شناسایی تنوع ژنوم در مرغ مرندی با استفاده از روش توالی یابی کل ژنوم

اسکندری طاهره، اسمعیلی زاده کشکوئیه علی، اسدی فوزی مسعود (1397) ﺷﻨﺎﺳﺎﯾﯽ ﻧﺸﺎﻧﮕﺮﻫﺎی ﺗﮏ ﻧﻮﮐﻠﺌﻮﺗﯿﺪی در ﻣﺮغ ﺑﻮﻣﯽ ﻓﺎرس ﺑﺎ اﺳﺘﻔﺎده از روش ﺗﻮاﻟﯽ ﯾﺎﺑﯽ ﮐﻞ ژﻧﻮم. مجله بیو تکنولوژی کشاورزی 10 (1)، 151-139. 

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 توالی یابی کل ژنوم. مجله ژنتیک نوین 14 (1)، 88-85. 

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.

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. Genomics112, 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. 

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. Genomics 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. J. Bioinform. 27, 2156-2158. 

Eskandari T, Esmailizadeh AK, Mohammadabadi MR, Sohrabi S (2018) Identification of single nucleotide polymorphisms in Fars native chicken using whole genome sequencing data. J. Agric. Biotech 10, 139-151 (In Persian). 

Fulton JE (2012) Genomic selection for poultry breeding. Anim Front. 2, 30-36. 

Gray IC, Campbell DA, Spurr NK (2000) Single nucleotide polymorphisms as tools in human genetics. Hum. Mol. Genet 9, 2403-2408. 

Guo Y, Li J, Li CI et al. (2012) The effect of strand bias in Illumina short-read sequencing data. BMC Genomics 13, 666.

Hillel J, Granevitze Z, Twito T et al. (2007) Molecular markers for the assessment of chicken biodiversity. World Poult SCI J 63, 33-45. 

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. 

Kijowski J, Niewiarowicz A (1978) Emulsifying properties of proteins and meat from broiler breast muscles as affected by their initial pH values. J Food Technol 13, 451-459. 

Kilian B, Graner A (2012) NGS technologies for analyzing germplasm diversity in genebanks. Brief Funct Genomics 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. J. Bioinform 25, 1754-1760. 

Li H, Handsaker B, Wysoker A et al. (2009) The sequence alignment/map format and sam tools. J. Bioinform 25, 2078-2079. 

Lin BZ, SasazaKi S, Mannen H (2018) Genetic diversity and structure in Bos taurus and Bos indicus populations analyzed by SNP markers. Ani Sci J 81, 281-289. 

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. 

Moazeni S, Mohammadabadi MR, Sadeghi M et 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. 

Mohammadabadi MR, Nikbakhti M, Mirzaee HR et al. (2010) Genetic variability in three native Iranian chicken populations of the Khorasan province based on microsatellite markers. Russ J Genet 46, 505-509. 

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. J. Agric. Biotech 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. 

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.

Ryman N, Utter F, Laikre L (1995) Protection of intraspecific biodiversity of exploited fishes. Rev Fish Biol Fish 5, 417–446. 

Sawai H, Kim HL, Kuno K et al. (2010) The Origin and Genetic Variation of Domestic Chickens with Special Reference to Junglefowls Gallus g. gallus and G. varius. PLoS One 5, e10639.  

Shahdadnejad N, Mohammadabadi MR, Shamsadini M (2016) Typing of Clostridium Perfringens Isolated from Broiler Chickens Using Multiplex PCR. Genet the 3rd millennium 14, 4. 

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, 559-570. 

Suh Y, Vijg J (2005) SNP discovery in associating genetic variation with human disease phenotypes. Mutat Res. 573, 41-53. 

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.