|
|
|
| Progress and Prospects of Jujube (Ziziphus jujuba) Omics Research |
| LI Bin1, HAN Lu1, ZHANG Shu-Feng1, LIU Meng-Jun1,2,*, YANG Meng1,2,* |
1 College of Horticulture, Hebei Agricultural University, Baoding 071000, China;
2 Research Center of Chinese Jujube, Hebei Agricultural University, Baoding 071000, China |
|
|
|
|
Abstract The omics-related research currently holds a prominent position in fruit tree studies. Collaborative investigations encompassing genomics, transcriptomics, proteomics, metabolomics, and so forth can enhance the efficiency of studies on various aspects of fruit trees. This includes exploring the origin and domestication history, understanding the mechanisms behind the formation of importantly economical traits, and identifying genes and molecular markers essential for molecular breeding practices and the molecular regulation of growth and development. The jujube (Ziziphus jujuba) is a native fruit tree that originated and was domesticated in China, and it is one of the fruit trees subjected to early whole-genome de novo sequencing. Its genome was sequenced in 2014, and since then, intensive studies through the way of multi-omics have been performed, leading to a new era in jujube research. This article systematically summarizes recent advancements in jujube genomics, transcriptomics, and metabolomics. Additionally, it outlines prospective avenues for multi-omics investigations of jujube. These insights collectively contribute to the future trajectory of jujube research, particularly in the realms of breeding and understanding the mechanisms controlling the formation of critical traits in jujube.
|
|
Received: 05 January 2023
|
|
|
|
Corresponding Authors:
*yangm@hebau.edu.cn; lmj1234567@aliyun.com
|
|
|
|
[1] 高玮林, 张力曼, 薛超玲, 等. 2022. 枣 E 类 MADS 基因在花和果中的表达及其蛋白互作研究[J]. 园艺学报, 49(4): 739-748.
(Gao W L, Zang L M, Xue C L, et al.2022. Expression of E-type MADS-box genes in flower and fruits and protein interaction analysis in Chinese jujube[J]. Acta Horticulturae Sinica, 49(4): 739-748.)
[2] 郭盛, 段金廒, 钱大玮, 等. 2013 枣属植物化学成分研究进展[J]. 国际药学研究杂志, 40(6): 702-710.
(Guo S, Duan J A, Qian D W, et al.2013. Chemical constituents of Ziziphus plants: Research advances[J]. Journal of International Pharmaceutical Research, 40(6): 702-710 .)
[3] 韩雅茹, 马亚平, 陈丽华, 等. 2022. 转录组和代谢组联合解析气温升高和干旱互作下灵武长枣果皮花青苷代谢机制[J]. 果树学报, 39(5): 811-825.
(Han Y R, Ma Y P, Chen L H, et al.2022. Transcriptome and metabolome combined analysis of anthocyanin metabolism in fruit peel of Ziziphus jujuba Mill. 'Lingwuchangzao' under the interaction of elevated temperature and drought[J]. Journal of Fruit Science, 39(5): 811-825.)
[4] 林明睿. 2017. 甜叶菊高密度遗传图谱构建及其分子标记筛选[D]. 硕士学位论文, 浙江农林大学, 导师: 吴建国, pp.34-36.
(Lin M R.2017. Construction of high density genetic map of Stevia rebaudiana and selection of molecular markers[D]. Thesis form M. S., Zhejiang Agriculture and Forestry University, Supervisor: Wu J G, pp.34-36.)
[5] 刘孟军. 2018. 枣产业转型期面临的挑战与对策[J]. 中国果树, (1): 1-4.
(Liu M J. 2018. The challenges and countermeasures of jujube industry during transition period[J]. China Fruits, (1): 1-4.)
[6] 刘孟军, 诚静容. 1994. 枣和酸枣的分类学研究[J]. 河北农业大学学报, 17(4).
(Liu M J, Cheng J R.1994 Taxonomic study on jujube and wild jujube[J]. Journal of Hebei Agricultural University, 17(4).)
[7] 刘孟军, 王玖瑞. 2019. 新中国果树科学研究70年-枣[J]. 果树学报, 36(10): 1369-1381.
