Analysis of Differential Expression Genes Related to Organic Acid in Fruits of Two Citrus Cultivars
WANG Jian-Hui1*, YANG Xin2, GONG Xiao-Yuan1, YU Jie-Lin1, HAN Dong-Mei1, LI Lin2, LI Xiang1, LIU Da-Yu1, LI Jing-Jing3, TANG Jiang4
1 College of Food and Biological Engineering, Chengdu University, Chengdu 610000, China; 2 College of Ecology and Environment, Chengdu University of Technology, Chengdu 610000, China; 3 The Sixth People's Hospital of Chengdu, Chengdu 610000, China; 4 Anyue Lemon Science and Technology Institute, Anyue County 642350, China
Abstract Fruit flesh of Citrus is rich in citrate and other nutrients. To better understand the effects of differential expression of genes (DEGs) on citrate and other important metabolites in Citrus, both fruit qualities and RNA-seq analysis were performed between 'Sweet lemon' and 'Eureka', respectively. The comparative analysis between 2 cultivars had been implemented using transcriptomics technology to identify the DEGs, which caused citrate accumulating in pulp. After transcriptomic sequencing for each fruit in 3 replicates, 73 678 unigenes had been obtained, out of which the total 4 044 unigenes were differentially expressed between 2 cultivars. Subsequently, DEGs were further enriched into different pathways by KEGG. The upregulating DGEs in 'Sweet lemon' with lower citrate contents were enriched into 24 pathways, including GABA shunt. Besides, upregulating DEGs in 'Eureka' with higher citrate contents were enriched into 13 pathways, including citrate cycle. At fruit ripening stage, the significantly differential expression of citrate synthase was not found between 2 cultivars. In addition, proton pump gene in 'Eureka' had higher transcription levels than 'Sweet lemon' at fruit ripening stage, so that it was benefit for vacuole acidification in fruit. It could be concluded that up-regulating expression of genes involved into citrate metabolism and proton transporting were correlated with organic acidity accumulations in Citrus fruits. This study provides an insight into organic acids metabolism in Citrus and is useful for breeding program in future.
WANG Jian-Hui,YANG Xin,GONG Xiao-Yuan, et al. Analysis of Differential Expression Genes Related to Organic Acid in Fruits of Two Citrus Cultivars[J]. 农业生物技术学报, 2023, 31(4): 718-729.
[1] 邓秀新. 2022. 中国柑橘育种 60 年回顾与展望[J]. 园艺学报, 49(10): 2063-2074. (Deng X X. 2022. A review and perspective for citrus breeding in China during the last six decades[J]. Acta Horticulturae Sinica, 49(10): 2063-2074. ) [2] 盛玲. 2017. GABA 支路调控柑橘果实柠檬酸代谢的机理研究[D]. 博士学位论文, 华中农业大学, 导师: 程运江, pp. 85-88. (Sheng L. 2017. Mechanism of gamma-ami-nobutyric acid shunt regulating citrate metabolism in cit-rus fruit[D]. Thesis for Ph. D., Huazhong Agricultural University, Supervisor: Cheng Y J, pp. 85-88. ) [3] 夏荣娜, 李凛, 杨鑫, 等. 2020. 血橙果肉 MYB 转录因子的克隆与表达分析[J]. 农业生物技术学报, 28(7): 11-20. (Xia R N, L L,Y X, et al. 2020. Cloning and expression analysis of MYB transcription factor in blood orange (Citrus sinensis)[J]. Journal of Agricultural Biotechnolo-gy, 28(7): 11-20. ) [4] 周媛. 2020. 柑橘果实糖酸代谢与镁的关系及其机制[D]. 博士学位论文, 华中农业大学, 导师: 胡承孝, pp. 57-59. (Zhou Y. 2020. The relationship between citrus fruit sug-ar and organic acid metabolism and magnesium and its mechanism[D]. Thesis for Ph. D., Huazhong Agricultural University, Supervisor: Hu C X, pp. 57-59. ) [5] Anders S, Huber W. Differential expression analysis for se-quence count data[J]. Genome Biology, 11(10): R106. Aprile A, Federici C, Close T J, et al. 2011. Expression of the H+-ATPase AHA10 proton pump is associated with cit-ric acid accumulation in lemon juice sac cells[J]. Func-tional & Integrative Genomics, 11(4): 