Transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition

Li, Baojun; Qiao, Liying; An, Lifeng; Wang, Weiwei; Liu, Jianhua; Ren, Youshe; Pan, Yangyang; Jing, Jiongjie; Liu, Wenzhong

doi:10.1186/s12864-018-4747-1

Cited by 77 publications

(94 citation statements)

References 81 publications

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“…Whether these candidate genes play an important role in lipid deposition remains to be studied [54]. In addition, although various pathways, such as the "Wnt signaling pathway," "MAPK signaling pathway," "AMPK signaling pathway" and "PPAR signaling pathway" were not significantly enriched, they were related to fat development and deposition [56][57][58][59]. Therefore, the differentially expressed lncRNAs involved in the aforementioned pathways may play an important role in the process of lipid deposition and deserve further study.…”

Section: Discussionmentioning

confidence: 99%

Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep

Han

Liu

et al. 2020

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Background: Intramuscular fat (IMF) content has become one of the most important indicators for measuring meat quality, and its level is affected by various genes. Long non-coding RNAs (lncRNAs) are widely expressed non-coding RNAs that play an important regulatory role in a variety of biological processes; however, research on lncRNAs involved in sheep intramuscular fat deposition is still in its infancy. Aohan fine-wool sheep (AFWS), China's representative meat-hair, dual-purpose sheep breed, provides a great model for studying the role of lncRNAs in the regulation of intramuscular fat deposition. We identified lncRNAs by RNA sequencing in sheep longissimus dorsi muscle(LDM) samples at two ages: 2 months (Mth-2) and 12 months .Results: We identified a total of 26,247 genes and 6,935 predicted novel lncRNAs in LDM samples of sheep. Among these, 606 mRNAs and 408 lncRNAs were differentially expressed. We then compared the structural characteristics of lncRNAs and mRNAs. We obtained targeted genes of differentially expressed lncRNAs and performed an enrichment analysis using Gene Ontology(GO) and the Kyoto Encyclopedia of Genes and Genomes(KEGG). We found these targeted mRNAs were primarily enriched in lipid metabolism, lipid transport, regulation of primary metabolic processes and developmental pathways, such as alpha-linolenic acid metabolism, biosynthesis of unsaturated fatty acids, phosphonate and phosphinate metabolism and cell proliferation. Based on the results of this enrichment analysis, we obtained candidate lncRNAs that potentially regulate lipid deposition and constructed a lncRNA-mRNA co-expression network. We speculated that these lncRNAs have important regulatory roles in intramuscular fat deposition. We randomly selected five mRNAs and five lncRNAs to verify the accuracy of sequencing results by qRT-PCR.Conclusions: Our study provided a list of the lncRNAs and mRNAs related to intramuscular lipid deposition in sheep and lay the foundation for future research on regulatory mechanisms. BackgroundWith improvements in living standards and changes in patterns of consumption, high-quality lamb meat is becoming increasingly popular. Currently, evaluations of the meat quality of livestock have revealed that the content of intramuscular fat (IMF) is lower in carcass fats, yet IMF has a critically 4 important influence on the edibility and flavor of muscle meat [1]. Indeed, the quantity of IMF has become one of the most critical parameters in meat quality indicators, as it is considered to be positively related to meat quality and texture [2,3]. When a certain amount of fat is deposited between the muscle bundles and muscle fibers, the marbled section of the meat has a high score, and the meat is fresh and juicy, which is often considered ideal [4, 5]. The selective deposition of fat can improve production efficiency and play a key role in improving meat quality. This practice is also a major focus and difficulty of modern livestock breeding [6]. Therefore, ensuring the appropriate deposition of IMF in le...

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Section: Discussionmentioning

confidence: 99%

Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep

Han

Liu

et al. 2020

Preprint

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“…9,30 In our previous studies, the roles of Lpin2/3, angiopoietin-like protein 4, miR-124-3p, and other genes and non-coding RNAs in the regulation of fat deposition from two fat-tailed sheep breeds had been discussed. [31][32][33][34] Therefore, this study mainly focuses on the crucial role of sterol regulatory element binding proteins (SREBPs) in fat-tailed sheep base on the dynamical changes of serum lipid metabolism indicators. SREBPs including SREBP-1a, SREBP-1c and SREBP2 are mainly responsible for regulating cellular lipogenesis and lipid homeostasis.…”

Section: Discussionmentioning

confidence: 99%

Expression Patterns of SREBF1 and SREBF2 in Liver and Adipose Tissues of Two Fat-Tailed Sheep Breeds

