基于转录组分析挖掘平凉红牛背最长肌肉质性状候选基因

doi:10.11843/j.issn.0366-6964.2023.11.015

Abstract

Abstract: The aim of this study was to mine the candidate genes related to nutrient contents of longissimus lumborum in Pingliang red cattle, so as to improve the meat quality. Forty steers with 30-months-old slaughter age and 750 kg weight under the same feeding conditions were selected, and the contents of 3 conventional nutrients were measured, i.e., protein, fat, and moisture. The high and low groups with extreme differences in phenotypic data were selected, respectively, with 3 replicates each group. Principal component analysis and comparative transcriptome analysis were used to screen significant factor loading genes (SFLGs) and differentially expressed genes (DEGs), and these genes were subjected to enrichment analysis. Weighted gene co-expression network analysis (WGCNA) was performed using all sample transcriptome data and phenotype data to screen target gene modules (r>0.35 and P<0.05) and hub genes (HGs) related to phenotypes. The 91, 81, and 80 SFLGs (the first principal component PC1 and the second principal component PC2) and 18, 85, and 338 DEGs were identified for protein, fat, and moisture content traits, respectively. Among them, 8, 4, and 3 SFLGs were shared in PC1 and PC2, and 1, 3, and 2 DEGs showed significant factor loading, respectively. The enrichment analysis results were related to the corresponding phenotype. WGCNA screened 2 target gene modules respectively as well as 10, 14, and 26 HGs for protein, fat, and moisture contents, and all identified key candidate genes such as MYADML2 and ZBTB14, which might play important roles in influencing the proportional relationship among 3 nutrients. In this study, key genes related to meat quality traits were found by identifying candidates affecting 3 conventional nutrients contents. The research result will provide a theoretical basis for the breeding work of Pingliang red cattle and also provide reference for the quality breeding of other beef cattle.

Key words: Pingliang red steer, longissimus lumborum, nutrient contents, transcriptome

CLC Number:

S823.2

WANG Wenxiang, DU Lili, HU Junwei, ZHANG Yanxiang, MA Minghao, DUAN Rui, QIAN Cong, WANG Xinyue, LI Sanlu, ZHANG Changqing, ZHANG Lupei, GAO Xue, XU Lingyang, LI Junya, GAO Huijiang. Mining Candidate Genes Related to Meat Quality Traits of Longissimus Lumborum in Pingliang Red Steer Based on Transcriptome[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4589-4604.

