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3个肉牛群体新转录本注释及功能解析
王正文1, 张凌云1, 安雪姣,等1
甘肃农业大学 动物科学技术学院
摘要:
【目的】挖掘肉牛(Bos taurus)新转录本,探讨其潜在功能,为进一步探明牛肉品质差异的遗传机制提供思路。【方法】以平凉红牛、杂交和牛(和牛×平凉红牛)和西门塔尔牛为研究对象,采集其背最长肌,进行RNA-seq测序,构建cDNA文库,将重新组装的测序数据与牛参考基因组序列进行比对分析,优化已注释转录本的信息,挖掘新转录本并对其进行功能富集分析。随机挑选9个显著差异表达的新转录本进行RT-qPCR验证。【结果】对1 081个转录本的5′非翻译区域(UTR)和1 586个转录本的3′UTR分别实现了延伸,并对1 038个转录本的5′和3′UTR都实现了延伸。挖掘新转录本442个,其中92个新转录本在不同群体间表达差异显著(P<0.05);GO分析显示,表达差异显著的新转录本在代谢过程、酶催化活性和细胞部分等显著富集;KEGG富集发现,显著差异表达的新转录本显著富集在味觉转导、过氧化物酶、河马(Hippo)和MAPK等信号通路中。RT-qPCR结果与RNA seq结果在定量方面存在差异,但变化趋势一致,说明转录组测序结果可靠。【结论】新转录本通过各种代谢途径和通路广泛参与调控牛肌肉生长、脂肪沉积、疾病和免疫等各项生命活动。
关键词:  平凉红牛  杂交和牛  西门塔尔牛  新转录本  肉质性状
DOI:
分类号:
基金项目:国家科技支撑计划项目(2015BAD03B04-4);甘肃省农业科技创新项目(GNCX-2014-32)
Annotation and function analysis on new transcripts of three beef cattle groups
WANG Zhengwen,ZHANG Lingyun,AN Xuejiao,et al
Abstract:
【Objective】This study discovered new transcripts of beef cattle (Bos taurus) and explored their potential functions to provide ideas for further research on genetic mechanism of beef quality differences.【Method】The longest dorsal muscle was collected for RNA-seq sequencing using Pingliang red cattle,crossbred Wagyu cattle (Wagyu×Pingliang Red Bull) and Simmental cattle as research subjects.The cDNA libraries were constructed,the reassembled sequencing data were compared with the bovine reference genome,the information of annotated transcripts was optimized,and new transcripts were searched to conduct functional enrichment analysis. Nine new transcripts with significant differences were randomly selected for RT-qPCR validation.【Result】Extensions were achieved for the 5′ untranslated region (UTR) of 1 081 transcripts and the 3′UTR region of 1 586 transcripts,including both regions of 1 038 transcripts.A total of 442 new transcripts were mined,92 of which were significantly (P<0.05) different expressed among groups.GO analysis showed that new transcripts with significantly differential expression were significantly enriched in metabolic processes,enzyme catalytic activity and cell parts.KEGG enrichment revealed that these new transcripts were significantly enriched in taste transduction,peroxisome,Hippo signaling pathway,and MAPK signaling pathway.The RT-qPCR results differed from the RNA-seq results in terms of quantification,but the trends were consistent,indicating that the transcriptome sequencing results were reliable.【Conclusion】These new transcripts widely involved in regulating cattle muscle growth,fat deposition,disease,immunity and other life activities through various metabolic pathways and pathways.
Key words:  Pingliang red cattle  crossbred Wagyu  Simmental cattle  new transcript  meat traits