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. 2020 Feb 10;11(2):183.
doi: 10.3390/genes11020183.

Comparative Transcriptome Analysis Identifying the Different Molecular Genetic Markers Related to Production Performance and Meat Quality in Longissimus Dorsi Tissues of MG × STH and STH Sheep

Shuru Cheng  1 , Xueying Wang  2 , Quanwei Zhang  3 , Yuqin He  3 , Xia Zhang  3 , Lei Yang  1 , Jinping Shi  1
Affiliations

Comparative Transcriptome Analysis Identifying the Different Molecular Genetic Markers Related to Production Performance and Meat Quality in Longissimus Dorsi Tissues of MG × STH and STH Sheep

Shuru Cheng et al. Genes (Basel). .

Abstract

Crossbred sheep have many prominent traits, such as excellent production performance and high-quality meat, when compared to local sheep breeds. However, the genetic molecular markers related to these characteristics remain unclear. The crossbred MG × STH (small-tailed Han sheep (STH) × Mongolian sheep (MG)) breed and the STH breed were selected to measure production performance and meat quality. We used 14 indexes of production performance and meat quality, which in the MG × STH population showed significant differences compared to the STH breed. Subsequently, the longissimusdorsi from the two sheep were subjected to comparative transcriptomic analyses to identify differentially expressed genes (DEGs) related to production performance and meat quality. A total of 874 DEGs were identified between the two sheep groups. A total of 110 unique DEGs related to sheep production performance and meat quality were selected as the candidate DEGs. We found 6 production-performance-related and 30 meat-quality-related DEGs through a correlation analysis, including SPARC, ACVRL1, FNDC5 and FREM1. The expression levels of 11 DEGs were validated by real-time PCR, and the results were in accordance with the results of the comparative transcriptomic and correlation analyses. These results will assist in understanding sheep heterosis and molecular marker-assisted selection.

Keywords: Ovis aries; crossbred; genetics; meat quality; production performance; transcriptome.

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Conflict of interest statement

The authors declare that no conflicts of interest exist. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Significantly different indexes related to production performance and meat quality between the Mongolian (MG) × small-tailed Han (STH) sheep and the STH sheep. (A–D) The indexes of chest circumference, live weight, carcass weight, and net meat mass used for evaluating the production performance of MG × STH and STH sheep. (E) The marbling of MG × STH and STH sheep. The black arrow shows the deposited fat in the marbling. (F–H) The indexes of cooking loss, yellowness (b*), and shear force used for assessing the meat quality of the MG × STH and STH sheep. **p < 0.001.
Figure 2
Figure 2
Identity and functional analysis of the differentially expressed genes (DEGs) from longissimus dorsi tissues in the MG × STH and STH sheep. (A) Total number of genes identified by transcriptome sequencing in the two sheep groups. (B) The number of DEGs compared to the STH sheep. (C) Volcano plot of the DEGs. (D) The significant gene ontology (GO) numbers of cellular components, molecular functions, and biological processes (p < 0.05). (E) Top 10 most significant pathways according to the DEGs in the two sheep groups (p < 0.05), where the x axis represents the number of DEGs.
Figure 3
Figure 3
Identification of candidate DEGs related to production performance and meat quality in the MG × STH and STH sheep. (A) Identification of the candidate DEGs related to growth and development in the two sheep groups. (B) A heatmap of the DEGs related to growth, development, and meat quality in each group. (C) A Venn diagram of DEGs related to growth, development, and meat quality. (D) The common DEGs involved in growth, development, and meat quality and their relative expression using a transcriptomic analysis. The x axis represents the relative expression by −log2(Fold Change).
Figure 4
Figure 4
A correlation analysis between DEGs and production performance and meat quality traits. (A) A heatmap of the gene–trait relationship established according to the Pearson correlation of DEGs and significantly different production performance and meat quality traits. (B) A Sankey diagram created with Pearson correlation coefficient thresholds >0.75 or <−0.75. (C,D) The relative expression of five candidate DEGs from RNA-seq data, where the expression value was calculated according to the log(FPKMs). FPKMs: Fragments per kilobase million.
Figure 5
Figure 5
Gene co-expression analyses of targeted DEGs related to sheep production performance and meat quality. (A) A Venn diagram of DEGs with Pearson correlation coefficient thresholds >0.75 or <−0.75 related to production performance and meat quality. (B) A heatmap of four DEGs related both to production performance and to meat quality. (C) The gene co-expression network of targeted DEGs (>0.75 or <−0.75) related to sheep production performance and meat quality.
Figure 6
Figure 6
Validation of 11 target DEGs in terms of transcriptome and correlation analysis data. (A) qRT-PCR analysis of six DEGs validated for transcriptome data. (B) qRT-PCR analysis of five DEGs validated for trait-associated correlation analysis data. The values were calculated using the 2−ΔΔCt method: * p < 0.05, ** p < 0.01.
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