(Liu M J, Wang J R.2019. Fruit scientific research in New China in the past 70 years: Chinese jujube[J]. Journal of Fruit Science, 36(10): 1369-1381.)
[8] 刘孟军, 王玖瑞, 刘平, 等. 2015. 中国枣生产与科研成就及前沿进展[J]. 园艺学报,42(9): 1683-1698.
(Liu M J, Wang J R, Liu P, et al.2015. Historical Achievements and Frontier Advances in the Production and Research of Chinese Jujube (Ziziphus jujuba) in China[J]. Folia Horticulturae, 42(9): 1683-1698.)
[9] 刘伟, 霍辰思, 王国平. 2021. 枣疯病导致的花异常发育相关基因鉴定及表达分析[J]. 山西农业大学学报(自然科学版), 41(6): 57-66.
(Liu W, Huo C S, Wang G P.2021. Identification and expression analysis of genes related to abnormal flower development induced by jujube madness disease[J].Journal of Shanxi Agricultural University(Natural Science Edition), 41(6): 57-66 .
[10] 仇倩倩. 2021. 'JMS2'×'邢16'杂交后代高密度遗传图谱构建及果实大小相关性状的QTL定位[D]. 硕士学位论文, 塔里木大学,导师: 吴翠云; 李新岗, pp.64-68.
(Chou Q Q.2021.Construction of high-density genetic mapping of 'JMS2'×'Xing16' hybrid offspring and QTL localization of fruit size-dependent traits[D]. Thesis form M. S., Tarim University, Supervisor: Wu C Y, pp.64-68.)
[11] 唐海霞, 高瑞, 王中堂, 等. 2021. 基于 SNP 标记的枣高密度遗传连锁图谱重新构建[J]. 园艺学报, 48(11): 2275-2285.
(Tang H X, Gao R, Wang Z T, et al.2021. High-density genetic linkage map reconstruction in jujube using SNP markers[J]. Acta Horticulturae Sinica, 48(11): 2275-2285.)
[12] 王晓铃, 许莉斯. 2012. AFLP分子标记在枣研究中的应用进展[J]. 农业与技术, 32(5): 62-63.
(Wang X L, Xu L S.2012. Application progress of AFLP molecular markers in jujube research[J]. Agriculture And Technology, 32(5): 62-63.)
[13] Di C, Yuan J, Wu Y, et al.2014. Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features[J]. Plant Journal, 80(5): 848-861.
[14] Dong X C, Tang H X, Zhang Q, et al.2022. Transcriptomic analyses provide new insights into jujube fruit quality affected by water deficit[J]. Scientia Horticulturae, (291): 110558
[15] Gao M J, Wang L H, Li M, et al.2021. Physiological and transcriptome analysis accentuates microtubules and calcium signaling in Ziziphus jujuba Mill 'Dongzao' autotetraploids with sensitive cold tolerance[J]. Scientia Horticulturae, (285): 110183.
[16] Guo M, Li S, Tian S, et al.2017. Transcriptome analysis of genes involved in defense against alkaline stress in roots of wild jujube (Ziziphus acidojujuba)[J]. PLoS One, 12(10): e0185732.
[17] Guo M, Zhang Z, Cheng Y, Li S, et al.2020. Comparative population genomics dissects the genetic basis of seven domestication traits in jujube[J]. Horticulture Research, 7(1): 89.
[18] Guo M, Zhang Z, Li S, et al.2021. Genomic analyses of diverse wild and cultivated accessions provide insights into the evolutionary history of jujube[J]. Plant Biotechnology Journal, 19(3): 517-531.
[19] Hao Q, Yang L, Fan D, et al.2021. The transcriptomic response to heat stress of a jujube (Ziziphus jujuba Mill.) cultivar is featured with changed expression of long noncoding RNAs[J]. PLoS One, 16(5): e0249663.
[20] Hou L, Chen W, Zhang Z, et al.2020. Genome-wide association studies of fruit quality traits in jujube germplasm collections using genotyping-by-sequencing[J]. Plant Genome, 13(3): e20036.
[21] Hou L, Li M, Zhang C, et al.2022. Comparative transcriptomic analyses of different jujube cultivars reveal the co-regulation of multiple pathways during fruit cracking[J]. Genes & Development, 13(1): 105.
