northwest North America. Plos Genet 10, e1004530.

Wang D, Sun Y, Stang P et al. (2009) Comparison of methods for correcting population stratification in a genome-wide association study of rheumatoid arthritis: principal-component analysis versus multidimensional scaling, BMC proceedings, BioMed Central 3, S109.

Wang DG, Fan JB, Siao CJ et al. (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Sci 280, 1077-1082.

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.