تجزیه و تحلیل غنی سازی مجموعه های ژنی جهت شناسایی مناطق ژنومی مرتبط با سازگاری محیطی در برخی از نژادهای گوسفندان ایرانی

نوع مقاله : مقاله پژوهشی

نویسندگان

1 گروه علوم دامی، دانشکده کشاورزی و محیط زیست، دانشگاه اراک

2 گروه علوم دامی، دانشکدگان کشاورزی و منابع طبیعی، دانشگاه تهران

3 گروه علوم دامی، دانشکده کشاورزی و منابع طبیعی، دانشگاه شهید باهنر کرمان

چکیده

پژوهش حاضر با هدف مطالعه ارتباط ژنومی (GWAS) بر اساس تجزیه و تحلیل غنی­سازی مجموعه‌­های ژنی جهت شناسایی جایگاه­‌های ژنی مؤثر بر صفات سازگاری با شرایط محیطی با استفاده از اطلاعات آرایه­‌های ژنومیOvine high-density 600K  Illumina انجام شد. به­این منظور از اطلاعات ژنوتیپی 139 رأس گوسفندان بومی ایرانی شامل نژادهای کرمانی (15 رأس)، سنجابی (14 رأس)، لری­بختیاری (15 رأس)، قزل (15 رأس)، قره­گل (15 رأس)، سیاه­کبود (15 رأس)، کبوده شیراز (9 راس)، افشاری (14 رأس)، شال (15 رأس) و بلوچی (12 رأس) استفاده شد. ابتدا، تجزیه GWAS برای صفات مورد مطالعه در برنامه PLINK انجام شد. سپس، ژن­های معنی­داری که در داخل و یا 50 کیلوباز بالا و پایین­دست نشانگرهای معنی­دار قرار داشتند، شناسایی شدند. در نهایت، تفسیر مجموعه ژنی با هدف شناسایی عملکرد زیستی ژن­‌های نزدیک به مناطق انتخابی از مسیر پایگاه‌­های بیوانفورماتیکی مختلف انجام شد. نتایج نشان داد که به­ترتیب 2431،  2244 و 2145 نشانگر SNP با صفات سازگاری با شرایط محیطی گرمسیری-سردسیری، پراکنش در مناطق با ارتفاع بالا-پایین از سطح دریا و پوشش بدنی پشمی-پوستی در گوسفندان بومی ایران مرتبط هستند (05/0>P). با تجزیه و تحلیل غنی­سازی مجموعه­های ژنی، مسیرهای زیستی (و ژن­های کاندیدای) مربوط به پاسخ دفاعی به عفونت­های باکتریایی (HSPA4L، DNAJB4 و MSRB3)، تنظیم پاسخ ایمنی به­واسطه ایمونوگلوبولین­ها (IL27A، TRAF3IP2 و LY96)، تنظیم فرآیند سیستم رشد و اتصالات سلولی (BMP2، THBS1 و MYH10)، تنظیم اندازه ساختار آناتومی (FGF2 و ACTR3)، تنظیم استخوان­سازی و توسعه اندام (PTBP1 و TMEM117)، و رشد اپیدرم پوست و پشم (KRT71، KR27 و KR25) شناسایی شدند. در مجموع، نتایج تحقیق حاضر می­توانند دیدگاه جدیدی در رابطه با معماری ژنتیکی صفات سازگاری در برنامه­های اصلاح­نژادی گوسفندان کشور فراهم آورند.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Gene-set enrichment analysis to identify genomic regions associated with environmental adaptation in some Iranian sheep breeds

نویسندگان [English]

  • A. Noroozi 1
  • M. H. Moradi 1 2
  • H. Mohammadi 1
  • A. H. Khaltabadi Farahani 1
  • A. K. Esmailizadeh 3
1 Department of Animal Science, Faculty of Agriculture and Environmental Sciences, Arak University, Arak, Iran
2 Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
3 Department of Animal Science, Faculty of Agriculture and Natural Resources, Shahid Bahonar University of Kerman, Kerman, Iran
چکیده [English]

