Biologia plantarum 67:189-199, 2023 | DOI: 10.32615/bp.2023.026
Progress of transcriptome sequencing of woody oil plants
- 1 College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin 150080, P.R. China
- 2 Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, P.R. China
- 3 Heilongjiang Provincial Key of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin 150080, P.R. China
- 4 State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin 150040, P.R. China
- 5 Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, P.R. China
Transcriptome is a collection of mRNA transcripts in a specific physiological state which has become one of the hotspots in biological research to evaluate the genes and networks in different kinds of plants. Transcriptome sequencing technology dates back to 1964 and has nearly 60 years of history. At present, the research mainly focuses on cultivating, breeding, molecular markers, and gene mining. With the increase in oil price, woody oil production can alleviate oil demand, but there are few review articles and molecular biology studies on the transcriptome of woody oil plants. In the past few decades, woody oil plants have made great progress in the development of transcriptome sequencing and bioinformatics. In this review, we reviewed the development history of sequencing technology and the research on the transcriptome of woody oil plants, mainly introducing the germplasm resources, molecular markers, and the application of important functional genes in woody oil plants. This paper not only provides ideas for mining functional genes of oil plants but also provides a reference for molecular breeding research of woody oil plants in the future.
Keywords: gene mining, germplasm resources, molecular markers, transcriptome sequencing technology, woody oil plants.
Received: February 2, 2023; Revised: May 8, 2023; Accepted: June 5, 2023; Published online: August 3, 2023 Show citation
References
- Ajambang W., Ardie S.W., Volkaert H. et al.: Comparative expression profiling of three early inflorescence stages of oil palm indicates that vegetative to reproductive phase transition of meristem is regulated by sugar balance. - Funct. Plant Biol. 42: 589-598, 2015.
Go to original source... - Beck T.F., Mullikin J.C., Biesecker L.G.: Systematic evaluation of Sanger validation of next-generation sequencing variants. - Clin. Chem. 62: 647-654, 2016.
Go to original source... - Burge C., Karlin S.: Prediction of complete gene structures in human genomic DNA. - J. Mol. Biol. 268: 78-94, 1997.
Go to original source... - Chang J., Wang K.L., Zhang C.C. et al.: Transcriptome analysis of resistant and susceptible pecan (Carya illinoinensis) reveals the mechanism of resistance to black spot disease (Colletotrichum fioriniae). - J. Agr. Food Chem. 71: 5812-5822, 2023.
Go to original source... - Chen C., Mitchell S.E., Elshire R.J. et al.: Mining conifers' mega-genome using rapid and efficient multiplexed high-throughput genotyping-by-sequencing (GBS) SNP discovery platform. - Tree Genet. Genom. 9: 1537-1544, 2013.
Go to original source... - Chen S.W., Li D.P., Chen S.S. et al.: Identifying and expression analysis of WD40 transcription factors in walnut. - Plant Genome 15: e20229, 2022.
Go to original source... - Chen Y.C., Yin H.F., Gao M. et al.: Comparative transcriptomics atlases reveals different gene expression pattern related to Fusarium wilt disease resistance and susceptibility in two Vernicia species. - Front. Plant Sci. 7: 1974, 2016.
Go to original source... - Dong L., Yin X., Huang B. et al.: The complete chloroplast genome of Camellia semiserrata Chi. (Theaceae), an excellent woody edible oil and landscaping species in South China. - Mitochondr. DNA B 6: 3013-3015, 2021.
Go to original source... - Dong X., Jiang X.D., Kuang G.Q. et al.: Genetic control of flowering time in woody plants: Roses as an emerging model. - Plant Divers. 39: 104-110, 2017.
Go to original source... - Du W., Ding J., Lu S.G. et al.: Identification of the key flavonoid and lipid synthesis proteins in the pulp of two sea buckthorn cultivars at different developmental stages. - BMC Plant Biol. 22: 299, 2022.
Go to original source... - Guo H.J., Jiao Y.N., Di C. et al.: [Discovery of Arabidopsis GRAS family genes in response to osmotic and drought stresses.] - Chin. Bull. Bot. 44: 290-299, 2009. [In Chinese]
- Gupta P.K., Varshney R.K., Sharma P.C., Ramesh B.: Molecular markers and their applications in wheat breeding. - Plant Breeding 118: 369-390, 1999.
Go to original source... - Hazzouri K.M., Flowers J.M., Visser H.J. et al.: Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop. - Nat. Commun. 6: 8824, 2015.
Go to original source... - He Y., Chen R., Yang Y. et al.: Sugar metabolism and transcriptome analysis reveal key sugar transporters during Camellia oleifera fruit development. - Int. J. Mol. Sci. 23: 822, 2022.
Go to original source... - Hsu W.-K., Lee S.-C., Lu P.-L.: A useful technical application of the identification of nucleotide sequence polymorphisms and gene resources for Cinnamomum osmophloeum Kaneh. (Lauraceae). - Forests 10: 306, 2019.
Go to original source... - Hu X.D., Pan B.Z., Fu Q.T. et al.: The complete chloroplast genome sequence of the biofuel plant Sacha Inchi, Plukenetia volubilis. - Mitochondr. DNA B 3: 328-329, 2018.
