Evaluation of Genetic Potential of Iranian Native Chicken Ecotypes; Insights for Conservation

Document Type : Research Paper

Authors

1 SHIRAZ UNIVERSITY

2 Ph.D. graduated, Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran

Abstract

Objective
Different climates and wide geographical area of Iran have caused considerable genetic diversity in Iranian chicken ecotypes. Artificial selection for genetic gain in economic traits leads to a reduction of genetic diversity in livestock and poultry breeds. On the other hand, by identifying the genetic potential of native ecotypes and managing breeding programs, it is possible to increase productivity in native chicken populations while maintaining genetic diversity. However, so far no genomic study has been performed to identify the genetic characteristics of native chickens. The aim of this study was to identify the genetic potential of Iranian native chicken ecotypes for appropriate targeting of breeding and genetic conservation programs.
 
Materials and methods
In this study, genomic data related to 51 native chicken ecotypes, 11 chickens of Arian line and 10 chickens of Leghorn breed were collected from the department of animal science at Shahid Bahonar University of Kerman. Mapping step against reference genome was done by BWA program. Identification of single nucleotide variants was performed by GTAK software. Phylogenetic analysis was investigated using the neighborhood joining method and Mega software. Fst and inbreeding coefficient among population were performed using Admixture and VCFtools programs.
 
Results
Percentage of alignment against the reference genome was reported between 83% and 95% for all samples and also 14.56 million single nucleotide variants were reported from the native and commercial chicken genomes. The results of phylogenetic tree analysis showed that almost all studied ecotypes were classified into separate groups. According to the reported results, it can be claimed that native chicken ecotypes are more genetically similar to the Arian line (compared to Leghorn breed). Findings obtained from admixture and Fst analysis also confirmed the results of phylogenetic analysis. For example, the highest Fst was estimated as 0.219 between Leghorn breed and Marandi ecotype.
 
Conclusions
Due to the genetic similarity of most native chicken ecotypes and Arian line, breeding programs can be organized based on meat production traits. By targeting breeding programs, genetic resources can be improved to increase productivity while preserving the genetic diversity of native chicken ecotypes.

