Abstract
Meat color is considered to be the most important indicator of meat quality, however, the molecular mechanisms underlying traits related to meat color remain mostly unknown. In this study, to elucidate the molecular basis of meat color, we constructed six cDNA libraries from biceps femoris (Bf) and soleus (Sol), which exhibit obvious differences in meat color, and analyzed the whole-transcriptome differences between Bf (white muscle) and Sol (red muscle) using high-throughput sequencing technology. Using DEseq2 method, we identified 138 differentially expressed genes (DEGs) between Bf and Sol. Using DEGseq method, we identified 770, 810, and 476 DEGs in comparisons between Bf and Sol in three separate animals. Of these DEGs, 52 were overlapping DEGs. Using these data, we determined the enriched GO terms, metabolic pathways and candidate genes associated with meat color traits. Additionally, we mapped 114 non-redundant DEGs to the meat color QTLs via a comparative analysis with the porcine quantitative trait loci (QTL) database. Overall, our data serve as a valuable resource for identifying genes whose functions are critical for meat color traits and can accelerate studies of the molecular mechanisms of meat color formation.
Highlights
Linkage mapping methods[4,5,6,7], and the fine mapping work for meat color QTLs were subsequently conducted[8,9]
To identify the candidate genes that influence meat color traits, we performed a comparative analysis of the whole transcriptomes of biceps femoris (Bf; white muscle) and soleus (Sol; red muscle), which are characterized by obvious color differences, using RNA-seq technology
We identified a series of differentially expressed genes (DEGs) between these two tissue types, which represent potential candidate genes affecting meat color traits
Summary
To screen for critical candidate genes related to meat color traits, we identified DEGs between Bf and Sol muscles using two methods, DEseq[2] and DEGseq. 115 DEGs obtained from the DEseq[2] method were mapped to 95 KEGG pathways, and 12 of these KEGG pathways were significantly enriched (q ≤ 0.1); “metabolic pathway (ko01100)” contained the most DEGs (20 unigenes) (Supplementary Table S12 and Fig. 8) Of these pathways, “vitamin B6 metabolism,” “glutathione metabolism,” “biosynthesis of unsaturated fatty acids,” and “fatty acid elongation” could all be related to the formation of meat color. Our data provide a comprehensive overview of the transcriptome of Bf and Sol muscles, which exhibit obvious meat color differences, and identify several potential metabolic pathways and many interesting candidate genes potentially involved in meat color traits. Our results lay a solid foundation for elucidating the mechanisms of meat color formation, and the DEGs identified represent the potential valuable candidate genes for meat color traits
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