Chen¹,

Qiao²,

Han³

et al. 2020

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Background The fat-tailed sheep is raised largely in China and other countries due to its high adaptability to nutritionally challenging environments and disease resistance as well as fat deposition in tails. So the purpose of the study is to explore the expression pattern and regulation mechanism of sterol regulatory element binding proteins (SREBPs) in liver and adipose tissues of fat-tailed sheep bases on its role in fat metabolism and deposition with sheep grown and development. Methods Two representative Chinese fat-tailed sheep breeds i.e. Guangling Large Tailed (GLT) and Small Tailed Han (STH) were employed to evaluate the ontogenetic expressions of SREBF1 and SREBF2 from seven different adipose tissues and liver at 4, 6, 8, 10 and 12 month by real-time PCR. Five serum indicators were detected, and the function speculation of SREBP1 and SREBP2 were evaluated by bioinformatics approaches. Results Serum indicators, especially total cholesterol TC and non-esterified fatty acid (NEFA) showed obvious differences and dynamical changes with the different development ages, gender factors only had a significant effect on serum NEFA concentrations. Both SREBF1 and SREBF2 mRNA expression in sheep were significantly affected by breed, tissue, age factors, and show a significant positive correlation (r = 0.286). Merely the expression of SREBF1 gene in STH is significantly higher than that in GLT, but SREBF2 gene expression is opposite. The expressions of SREBF1/2 in liver are extremely higher than that in seven adipose tissues, the interaction of two factors between breed and month age, breed and tissue, and tissue and gender also significantly affects its expression. Subcellular locations and function prediction imply that SREBP1/2 expressions are closely related with metabolism processes in cells. Conclusions The mRNA expression profiling of SREBF1 and SREBF2 showing a breed-specific, gender-specific, and temporal and spatial expressions differences, which imply that SREBF1/2 play a crucial role in lipid metabolism regulation during growth and development of two fat-tailed sheep. This study provides a phenotypic basis for further revealing the genetic mechanism in lipid metabolism and fat deposition that causes differences in ovine tail types, which also provides a novel insight for improving quality of meat.

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“…Using RNA-seq, a total of 19,878 genes were identi ed in tail fat tissues, among which 8,042 were differentially expressed between the two sheep breeds (FDR ≤ 0.001 and |Log 2 Ratio| ≥ 1). Li and co-workers reported 5,395 DEGs between tail fat tissues of Guangling large-tailed and small-tailed Han sheep [27]. In addition, 646 DEGs between Kazak and Tibetan sheep were reported by Wang et al [26], 390 DEGs between Lanzhou Fat-Tailed and Tibetan sheep by Ma et al [29] and 602 DEGs between Small-Tailed Han and Dorset sheep by Miao et al [28].…”

Section: Detection Of Variants In Candidate Genes Related To Tail-fatmentioning

confidence: 99%

“…Guangling Large-Tailed sheep and Small-Tailed Han sheep are two typical fat-tailed breeds in China. Upon application of RNA-Seq, a total of 4131 differentially expressed genes were determined in tail fat tissues of these two breeds, with FABP4, FABP5, ADIPOQ and CD36 identi ed as the four most highly transcribed genes [27]. Research on Small-Tailed Han and Dorset sheep revealed 602 differentially expressed genes, and GO analysis showed that several of these genes were enriched in the triglyceride biosynthetic process [28].…”

Section: Introductionmentioning

confidence: 99%

Comparative tail fat transcriptome analysis of key genes and pathways activated in response to fat deposition in two sheep breeds with extreme fat-tail phenotype differences

Zhang¹,

Xu²,

Wang³

et al. 2020

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Background Fat tail in sheep presents a valuable energy reserve that has historically facilitated adaptation to harsh environments. However, in modern intensive and semi-intensive sheep industry systems, breeds with leaner tails are preferred. For efficient selection of lean sheep breeds, clarification of the regulatory mechanisms underlying tail fat deposition of sheep is crucial. Altay and Xinjiang Fine Wool (XFW) sheep, two important breeds with distinct tail fat deposition properties, are mainly distributed in the Xinjiang district of China, and serve as ideal models for investigating the mechanisms of tail fat deposition. In the present study, RNA-Seq was applied to determine the transcriptome profiles of tail fat tissues in these two breeds, followed by analysis of differentially expressed genes (DEGs) and their sequence variations. Results In total, 21,527 genes were detected, among which 3,965 displayed significant expression variations in tail fat tissues of the two sheep breeds, including 707 upregulated and 3,258 downregulated genes. Gene Ontology (GO) analysis disclosed that 198 DEGs were related to fat metabolism. In Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the majority were significantly enriched in adipocytokine signaling, PPAR signaling, and metabolic pathways, with some genes being involved in multiple pathways. Among the 198 DEGs, 22 genes were markedly up or down regulated in tail fat tissue of Altay sheep, supporting their association with the fat tail trait of this breed. A total of 41,724 and 42,193 SNPs were detected in tail fat tissue transcriptomes of Altay and XFW sheep, respectively. The distribution of 7 SNPs in the coding regions of the 22 candidate genes was further investigated in three sheep populations with distinct tail types. In particular, the g.18167532 T/C mutation of ABCA1 and g.57036072 G/T mutation of SLC27A2 showed significantly different distributions and were closely associated with tail type. Conclusions The present study provides transcriptomic evidence explaining the differences in fat- and thin-tailed sheep breeds and reveals numerous DEGs and SNPs associated with tail type. Our data provide a valuable theoretical basis for selection of lean sheep breeds.

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Transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition

Cited by 77 publications

References 81 publications

Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep

Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep

Expression Patterns of SREBF1 and SREBF2 in Liver and Adipose Tissues of Two Fat-Tailed Sheep Breeds

Comparative tail fat transcriptome analysis of key genes and pathways activated in response to fat deposition in two sheep breeds with extreme fat-tail phenotype differences

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