اسکندری طاهره، اسمعیلی زاده کشکوئیه علی، اسدی فوزی مسعود (1397) ﺷﻨﺎﺳﺎﯾﯽ ﻧﺸﺎﻧﮕﺮﻫﺎی ﺗﮏ ﻧﻮﮐﻠﺌﻮﺗﯿﺪی در ﻣﺮغ ﺑﻮﻣﯽ ﻓﺎرس ﺑﺎ اﺳﺘﻔﺎده از روش ﺗﻮاﻟﯽﯾﺎﺑﯽ ﮐﻞ ژﻧﻮم. مجله بیو تکنولوژی کشاورزی 10 (1)، 151-139.
اکبری رسول، اسمعیلی زاده کشکوئیه علی، امیری قنات سامان زینب، آیت اللهی مهجردی احمد (1399) شناسایی تنوع ژنوم در مرغ مرندی با استفاده از روش توالییابی کل ژنوم. مجله بیو تکنولوژی کشاورزی 12 (1)، 161-176.
امیری قنات سامان زینب، اسمعیلی زاده کشکوئیه علی، اسدی فوزی مسعود (1395) بررسی تنوع ساختاری ژنگان سگ و گرگ بومی ایران با روش توالییابی کل ژنوم. مجله علوم دامی ایران 47 (2)، 271-277.
امیری قنات سامان زینب، اسمعیلی زاده کشکوئیه علی، اسدی فوزی مسعود (1398) شناسایی ایندلها در ژنوم سگ و گرگ بومی ایران با روش توالییابی کل ژنوم. مجله ژنتیک نوین 14 (1)، 88-85.
بازگیر حمیده (1396) نقشه یابی نشانگرهای تک نوکلئوتیدی در مرغ نژاد لاری با استفاده از توالی یابی ژنوم. پایان نامه کارشناسی ارشد، دانشگاه شهید باهنر کرمان. 20-15.
نصیری محمد رضا، رودباری زهرا (1393) تجزیه و تحلیل ناحیه سیتوکروم b در مرغ بومی خراسان. مجله بیوتکنولوژی کشاورزی 6(2)، 189-198.
محمدی فر آمنه، فقیه ایمانی سید علی، محمد آبادی محمد رضا، سفلایی محمد (1392) تاثیر ژن TGFB3 بر ارزشهای فنوتیپی و ارثی صفات وزن بدن در مرغ بومی فارس. مجله بیوتکنولوژی کشاورزی 5 (4)، 125-136.
References
Abadi MRM, Askari N, Baghizadeh A, Esmailizadeh AK (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, 146-151.
Akbary R, Esmaeelizadeh A, Amiri Ghanatsaman Z, Ayetollahi Mehrjerdi A (2020) Identification of genome diversity in marandi chicken using whole genome sequencing method. Agric Biotech J 12,161-176 (In Persian).
Alkan C, Coe BP, Eichler EE (2011) Genome structural variation discovery and genotyping.. Nat Rev Genet 12, 363-376.
Amiri Ghanatsaman Z, Esmailizadeh Koshkoiyeh A, Asadi Fozi M (2016) Study of structural diversity of genome Iranian native dog and wolf with the method whole genome sequencing. Iran J Anim Sci 47, 271-277 (In Persian).
Amiri Ghanatsaman Z, Esmailizadeh Koshkoiyeh A, Asadi Fozi M (2019) Detection of deletions and insertions in genome of Iranian dogs and wolves with the method whole genome sequencing. Mod Genet 14, 85-88 (In Persian).
Asadollahpour Nanaei H, Dehghani Qanatqestani M, Esmailizadeh A (2020) Whole-genome resequencing reveals selection signatures associated with milk production traits in African Kenana dairy zebu cattle. Genomics 112, 880-5.
Bainbridge MN, Wang M, Wu Y et al. (2011) Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities. Genome Biol 12, 68.
Bazgir H (2017) Mapping of single nucleotide markers in Lari chickens using genome sequencing. Master of Science Thesis, Shahid Bahonar University of Kerman. Kerman, Iran. Pp. 15-20 (In Persian).
Buysse K, Delle Chiaie B, Van Coster R et al. (2009) Challenges for CNV interpretation in clinical molecular karyotyping: lessons learned from a 1001 sample experience. Eur J Med Genet 52, 398-403.
Cingolani P, Platts A, Wang LL et al. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, snpeff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6, 80-92.
Collins DW, Jukes TH (1994) Rates of transition and transversion in coding sequences since the human-rodent divergence. Genomic 20, 386-396.
Da Silva JM, Giachetto PF, da Silva LOC et al. (2015) Genomic variants revealed by invariably missing genotypes in Nelore cattle. Plos One 10, 0136035.
Danecek P, Auton A, Abecasis G et al. (2011) The variant call format and vcftools. Bioinformatic 27, 2156-2158.
Deng J, Xie XL, Wang DF et al. (2020) Paternal origins and migratory episodes of domestic sheep. Curr Biol 30, 4085-4095.
Dohner, J.V. (2001) The encyclopedia of endangered livestock and poultrybreeds. New Haven (CT): Yale University Press.
Engelsma KA, Veerkamp RF, Calus MPL, Windig JJ (2011) Consequences for diversity when prioritizing animals for conservation with pedigree or genomic information. J Anim Breed Genet 128, 473–481.