Introduction: Environmental adaptations that allow different breeds to thrive in different ecological conditions are significant in sheep breeding. Understanding the genetic basis for such adaptations can greatly enhance breeding programs aimed at improving resilience and productivity. Various indigenous sheep breeds exhibit unique traits suited for their respective habitats in Iran. This study aimed to identify genomic loci associated with environmental adaptation through genome-wide association studies (GWAS) based on gene-set enrichment (GSE) analysis. By leveraging high-density single-nucleotide polymorphism (SNP) arrays, we explored the genetic mechanisms underlying thermotolerance, altitude adaptation, and coat type differentiation, which are critical for sustaining sheep production under Iran’s heterogeneous climates. These adaptations are particularly relevant given Iran’s diverse topography, where temperatures range from -20°C in mountainous regions to +50°C in deserts, creating strong selective pressures on local breeds.
Materials and methods: The Illumina HD ovine SNP600K BeadChip genomic arrays were utilized to analyze 139 animals from nine Iranian sheep breeds, namely Kermani (n=15), Sanjabi (n=14), Lori-Bakhtiari (n=15), Qezel (n=15), Gharagol (n=15), SiahKabod (n=15), GrayShiraz (n=9), Afshari (n=14), Shal (n=15), and Baluchi (n=12). Animals were grouped based on three adaptive traits: (1) tropical vs. cold climate resilience, (2) high vs. low altitude distribution, and (3) wool vs. skin coat type. Quality control filters included minor allele frequency (MAF) > 0.05, SNP call rate > 95%, and removal of markers with unknown genomic positions. To assess the relationship between specific traits and SNP variations across the genome, GWAS was conducted based on logistic regression models using PLINK software (v 1.9), with principal component analysis (PCA) to correct for population stratification. SNPs were assigned to respective genes based on their locations within the genomic sequence or a flanking region of 50 kb upstream and downstream of each significant SNP. Following this analysis, we employed various bioinformatics databases to interpret gene sets and ascertain their biological functions related to selected genomic regions.
Results and discussion: The results of the GWAS showed that 2431, 2244, and 2145 SNP markers were associated with adaptation to tropical-cold environmental conditions, distribution in areas with high-low height of sea level, and wool-skin body covering in Iranian indigenous sheep, respectively (P<0.05). Gene-set enrichment analysis identified the biological pathways (and candidate genes) of defense response to gram-positive bacterium (HSPA4L, DNAJB4, MSRB3), regulation of immunoglobulin mediated immune response (IL27A, TRAF3IP2, LY96), regulation of muscle system process and cell junction (BMP2, THBS1, MYH10), regulation of anatomical structure size (FGF2, ACTR3), regulation of ossification and organ growth (TMEM117, PTBP1), and skin epidermis development (KR25, KR27, KRT71). The pathways identified in the current study for adaptation traits in indigenous breeds played an important role in the regulation of the immune system, muscle structure development, osteoclast differentiation, body size, and regulation of wool growth. The insights gained from this study greatly extend our understanding of how specific genetic determinants contribute toward functional adaptations in Iranian sheep breeds under diverse environments. For example, the identification of HSPA4L in thermotolerance aligns with its known role in heat shock response, while novel candidates like TMEM117 may represent breed-specific adaptations. Some genes have also not been well-established in their biological function, and there may be potential mutual effects that are not yet understood in this context. Therefore, to determine the precise role of these genes, it is essential to conduct further comprehensive functional studies and biological system analyses.
Conclusions: In general, our findings provide valuable knowledge on genomic regions linked with vital adaptation traits among indigenous Iranian sheep breeds. The integration of GWAS and pathway analysis revealed not only expected candidates (e.g., KRT genes for wool) but also novel genes (e.g., LY96 for immunity) that broaden our understanding of genomic adaptability. These results may serve future research endeavors focused on dissecting genetic architectures underlying adaptability, particularly for marker-assisted selection in breeding programs. However, the study’s limitations, including sample size and the need for functional validation of candidate genes, highlight opportunities for future work. A pivotal component influencing successful breeding strategies aimed at improving these animals' resilience while considering changing global climates.

کلیدواژه‌ها [English]

  • Pathway analysis
  • Candidate gene
  • Iranian sheep
  • Genome-wide association analysis

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تحقیقات تولیدات دامی
دوره 14، شماره 2
مرداد 1404
صفحه 1-18

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