Identification of selective signatures, detection of ROH Islands and related genes associated with the number of lambs per lambing in Zandi ewes

Document Type : Research Paper

Authors

1 Assistant Professor, Department of Animal Sciences, Faculty of Agriculture and Environmental Sciences, Arak University, Arak, Iran.

2 Assistant Professor, Department of Animal Sciences, University College of Agriculture and Natural Resources, University of Tehran

3 Associate Professor, Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran.

Abstract

Abstract
Objective
The locations of ROHs which are under positive selection, or laboring favorable allele in population, tend to be fixed in the genome and formation of ROH Island during long times. Also, selection not only increases the frequency of new-useful mutations but also remains some signals throughout the genome. Since these regions are often control economically important traits, identifying and tracking these regions is the most important subject in the animal genetics.
Materials and methods
In order to identify the signatures of selection and ROH Islands, 81 native Zandi sheep including prolific ewes (42 animal) and others with only singleton records (39 animal) were genotyped using the medium-density Illumina Ovine SNP50 array. Theta unbiased statistical method in R software was used to identify selection signatures. Candidate genes were identified by SNPs located at 0.1% upper range of Theta using BioMart software in ensemble 109. Also the detectRUNS package of R was useful to find the proportions of the homozygous genome and one percent of SNP with the highest frequency in ROH were considered as ROH Islands.
Results
Based on the results of obtained Theta values genomic regions on chromosomes 1(3 regions), 2 (2 regions), 5, 6 (2 regions), 8 (2 region), 10 and 25 were identified. A total of 17 ROH Islands with length: 270.46 Kb to 8.25 Mb related to studied trait were identified, which covering less than 1% of the sheep genome. The ROH Islands was not distributed across the genome uniform. The highest number ROH Island was observed on chromosome 1, while the lowest was on chromosome 24. Candidate genes PER2, KCNH7, CLCN3, UTG8 and EPHA5 obtained these regions. Further investigation using bioinformatics tools showed these genomic regions overlapped with the genes associated with development of ovarian granulosa cells, ovulation rate, lipid transport in Sertoli cells and early growth fetus.
Conclusions
The results of this study revealed that, the selection processes in different sheep breeds for economic traits during several years, has led to the formation of many ROH islands in sheep genome, therefore scanning these regions at the genome level can be an alternative strategy to identify genes and associated loci with economic traits. However, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes.

