Abstract
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.
Highlights
Splicing of pre-mRNA is a crucial post-transcriptional process that increases proteome diversity in eukaryotes
Alternative splicing (AS) events were quantified as percent spliced-in (PSI) and classified into five types―alternative 3′ splice sites (A3SS), alternative 5′ splice sites (A5SS), mutually exclusive exons (MXE), RI, and SE―while statistically significant differences between White Leghorn (WL) and Cornish Game (CG) were identified
SE formed a large proportion of splicing in the brain and muscle tissues, A3SS was slightly higher than SE in the liver tissue, and RI only accounted for 3% of the tissues. 28, 38, and 44% of genes only underwent one splicing, and over 56% of events among the tissues were complex events (Figure 2A)
Summary
Splicing of pre-mRNA is a crucial post-transcriptional process that increases proteome diversity in eukaryotes. Alternative splicing (AS) generates multiple isoforms from a single gene using different combinations of exons. AS is a widespread and complex component of gene regulation in humans and domestic animals, and increasing evidence suggests that aberrant AS functionality can be the cause or consequence of many diseases, and may associating with economically important traits in domestic animals (Pan et al, 2008; Merkin et al, 2012; Gao et al, 2018; Dlamini et al, 2021). Splice-altering therapies using animal models have been extensively studied for many diseases such as neurodegeneration and muscular dystrophies, and AS events have emerged as Splicing Patterns in F1 Chickens new biomarkers in some circumstances (Montes et al, 2019; Zhao, 2019). It is important to study the AS regulatory mechanisms in birds
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