Screening and Characterization of LncRNA Associated with Marbling Grade in Beef Cattle

doi:10.7668/hbnxb.20193934

Abstract

Abstract:

Beef marbling is an important meat quality trait regulated by multiple genes and is one of the conditions to measure the quality of high grade beef.LncRNA is an important non-coding RNA that plays an important role in regulating the biological processes related to fat deposition.To understand the potential biological role of lncRNA in different marbling phenotypes in beef cattle,this study collected crossbred and the longest dorsal muscle tissues from two extreme grades of high(A5)and low(A1)marbling,and used high-throughput sequencing to detect differential lncRNA associated with meat marbling,predict the trans-acting target genes of differential lncRNA,and perform functional enrichment for the analysis.The results showed that a total of 45 significantly different lncRNA were screened in two grades of marbled beef tissues,including 21 and 24 significantly up- and down-regulated lncRNA in high-grade marbled tissues,respectively,including MSTRG.9509.3,ENSBTAT00000077612,ENSBTAT00000072841 and other lncRNA associated with lipid deposition.Functional enrichment analysis of trans-acting target genes showed that predicted target genes were significantly enriched to lipopolysaccharide binding,lipolysis and other biological processes associated with lipid deposition.Differential lncRNA may be involved in regulating beef marbling phenotypic traits by targeting fat deposition-related genes(FABP4,PLIN1,LIPE,etc.)through trans-activation.The detection of beef marbling-related differential lncRNA,predicted target genes and their enrichment pathways would provide a basis for expanding the understanding of the biological functions of non-coding RNAs and their relationship with beef marbling characteristics,as well as a reference for the analysis of quality traits and breeding of new breeds in agricultural livestock.

Key words: Beef cattle, Marbling, LncRNA, Intramuscular fat, Meat quality

ZENG Ling, ZHANG Yanfeng, LI Chenglong, DING Yanling, ZHOU Xiaonan, MING Wenxuan, SU Zonghua, QU Chang, XU Junjie, SHI Yuangang, KANG Xiaolong. Screening and Characterization of LncRNA Associated with Marbling Grade in Beef Cattle[J]. Acta Agriculturae Boreali-Sinica, 2023, 38(S1): 371-380. doi: 10.7668/hbnxb.20193934.

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URL: http://www.hbnxb.net/EN/10.7668/hbnxb.20193934

http://www.hbnxb.net/EN/Y2023/V38/IS1/371

Figures/Tables 10

Fig.1 Marbling grade phenotypes of crossbred Wagyu cattle A.Muscle tissue with a marbling grade of A1;B.Muscle tissue with a marbling grade of A5.

Tab.1 Primer information of quantitative validation for lncRNA

引物名称 Primer name	引物序列(5'—3') Primer sequences(5'—3')	产物长度/bp Product length	退火温度/℃ Annealing temperature
MSTRG.9911.1	F:CCCTCTGTGCCTGCTATT	187	54.0
	R:GGTTCCCGATGTAAGTGTC
MSTRG.9509.3	F:CACCTTGGCTGGTAACGC	352	56.3
	R:GGAGGGATCTCGGATTGG
ENSBTAT00000071741	F:ACTTCCGCCTTGCTTTCAG	141	57.0
	R:CCTTCCCTCAGCGTTGGT
MSTRG.1867.3	F:GCCCTTGTGCCCTGTAGAAA	222	59.0
	R:CCAAGCCCAGTGTCAGTGTCT
ENSBTAT00000077612	F:CATAGGGACTGTCGTGATT	141	50.4
	R:TTCCGATTCTTCTGCTTT
MSTRG.2227.1	F:CCTCATTCCCTGTTGGTT	189	50.3
	R:TATTGGCACTTTGGCTTC
ENSBTAT00000079684	F:GGGTTACATAAGGATTCAAGTT	222	52.0
	R:AAGTAAGAGGTTAGGCAGGTC
ENSBTAT00000072841	F:GGGCAACGCTGAGGTCTA	158	55.0
	R:GCACGAACTCGAAACAATCT
MSTRG.9442.3	F:CCCATGAGACCAGTTGAT	419	51.3
	R:TGAAGGAAAGACAGAGGC
GAPDH	F:TCGGAGTGAACGGATTCGGC	82	54.0
	R:ATGGCGACGATGTCCACTTT

Tab.2 Statistical analysis of sequencing data quality control

样品 Samples	原始序列 Raw reads	纯净序列 Clean reads	纯净序列/原始序列/% Clean reads/Raw reads	Q20/%	Q30/%
A1-1	111 554 164	111 194 184	99.68	97.54	93.56
A1-2	101 269 128	100 892 594	99.63	97.22	92.88
A1-3	96 917 862	96 549 646	99.62	97.14	92.69
A5-1	90 769 326	90 410 038	99.60	97.22	93.00
A5-2	96 145 566	95 822 408	99.66	97.26	93.13
A5-3	91 064 624	90 728 852	99.63	97.39	93.25

