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| Identification of Candidate Genes Related to Meat Flavor in Liancheng White Duck (Anas platyrhynchos) Based on RNA-seq |
| ZHANG Lin-Li, LI Li, ZHU Zhi-Ming, MIAO Zhong-Wei, XIN Qing-Wu*, ZHENG Nen-Zhu* |
| Institute of Animal Science and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China |
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Abstract Liancheng white duck (Anas platyrhynchos) is a precious and rare waterfowl resource in China, and has high meat quality and unique flavor, while the formation mechanism of meat quality is still unclear. Exploring the genes related to meat quality and flavor can not only be helpful for the development and utilization of Liancheng white duck, but also provide a reference for breeding and meat quality evaluation of meat ducks. In this study, RNA-seq was used for transcriptome sequencing to screen differentially expressed genes in breast muscle transcriptome of Liancheng white duck and Cherry Valley duck; and functional annotation, enrichment analysis and qRT-PCR verification were carried out to explore the potential regulatory genes of meat quality formation in Liancheng white duck. A total of 44.31 Gb clean data was obtained by sequencing, and the mapping rate with reference genome was over 77.54%. The edge R analysis identified 912 differentially expressed genes between the two breeds, among which 424 were highly expressed genes and 488 were low expressed genes in Liancheng white duck. In Gene Ontology (GO) annotation, 772 differentially expressed genes were annotated, including 12 biological processes related to the formation of meat flavor substances, such as lipid metabolism, fatty acid metabolism, threonine catabolism, and carboxylic acid metabolism. KEGG pathway analysis showed that the differentially expressed genes were enriched in 179 signaling pathways, among which 12 pathways were significantly enriched, including flavor-related pathways such as the interaction between cytokines and receptors, linoleic acid metabolism and histidine metabolism, glycerophosphate metabolism and transforming growth factor (TGFβ) signaling pathway. According to the annotation of pathway function, the genes such as acidic amino acid decarboxylase 1 (GADL1), coiled-coil domain-containing protein 57 (CCDC57), and pyruvate dehydrogenase kinase, isozyme 4 (PDK4) were screened out and might play an important role in regulating the formation of delicious amino acids and fatty acids in Liancheng white duck, and further affecting the formation of chest muscle quality. Furthermore, 2 high expressed genes and 3 low expressed genes were selected for qRT-PCR verification, and the results were consistent with that of transcriptome sequencing, which indicated that the sequencing results were reliable. The present study provides a reference for further studying on the formation mechanism of meat flavor of Liancheng white duck and selection of genetic markers.
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Received: 25 September 2020
Published: 01 April 2021
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Corresponding Authors:
* xinqingwu6656@126.com; zhengnz@163.com
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[1] 邓文艺. 2019. 丙酮酸脱氢酶激酶4介导FXR调节肝脂质代谢的机制研究[D]. 硕士学位论文, 南华大学, 导师: 屈顺林, pp. 1-80.
(Deng W Y.2019. Mechanism of pyruvate dehydrogenase kinase 4 mediated FXR regulation of hepatic lipid metabolism[D]. Thesis for M.S., University of South China, Supervisor: Qu S L, pp. 1-80.)
[2] 何宗亮, 郗正林, 虞德兵, 等. 2015. 连城白鸭杂交后代肌肉氨基酸含量测定及评价[J]. 安徽农业科学, 43(14): 124-126.
(He Z L, Xi Z L, Yu D B, et al.2015. Content determination and evaluation of amino acids in hybrid offsprings of Liancheng white duck[J]. Journal of Anhui Agricultural Science, 43(14): 124-126.)
[3] 侯水生, 刘灵芝. 2019年水禽产业现状、未来发展趋势与建议[J]. 中国畜牧杂志, 2020, 56(03): 130-135.
(Hou S S, Liu L Z.2020. Current status, future development trends and recommendations of the waterfowl industry in 2019[J]. Chinese Journal of Animal Science, 56(03): 130-135.)
[4] 李颖慧, 李凤娜, 林彬彬, 等. 2014. IL-15 参与调控肌肉与脂肪组织代谢的新进展[J]. 细胞与分子免疫学杂志, 30(11): 1217-1220.
(Li Y H, Li F N, Lin B B, et al.2014. New progress of IL-15 in regulating muscle and fat tissue metabolism[J]. Chinese Journal of Cellular and Molecular Immunology, 11: 1217-1220.)
[5] 孟宪然, 杜琛, 王静, 等. 基于RNA_Seq识别山羊肉品质候选基因[J]. 畜牧兽医学报, 2015, 8(46): 1300-1307.
(Meng X R, Du C, Wang J, et al.2015. RNA-Seq approach for identifying cadidate genes of meat quality in goats[J]. Acta Veterinaria et Zootechnica Sinica, 8(46): 1300-1307.)
[6] 缪中纬, 朱志明, 辛清武, 等. 2014. 连城白鸭肉用新品系屠宰性能及肉质特性[J]. 福建农业学报, 29(02): 117-122.
(Miao Z W, Zhu Z M, Xin Q W, et al.2014. Slaughter performance and meat quality of new meat lines of Liancheng whith duck[J]. Fujian Journal of Agriculture Sciences, 29(02): 117-122.)