551-63. [6] Avi S, Esther D, Etti O, et al. 2000. NADP+ -isocitrate dehydro-genase gene expression and isozyme activity during citrus fruit development[J]. Plant Science, 158(1): 173-181. [7] Bo L, Colin N D. 2011. RSEM: Accurate transcript quantifica-tion from RNA-Seq data with or without a reference ge-nome[J]. BMC Bioinformatics, 12: 323. [8] Butelli E, Garcia-Lor A, Licciardello C, et al. 2017. Changes in anthocyanin production during domestication of citrus[J]. Plant physiology, 173(4): 2225-2242. [9] Butelli E, Concetta L, Chandrika R, et al. 2019. Noemi con-trols production of flavonoid pigments and fruit acidity and illustrates the domestication routes of modern citrus varieties[J]. Current Biology, 29(1): 158-164. [10] Grabherr M G, Haas B J, Yassour M, et al. 2011. Full-length tran-scriptome assembly from RNA-seq data without a refer-ence genome[J]. Nature Biotechnology, 29(7): 644-652. [11] Li S J,Yin X R,Wang W L,et al. 2017. Citrus CitNAC62 co-operates with CitWRKY1 to participate in citric acid degradation via up-regulation of CitAco3[J]. Journal of Experimental Botany, 68(13): 3419-3426. [12] Luo A C, Yang X H, Deng Y Y, et al. 2003. Organic acid con-centrations and the relative enzymatic changes during the development of the citrus fruits[J]. Agricultural Sci-ences in China, (06): 66-70. [13] Ma X, Li N, Guo J, et al. 2020. Involvement of CsPH8 in ci-trate accumulation directly related to fruit storage perfor-mance of 'Bingtang' sweet orange mutants[J]. Posthar-vest Biology and Technology, 170: 111316. [14] Mao X Z, Tao C,Wei L P. 2005. Automated genome annota-tion and pathway identification using the KEGG Orthol-ogy (KO) as a controlled vocabulary[J]. Bioinformatics, 21(19): 3787-3793. [15] Strazzer P, Spelt CE, Li S, et al. 2019. Hyperacidification of Citrus fruits by a vacuolar proton-pumping P-ATPase complex[J]. Nature Communication, 10(1): 744. [16] Sheng L,Shen D D,Yang W,et al. 2017. GABA pathway rate-limit citrate degradation in postharvest citrus fruit evi-dence from HB pumelo (Citrus grandis) × Fairchild (Cit-rus reticulata) hybrid population[J]. Journal of Agricul-tural and Food Chemistry, 65(8): 1669-1676. [17] Shi C Y, Hussain S B, Guo L X, et al. 2018. Genome-wide identification and transcript analysis of vacuolar-ATPase genes in citrus reveal their possible involvement in ci-trate accumulation[J]. Phytochemistry, 155: 147-154. [18] Shi C Y, Song R Q, Hu X M, et al. Citrus PH 5-like H+-ATPase genes: Identification and transcript analysis to investi-gate their possible relationship with citrate accumulation in fruits[J]. Frontiers in Plant Science, 6: 135. [19] Tanaka T. 1969. Misunderstanding with regards Citrus classifi-cation and nomenclature[J]. Bulletin of University of Osaka Prefecture, 21: 139-145. [20] Wang J H, Liu J J, Chen K L, et al. 2017. Comparative tran-scriptome and proteome profiling of two Citrus sinensis cultivars during fruit development and ripening[J]. BMC Genomics, 18(1): 1-13. [21] Wang J H, Liu J J,Chen K L,et al. 2016. Anthocyanin biosyn-thesis regulation in the fruit of Citrus sinensis cv. Tarocco[J]. Plant Molecular Biology Reporter, 34(6): 1043-1055. [22] Wang J H, Xi D H, Liu J J, et al. 2012. Genetic variability in the grapevine virus A from Vitis vinifera L. × Vitis labrus-ca L[J]. Turkish Journal of Biology, 36(5): 542-551. [23] Wu G A, Terol J, Ibanez V, et al. 2018. Genomics of the origin and evolution of Citrus[J]. Nature, 554(7692): 311-316. [24] Wu S, Zhang C, Li M, et al. 2021b. Effects of potassium on fruit soluble sugar and citrate accumulations in Cara cara navel orange (Citrus sinensis L. Osbeck)[J]. Scien-tia Horticulturae, 283: 110057.