Go to original source... - Hu Y., ©marda P., Liu G. et al.: High-depth transcriptome reveals differences in natural haploid Ginkgo biloba L. due to the effect of reduced gene dosage. - Int. J. Mol. Sci. 23: 8958, 2022.
Go to original source... - Islam A.S.M.F., Sanders D., Mishra A.K., Joshi V.: Genetic diversity and population structure analysis of the USDA olive germplasm using genotyping-by-sequencing (GBS). - Genes 12: 2007, 2021.
Go to original source... - Ji F.Y., Ma Q.G., Zhang W.T. et al.: A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits. - Genome Biol. 22: 300, 2021.
Go to original source... - Jia B.G., Lin Q., Zhang L. et al.: Development of 15 genic-SSR markers in oil-tea tree (Camellia oleifera) based on transcriptome sequencing. - Genetika 46: 789-797, 2014.
Go to original source... - Jia Z., Wang G., Xuan J. et al.: Comparative transcriptome analysis of pecan female and male inflorescences. - Russ. J. Plant Physiol. 65: 186-196, 2018.
Go to original source... - Kang Y.N., Kang C.S., Kim C.S.: History of nucleotide sequencing technologies: advances in exploring nucleotide sequences from Mendel to the 21st century. - Korean J. Hortic. Sci. Technol. 37: 549-558, 2019.
Go to original source... - Kumar J., Heikrujam M., Sharma K., Agrawal V.: SRAP and SSR marker-assisted genetic diversity, population structure analysis and sex identification in jojoba (Simmondsia chinensis). - Ind. Crop. Prod. 133: 118-132, 2019.
Go to original source... - Lang Y.H., Liu Z., Zheng Z.M.: Investigation of yellow horn (Xanthoceras sorbifolia Bunge) transcriptome in response to different abiotic stresses: a comparative RNA-Seq study. - RSC Adv. 10: 6512-6519, 2020.
Go to original source... - Li J.B., Xiong C.W., Ruan D. et al.: Identification of Camellia oleifera WRKY transcription factor genes and functional characterization of CoWRKY78. - Front. Plant Sci. 14: 1110366, 2023b.
Go to original source... - Li J.B., Zhao S., Yu X. et al.: Role of Xanthoceras sorbifolium MYB44 in tolerance to combined drought and heat stress via modulation of stomatal closure and ROS homeostasis. - Plant Physiol. Biochem. 162: 410-420, 2021.
Go to original source... - Li J.B., Zhou H., Xiong C.W. et al.: Genome-wide analysis R2R3-MYB transcription factors in Xanthoceras sorbifolium Bunge and analysis of XsMYB30 in drought and salt stresses tolerance. - Ind. Crop. Prod. 178: 114597, 2022.
Go to original source... - Li J.B., Zhou X.D., Xiong C.W. et al.: Yellowhorn Xso-miR5149-XsGTL1 enhances water-use efficiency and drought tolerance by regulating leaf morphology and stomatal density. - Int. J. Biol. Macromol. 237: 124060, 2023a.
Go to original source... - Li Z.T., Zhong Y.D., Yu F.X., Xu M.: Novel SSR marker development and genetic diversity analysis of Cinnamomum camphora based on transcriptome sequencing. - Plant Genet. Resour. 16: 568-571, 2018.
Go to original source... - Lin P., Yin H.F., Yan C. et al.: Association genetics identifies single nucleotide polymorphisms related to kernel oil content and quality in Camellia oleifera. - J. Agr. Food Chem. 67: 2547-2562, 2019.
Go to original source... - Liu N., Cheng F.Y.: Association mapping for yield traits in Paeonia rockii based on SSR markers within transcription factors of comparative transcriptome. - BMC Plant Biol. 20: 245, 2020.
Go to original source... - Liu Y.L., Huang Z.D., Ao Y. et al.: Transcriptome analysis of yellow horn (Xanthoceras sorbifolia Bunge): a potential oil-rich seed tree for biodiesel in China. - PLoS ONE 8: e74441, 2013.
Go to original source... - Ma Y.Z., Wang J., Hu Q.J. et al.: Ancient introgression drives adaptation to cooler and drier mountain habitats in a cypress species complex. - Commun. Biol. 2: 213, 2019.
Go to original source... - Margulies M., Egholm M., Altman W.E. et al.: Genome sequencing in microfabricated high-density picolitre reactors. - Nature 437: 376-380, 2005.
Go to original source... - Masura S.S., Rasid O.A., Shaharuddin N.A. et al.: Identification of oil palm root-specific genes through mining of RNA-Seq data and RT-qPCR analysis. - J. Oil Palm Res. 6: 261-275, 2022.
- Mattison C.P., Rai R., Settlage R.E. et al.: RNA-Seq analysis of developing pecan (Carya illinoinensis) embryos reveals parallel expression patterns among allergen and lipid metabolism genes. - J. Agr. Food Chem. 65: 1443-1455, 2017.