References 41

[1]	GAJAWEERA C,CHUNG K Y,LEE S H,et al.Assessment of carcass and meat quality of longissimus thoracis and semimembranosus muscles of Hanwoo with Korean beef grading standards[J].Meat Sci,2020,160:107944.
[2]	KIM N K,CHO S,LEE S H,et al.Proteins in longissimus muscle of Korean native cattle and their relationship to meat quality[J]. Meat Sci,2008,80(4):1068-1073.
[3]	MAO Y W,HOPKINS D L,ZHANG Y M,et al.Beef quality with different intramuscular fat content and proteomic analysis using isobaric tag for relative and absolute quantitation of differentially expressed proteins[J].Meat Sci,2016,118:96-102.
[4]	WANG Y J,WANG Z S,HU R,et al.Comparison of carcass characteristics and meat quality between Simmental crossbred cattle,cattle-yaks and Xuanhan yellow cattle[J].J Sci Food Agric,2021,101(9):3927-3932.
[5]	GAO Y H,WANG S Z,MA Y F,et al.Circular RNA regulation of fat deposition and muscle development in cattle[J].Vet Med Sci,2022,8(5):2104-2113.
[6]	王子渲,王巧,张锦,等.基于脾脏转录组筛选北京油鸡和广明白鸡抗热应激相关功能基因[J].畜牧兽医学报,2023,54(5): 1905-1914.WANG Z X,WANG Q,ZHANG J,et al.Transcriptome based screening of functional genes related to heat stress resistance in Beijing you chickens and Guangming broilers[J].Acta Veterinaria et Zootechnica Sinica,2023,54(5):1905-1914.(in Chinese)
[7]	CHEN S F,ZHOU Y Q,CHEN Y R,et al.Fastp:an ultra-fast all-in-one FASTQ preprocessor[J].Bioinformatics,2018, 34(17): i884-i890.
[8]	KIM D,LANGMEAD B,SALZBERG S L.HISAT:a fast spliced aligner with low memory requirements[J].Nat Methods,2015, 12(4): 357-360.
[9]	LIAO Y,SMYTH G K,SHI W.featureCounts:an efficient general purpose program for assigning sequence reads to genomic features[J].Bioinformatics,2014,30(7):923-930.
[10]	PERTEA M,PERTEA G M,ANTONESCU C M,et al.StringTie enables improved reconstruction of a transcriptome from RNA-seq reads[J].Nat Biotechnol,2015,33(3):290-295.
[11]	NIHASHI Y,UMEZAWA K,SHINJI S,et al.Distinct cell proliferation,myogenic differentiation,and gene expression in skeletal muscle myoblasts of layer and broiler chickens[J].Sci Rep,2019,9(1):16527.
[12]	LOVE M I,HUBER W,ANDERS S.Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2[J]. Genome Biol,2014,15(12):550.
[13]	WU T Z,HU E Q,XU S B,et al.clusterProfiler 4.0:a universal enrichment tool for interpreting omics data[J].Innovation (Camb), 2021,2(3):100141.
[14]	LANGFELDER P,HORVATH S.WGCNA:an R package for weighted correlation network analysis[J].BMC Bioinformatics,2008, 9: 559.
[15]	WANG Z W,AN X J,YANG Y H,et al.Comprehensive analysis of the longissimus dorsi transcriptome and metabolome reveals the regulatory mechanism of different varieties of meat quality[J].J Agric Food Chem,2023,71(2):1234-1245.
[16]	IIDA F,SAITOU K,KAWAMURA T,et al.Effect of fat content on sensory characteristics of marbled beef from Japanese black steers[J].Anim Sci J,2015,86(7):707-715.
[17]	DOS SANTOS SILVA D B,FONSECA L F S,PINHEIRO D G,et al.Prediction of hub genes associated with intramuscular fat content in Nelore cattle[J].BMC Genomics,2019,20(1):520.
[18]	YANG S,LI C,XIE Y,et al.Detection of functional polymorphisms influencing the promoter activity of the SAA2 gene and their association with milk production traits in Chinese Holstein cows[J].Anim Genet,2015,46(6):591-598.
[19]	ANTONICKA H,SHOUBRIDGE E A.Mitochondrial RNA granules are centers for posttranscriptional RNA processing and ribosome biogenesis[J].Cell Rep,2015,10(6):920-932.
[20]	ZIENTARA-RYTTER K,SUBRAMANI S.The roles of ubiquitin-binding protein shuttles in the degradative fate of ubiquitinated proteins in the ubiquitin-proteasome system and autophagy[J].Cells,2019,8(1):40.
[21]	NGUYEN H A,VU S H,JUNG S,et al.SERTAD1 sensitizes breast cancer cells to doxorubicin and promotes lysosomal protein biosynthesis[J].Biomedicines,2022,10(5):1148.
