نوع مقاله : مقاله پژوهشی
نویسندگان
1 استادیار، گروه علوم دامی، دانشکده کشاورزی و محیط زیست، دانشگاه اراک، اراک، ایران.
2 دانشیار، گروه علوم دامی، دانشکده کشاورزی و محیط زیست، دانشگاه اراک، اراک، ایران.
3 استادیار، گروه علوم دام و طیور، پردیس ابوریحان، دانشگاه تهران، پاکدشت، ایران.
چکیده
درک کنترل ژنتیکی خلق‌وخوی به‌عنوان یک صفت پیچیده و دارای همبستگی با صفات اقتصادی یکی از اهداف اصلاح نژادی در صنعت گاو گوشتی است. هدف پژوهش حاضر، مطالعه پویش کل ژنوم بر مبنای تجزیه و تحلیل غنیسازی مجموعه ژنی جهت شناسایی جایگاههای ژنی مؤثر بر صفات مرتبط با خلق‌وخوی گاو نژاد براهمن بود. بدین منظور از اطلاعات ژنوتیپی 1370 رأس گاو براهمن و رکوردهای فنوتیپی شامل سرعت خروج، امتیاز پن و امتیاز خلق‌وخوی استفاده شد. ارزیابی پویش کامل ژنوم با PLINK نسخه 1/90 انجام شد. تجزیه و تحلیل غنی سازی مجموعه های ژنی به‌وسیله بسته نرمافزاری goseq برنامه R با هدف شناسایی مسیرهای زیستی ژن‌های نزدیک در مناطق انتخابی کاندیدا انجام شد. در نهایت تجزیه و تحلیل بیوانفورماتیکی از پایگاههای برخط GO، Metacyc، KEGG، Reactome و Panther استفاده شد. با تجزیه و تحلیل غنیسازی مجموعههای ژنی، مسیرهای بیوشیمیایی و )ژن‌های کاندیدای( neurotransmitter secretion (NRXN3 و CACNG3)،Cycle Dopamine Neurotransmitter Release (PPFIA2)، regulation of neuron projection development (GRID2)، neuron projection (SLC8A1 و KCNQ2)، Axonal growth inhibition (RTN4R)، Neurotrophin signaling pathway (MAP2K2، MAP3K5 و PSEN1) و Focal adhesion (TLN2) مرتبط با سرعت خروج شناسایی شدند. ژن‌های کاندیدای شناسایی‌شده نقش مهمی در تفرق و تمایز سیناپسها، انتقال‌دهندههای عصبی، بیماریهای عصبی و اختلال روانی، استرسهای اکسیداتیو و محیطی، گیرندههای هورمونی و هموستازی گلوکز داشتند. با توجه به تأیید مناطق قبلی پویش ژنومی و شناسایی مناطق ژنومی جدید، استفاده از یافتههای این پژوهش میتواند در انتخاب ژنتیکی حیوانات با تولید بالاتر از طریق دامهای آرام مفید باشد.
کلیدواژه‌ها
عنوان مقاله [English]
Genome-wide association study by gene set enrichment analysis to identify genes and pathways associated with temperament in Brahman cattle
نویسندگان [English]
- Hossein Mohammadi 1
- Amir Hossein khaltabadi farahani 2
- Mhammad hossein Moradi 2
- Abouzar Najafi 3
1 Department of Animal Sciences, Faculty of Agriculture and Environmental Sciences, University of Arak
2 University of arak
3 Tehran University
چکیده [English]
Understanding the genetic control of temperament as a complex trait and correlated with economic traits is one of the breeding goals in beef cattle industry. The aim of the current study was genome wide association studies (GWAS) based on Gene set enrichment analysis for detecting the loci associated with temperament traits in Brahman cattle breed. Therefore, 1370 Brahman cattle and phenotype records associated with temperament traits including Exit velocity, Pen Score, and Temperament Score were used. The evaluation of genome-wide association was carried out using PLINK package 1.90. The gene enrichment analysis was performed by the goseq R package for identifying biological pathways of nearby genes in selected candidate regions and finally, GO, Metacyc, KEEG, Reactome and panther databases were applied for bioinformatics analysis. By Gene set enrichment analysis, the biological pathways and candidate genes of neurotransmitter secretion (NRXN3 and CACNG3), Dopamine Neurotransmitter Release Cycle (PPFIA2), regulation of neuron projection development (GRID2), neuron projection (SLC8A1 and KCNQ2), Axonal growth inhibition (RTN4R), Neurotrophin signaling pathway (MAP2K2, MAP3K5 and PSEN1) and Focal adhesion (TLN2) were identified. The detected candidate genes played an important role in differentiation of synapse, neurotransmitters, neurological diseases and disorders, oxidative and environmental stresses, hormone receptors and glucose homeostasis. Considering the confirmation of the previous region of genome wide association and the identification of new genomic regions, the findings of this study can be useful in the genetic selection of higher production cattle through calm animals.
کلیدواژه‌ها [English]
- Behaviour
- Bos indicus
- Candidate gene
- Gene ontology
- SNPchip
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