Keywords


جعفری احمدآبادی سید علی اصغر، عسکری­همت حشمت­اله، محمدآبادی محمدرضا (1402) تاثیر شاهدانه بر بیان ژن DLK1 در بافت‌ قلب بره‌های کرمانی. مجله بیوتکنولوژی کشاورزی، 15(1)، 217-234.
عرب پور رق­آبادی زهرا، محمدآبادی محمدرضا، خضری امین (1400) الگوی بیانی ژن p32 در بافت‌های ران، دست، راسته و چربی پشت بره کرمانی. مجله بیوتکنولوژی کشاورزی، 13(4)، 183-200.
کوروش‌نیا حمیدرضا، مرادی شهربابک حسین، صادقی مصطفی (1397) بررسی همگنی ساختار ژنتیکی در جمعیت گوسفند نژاد زندی با استفاده از داده‌های ژنومی. نشریه علوم دامی (پژوهش و سازندگی) 31 (121)، 76-67.
محمدی فر آمنه، محمدآبادی محمدرضا (1390) کاربرد نشانگرهای ریزماهواره برای مطالعه ژنوم گوسفند کرمانی. مجله علوم دا‌می‌ایران 42(4)، 344-337.
محمودی مریم­، آیت اللهی مهرجردی احمد ، محمدآبادی محمدرضا (1396) بررسی اگزون چهارم ژن کاپاکازئین گوسفند کرمانی با تکنیک PCR-RFLP. مجله بیوتکنولوژی کشاورزی، 9(3)، 128-119.
نصرتی مریم، محمدآبادی محمد رضا (1401) پویش ژنومی جزایر همخونی و ژن­های مرتبط با آن در جمعیت­ گوسفندان دنیا. مجله پژوهش­های تولیدات دامی، 13 (36)، 146-137.
References
Addo S, Klingel S, Thaller G, Hinrichs D (2021) Genetic diversity and the application of runs of homozygosity-based methods for inbreeding estimation in German White-headed Mutton sheep. PLoS One 16, e0250608.
Akey JM, Zhang G, Zhang K, Jin L, Shriver MD (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Res 12(12), 1805-1814.
Al-Abri M, Kharousi KA, Toobi AGA, Salem MM (2023) Genome wide association analysis for twinning ability in Jabal Akhdar Omani goats. Small Rum Res (221), 106951.
Almamun HA, Clark SA, Kwan P, Gondro C (2015) Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep. Genet Sel Evol 47, 90.
Amiri Roudbar M, Mohammadabadi MR, Mehrgardi AA, Abdollahi-Arpanahi A (2017) Estimates of variance components due to parent-of-origin effects for body weight in Iran-Black sheep. Small Rum Res 149, 1-5.
Amiri Roudbar M., Abdollahi-Arpanahi R., Ayatollahi Mehrgardi A., et al. (2018) Estimation of the variance due to parent-of-origin effects for productive and reproductive traits in Lori-Bakhtiari sheep. Small Rumin Res 160, 95-102.
Arabpour Z, Mohammadabadi M, Khezri A (2021) The expression pattern of p32 gene in femur, humeral muscle, back muscle and back fat tissues of Kermani lambs. Agric Biotechnol J 13 (4), 183-200 (In Persian).
Bahrampour V, Mohammadabadi MR, Mirzaei HR, et al. (2008) Molecular analysis of Calpastatin gene in Kermani sheep herds. J Agric Sci Nat Resource 15 (4), 124-131.
Biscarini F, Cozzi P, Gaspa G, Marras G, (2019) detectRUNS: Detect Runs of Homozygosity and Runs of Heterozygosity in Diploid Genomes. R Package Version 0.9.6.
Curik I, Ferenčaković M, Sölkner J, (2014) Inbreeding and runs of homozygosity: a possible solution to an old problem. Livest Sci 166, 26-34.
Eydivandi S, Roudbar MA, Karimi MO, Sahana G (2021) Genomic scans for selective sweeps through haplotype homozygosity and allelic fixation in 14 indigenous sheep breeds from Middle East and South Asia. Sci Rep 11(1), 2834.
Gomez-Raya L, Rodríguez C, Barragán C, Silió L (2015) Genomic inbreeding coefficients based on the distribution of the length of runs of homozygosity in a closed line of Iberian pigs. Genet Sel Evol 47, 81.
Jafari Ahmadabadi SAA, Askari-Hemmat H, Mohammadabadi M, et al. (2023) The effect of Cannabis seed on DLK1 gene expression in heart tissue of Kermani lambs. Agric Biotechnol J 15 (1), 217-234 (In Persian).
Kim E, Elbeltagy A, Aboul-Naga A, Rischkowsky B, Sayre B, Mwacharo J, Rothschild M. (2015b). Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment. Heredity 116, 255–264.
Kim H, Song KD, Kim HJ, Park W, Kim J, Lee T, (2015a) Exploring the Genetic Signature of Body Size in Yucatan Miniature Pig. PLoS one 10, 4e0121732.
Kulus J, Kulus M, KrancW, Jopek K, Zdun M, Józkowiak M, Ja´skowski JM, Piotrowska Kampisty H, Bukowska D, Antosok P. (2021)Transcriptomic profile of new gene markers encoding proteins responsible for structure of porcine ovarian granulosa cells. Biology 10, 1214.
Li Y, Chen Z, Fang Y, Cao C, Zhang Z, Pan Y, Wang Q. (2022) Runs of Homozygosity Revealed Reproductive Traits of Hu Sheep. Genes 13, 1848.
Lin J, Zhang W, Zhang X, Wang C (2022) Signatures of selection in recently domesticated macadamia. Nat Commun 13(24), 224.
