Genome-wide association study associated with first lambing age and lambing interval traits in Zandi sheep

Document Type : Research Paper

Authors

1 department of animal science

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

Abstract

First lambing age and lambing interval are among the most important reproductive traits affecting profitability of sheep breeding systems. The present study aimed to conduct a genome wide association studies (GWAS) for identifying the loci associated with first lambing age and lambing interval in Zandi native sheep using the 50K arrays.
Materials and methods
For this purpose, phenotypes records and genotypic data related to first lambing age and lambing interval were obtained from 96 Zandi sheep. Different steps of quality control and identification of independent SNP markers were performed by PLINK software. After quality control, 94 animals and 36070 markers were identified for further analysis. Genome wide association study was performed with reproductive traits using GEMMA software. Using the Genome Data Viewer software from NCBI database based on last assembly (ARS-UI_Ramb_v2.0) the SNP were assigned to genes if they were within the genomic sequence of the gene or within a flanking region of 300 kb up- and downstream of the gene. Finally, from online bioinformatics databases for the assignment of the genes to functional categories, DAVID and PANTHER databases were used.
Results
In this research, seven SNP markers on chromosomes 1, 2, 3, 6, 11 and 23 were identified. Also, we identified different sets of candidate genes related to reproductive traits: UMPS, ITGB, SMARCAL1, APAF1, UGT8 and ST8SIA5 in Zandi sheep. Some of the found genes, are consistent with some of the previous studies related to reproductive traits. Some of the genes were found are consistent with some previous studies and to be involved biological pathways related to fertilization, ovulation rate, estrogen biosynthesis, conception rate, skeletal muscle development, early development of the fetus and puberty.
Conclusion
The results of our research can be used to understand the genetic mechanism controlling reproductive traits and considering, this study supported previous results from GWAS of reproductive traits, also revealed additional regions, using these findings could potentially be useful for genetic selection in sheep for age at first lambing.

