Comparison of transcriptome between high- and low-marbling fineness in longissimus thoracis muscle of Korean cattle

Abstract

Objective: This study compared differentially expressed genes (DEGs) between groups with high and low numbers of fine marbling particles (NFMP) in the longissimus thoracis muscle (LT) of Korean cattle to understand the molecular events associated with fine marbling particle formation. Methods:The size and distribution of marbling particles in the LT were assessed with a computer image analysis method. Based on the NFMP, 10 LT samples were selected and assigned to either high-(n = 5) or low-(n = 5) NFMP groups. Using RNA sequencing, LT transcriptomic profiles were compared between the high-and low-NFMP groups. DEGs were selected at P < 0.05 and |fold change| > 2 and subjected to functional annotation. Results:In total, 328 DEGs were identified, with 207 up-regulated and 121 down-regulated genes in the high-NFMP group. Pathway analysis of these DEGs revealed five significant (P < 0.05) Kyoto Encyclopedia of Genes and Genomes pathways; the significant terms included endocytosis (P = 0.023), protein processing in endoplasmic reticulum (P = 0.019), and adipocytokine signaling pathway (P = 0.024), which are thought to regulate adipocyte hypertrophy and hyperplasia. The expression of sirtuin4 (P < 0.001) and insulin receptor substrate 2 (P = 0.043), which are associated with glucose uptake and adipocyte differentiation, was higher in the high-NFMP group than in the low-NFMP group. Conclusion:Transcriptome differences between the high-and low-NFMP groups suggest that pathways regulating adipocyte hyperplasia and hypertrophy are involved in the marbling fineness of the LT.

Recent developments and future directions in meta-analysis of differential gene expression in livestock RNA-Seq

“…For longer transcripts with many isoforms or non-poly(A) transcripts, traditional RNA-Seq may be more appropriate. To date, QuantSeq has been deployed in transcriptomic studies of multiple livestock species, including cattle ( Pascottini et al, 2021 ; Beak and Baik, 2022 ; Busato et al, 2022 ; Pedroza et al, 2022 ), sheep ( Kubik et al, 2018 ), chicken ( Ibrahim et al, 2021 ) and pigs ( Dong et al, 2018 ; Kroeske et al, 2021 ; Schroyen et al, 2021 ; Kramer et al, 2022 ).…”

— Invited Review — Factors affecting beef quality and nutrigenomics of intramuscular adipose tissue deposition

“…We compared the transcriptomes of high-and low-marbling-fineness groups of longissimus thoracis (LT) muscle from Korean cattle. We identified 328 differentially expressed genes (DEGs), analysis of which revealed that pathways regulating adipocyte hyperplasia and hypertrophy are involved in the marbling fineness of the LT [19].…”

Identification of several lncRNA-mRNA pairs associated with marbling trait between Nanyang and Angus cattle

“…At present, studies have screened out differential lncRNAs related to intramuscular fat deposition in muscle samples of beef cattle and other livestock via transcriptome sequencing, and combined this with functional enrichment pathway analysis to regulate the biological processes of intramuscular fat deposition associated with marbling formation. Research has discovered that pathways related to fat proliferation, fat droplet hypertrophy, and adipocyte differentiation are implicated in the formation of marbling patterns in beef cattle muscle tissue [ 15 ]. In Hanwoo beef cattle, three types of samples, namely muscle, intramuscular adipose, and subcutaneous adipose, were taken for RNA sequencing, with the aim of identifying the lncRNAs associated with shear force, body weight, and muscle function [ 16 ].…”