Liu J, Shi L, Li Y, Chen L, Garrick D, Wang L Zhao F (2021) Estimates of genomic inbreeding and identification of candidate regions that differ between Chinese indigenous sheep breeds. J Anim Sci 12(1), 95.
Machová K, Marina H, Arranz JJ, Pelayo R, Rychtářová J, Milerski M, Vostrý L, Suárez-Vega A, (2023) Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphisms. Animal 17(1), 100690.
Mahmoodi M, Ayatollahi A, Mohammadabadi MR (2018) Studying exon 4 of kappa-casein gene in Kermani sheep using PCR-RFLP. Agric Biotechnol J 9 (3), 119-128 (In Persian).
Masoudzadeh SH, Mohammadabadi MR, Khezri A, et al. (2020) Dlk1 Gene Expression in Different Tissues of Lamb. Iran J Appl Anim Sci 10 (4), 669-677.
Mastrangelo SE, Ciani MT, Sardina G, Sottile F, Portolano B (2018) Runs of homozygosity reveal genome-wide autozygosity in Italian sheep breeds. Anim Genet 49, 71-81.
Mohamadipoor Saadatabadi L, Mohammadabadi M, Amiri Z, et al. (2021) Signature selection analysis reveals candidate genes associated with production traits in Iranian sheep breeds. BMC Vet Res 17 (1), 1-9.
Mohammadabadi MR (2016) Role of clostridium perfringens in pathogenicity of some domestic animals. J Adv Agric 7 (3), 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 (2), e154.
Mohammadifar A, Mohammadabadi MR (2011) Application of Microsatellite Markers for a Study of Kermani Sheep Genome. Iran J Anim Sci 42 (4), 337-344 (In Persian).
Mohammadi H, Rafat SA, Moradi Shahrbabak H, Shodja J, Moradi MH (2020) Genome-wide association study and gene ontology for growth and wool characteristics in Zandi sheep. J Livest Sci Technol 8(2), 45-55.
Nosrati M, Mohammad Abadi MR (2022) Genome-Wide Scans of ROH Islands and Related Genes in the World's Sheep Populations. Research on Animal Production 13 (36), 137-146. (In Persian)
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 81, 559-575.
Purfield DC, McParland S, Wall E, Berry DP, (2017) The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds. PLoS One, 12, e176780.
Safaei SMH, Dadpasand M, Mohammadabadi M, et al. (2023) An Origanum majorana Leaf Diet Influences Myogenin Gene Expression, Performance, and Carcass Characteristics in Lambs. Animals 13 (1), 14
Sánchez-Ramos R, Trujano-Chavez MZ, Gallegos-Sánchez J, Becerril-Pérez CM, Cadena-Villegas S, Cortez-Romero C, (2023) Detection of Candidate Genes Associated with Fecundity through Genome-Wide Selection Signatures of Katahdin Ewes. Animals (Basel) 13(2), 272.
Saravanan KA, Panigrahi M, Kumar H, Parida S, Bhushan B, Gaur GK, Dutt T, Mishra BP, Singh RK, (2021) Genomic scans for selection signatures revealed candidate genes for adaptation and production traits in a variety of cattle breeds. Genomics 113(3), 955-963. 
Shahsavari M, Mohammadabadi M, Khezri A, et al. (2021) Correlation between insulin-like growth factor 1 gene expression and fennel (Foeniculum vulgare) seed powder consumption in muscle of sheep. Anim Biotechnol 1-11.
Shahsavari M, Mohammadabadi M, Khezri A, et al. (2022) Effect of Fennel (Foeniculum Vulgare) Seed Powder Consumption on Insulin-like Growth Factor 1 Gene Expression in the Liver Tissue of Growing Lambs. Gene Expr 21(2), 21-26.
Tenghe AMM, Bouwman AC, Berglund B, Strandberg E, de Koning DJ, Veerkamp RF (2016) Genome-wide association study for endocrine fertility traits using single nucleotide polymorphism arrays and sequence variants in dairy cattle. J Dairy Sci 99(7), 5470-5485.
Wang JJ, Zhang T, Chen QM, Zhang RQ, Li L, Cheng SF, Shen W, Lei CZ (2020) Genomic Signatures of Selection Associated With Litter Size Trait in Jining Gray Goat. Front Genet 11, 286.
Weir BS, Cockerham CC (1984) Estimating F‐statistics for the analysis of population structure. Evolution 38(6), 1358-1370.
Wright S (1965) The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 1, 395-420.
Yurchenko AA, Daetwyler HD, Yudin N, (2018) Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation. Sci Rep 8, 12984.
Zhang Z, Sui Z, Zhang J, Li Q, Zhang Y, Wang C, Li X, Xing F (2022) Identification of Signatures of Selection for Litter Size and Pubertal Initiation in Two Sheep Populations. Animals (Basel) (19), 2520.
Zhu C, Fan H, Yuan Z, Hu S, Zhang L, Wei C, Zhang Q, Zhao F, Du L (2015) Detection of Selection Signatures on the X chromosome in Three Sheep Breeds. Int J Mol Sci. 16, 20360-20374.