[22]	YU H,FAN M H,CHEN X Y,et al.Activated autophagy-lysosomal pathway in dairy cows with hyperketonemia is associated with lipolysis of adipose tissues[J].J Dairy Sci,2022,105(8):6997-7010.
[23]	LI Z,ZHOU T,WU Y,et al.Investigation of the activity of cathepsin B in red shrimp (Solenocera crassicornis) and its relation to the quality of muscle proteins during chilled and frozen storage[J].J Food Sci,2022,87(4):1610-1623.
[24]	SKUGOR A,KJOS N P,SUNDARAM A Y M,et al.Effects of long-term feeding of rapeseed meal on skeletal muscle transcriptome,production efficiency and meat quality traits in Norwegian landrace growing-finishing pigs[J].PLoS One,2019,14(8): e0220441.
[25]	LÓPEZ-PEDROUSO M,LORENZO J M,DI STASIO L,et al.Quantitative proteomic analysis of beef tenderness of piemontese young bulls by SWATH-MS[J].Food Chem,2021,356:129711.
[26]	SHAFIEE G,ASGARI Y,SOLTANI A,et al.Identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysis[J].PeerJ,2018,6:e5239.
[27]	XU Z Y,CHEN W T,WANG L Y,et al.Cold exposure affects lipid metabolism,fatty acids composition and transcription in pig skeletal muscle[J].Front Physiol,2021,1:748801.
[28]	MILIARA X,GARNETT J A,TATSUTA T,et al.Structural insight into the TRIAP1/PRELI-like domain family of mitochondrial phospholipid transfer complexes[J].EMBO Rep,2015,16(7):824-835.
[29]	EBERLEIN A,KALBE C,GOLDAMMER T,et al.Analysis of structure and gene expression of bovine CCDC3 gene indicates a function in fat metabolism[J].Comp Biochem Physiol B Biochem Mol Biol,2010,156(1):19-25.
[30]	ZHAO Y H,CHEN S K,YUAN J N,et al.Comprehensive analysis of the lncRNA-miRNA-mRNA regulatory network for intramuscular fat in pigs[J].Genes (Basel),2023,14(1):168.
[31]	DANG Y L,DONG Q,WU B W,et al.Global landscape of m6A methylation of differently expressed genes in muscle tissue of liaoyu white cattle and simmental cattle[J].Front Cell Dev Biol,2022,10:840513.
[32]	ZHANG J,WANG J Y,MA C,et al.Comparative transcriptomic analysis of mRNAs,miRNAs and lncRNAs in the Longissimus dorsi muscles between fat-type and lean-type pigs[J].Biomolecules,2022,12(9):1294.
[33]	CARDOSO T F,QUINTANILLA R,CASTELLÓ A,et al.Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles[J].BMC Genomics,2018,19(1):145.
[34]	ÖZMEN Ö,KARAMAN K.Transcriptome analysis and potential mechanisms of bovine oocytes under seasonal heat stress[J]. Anim Biotechnol,2023,34(4):1179-1195.
[35]	ZHAO H H,SOUFAN O,XIA J G,et al.Transcriptome and physiological analysis reveal alterations in muscle metabolisms and immune responses of grass carp (Ctenopharyngodon idellus) cultured at different stocking densities[J].Aquaculture,2019, 503:186-197.
[36]	BRYSON T D,HARDING P.Prostaglandin E2 EP receptors in cardiovascular disease:an update[J].Biochem Pharmacol,2022,195: 114858.
[37]	YIN C Y,LIU W H,LIU Y S,et al.PID1 alters the antilipolytic action of insulin and increases lipolysis via inhibition of AKT/PKA pathway activation[J].PLoS One,2019,14(4):e0214606.
[38]	HU Z G,LIU X L.Integration of transcriptomics and non-targeted metabolomics reveals the underlying mechanism of skeletal muscle development in duck during embryonic stage[J].Int J Mol Sci,2023,24(6):5214.
[39]	PALOMBO V,MILANESI M,SGORLON S,et al.Genome-wide association study of milk fatty acid composition in Italian Simmental and Italian Holstein cows using single nucleotide polymorphism arrays[J].J Dairy Sci,2018,101(12):11004-11019.
[40]	NYLÉN C,AOI W,ABDELMOEZ A M,et al.IL6 and LIF mRNA expression in skeletal muscle is regulated by AMPK and the transcription factors NFYC,ZBTB14,and SP1[J].Am J Physiol Endocrinol Metab,2018,315(5):E995-E1004.
[41]	CHEN Z T,TENG J Y,DIAO S Q,et al.Insights into the architecture of human-induced polygenic selection in Duroc pigs[J].J Anim Sci Biotechnol,2022,13(1):99.

Mining Candidate Genes Related to Meat Quality Traits of Longissimus Lumborum in Pingliang Red Steer Based on Transcriptome

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