[22] Huang J, Chen X, He A, et al.2021. Integrative morphological, physiological, proteomics analyses of jujube fruit development provide insights into fruit quality domestication from wild jujube to cultivated jujube[J]. Frontiers in Plant Science, 24(12): 773825.
[23] Huang J, Zhang C, Zhao X, et al.2016. The jujube genome provides insights into genome evolution and the domestication of sweetness/acidity taste in fruit trees[J]. PLoS Genetics, 12(12): e1006433.
[24] Li B Y, Li H, Xu Z H, et al.2022a. Transcriptome profiling and identification of the candidate genes involved in early ripening in Ziziphus jujuba[J]. Frontiers in Plant Science, (13): 23
[25] Li N, Song Y, Li J, et al.2021a. Resequencing and transcriptomic analysis reveal differences in nitrite reductase in jujube fruit (Ziziphus jujuba Mill.)[J]. Plant Methods, 17(1): 75.
[26] Li M, Guo Y, Liu S, et al.2019. Autotetraploidization in Ziziphus jujuba Mill. var. spinosa enhances salt tolerance conferred by active, diverse stress responses[J]. Environmental And Experimental Botany, 165: 92-107.
[27] Li M, Hou L, Zhang C, et al.2022b. Genome-wide identification of direct targets of ZjVND7 reveals the putative roles of whole-genome duplication in sour jujube in regulating xylem vessel differentiation and drought tolerance[J]. Plant Science Today, 13: 829765.
[28] Li M, Zhang C, Hou L, et al.2021b. Multiple responses contribute to the enhanced drought tolerance of the autotetraploid Ziziphus jujuba Mill. var. spinosa[J]. Cell and Bioscience. (11): 119.
[29] Li Y, Xu C, Lin X, et al.2014. De novo assembly and characterization of the fruit transcriptome of Chinese jujube (Ziziphus jujuba Mill.) Using 454 pyrosequencing and the development of novel tri-nucleotide SSR markers[J]. PLoS One, 9(9): e106438
[30] Liao L, Zhang W H, Zhang B, et al.2021. Unraveling a genetic roadmap for improved taste in the domesticated apple[J]. Plant Molecular Biology, 14(9): 1454-1471.
[31] Liu M J, Zhao J, Cai Q L, et al.2014. The complex jujube genome provides insights into fruit tree biology[J]. Nature Communications, 28(5): 5315.
[32] Liu Y, Zhang P, Geng Y, et al.2020. Cracking of jujube fruits is associated with differential expression of metabolic genes[J]. FEBS Open Bio, 10(9): 1765-1773.
[33] Lu D Y, Wu Y, Pan Q H, et al.2022a. Identification of key genes controlling L-ascorbic acid during Jujube (Ziziphus jujuba Mill.) fruit development by integrating transcriptome and metabolome analysis[J]. Frontiers in Plant Science, (13): 952698.
[34] Lu D Y, Zhang L, Wu Y, et al.2022b. An integrated metabolome and transcriptome approach reveals the fruit flavor and regulatory network during jujube fruit development[J]. Frontiers in Plant Science, 2022, (13): 952698.
[35] Lu H, Wu C, Zhang Z Y, et al.2020. Genome-wide association studies of fruit quality traits in jujube germplasm collections using genotyping-by-sequencing[J]. Plant Genome, 13(3): e20036.
[36] Ma F L, Huang J Q, Yang J, et al.2020. Identification, expression and miRNA targeting of auxin response factor genes related to phyllody in the witches broom disease of jujube[J]. Gene, 1(749): 144656.
[37] Meng X, Li Y, Yuan Y, et al.2020. The regulatory pathways of distinct flowering characteristics in Chinese jujube[J]. Horticulture Research, 1(7): 123.
[38] Shao F X, Yin H F, Wang S, et al.2022. Transcriptomic analysis reveals key candidate genes related to seed abortion in Chinese jujube (Ziziphus jujuba Mill)[J]. Current Genomics, 23(1): 26-40.
