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

Abstract

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.

Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differential isoform in skin tissues of different hair length Yak

“…In this study, a total of 9,845 novel genes and 66,989 isoforms were identified by PacBio seq, and nearly half of the gene loci were equal to or greater than 3Kb. Consistently with previous studies, PacBio identified more long transcripts than reference annotated transcripts [24,25]. In addition, numerous novel lncRNA was predicted from the Iso-seq.…”

Full-Length Transcriptome and Gene Expression Analysis of Different Ovis aries Adipose Tissues Reveals Transcript Variants Involved in Lipid Biosynthesis

“…Sequencing and data analysis procedures are shown in Figure 1 . Library preparation and sequencing followed previously reported methods with slight modifications [ 10 ]. Total RNA was extracted from frozen adipose tissues using TRIzol (Takara, Dalian, China) [ 12 ].…”

“…Gene transcripts undergo diverse splicing to generate various isoforms. With the commercialization of sequencing platforms and the reduced sequencing costs, transcriptome sequencing technology has found widespread application in animal transcriptome studies, including pigs [ 7 ], chickens [ 8 ], beef cattle [ 9 ], goats [ 10 ], and sheep [ 11 ]. Previous studies on sheep fat metabolism have primarily focused on short-read RNA-seq data from second-generation sequencing platforms [ 11 , 12 , 13 ].…”

Temporal Transcriptome Dynamics of Longissimus dorsi Reveals the Mechanism of the Differences in Muscle Development and IMF Deposition between Fuqing Goats and Nubian Goats

“…Mass accounts for 40–60% of the body weight of mammals, and skeletal muscle is considered the most important tissue for producing meat livestock. Many studies have focused on the growth and development of skeletal muscle to identify relevant biological mechanisms underlying meat yield and quality and offer the possibility of improving growth traits in goats [ 6 , 7 , 8 , 9 ]. In addition, skeletal muscle development in mammals can be divided into prenatal and postnatal stages; the number of muscle fibers increases before birth and the volume of muscle fibers increases after birth [ 10 ].…”

“…RNA sequencing is a high-throughput sequencing method for characterizing gene expression in specific tissues that provides accurate counts of transcripts to measure relative expression and to discover new exons or genes [ 16 ]. This approach is widely used for research on gene expression profiles revealing muscle growth and development, and the transcriptome profiles of different breeds and muscle tissues are becoming increasingly clear in goats [ 6 , 7 , 8 , 17 , 18 ]. Some functional differentially expressed genes (DEGs) from different kinds of materials in KEGG pathways, such as the Jak-STAT signaling pathway [ 18 ], MAPK signaling pathway [ 19 ], and PI3K-Akt signaling pathway [ 7 , 20 ], have been found to play crucial roles in muscle growth and development in goats.…”