تجزیه و تحلیل مجموعه‌های‌ ژنی جهت شناسایی ژن‌ها و مسیرهای زیستی مرتبط با صفات وزن تخم‌مرغ در کل دوره تولید

نوع مقاله : مقاله پژوهشی

نویسندگان

1 دانشجوی کارشناسی ارشد گروه علوم دامی، دانشکده کشاورزی و منابع طبیعی، دانشگاه اراک، اراک، ایران.

2 گروه علوم دامی

3 استادیار گروه علوم دامی، دانشکده کشاورزی و منابع طبیعی، دانشگاه اراک، اراک، ایران

4 دانش آموخته دکتری ژنتیک و اصلاح دام، گروه علوم دامی، دانشکده کشاورزی، دانشگاه تبریز. تبریز، ایران.

چکیده

هدف: شناسایی ژن­‌های بزرگ اثر مؤثر بر صفات مهم اقتصادی یکی از مهم‌‌ترین اهداف اصلاح نژادی در پرورش مرغ است. پژوهش حاضر به منظور مطالعه پویش ژنومی بر اساس آنالیز مجموعه‌­های ژنی برای شناسایی جایگاه­‌های ژنی مؤثر بر صفات مرتبط با وزن تخم­مرغ نژاد رُد آیلند رِد با استفاده از آرایه­‌های ژنومی با تراکم بالا بوده است.
مواد و روش­ها: اطلاعات رکورد‌های فنوتیپی و ژنوتیپی مرتبط با وزن تخم­مرغ نمونه­‌ها از پایگاه ذخیره ژنومی برخط Figshare استفاده شد. آنالیز پویش کل ژنومی بر پایه آنالیز مسیر در سه مرحله تعیین مکان SNPهای معنی­‌دار با ژن، ارتباط ژن‌­ها به طبقات عملکردی و مسیرهای بیوشیمیایی و پویش کل ژنومی بر پایه آنالیز مسیر انجام می‌­شود. بر این اساس، مطالعه پویش ژنومی برای صفات وزن تخم­مرغ در اولین تخم­گذاری و 28، 36، 56، 66، 72 و 80 هفتگی در 1078 قطعه مرغ در برنامه GenABEL انجام شد. سپس با استفاده از بسته نرم افزاری biomaRt2 ژن­های معنی­داری که در داخل و یا 20 کیلوباز بالادست یا پایین دست نشانگرهای SNP معنی­دار قرار داشتند، شناسایی گردید. در نهایت تفسیر مجموعه ژنی با بسته نرم افزاری goseq برنامه R با هدف شناسایی عملکرد بیولوژیکی ژن­‌های نزدیک به مناطق انتخابی و ژن‌­های کاندیدا از طریق پایگاه‌­های GO، KEGG، DAVID و PANTHER انجام شد.
نتایج: در این پژوهش تعداد 9 نشانگر تک نوکلئوتیدی واقع روی کروموزوم­‌‌های 3، 4، 6، 7، 8، 9، 19، 20 و 22 شناسایی شدند که با ژن‌­هایMC3R ،­LEPR ، ECT2، SH3GL2، KCNMA1، SPP1، PCK1، MMP9، PPP1CB، ACOX1 و IGFBP2 مرتبط بودند. تعدادی از این نشانگرهای شناسایی شده در مناطق ژنومی معنی­‌دار با مطالعه پیشین مرتبط با وزن تخم­مرغ هم­خوانی داشتند. در تفسیر مجموعه ژنی تعداد 28 مسیر هستی شناسی ژنی و بیوشیمیایی با صفات وزن تخم­مرغ شناسایی شد (P˂0.01). از این بین، مسیرهایRegulation of feeding behavior،­Positive Regulation of apoptotic process،Positive regulation of protein phosphorylation osteoblast differentiation، Positive regulation of gluconeogenesis، Cell-cell junction وFocal adhesion عملکرد‌های مهمی را در ارتباط با وزن تخم­مرغ و فرآیند تولید تخم مرغ از طریق رشد اووسیت و تخمک­اندازی، تشکیل پروتئین آلبومین و تشکیل پوسته تخم مرغ بر عهده داشتند.
نتیجه ­گیری: با توجه به تأیید نتایج حاصل از مطالعه قبلی در زمینه پویش ژنومی صفات وزن تخم­مرغ و شناسایی مناطق ژنومی جدید استفاده از یافته­های این تحقیق می­تواند در انتخاب ژنتیکی برنامه­های اصلاح نژادی مرغ مفید باشد.

کلیدواژه‌ها

عنوان مقاله [English]

Gene-set enrichment analysis to identify genes and biological pathways associated with egg weight in the whole laying period

نویسندگان [English]

  • Ali Reza Jafarymanesh 1
  • Amir Hossein Khaltabadi Farahani 2
  • Mohammad Hossein Moradi 3
  • Hossein Mohammadi 4
1 MSc Student, Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
2 department of animal science
3 Assistant Professor, Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
4 Ph.D Graduated, Department of Animal Science, Faculty of Agricultural Sciences, University of Tabriz, Tabriz, Iran
چکیده [English]

Objective
Identifying genes with large effects on economically important traits, has been one of the important goals in chicken breeding. The present study aimed to conduct a genome wide association studies (GWAS) based on Gene-set enrichment analysis for identifying the loci associated with egg weight in Rhode Island Red chicken using the high-density SNPs.
 
Materials and methods
Phenotypes records and genotypic data were obtained from the Figshare online public repository. The gene set analysis consists basically in three different steps: the assignment of SNPs to genes, the assignment of genes to functional categories, and finally the association analysis between each functional category and the phenotype of interest. Genome wide association study for 1,078 hens was performed with egg weight including first egg weight, eggs weight at 28, 36, 56, 66, 72, and 80 weeks of age using GenABEL software. Using the biomaRt2 R package the SNP were assigned to genes if they were within the genomic sequence of the gene or within a flanking region of 20 kb up- and downstream of the gene. Subsequently, gene enrichment analysis was performed with the goseq R package and bioinformatics analysis was implemented to identify the biological pathways performed in GO, KEEG, DAVID and PANTHER databases.
 
Results
In this research, 9 SNP markers on chromosomes 3, 4, 6, 7, 8, 9, 19, 20 and 22 located in MC3R, LEPR, ECT2, SH3GL2, KCNMA1, SPP1, PCK1, MMP9, PPP1CB, ACOX1, and IGFBP2 genes were identified. Some of the genes that were found are consistent with some previous studies related to egg weights. According to pathway analysis, 28 pathways from gene ontology and biological pathways were associated with the egg weight (P˂0.01). Among these pathways, the regulation of feeding behavior, positive regulation of the apoptotic process, positive regulation of protein phosphorylation, osteoblast differentiation, positive regulation of gluconeogenesis, cell-cell junction, and focal adhesion have important functions in creating the egg weight and process production through the development and ovulation of the oocytes, the formation of albumen, and the formation of eggshell.
 
Conclusions
 In total, this study supported previous results from GWAS of egg weights, also revealed additional regions in the chicken genome associated with these economically important traits, using these findings could potentially be useful for genetic selection in the breeding programs.

کلیدواژه‌ها [English]

  • Egg weight
  • Genome scan
  • Gene ontology
  • Pathway-based analysis

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مجله بیوتکنولوژی کشاورزی
دوره 12، شماره 3
آبان 1399
صفحه 91-116

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