[39] Shen L Y, Luo H, Wang X L, et al.2021. Chromosome-scale genome assembly for Chinese sour jujube and insights into its genome evolution and domestication signature[J]. Frontiers in Plant Science, 12(7): 73090.
[40] Shi Q Q, Li X, Du J T, et al.2022. Association of bitter metabolites and flavonoid synthesis pathway in jujube fruit[J]. Frontiers in Nutrition, 9: 901756.
[41] Wang B, Yang X F, Jia Y Y, et al.2021. High-quality Arabidopsis thaliana genome assembly with nanopore and hifi long reads[J]. Genomics Proteomics Bioinformatics, (21): 174-181.
[42] Wang H Y, Ye X, Li J D, et al.2018. Transcriptome profiling analysis revealed co-regulation of multiple pathways in jujube during infection by 'Candidatus Phytoplasma ziziphi'[J]. Gene, (665): 82-95.
[43] Wang L X, Li M, Liu Z G, et al.2020. Genome-wide identification of CNGC genes in Chinese jujube (Ziziphus jujuba Mill.) and ZjCNGC2 mediated signalling cascades in response to cold stress[J]. BMC Genomics, 21(1): 191.
[44] Wang Z T, Zhang Z, Tang H X, et al.2019a. Genetic variation in leaf characters of F1 hybrids of Chinese jujube[J]. Scientia Horticulturae, (224): 372-378.
[45] Wang Z T, Zhang Z, Tang H X, et al.2019b. High-density genetic map construction and QTL mapping of leaf and needling traits in Ziziphus jujuba Mill.[J]. International Journal of Plant Sciences, 22(10): 1424.
[46] Xu Q, Liu C Y, Manosh K B, et al.2014. Recent advances in fruit crop genomics[J]. Frontiers of Agricultural Science and Engineering, 1(1): 21.
[47] Xue X, Zhao A, Wang Y, et al.2021. Composition and content of phenolic acids and flavonoids among the different varieties, development stages, and tissues of Chinese jujube (Ziziphus jujuba Mill.)[J]. PLoS One, 16(10): e0254058.
[48] Ye X, Wang H Y, Chen P, et al.2017. Combination of iTRAQ proteomics and RNA-seq transcriptomics reveals multiple levels of regulation in phytoplasma-infected Ziziphus jujuba Mill.[J]. Horticulture Research, (4): 17080.
[49] Yu Y, Guan J T, Xu Y G, et al.2021. Population-scale peach genome analyses unravel selection patterns and biochemical basis underlying fruit flavor[J]. Nature Communications, 12(1): 3604.
[50] Zhang Q, Wang L, Liu Z, et al.2020. Transcriptome and metabolome profiling unveil the mechanisms of Ziziphus jujuba Mill. peel coloration[J]. Food Chemistry, 312: 125903.
[51] Zhang Q, Wang L, Wang Z, et al.2021. The regulation of cell wall lignification and lignin biosynthesis during pigmentation of winter jujube[J]. Horticulture Research, 8(1): 238.
[52] Zhang Z, Kang C, Zhang S, et al.2019. Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube[J]. BMC Plant Biology, 19(1): 189.
[53] Zhang Z, Shi Q Q, Wang B, et al.2022. Jujube metabolome selection determined the edible properties acquired during domestication[J]. The Plant Juornal, 109(5): 1116-1133.
[54] Zhao J, Jian J B, Liu G N, et al.2014. Rapid SNP discovery and a RAD-based high-density linkage map in jujube (Ziziphus Mill.)[J]. PloS One, 9(10): e109850.
[55] Zhou H, He Y, Zhu Y, et al.2020. Comparative transcriptome profiling reveals cold stress responsiveness in two contrasting Chinese jujube cultivars[J]. BMC Plant Biology, 20(1): 240. |
| [1] |
LOU Meng-Yu, LU Jia-Ni, DUAN Qin, YANG Wang-Xin, ZHENG Qi, ZHU Cui-Yun, ZHANG Si-Huan, LI Shuang, LING Ying-Hui. Transcriptome Analysis Reveals Differences in Skeletal Muscle Gene Expression in Sheep (Ovis aries) of Different Genders[J]. 农业生物技术学报, 2024, 32(1): 158-167. |
|
|
|
|
