بررسی اثر ژن‌های مرتبط با میتوپروتئوم‌ بر رشد ماهیچه سینه مرغ بومی اصفهان به‌وسیله داده RNA-seq

نوع مقاله : علمی پژوهشی- ژنتیک و اصلاح دام و طیور

نویسندگان

1 فردوسی مشهد

2 دانشگاه تهران

3 دانشگاه فردوسی مشهد

4 مرکز تحقیقات علوم دامی کشور

چکیده

این آزمایش به منظور بررسی و شناسایی تفاوت‌های ژنتیکی و مسیرهای متابولیکی مرتبط با میتوکندری بین توده مرغ بومی اصفهان و یک سویه جوجه تجاری راس 708 با سرعت رشدهای متفاوت، انجام شد. بدین منظور از روش توالی‌یابی RNA-seq با استفاده از چهار نمونه ماهیچه سینه 28 روزگی استفاده شد. مقایسه آماری بیان ژن‌های توالی‌یابی شده در مرغ بومی و جوجه تجاری، 606 ژن با تفاوت معنی‌دار را مشخص نمود و از این تعداد 249 ژن در مرغ بومی و 357 ژن در جوجه تجاری افزایش بیان داشتند. بر اساس نتایج بیان ژن‌ها در مرغ بومی، فاکتور رونویسی FoxO3 موجب فعال شدن مسیر آتروفی لیگازهای یوبیکویتینی E3 و افزایش شکست پروتئین و در نتیجه کاهش حجم ماهیچه اسکلتی در مقایسه با جوجه تجاری شده است. هیپوکسی و تنظیم فرآیند متابولیکی گونه‌های اکسیژن فعال (ROS) از مهم‌ترین فرآیندهای بیولوژیکی فعال در مرغ بومی بودند. بررسی و مقایسه ژن‌های مرتبط با پروتئوم میتوکندریایی نشان داد در این مرغ تغییرات معنی‌داری در بیان بسیاری از پروتئین‌های وابسته به رشد و تنظیم‌کننده رونویسی وجود دارد. این تغییرات نشان‌دهنده برنامه سازگاری پیچیده‌ای است که شکست پروتئین را تسهیل نموده و سوخت گلوکز در ماهیچه را کاهش می‌دهد. این مسیرهای متابولیسمی در جهت کاستن سطح نیازمندی‌های مرغ بومی به گونه‌ای تکامل یافته‌اند تا توان این مرغ را در غلبه بر شرایط و تنش‌های محیطی و تحمل کمبودهای غذایی تقویت نمایند.

کلیدواژه‌ها


عنوان مقاله [English]

The Effect of Mitoproteum Genes on Breast Muscle Growth of Isfahan Native Chickens by RNA-seq Data

نویسندگان [English]

  • seyed nader albooshoke 1
  • Mojtaba Tahmoorespur 1
  • Mohammad Reza Bakhtiyarizadeh 2
  • Mohammad Reza Nassiry 3
  • Saied Esmaeilkhanian 4
1 Ferdowsi university of mashhad
2 University of Tehran
3 Ferdowsi Mashhad
4 Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
چکیده [English]

Introduction Native chicken breeds are important genetic resource and well adapted to the local environmental conditions. However, growth rate and feed efficiency of these breeds are not appropriate. On the other hand modern broilers grow faster and offer a higher nutritional efficiency than the indigenous chicken breeds. This advantage is the result of the severe genetic selection programs, which were designed to increase production. In this study, a systematic identification of mitoProteome genes and new pathways related to growth rate of pectoralis muscle in chicken has been made using gene expression profiles of two distinct breeds: Isfahan native, a slow-growing Iranian breed possessing low growth rate and Ross 708, a commercial fast-growing broiler line.
Materials and Methods All the birds were reared under the same management, environmental and nutritional conditions. The diet was the same throughout the whole experiment and formulated to contain 20% CP and 3000 kcal ME/kg. The birds received feed and water freely (ad libitum). On day 28 post-hatch, six birds were randomly selected from each breed, weighed and sacrificed. From each bird, 1 to 2 g of tissue was excised from the posterior region of the left pectoralis major muscle. Total RNA was isolated from breast muscle samples. Using Truseq Stranded RNA Prep kit (Illumina), each sample was converted to a uniquely indexed cDNA library, and the resulting cDNA libraries were pooled and sequenced on an Illumina Hiseq 2000 sequencer. An average of 70 million paired end reads (150 bp) were produced from all sample, 70% of which were properly mapped to the reference genome (EnsemblGalgal4). We analyzed the sequence data using bioinformatics tools Hisat2 and Cufflinks. Using Hisat2 aligner, more than 72% of clean reads (in average) were mapped back to the Galgal4 reference genome. In addition, about 90% of reads were aligned concordantly.
Results and Discussion On the first day after hatching, the weight of commercial chicks were heavier than native. This process continued until the end of the test, 28 days. The commercial chickens have a heavier weight, higher growth rate, and lower feed conversion rates than native chickens. The RNA-Seq of four muscle samples yielded around 131,590,636 million of raw 150 bp paired end reads, of which 94,483,431 and 37,107,205 reads were for native and commercial breeds, respectively. We identified 606 differentially expressed genes (DEGs) between two breeds with at least 2-fold differences (P-adjusted (Benjamini) ≤ 0.05, log2FC ≥ 2). Of these, 249 and 357 genes were up-regulated in native and commercial broilers, respectively. In the native chickens, FoxO3 transcription factor activated the atrophy pathway related to E3 ubiquitin ligases and led to increased proteolysis and reduced the skeletal muscle size as compared to the commercial broilers. Hypoxia and regulation of the metabolic process of the reactive oxygen species (ROS) were among the most important significant biological processes in native chickens. The analysis of the genes associated with the mitoProteome revealed significant changes in the expression of many genes involved in transcription regulation and growth. Also the increased expression of FoxO3 gene and the releasing of amino acids caused by the degradation of proteins, increased the expression of amino acid catabolism enzyme's (such as MCCC2 and TDH), as well increased expression of pyruvate dehydrogenase kinases (PDK4 and PDK3). This led to reducing of the aerobic oxidation of pyruvate and increasing gluconeogenesis. Increasing the UCP3 gene expression in native chickens can partly reduce mitochondrial efficiency and inappropriate feed conversion ratio compared to commercial chickens. These changes were also reflective of a complicated adaptation program that facilitates proteolysis and reduces oxidative metabolism of glucose and pyruvate in the muscles. These metabolic pathways have evolved to reduce the requirements of indigenous chickens and increase the ability of these strains to overcome the circumstances and environmental stress and resist nutritional deficits.
Conclusion Our results suggested that different expression patterns of some genes including SGK1, FBXO32, FBX030, IRS2 ، SP3, CUL, PIK3IP1 and FoxO3 in native breed might represent a cause for the poor growth performance for this breed than commercial breed. Hence, evaluation of native chicken based on these candidate genes would accelerate the efficient native chicken breed in near future. These results expand our knowledge of the genes transcribed in the breast muscle of two breeds and provide a basis for future research of the molecular mechanisms underlying the chicken breed differences.

کلیدواژه‌ها [English]

  • Breast muscle
  • Native chicken
  • Mitoproteome
  • RNA-seq
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