Tab.3 Sequencing data genome alignment statistics

样品 Samples	总数据/条 Total reads	比对量/条 Map reads	比对率/% Map rate	唯一比对/条 Unique mapped	唯一比对率/% Unique mapped rate
A1-1	110 637 006	104 215 448	94.20	99 466 504	89.90
A1-2	100 489 580	94 541 731	94.08	89 773 862	89.34
A1-3	95 736 800	89 862 658	93.86	84 910 423	88.69
A5-1	89 742 628	84 181 762	93.80	79 015 339	88.05
A5-2	95 508 118	89 146 832	93.34	84 419 850	88.39
A5-3	90 293 804	85 179 073	94.34	80 724 889	89.40

Fig.2 Distribution of lncRNA expression abundance and identification of novel lncRNA A.The horizontal coordinate is log₁₀FPKM,the higher values,higher gene expression;the vertical coordinate is the density of genes,i.e.the number of genes corresponding to a certain of expression level on the horizontal axis;The peak indicates the highest number of protein-coding genes at this expression level;B.Violin plots of gene expression levels for each sample:the length of the vertical axis represents the degree of data dispersion,and the width of the horizontal axis represents the distribution of data at a given vertical coordinate position;C.Venn diagram of CNCI and CPC2 annotation;D.Statistical plot of new lncRNA transcript types.

Fig.3 Expression patterns of differential lncRNA associated with extreme grades of marbling A.Statistics of the number of differential lncRNA in A1 and A5 groups;B.Differential lncRNA volcano plot:y-axis is the logarithm of Padj,x-axis is the difference multiplier;C.Heatmap of differential lncRNAs in A1 and A5 groups.Each column represents one sample,each row represents one lncRNA;genes expression in different samples are indicated by different colors,red for high expression and blue for low expression.

Fig.4 GO functional enrichment of marbling-associated differential lncRNA for target gene A:1.Plasma membrane part;2.Cell surface;3.External side of plasma membrane;4.Side of membrane;5.Extracellular region part;6.Extracellular region;7.Intrinsic component of plasma membrane;8.Cell periphery;9.Plasma membrane;10.Integral component of plasma membrane;11.Extracellular space;12.Plasma membrane protein complex;13.Membrane part;14.Plasma membrane region;15.Intrinsic component of membrane;16.Collagen-containing extracellular matrix;17.Synaptic membrane;18.Extracellular matrix;19.Plasma membrane receptor complex;20.Receptor complex.B:1.Transmembrane transporter activity;2.Signaling receptor binding;3.Transporter activity;4.Motor activity;5.Lipopolysaccharide binding;6.C-C Chemokine receptor activity;7.C-C Chemokine binding;8.Cytokine receptor activity;9.Non-membrane spanning protein tyrosine kinase activity;10.ATP-dependent Microtubule motor activity;11.Microtubule motor activity;12.G Protein-coupled chemoattractant receptor activity;13.Chemokine receptor activity;14.Androsterone dehydrogenase activity;15.Cell adhesion molecule binding;16.Chemokine activity;17.Monooxygenase activity;18.Inorganic molecular entity transmembrane transporter activity;19.Active transmembrane transporter activity;20.Cation transmembrane transporter activity.C:1.Immune system process;2.Immune response;3.Regulation of immune system process;4.Cell activation;5.Response to external stimulus;6.Defense response;7.Leukocyte activation;8.Positive regulation of immune system process;9.Regulation of cell activation;10.Lymphocyte activation;11.Cell surface receptor signaling pathway;12.Response to other organism;13.Response to external biotic stimulus;14.Response to biotic stimulus;15.Immune effector process;16.Regulation of leukocyte activation;17.Biological adhesion;18.Regulation of response to stimulus;19.Innate immune response;20.Regulation of immune response.

Fig.5 KEGG pathway enrichment of target gene from differential lncRNA 1.Herpes simplex infection;2.Viral protein interaction with cytokine and cytokine receptor;3.Base excision repair;4.Cytokine-cytokine receptor interaction;5.Apoptosis;6.Cell adhesion molecules(CAMs);7.Longevity regulating pathway-worm;8.Chemokine signaling pathway;9.Ovarian steroidogenesis;10.Bile secretion;11.Graft-versus-host disease;12.Hematopoietic cell lineage;13.Kaposi sarcoma-associated Herpesvirus infection;14.Natural killer cell mediated cytotoxicity;14.Regulation of lipolysis in adipocyte;16.Antigen processing and presentation;17.IL-17 Signaling pathway;18.TypeⅠ diabetes mellitus;19.Complement and coagulation cascades;20.Antifolate resistance.

Fig.6 A regulatory network of fat deposition-associated lncRNA-target gene-biological processes Rectangles.Differentially expressed lncRNA;Diamonds.Target genes;Triangles.Biological processes associated with fat deposition;Green.Up-regulated gene expression;Red.Down-regulated gene expression.

Fig.7 Comparison of RNA-seq and qRT-PCR results

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