Keywords

References

پژمان لیلا، زمانی پویا (1391) برآورد اجزای واریانس و پارامترهای ژنتیکی برخی صفات تولید­مثلی در گوسفند نژاد مهربان با کمک مدل­های تک متغیره. نشریه پژوهش­های علوم دامی، 22­(3)، 35-27.
خلت­آبادی فراهانی، امیرحسین محمّدی، حسین، مرادی محمد حسین (1399) تجزیه و تحلیل غنی‌سازی مجموعه‌های ژنی با استفاده از مطالعات پویش کل ژنومی جهت شناسایی ژن‌ها و مسیرهای مرتبط با تعداد نتاج در نژادهای مختلف گوسفند. تولیدات دامی، 22(3)، 325-335.
محمّدی حسین، مرادی شهربابک حسین، طاهری یگانه امیر (1401) پویش کل ژنوم بر پایه روش آماری غنی‌سازی شبکه ژنی (آنالیز مسیر) مرتبط با تعداد بره متولد شده در هر زایش متعلق به گوسفند زندی. مجله بیوتکنولوژی کشاورزی، 14(1)، 101-116.­
References
Abdoli R, Mirhoseini SZ, Ghavi Hossein-Zadeh N, et al. (2018) Genome-wide association study to identify genomic regions affecting prolificacy in Lori-Bakhtiari sheep. Anim Genet 49(5), 488-491.
Abdoli R, Mirhoseini SZ, Ghavi Hossein-Zadeh N, et al. (2019). Genome-wide association study of first lambing age and lambing interval in sheep. Small Rum Res 178, 43-45.
Amiri Roudbar M, Mohammadabadi MR, Mehrgardi AA, et al. (2017) Estimates of variance components due to parent-of-origin effects for body weight in Iran-Black sheep. Small Rum Res 149, 1-5.
Bohlouli M, Mohammadi H, Alijani S (2013) Genetic evaluation and genetic trend of growth traits of Zandi sheep in semi-arid Iran using random regression models. Small Rum Res 114, 195–201.
Cai Z, Guldbrandtsen B, Lund MS, et al. (2019) Prioritizing candidate genes for fertility in dairy cows using gene-based analysis, functional annotation and differential gene expression. BMC Genom 20, 255.
Dolebo AT, Khayatzadeh N, Melesse A, et al. (2019) Genome-wide scans identify known and novel regions associated with prolificacy and reproduction traits in a sub-Saharan African indigenous sheep (Ovis aries). Mamm Genome (11), 339-352.
Fortes MRS, Reverter A, Kelly M, et al. (2013) Genome-wide association study for inhibin, luteinizing hormone, insulin-like growth factor 1, testicular size and semen traits in bovine species. Andrology 1, 644–650.
Gangwar M, Kumar S, Ferdous Ahmad A, et al. (2023) Identification of genetic variants affecting reproduction traits in Vrindavani cattle. Res Sq 1, 29.
Galliou JM, Kiser JN, Oliver KF, et al (2020) Identification of Loci and Pathways Associated with Heifer Conception Rate in U.S. Holsteins. Genes (Basel) 11, 767.
Hernández-Montiel W, Martínez-Núñez MA, Ramón-Ugalde JP, et al. (2020) Genome-Wide Association Study Reveals Candidate Genes for Litter Size Traits in Pelibuey Sheep. Animals (Basel) 10(3), 434.
Johnston SE, McEwan JC, Pickering NK, et al. (2011) Genome-wide association mapping identifies the genetic basis of discrete and quantitative variation in sexual weaponry in a wild sheep population. Mol Ecol 20, 2555–2566.
Kominakis A, Hager-Theodorides AL, Zoidis E, et al. (2017) Combined GWAS and 'guilt by association'-based prioritization analysis identifies functional candidate genes for body size in sheep. Genet Sel Evol 49(1), e41. 
Messer LA, Wang L, Yelich J, et al. (1996) Linkage mapping of the retinol binding protein 4 (RBP4) gene to porcine chromosome 14. Mammalian Genome 7, 396-410.
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.
Mohammadi H, Khaltabadi Farahani HK, Moradi MH, et al. (2022) Weighted Single-Step Genome-Wide Association Study Uncovers Known and Novel Candidate Genomic Regions for Milk Production Traits and Somatic Cell Score in Valle del Belice Dairy Sheep. Animals (Basel) 12(9), 11-55.
Pasandideh M, Gholizadeh M, Rahimi-Mianji G (2020) Identification of two novel SNPs affecting lambing traits in sheep by using a 50K SNP-Chip. Small Rum Res 191, e106193.
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(3), 559-575.
Ramos Z, Garrick DJ, Blair HT, et al. (2023) Genomic Regions Associated with Wool, Growth and Reproduction Traits in Uruguayan Merino Sheep. Genes 14, 167. 
Salazar-Carranza M, Castillo-Badilla G, Murillo-Herrera J, et al. (2014) Effect of age at first calving on first lactation milk yield in Holstein cows from Costa Rican specialized dairy herds. Open J Vet Med 4(09), e197.
Tsartsianidou V, Pavlidis A, Tosiou E, et al. (2023) Novel genomic markers and genes related to reproduction in prolific Chios dairy sheep: a genome-wide association study. Animal (3), e100723. 
Xu SS, Gao L, Xie XL, et al. (2018). Genome-Wide Association Analyses Highlight the Potential for Different Genetic Mechanisms for Litter Size Among Sheep Breeds. Front Genet 9, e118.
Uzun A, Rodriguez-Osorio N, Kaya A, et al. (2009) Functional genomics of HMGN3a and SMARCAL1 in early mammalian embryogenesis. BMC Genom 10, e183.
Vatankhah M, Talebi MA, Edriss MA (2008) Estimation of genetic parameters for reproductive traits in Lori-Bakhtiari sheep. Small Rum Res 74, 216-220.
Wang S, Dvorkin D, Da Y (2012) SNPEVG: A graphical tool for GWAS graphing with mouse clicks. BMC Bioinform 13, e319.
Zhang Z, Sui Z, Zhang J, et al. (2022) Identification of Signatures of Selection for Litter Size and Pubertal Initiation in Two Sheep Populations. Animals 12, e2520.
Agricultural Biotechnology Journal
Volume 16, Issue 1
February 2024
Pages 195-208

Files

Share

How to cite

Statistics