Abstract
Meat quality is one of the most important economic traits in pig breeding and production. Intramuscular fat (IMF) is a major factor that improves meat quality. To better understand the alternative splicing (AS) events underlying meat quality, long-read isoform sequencing (Iso-seq) was used to identify differential (D)AS events between the longissimus thoracis (LT) and semitendinosus (ST), which differ in IMF content, together with short-read RNA-seq. Through Iso-seq analysis, we identified a total of 56,789 novel transcripts covering protein-coding genes, lncRNA, and fusion transcripts that were not previously annotated in pigs. We also identified 456,965 AS events, among which 3930 were DAS events, corresponding to 2364 unique genes. Through integrative analysis of Iso-seq and RNA-seq, we identified 1174 differentially expressed genes (DEGs), among which 122 were DAS genes, i.e., DE-DAS genes. There are 12 overlapped pathways between the top 20 DEGs and DE-DAS genes, as revealed by KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, indicating that DE-DAS genes play important roles in the differential phenotype of LT and ST. Further analysis showed that upregulated DE-DAS genes are more important than downregulated ones in IMF deposition. Fatty acid degradation and the PPAR (peroxisome proliferator-activated receptor) signaling pathway were found to be the most important pathways regulating the differential fat deposition of the two muscles. The results update the existing porcine genome annotations and provide data for the in-depth exploration of the mechanisms underlying meat quality and IMF deposition.
Highlights
Meat quality is emerging as one of the most important economic traits in pig breeding and production, owing to the demands of consumers
36,499,249 filtered subread reads with an average length of 1383 bp and 395,182 circular consensus sequences (CCSs) with an average length of 1769 bp were obtained
CCSs were further classified into non-FL (88,282), FL (306,900), full-length nonconcatemer (FLNC) (293,556), and FLNC_polyA (293,459) reads based on the presence of
Summary
Meat quality is emerging as one of the most important economic traits in pig breeding and production, owing to the demands of consumers. Meat quality is a comprehensive indicator composed of the intramuscular fat (IMF) content, pH, tenderness, meat color, water-holding capacity, muscle fiber composition, etc. Most traits of meat quality exhibit low to moderate heritability [1,2], and they are expensive to measure. Selecting a meat quality using traditional methods, such as best linear unbiased prediction, is difficult. Molecular biology techniques have been developed to improve meat quality through molecular breeding strategies, for example, molecular marker-assisted selection. Many studies have focused on revealing the mechanisms underlying meat quality, which are the prerequisite for the molecular selection of the trait
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