Hybrid Sequencing in Different Types of Goat Skeletal Muscles Reveals Genes Regulating Muscle Development and Meat Quality.

Yangyang Pan,Jianhua Liu,Kaijie Yang,Sijia Chen,Xilin Bi,Shu Niu,Liying Qiao,Wenzhong Liu

doi:10.3390/ani11102906

Yangyang Pan, Jianhua Liu + Show 6 more

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https://doi.org/10.3390/ani11102906

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Abstract

Simple SummarySkeletal muscle development and meat quality are key traits of considerable importance to consumers and farmers. In the past, second-generation sequencing technology has been used to study genes regulating muscle development and meat quality. However, with the limitation of read length, goat transcriptome was constructed mainly on the basis of the merging of short reads, resulting in an insufficient understanding of goat transcriptome structures. Identification of full-length transcript structure was still a challenge. Therefore, in this study, a hybrid sequencing was conducted that combined the long-reading character of third-generation sequencing with the quantification ability of second-generation sequencing. By comparing the longissimus dorsi and biceps femoris muscles, genes and transcript isoforms regulating meat quality and muscle development of goat were identified. A large number of novel loci and isoforms were identified in the goats. Functional annotation of these genes showed that they were associated with skeletal muscle development and lipid metabolism.Domestic goats are commonly reared for meat and milk production in several regions of the world. However, the genetic mechanism underlying muscle development and meat quality of goats is limited. Therefore, the aim of this study was to identify known and novel genes regulating muscle development and meat quality of goats using second- and third-generation sequencing technologies. To achieve this, the meat quality and transcriptomes of longissimus dorsi (LD) and biceps femoris (BF) muscle tissues of Lingqiu Greyback goats were examined and compared. Differentially expressed genes (DEGs) and isoforms (DEIs) were functionally annotated. Results showed that 45,574 full-length transcripts covering 18,491 loci were characterized, and 12,566 genes were co-expressed in all samples. Differential expression analysis identified 231 DEGs, including 45 novel genes in the LD and BF muscles of the goats. Additionally, 1173 DEIs were found, in which 642 novel isoforms were identified in this study. Functional annotation and pathway analysis of the DEGs and DEIs revealed that some of them were associated with muscle growth and lipid metabolism. Overall, the findings of this study contribute to the understanding of the transcriptomic diversity underlying meat quality and muscle development of goat.

Highlights

Goats (Capra hircus) are reared in several countries, especially in mountainous regions and developing countries in subtropical and arid regions, for their meat, milk, and wool.goats possess high adaptability to harsh environmental conditions [1] and are consumed for their flavor and palatability
Meat quality parameters of the longissimus dorsi (LD) and biceps femoris (BF) muscles were analyzed after slaughter
There were no significant differences in the lightness and yellowness of two muscle types; the redness of BF muscle was significantly more intense (p < 0.05) than that of the LD muscle

Summary

Introduction

Goats (Capra hircus) are reared in several countries, especially in mountainous regions and developing countries in subtropical and arid regions, for their meat, milk, and wool.goats possess high adaptability to harsh environmental conditions [1] and are consumed for their flavor and palatability. Meat yield and quality are key traits of considerable importance to farmers and consumers; they are controlled by both genetic and environmental factors [2]. Compared with meat from other domestic animals, such as sheep, goat meat possesses higher dietetic qualities [8], such as leaner carcass and lower fat and intramuscular fat content [9]. The growth rate of goat muscle is usually lower than that of sheep. Meat tenderness is another quality trait of importance to consumers [10]; the level of tenderness differs considerably between muscle types [11]. It has been reported that the biceps femoris (BF) is tougher than the longissimus dorsi (LD) muscle in cattle [12]

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