تجزیه و تحلیل مجموعه های ژنی جهت شناسایی ژن ها و مسیرهای زیستی مرتبط با صفات وزن بدن در مرغ

نوع مقاله : مقاله پژوهشی

نویسندگان

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

2 دانشیار گروه علوم دامی، دانشکده کشاورزی و منابع طبیعی، دانشگاه اراک

چکیده

این پژوهش به منظور مطالعه پویش کل ژنوم بر پایه تجزیه و تحلیل غنی­سازی مجموعه ژنی جهت شناسایی جایگاه­های ژنی مؤثر بر وزن بدن در سنین مختلف چهار نژاد مرغ چوآ، سیلک، لنگشن و بیرد با استفاده از آرایه­های ژنومی با تراکم بالا انجام شد. اطلاعات رکوردهای فنوتیپی و ژنوتیپی نمونه­ها از پایگاه ذخیره ژنومی برخط Frontiersin استفاده شد. مطالعه پویش کل ژنومی از 402 قطعه مرغ و خروس با صفات وزن بدن از هفته اول تا 15 هفتگی در برنامه GenABEL ارزیابی شد. در مرحله بعد، تجزیه غنی­سازی مجموعه ژنی با بسته نرم افزاری goseq برنامه R با هدف شناسایی عملکرد زیستی ژن­های نزدیک در مناطق انتخابی کاندیدا با پایگاه­های GO، KEGG، DAVID و PANTHER انجام شد. در این پژوهش، تعداد 10 نشانگر تک نوکلئوتیدی واقع روی کروموزوم­های 1، 2، 5، 7، 10، 14، 18، 19، 20 و 27 شناسایی شدند که با ژن­های ABCG1، MYOD1، MYH10، MYH11، MYO1B، MYO1C، MYO1E، MYL1، MYL2، MYL3، SLC2A8، ACACA، ACOX1، ACOX2 و PNPLA2 مرتبط بودند. برخی از این ژن­ها در مناطق معنی­دار با مطالعات قبلی هم­خوانی داشتند. در تجزیه غنی­سازی مجموعه ژنی، تعداد 17 مسیر هستی­شناسی ژنی و بیوشیمیایی با صفات وزن بدن شناسایی شدند (01/0P˂). از این بین، مسیرهای cytoskeletal protein binding،anatomical structure development  و Tricarboxylic acid cycle نقش مهمی در توسعه الیاف عضلانی اسکلتی و سوخت و ساز چربی داشتند. با توجه به تأیید مناطق قبلی پویش ژنومی صفات وزن بدن و شناسایی مناطق ژنومی جدید، استفاده از یافته­های این تحقیق می­تواند سبب تسریع در پیشرفت ژنتیکی برنامه­های اصلاح نژادی مرغ شود. 

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Gene set enrichment analysis to identify genes and biological pathways associated with body weight in chicken

نویسندگان [English]

  • A. H. Khaltabadi Farahani 1
  • H. Mohammadi 1
  • M. H. Moradi 1
  • H. A. Ghasemi 2
  • I. Hajkhodadadi 1
1 Assistant Professor, Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
2 Associate Professor, Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
چکیده [English]

The aim of the present study was to conduct a genome wide association studies (GWAS) based on gene set enrichment analysis for identifying the loci associated with body weight in four chicken breeds including Chahua, Silkie, Langshan, and Beard using the high throughput single nucleotide polymorphisms (SNPs). Phenotypic and genotypic data were obtained from the Frontiersin online public repository. In this study, the 402 cocks and hens were used with body weight from 1 to 15 weeks using GenABEL software. The gene enrichment analysis was performed with the goseq R package. In the next step, a bioinformatics analysis was implemented to identify the biological pathways performed in GO, KEEG, DAVID and PANTHER databases. Ten SNP markers on  chromosomes 1, 2, 5, 7, 10, 14, 18, 19, 20 and 27 located in ABCG1, MYOD1, MYH10, MYH11, MYO1B, MYO1C, MYO1E, MYL1, MYL2, MYL3, SLC2A8, ACACA, ACOX1, ACOX2, and PNPLA2 genes were identified. Some of the genes were found are consistent with some previous studies and to be involved in biological pathways related to body weight. According to pathway analysis, 17 pathways from gene ontology and KEGG pathway were associated with the body weight (P˂0.01). Among those pathways, the cytoskeletal protein binding, anatomical structure development and tricarboxylic acid cycle had significant association with skeletal muscle fiber and metabolism lipid traits. In total, this study supported previous results from GWAS of body weight; also revealed additional regions in the chicken genome associated with these economically important traits. The use of these findings can accelerate the genetic progress in the breeding programs.

کلیدواژه‌ها [English]

  • Pathway-based analysis
  • Candidate gene
  • Chicken
  • Body weight

مراجع

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تحقیقات تولیدات دامی
دوره 9، شماره 3
آذر 1399
صفحه 47-57

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