[7] 王继文, 李亮, 刘贺贺. 2019. 我国优质麻鸭育种研究现状[J]. 中国家禽, 41(15): 1-5.
(Wang J W, Li L, Liu H H.2019. Research status of high-quality shelduck breeding in China[J]. China Poultry, 41(15): 1-5.)
[8] 祖道海, 宋焕禄, 江新业. 2006. 连城白鸭肉质的研究[J]. 中国禽业导刊, 23(3): 40.
(Zu D H, Song H L, Jiang X Y.Study on the meat quality of Liancheng white duck[J]. Guide to Chinese Poultry, 2006(23): 40.)
[9] Bhuiyan M S A, Kim Y K, Kim H J, et al.2018. Genome-wide association study and prediction of genomic breeding values for fatty-acid composition in Korean Hanwoo cattle using a high-density single-nucleotide polymorphism array[J]. Journal of Animal Science, 96(10): 4063-4075.
[10] Bouwman A C, Visker M H, van Arendonk J M, et al.2014. Fine mapping of a quantitative trait locus for bovine milk fat composition on Bos taurus autosome 19[J]. Journal of Dairy Science, 97(2): 1139-1149.
[11] Brewer M S.2009. Irradiation effects on meat flavor: A review[J]. Meat Science, 81(1): 1-14.
[12] Chumngoen W, Tan F J.2015. Relationships between descriptive sensory attributes and physicochemical analysis of broiler and Taiwan native chicken breast meat[J]. Asian-Australasian Journal of Animal Sciences, 28(7): 1028-1037.
[13] de Jager N.2012. Gene expression studies in bovine skeletal muscle: Investigations into the effects of hormone growth promotant treatment, environment and tenderness genotype associated with tenderness and marbling[D]. Thesis for Ph.D., The University of Queensland, Suppervisor: Dalrympl B P, pp.1-261.
[14] Gardin A, White J.2010. The sanger mouse genetics programme: High throughput characterisation of knockout mice[J]. Acta Ophthalmologica, 89(s248): 925.
[15] Gasic S, Tian B.1999. Green A Tumor necrosis factor α stimulates lipolysis in adipocytes by decreasing Gi protein concentrations[J]. Journal of Biological Chemistry, 274(10): 6770-6775.
[16] He M, Wu P, Chen F, et al.2020. Transcriptome analysis of leg muscles in fast and slow growth Bian chickens[J]. Animal Biotechnology, 31(4): 295-305.
[17] Kumar A, Ruan M, Clifton K, et al.2012. TGF-β mediates suppression of adipogenesis by estradiol through connective tissue growth factor induction[J]. Endocrinology, 153(1): 254-263.
[18] Li W, Zhang X Y, Du J, et al.2020. RNA-seq-based quanitative transcriptome analysis of meat color and taste from chickens administered by eucalyptus leaf polyphenols extract[J]. Journal of Food Science, 85(4): 1319-1327.
[19] Liu P, Ge X M, Ding H Z, et al.2012. Role of glutamate decarboxylase-like protein 1 (gadl1) in taurine biosynthesis[J]. Journal of Biological Chemistry, 287(49): 40898-40906.
[20] Mahootchi E, Himaei S C, Kleppe R, et al.2020. GADL1 is a multifunctional decarboxylase with tissue specific roles in β-alanine and carnosine production[J]. Science Advances, 6(29): 1-19.
[21] Nam D, Guo B, Chatterjee S, et al.2015. The adipocyte clock controls brown adipogenesis through the TGF-β and BMP signaling pathways[J]. Journal of Cell Science, 128(9): 1835-1847.
[22] Piórkowska K, Żukowski K, Ropka-Molik K, et al.2018. A comprehensive transcriptome analysis of skeletal muscles in two Polish pig breeds differing in fat and meat quality traits[J]. Genetics and Nolecular Biology, 41(1): 125-136.
[23] Schulze S K, Kanwar R, Golzenleuchter M, et al.2012. SERE: Single-parameter quality control and sample comparison for RNA-Seq[J]. BMC Genomics, 13(1): 524-524.
[24] Shackelford S D, King A, Snelling W, et al.2019. Awardee talk-genomic control of fatty acid profile in beef[J]. Journal of Animal Science, 97(Supplement_3): 108.
[25] Shin S M, Kim K Y, Kim J K, et al.2003. Dexamethasone reverses TGF-β- mediated inhibition of primary rat preadipocyte differentiation[J]. FEBS letters, 543(1-3): 25-30.
[26] Smith D P, Northcutt J K, Qudsieh R I, et al.2015. Effect of strain on duck breast meat quality[J]. Journal of Applied Poultry Research, 24(3): 401-407.
[27] Sodhi S S, Song K D, Ghosh M, et al.2014. Comparative transcriptomic analysis by RNA-seq to discern differential expression of genes in liver and muscle tissues of adult Berkshire and Jeju Native pig[J]. Gene, 546(2): 233-242.
[28] Thoudam T, Ha C M, Leem J, et al.2019. PDK4 augments ER-mitochondria contact to dampen skeletal muscle insulin signaling during obesity[J]. Diabetes, 68(3): 571-586.
[29] Yu H, Zhao Z, Yu X, et al.2017. Bovine lipid metabolism related gene GPAM: Molecular characterization, function identification, and association analysis with fat deposition traits[J]. Gene, 609: 9-18. |
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