Keywords


عسکری ناهید؛ باقی زاده امین؛ محمدآبادی محمد رضا (1389) بررسی تنوع ژنتیکی در چهار جمعیت بز کرکی رائینی با استفاده از لوکوس‌های بین ریزماهواره ISSR. فصلنامه ژنتیک نوین 5، 58-49.
جمالپور مهرنسا؛ دادپسند محمد؛ آتشی‌هادی؛ نیازی علی؛ خراتی کوپایی حامد؛‌ هاشمی سیدمحمدرضا (1397) واکاوی بیوانفورماتیکی و فیلوژنی ناحیه 5`UTR ژن نوروپپتید وای ( Neuropeptide Y) و ارتباط آن با صفات تولیدی در مرغ‌ بومی فارس. مجله علوم دامی ایران 49(3)، 458-453.
خراتی کوپایی حامد؛ ابراهیمی اسماعیل؛ دادپسند محمد؛ نیازی علی؛ اسمعیلی زاده علی (1397) شناسایی واریانت‌های ژنتیکی در لاین آرین و بررسی عملکرد آنها با استفاده از توالی یابی کل ژنوم. مجله بیوتکنولوژی کشاورزی (3)10 ، 60-46.
خراتی کوپایی حامد؛ محمد آبادی محمدرضا؛ ترنگ علیرضا؛ خراتی کوپایی محمود؛ اسمعیلی زاده کشکوییه (1391) بررسی ارتباط چند شکلی آللی ژن DGAT1 با بیماری ورم پستان در جمعیت گاو‌های هلشتاین ایران. فصلنامه ژنتیک نوین (1)7، 104-101.
محمدآبادی محمدرضا (1399) پروفایل بیانیmRNA مختص بافت ژن ESR2 در بز. مجله بیوتکنولوژی کشاورزی 12(4)، 184-169.
محمدآبادی محمدرضا؛ اسدالله پور نعنایی حجت (1400) بیان ژن لپتین در بز کرکی راینی با استفاده از Real Time PCR. مجله بیوتکنولوژی کشاورزی 13(1)، 214-197.
محمدی پور سعادت آبادی لیلا ؛ محمدآبادی محمدرضا؛ اسدالله پور نعنائی حجت؛ امیری قنات سامان زینب (1400) معرفی ژن های کاندیدا مرتبط با صفات تولید شیر و پشم در گوسفند. مجله ژنتیک نوین 16(3)، 281-297.
References
Asadollahpour Nanaei H, Kharrati-Koopaee H, Esmailizadeh A (2022) Genetic diversity and signatures of selection for heat tolerance and immune response in Iranian native chickens. BMC Genomics 23, e224.
Askari N, Baghizadeh A, Mohammadabadi MR (2010) Study of genetic diversity in four populations of Raeini cashmere goat using ISSR markers. Modern Genet 5, 49-56 (In Persian).
Albuquerque F, Beier P (2015) Global patterns and environmental correlates of high-priority conservation areas for vertebrates. J Biogeogr 42(8), 1397-1405.
Alkan C, Coe BP, Eichler EE (2011) Genome structural variation discovery and genotyping. Nat Rev Genet 12(5), 363-76.
Esfandiari P, Dadpasand M, Kharrati-Koopaee H et al. (2020) Bioinformatics, phylogenetic and variant association analysis of Ovocalyxin-32 gene reveals its contribution to egg production traits in native chickens. Anim Genet 17-18, e200108.
Jamalpour M, Dadpasand M, Atashi H et al. (2018) Bioinformatics and phylogenetic analysis for 5′ UTR region of neuropeptide Y gene and its association with body weight and egg production traits in Fars native chickens. Iran J Anim Sci 49(3), 453-458 (In Persian).
Kharrati-Koopaee H, Ebrahimie E, Dadpasand M et al. (2019) Genomic analysis reveals variant association with high altitude adaptation in native chickens. Sci Rep 9(1),1-22.
Kharrati-Koopaee H, Ebrahimi E, Dadpasand M et al. (2018) Identification of genetic variants in Arian line and investigation of their performance using whole genome sequencing. Agri Bio J 10(3), 46-60 (In Persian).
Kharrati-Koopaee H, Mohammadabadi MR, Tarang A et al. (2012) Study of the association between the allelic variations in DGAT1 gene with mastitis in Iranian Holstein cattle. Modern Genet 7(1), 101-104 (In Persian).
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 25,754-60.
Masoudzadeh SH, Mohammadabadi M, Khezri A, et al. (2020) Effects of diets with different levels of fennel (Foeniculum vulgare) seed powder on DLK1 gene expression in brain, adipose tissue, femur muscle and rumen of Kermani lambs. Small Rumin Res193, e106276.
Miller SA, Dykes DD, Polesky HF (1988) A simple salting-out procedure for extracting DNA from human nucleated cells. Nucl Acids Res 16, 1215.
Moazeni SM, Mohammadabadi MR, Sadeghi M, Moradi Shahrbabak H, Esmailizadeh AK, Bordbar F (2016) Association between UCP Gene Polymorphisms and Growth, Breeding Value of Growth and Reproductive Traits in Mazandaran Indigenous Chicken. J Anim Sci 6, 1-8.
Mohamadipoor Saadatabadi L, Mohammadabadi M, Amiri Z, Babenko O, Stavetska R, Kalashnik O, Kucher D, Kochuk-Yashchenko O, Asadollahpour Nanaei H (2021) Signature selection analysis reveals candidate genes associated with production traits in Iranian sheep breeds. BMC Vet Res 17 (1), 1-9
Mohammadabadi MR (2021) Tissue-specific mRNA expression profile of ESR2 gene in goat. Agric Biotechnol J 12, 169-184 (In Persian).
Mohammadabadi MR, Asadollahpour Nanaei H (2021) Leptin gene expression in Raini Cashmere goat using Real-Time PCR. Agric Biotechnol J 13, 197-214 (In Persian).
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. 
Mohammadipour SAL, Mohammadabadi M, Asadollahpour Nanaei H, Amiri Z (2020) Introducing candidate Genes Associated with the Milk and Wool Production Traits in Sheep. Modern Genet 16 (2), 281-297 (In Persian).
Price MN, Dehal PS, Arkin AP (2010) FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE  53: e9490.
Taberlet P, Coissac E, Pansu J, Pompanon F (2011) Conservation genetics of cattle, sheep, and goats. CR Biol 334, 247-254.
Wang MS, Thakur M, Peng MS et al. (2020) 863 genomes reveal the origin and domestication of chicken. Cell Res 30(8), 693-701.
Wang, MS., Zhang, JJ., Guo, X. et al. (2021) Large-scale genomic analysis reveals the genetic cost of chicken domestication. BMC Biol 19, 118.
Weir BS, Cockerham CC (1984) Estimating F-statistic for the analysis of population stricter 38, 1358-1370.