The genome variation and developmental transcriptome maps reveal genetic differentiation of skeletal muscle in pigs.

Yalan Yang,Shuaicheng Li,Yongchao Niu,Jiaxing Chen,Kui Li,Guoqiang Yi,Xinhao Fan,Junyu Yan,Lixian Wang,Xiaoqin Liu,Yuwen Liu,Zishuai Wang,Longchao Zhang,Zhonglin Tang,Leif Andersson

doi:10.1371/journal.pgen.1009910

Abstract

Natural and artificial directional selections have resulted in significantly genetic and phenotypic differences across breeds in domestic animals. However, the molecular regulation of skeletal muscle diversity remains largely unknown. Here, we conducted transcriptome profiling of skeletal muscle across 27 time points, and performed whole-genome re-sequencing in Landrace (lean-type) and Tongcheng (obese-type) pigs. The transcription activity decreased with development, and the high-resolution transcriptome precisely captured the characterizations of skeletal muscle with distinct biological events in four developmental phases: Embryonic, Fetal, Neonatal, and Adult. A divergence in the developmental timing and asynchronous development between the two breeds was observed; Landrace showed a developmental lag and stronger abilities of myoblast proliferation and cell migration, whereas Tongcheng had higher ATP synthase activity in postnatal periods. The miR-24-3p driven network targeting insulin signaling pathway regulated glucose metabolism. Notably, integrated analysis suggested SATB2 and XLOC_036765 contributed to skeletal muscle diversity via regulating the myoblast migration and proliferation, respectively. Overall, our results provide insights into the molecular regulation of skeletal muscle development and diversity in mammals.

Highlights

Skeletal muscle development is a complex and dynamically regulated process of temporally separated but highly coordinated events including the determination of myogenic progenitor cells, myoblast proliferation and differentiation, myoblast fusion, and muscle growth and maturation [1]
All these events are precisely controlled by complex networks of spatially and temporally expressed genes according to strict time-sequence expression [7,8], including the Pax family (Pax3 and Pax7), the myogenic regulatory factor (MRF) family, and the myocyte enhancer factor 2 (MEF2) family [9]
Using strict criteria for long noncoding RNA identification as described previously [18,19], we identified a total of 1,661 novel long intergenic noncoding RNA, corresponding to 3,269 transcripts in skeletal muscle (S3 Table)

Summary

Introduction

Skeletal muscle development is a complex and dynamically regulated process of temporally separated but highly coordinated events including the determination of myogenic progenitor cells, myoblast proliferation and differentiation, myoblast fusion, and muscle growth and maturation [1]. Commercial Western breeds, such as Landrace pigs, have been intensively selected for rapid, large, and efficient accretion of muscle, while Chinese indigenous breeds, such as Tongcheng pigs, have lower growth rates, higher fat content and better meat quality [15]. These differences make them as an exceptional model to elucidate the underlying mechanisms of phenotype differentiation within species, especially in muscle mass and quality [15,16,17]. The genetic basis of transcriptome dynamic and diversity in skeletal muscle development remain unclear

Methods

Results

Conclusion