Circular RNA, microRNA and Protein Profiles of the Longissimus Dorsi of Germany ZIKA and Sichuan White Rabbits.

Xiangyu Zhang,Congyan Li,Min Lei,Xiaohong Xie,Zhiqiang Guo,Chao Yang,Dengping Huang,Liangde Kuang,Li Tang,Yongjun Ren,Yang Ji,Xiaodong Deng,Jie Zheng,Cuixia Zhang,Gaofu Wang

doi:10.3389/fgene.2021.777232

Xiangyu Zhang, Congyan Li + Show 13 more

Open Access

https://doi.org/10.3389/fgene.2021.777232

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Abstract

Due to the dietetic properties and remarkable nutritive value of rabbit meat, its industry is increasing rapidly. However, the association between circular RNAs, microRNAs, and proteins and muscle fiber type, and meat quality of rabbit is still unknown. Here, using deep sequencing and iTRAQ proteomics technologies we first identified 3159 circRNAs, 356 miRNAs, and 755 proteins in the longissimus dorsi tissues from Sichuan white (SCWrabs) and Germany great line ZIKA rabbits (ZIKArabs). Next, we identified 267 circRNAs, 3 miRNAs, and 29 proteins differentially expressed in the muscle tissues of SCWrabs and ZIKArabs. Interaction network analysis revealed some key regulation relationships between noncoding RNAs and proteins that might be associated with the muscle fiber type and meat quality of rabbit. Further, miRNA isoforms and gene variants identified in SCWrabs and ZIKArabs revealed some pathways and biological processes related to the muscle development. This is the first study of noncoding RNA and protein profiles for the two rabbit breeds. It provides a valuable resource for future studies in rabbits and will improve our understanding of the molecular regulation mechanisms in the muscle development of livestock. More importantly, the output of our study will benefit the researchers and producers in the rabbit breeding program.

Highlights

As a functional food, rabbit meat can provide properties and be remarkably nutritive (Dalle Zotte and Szendro, 2011)
We found that 1905 circRNAs were expressed in the muscle tissues of both rabbit breeds and that 426 and 828 circRNAs were expressed in Sichuan white rabbits (SCWrabs) and ZIKArabs, respectively
Using edgeR we identified 120 upregulated and 147 down-regulated circRNAs in the muscle tissues of SCWrabs compared to ZIKArabs (Figure 1D; Supplementary Table S2)

Summary

Introduction

Rabbit meat can provide properties and be remarkably nutritive (Dalle Zotte and Szendro, 2011). The rabbit industry for meat production is developing rapidly (van Harten and Cardoso, 2010; Paci et al, 2013) and has reached 200 million tons of meat every year, because rabbit meat has characteristics of rich protein, low cholesterol, and low fat. Improving the yield and quality of rabbit meat is important for the breeding program. Sichuan white rabbits (SCWrabs) are a unique Chinese domestic breed which has excellent characteristics, including strong adaptability, fecundity, and resistance to disease, easy to feed, and tender meat (Li S. et al, 2018). ZIKA rabbits (ZIKArabs) are a rabbit breed developed in Germany as a high yielding hybrid for the meat industry and can attend a weight of 3.2 kg in 84 days (Kuang et al, 2014). SCWrabs and ZIKArabs have significant differences in the growth rate, adult weight, and meat quality

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