College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, People's Republic of China.
Department of Animal Sciences, Washington Center for Muscle Biology, Washington State University, Pullman, Washington, 99164-6310, USA.
BMC Genomics. 2022 Sep 9;23(1):644. doi: 10.1186/s12864-022-08857-2.
Donkey meat has low fat and high protein contents and is rich in various unsaturated fatty acids and trace elements that are beneficial to human digestion and absorption. IMF (intramuscular fat), also known as marbling, is an important indicator of the lean meat to fat ratio, which directly affects the tenderness and juiciness of the meat. At present, the underlying molecular variations affecting IMF content among donkey breeds are unclear. The Guangling donkey is an indigenous species in China. This study explored candidate regulatory genes that affect IMF content in Guangling donkeys. The IMF content of the longissimus dorsi muscle in 30 Guangling donkeys was measured. Six donkeys of similar age were selected according to age factors and divided into two groups, the high (H) and low (L) fat groups, according to their IMF content.
RNA-seq technology was used to compare the muscle transcriptome between the two groups. More than 75.0% of alternative splicing (AS) events were of the skipped exon (SE) type. A total of 887 novel genes were identified; only 386 novel genes were aligned to the annotation information of various databases. Transcriptomics analysis revealed 167 differentially expressed genes (DEGs), of which 64 were upregulated and 103 were downregulated between the H and L groups. Gene ontology analysis showed that the DEGs were enriched in multiple biological processes and pathways that are related to adipocyte differentiation, lipid synthesis, and neutral lipid metabolism. KEGG pathway analysis suggested that arachidonic acid metabolism, the HIF-1 signalling pathway, fructose and mannose metabolism, glycerophospholipid metabolism, and the AMPK signalling pathway were involved in lipid deposition. In addition, a gene-gene interaction network was constructed that revealed that the DEGs, including SCD, LEPR, CIDEA, DLK1, DGAT2, ITGAL, HMOX1, WNT10B, and DGKA, had significant roles in adipocyte differentiation and adipogenesis. The selected DEGs were further validated by qRT-PCR.
This study improves the in-depth understanding of gene regulation and protein expression regarding IMF deposition and lays a basis for subsequent molecular breeding studies in Guangling donkeys.
驴肉脂肪含量低，蛋白质含量高，富含多种对人体消化吸收有益的不饱和脂肪酸和微量元素。IMF（肌内脂肪），又称大理石纹，是瘦肉与脂肪比例的重要指标，直接影响肉质的嫩度和多汁性。目前，影响驴品种 IMF 含量的潜在分子变异尚不清楚。广灵驴是中国的本土品种。本研究探讨了影响广灵驴 IMF 含量的候选调控基因。测量了 30 头广灵驴背最长肌的 IMF 含量。根据年龄因素选择了 6 头年龄相近的驴，根据其 IMF 含量分为高（H）、低（L）脂肪组。
采用 RNA-seq 技术比较两组肌肉转录组。超过 75.0%的选择性剪接（AS）事件为外显子跳过（SE）类型。共鉴定出 887 个新基因；只有 386 个新基因与各种数据库的注释信息对齐。转录组分析显示 167 个差异表达基因（DEGs），其中 H 组与 L 组相比，上调基因 64 个，下调基因 103 个。基因本体论分析表明，DEGs 富集在多个与脂肪细胞分化、脂质合成和中性脂质代谢相关的生物学过程和途径中。KEGG 通路分析表明，花生四烯酸代谢、HIF-1 信号通路、果糖和甘露糖代谢、甘油磷脂代谢和 AMPK 信号通路参与了脂质沉积。此外，构建了基因-基因相互作用网络，揭示了 SCD、LEPR、CIDEA、DLK1、DGAT2、ITGAL、HMOX1、WNT10B 和 DGKA 等 DEGs 在脂肪细胞分化和脂肪生成中具有重要作用。通过 qRT-PCR 进一步验证了所选 DEGs。
本研究加深了对 IMF 沉积相关基因调控和蛋白表达的深入了解，为后续广灵驴分子育种研究奠定了基础。