Eskandari T, Esmailizadeh AK, Mohammadabadi MR, Sohrabi S (2018) Identification of single nucleotide polymorphisms in Fars native chicken using whole genome sequencing data. Agric Biotech J 10, 139-151 (In Persian).
Gray IC, Campbell DA, Spurr NK (2000) Single nucleotide polymorphisms as tools in human genetics. Hum Mol Genet 9, 2403-2408.
Groeneveld LF, Lenstra JA, Eding H et al. (2010) Genetic diversity in farm animals- a review. Anim Genet 41, 6-31.
Guo Y, Li J, Li CI et al. (2012) The effect of strand bias in Illumina short-read sequencing data. BMC Genomics 13(1), 666.
Karimi K, Strucken EM, Moghaddar N et al.(2016) Local and global patterns of admixture and population structure in Iranian native cattle. BMC Genet, 17:108.
Kerstens HHD, Crooijmans RPMA, Veenendaal A et al. (2009) Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey. BMC Genomics, 10: 479-10.
Kilian B, Graner A (2012) NGS technologies for analyzing germplasm diversity in genebanks. Brief Funct Genom. 11, 38-50.
Li D, Li Y, Li M et al. (2019) Population genomics identifies patterns of genetic diversity and selection in chicken. BMC genomics 20, 263.
Li G, Ma L, Song C et al. (2009) The YH database: the first Asian diploid genome database. Nucleic Acids Res. 37, 1025-1028.
Li H, Durbin R (2009) Fast and accurate short read alignment with burrows–wheeler transform. Bioinformatics 25, 1754-1760.
Li H, Handsaker B, Wysoker A et al. (2009) The sequence alignment/map format and sam tools. Bioinformatics 25, 2078-2079.
McKenna A, Hanna M, Banks E et al. (2010) The genome analysis toolkit, a mapreduce frame work for analyzing next-generation dna sequencing data. Genome Res 20, 1297-1303.
Metzker ML (2010) Sequencing technologies - the next generation. Nat Rev Genet 11, 31-46.
Moazeni S, Mohammadabadi MR, Sadeghi Met al. (2016a) Association between UCP Gene Polymorphisms and Growth, Breeding Value of Growth and Reproductive Traits in Mazandaran Indigenous Chicken. Open J Anim Sci 6, 1-8.
Moazeni SM, Mohammadabadi MR, Sadeghi M et al. (2016b) Association of the melanocortin-3(MC3R) receptor gene with growth and reproductive traits in Mazandaran indigenous chicken. J Livest Sci Technol 4, 51-56.
Mohammadifar A, Faghih Imani SA, Mohammadabadi MR, Soflaei M (2014) The effect of TGFb3 gene on phenotypic and breeding values of body weight traits in Fars native fowls. Agric Biotech J 5, 125-136 (In Persian).
Mohammadifar A, Mohammadabadi MR )2017( The Effect of Uncoupling Protein Polymorphisms on Growth, Breeding Value of Growth and Reproductive Traits in the Fars Indigenous Chicken. Iran. J Appl Anim Sci 7, 679-685.
Moradian H, Koshkoiyeh AE, Mohammadabadi M, Fozi MA (2020) Whole genome detection of recent selection signatures in Sarabi cattle: a unique Iranian taurine breed. Genes Genom 42(2), 203-215.
Nassiri MR, Roudbari Z (2014) Genetic analysis of cytochrome b region in native chicken of Khorasan. Agric Biotech J 6,189-198 (In Persian).
Nosrati M, Asadollahpour Nanaei H, Amiri Ghanatsaman Z, Esmailizadeh A (2019) Whole genome sequence analysis to detect signatures of positive selection for high fecundity in sheep. Reprod Domest Anim 54, 358-64.
Ramos AM, Crooijmans RPMA, Affara NA et al. (2009) Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology. PLoS One 4, e6524.
Ruiz-Larrañaga O, Nanaei HA, Montes I et al. (2020) Genetic structure of Iranian indigenous sheep breeds: insights for conservation. Trop Anim Health Prod 52, 2283-2290.
Sohrabi SS, Mohammadabadi MR, Wu DD, Esmailizadeh A (2018) Detection of breed-specific copy number variations in domestic chicken genome. Genome 61, 7-14.
Stothard P, Choi J-W, Basu U et al. (2011) Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics 12, 559-10.
Suh Y, Vijg J (2005) SNP discovery in associating genetic variation with human disease phenotypes. Mutat Res 573, 41-53.
Weldenegodguad M, Popov R, Pokharel K et al. (2019) Whole-genome sequencing of three native cattle breeds originating from the northernmost cattle farming regions. Front Genet 9, 728.
You F, Huo N, Deal K et al. (2011) Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. BMC Genomics 12, 59.
Zandi E, Mohammadabadi MR, Ezzatkhah M, Esmailizadeh AK (2014) Typing of Toxigenic Isolates of Clostridium Perfringens by Multiplex PCR in Ostrich. Iran J Appl Anim Sci 4, 509-514.
Zeng L, Tu XL, Dai H et al. (2019) Whole genomes and transcriptomes reveal adaptation and domestication of pistachio. Genome Biol 20, 1-13.
Zhang H, Wang SZ, Wang ZP et al. (2012) A genome-wide scan of selective sweeps in two broiler chicken lines divergently selected for abdominal fat content. BMC Genet 13, 704.