Qi Xin, Gu Hongchang, Qu Lujiang
Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
Front Genet. 2021 Dec 3;12:774240. doi: 10.3389/fgene.2021.774240. eCollection 2021.
Transcriptome analysis has been used to investigate many economically traits in chickens; however, alternative splicing still lacks a systematic method of study that is able to promote proteome diversity, and fine-tune expression dynamics. Hybridization has been widely utilized in chicken breeding due to the resulting heterosis, but the dynamic changes in alternative splicing during this process are significant yet unclear. In this study, we performed a reciprocal crossing experiment involving the White Leghorn and Cornish Game chicken breeds which exhibit major differences in body size and reproductive traits, and conducted RNA sequencing of the brain, muscle, and liver tissues to identify the inheritance patterns. A total of 40 515 and 42 612 events were respectively detected in the brain and muscle tissues, with 39 843 observed in the liver; 2807, 4242, and 4538 events significantly different between two breeds were identified in the brain, muscle, and liver tissues, respectively. The hierarchical cluster of tissues from different tissues from all crosses, based on the alternative splicing profiles, suggests high tissue and strain specificity. Furthermore, a comparison between parental strains and hybrid crosses indicated that over one third of alternative splicing genes showed conserved patterns in all three tissues, while the second prevalent pattern was non-additive, which included both dominant and transgressive patterns; this meant that the dominant pattern plays a more important role than suppression. Our study provides an overview of the inheritance patterns of alternative splicing in layer and broiler chickens, to better understand post-transcriptional regulation during hybridization.
转录组分析已被用于研究鸡的许多经济性状；然而，可变剪接仍缺乏一种系统的研究方法，该方法能够促进蛋白质组多样性并微调表达动态。杂交由于产生杂种优势而在鸡育种中被广泛应用，但在此过程中可变剪接的动态变化显著却不清楚。在本研究中，我们进行了一项涉及白来航鸡和科尼什斗鸡品种的正反交实验，这两个品种在体型和繁殖性状上存在重大差异，并对脑、肌肉和肝脏组织进行了RNA测序以确定遗传模式。在脑和肌肉组织中分别检测到总共40515和42612个事件，在肝脏中观察到39843个；在脑、肌肉和肝脏组织中分别鉴定出两个品种之间有2807、4242和4538个事件存在显著差异。基于可变剪接谱对所有杂交组合不同组织的组织进行层次聚类，表明具有高度的组织和品系特异性。此外，亲本品系与杂交组合之间的比较表明，超过三分之一的可变剪接基因在所有三个组织中呈现保守模式，而第二常见的模式是非加性的，包括显性和超亲模式；这意味着显性模式比抑制作用发挥更重要的作用。我们的研究概述了蛋鸡和肉鸡中可变剪接的遗传模式，以更好地理解杂交过程中的转录后调控。