Go to original source... - McCarthy A.: Third generation DNA sequencing: Pacific Biosciences' Single Molecule Real Time technology. - Chem. Biol. 17: 675-676, 2010.
Go to original source... - Niu E., Jiang C.Y., Wang W. et al.: Chloroplast genome variation and evolutionary analysis of Olea europaea L. - Genes 11: 879, 2020.
Go to original source... - Pereira V.M., Filho J.A.F., Leão A.P. et al.: American oil palm from Brazil: Genetic diversity, population structure, and core collection. - Crop Sci. 60: 3212-3227, 2020.
Go to original source... - Pompelli M.F., Jarma-Orozco A., Rodríguez-Páez L.A.: Salinity in Jatropha curcas: A review of physiological, biochemical, and molecular factors involved. - Agriculture 12: 594, 2022.
Go to original source... - Quan W.X., Ding G.J.: Root tip structure and volatile organic compound responses to drought stress in Masson pine (Pinus massoniana Lamb.). - Acta Physiol. Plant. 39: 258, 2017.
Go to original source... - Rhoads A., Au K.F.: PacBio sequencing and its applications. - Genomics Proteomics Bioinformatics 13: 278-289, 2015.
Go to original source... - Russell J.R., Kadu C.A.C., Jamnadass R. et al.: AFLP and SSR diversity in the African fruit tree Allanblackia: implications for management of a genus newly subject to domestication for the edible oil industry. - Tree Genet. Genom. 5: 517-527, 2009.
Go to original source... - Sanger F., Coulson A.R.: A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. - J. Mol. Biol. 94: 441-448, 1975.
Go to original source... - Sanger F., Nicklen S., Coulson A.R.: DNA sequencing with chain-terminating inhibitors. - PNAS 74: 5463-5467, 1977.
Go to original source... - Smith C.C., Wang Q., Chin C.-S. et al.: Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia. - Nature 485: 260-263, 2012.
Go to original source... - Sun J., Jia H., Wang P. et al.: Exogenous gibberellin weakens lipid breakdown by increasing soluble sugars levels in early germination of zanthoxylum seeds. - Plant Sci. 280: 155-163, 2019.
Go to original source... - The Arabidopsis Genome Initiative: Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. - Nature 408: 796-815, 2000.
Go to original source... - Tuskan G.A., Difazio S., Jansson S. et al.: The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). - Science 313: 1596-1604, 2006.
Go to original source... - Wang H.B., Zou Z.R., Wang S.S., Gong M.: Global analysis of transcriptome responses and gene expression profiles to cold stress of Jatropha curcas L. - PLoS ONE 8: e82817, 2013.
Go to original source... - Wang Y.L., Li Y.: Population genetics and development of a core collection from elite germplasms of Xanthoceras sorbifolium based on genome-wide SNPs. - Forests 13: 338, 2022.
Go to original source... - Wang Y.L., Zhu L.Z., Li Y.: Genetic relationships among 15 Xanthoceras sorbifolium cultivars using SSR markers and phenotypic traits. - J. Anim. Plant Sci. 33: 358-366, 2023.
Go to original source... - Wang Z.Q., Yu A.M., Li F. et al.: Bulked segregant analysis reveals candidate genes responsible for dwarf formation in woody oilseed crop castor bean. - Sci. Rep.-UK 11: 6277, 2021.
Go to original source... - Xia E.H., Jiang J.J., Huang H. et al.: Transcriptome analysis of the oil-rich tea plant, Camellia oleifera, reveals candidate genes related to lipid metabolism. - PLoS ONE 9: e104150, 2014.
Go to original source... - Xia T.F., Wang L., Xu J.Q. et al.: [The genotypic diversity analysis of 267 six-rowed hulless barley accessions from the Qinghai-Tibetan Plateau.] - Acta Agric. Bor.-Occident. Sin. 27: 182-193, 2018. [In Chinese]
- Xiong C.W., Zhao S., Yu X. et al.: Yellowhorn drought-induced transcription factor XsWRKY20 acts as a positive regulator in drought stress through ROS homeostasis and ABA signaling pathway. - Plant Physiol. Biochem. 155: 187-195, 2020.
Go to original source... - Xu W., Yang T.Q., Qiu L.J. et al.: Genomic analysis reveals rich genetic variation and potential targets of selection during domestication of castor bean from perennial woody tree to annual semi-woody crop. - Plant Direct 3: e00173, 2019.
Go to original source... - Yan R., Ruan C., Zhao S. et al.: SNP discovery of Camellia oleifera based on RNA-seq and its application for identification of genetic relationships and locus for oil content among different cultivars. - J. Hortic. Sci. Biotech. 95: 687-702, 2020.
Go to original source... - Yang G.Y., Peng S.B., Wang T.Y. et al.: Walnut ethylene response factor JrERF2-2 interact with JrWRKY7 to regulate the GSTs in plant drought tolerance. - Ecotox. Environ. Safe. 228: 112945, 2021.
Go to original source... - Yang T.Q., Yu Q., Xu W. et al.: Transcriptome analysis reveals crucial genes involved in the biosynthesis of nervonic acid in woody Malania oleifera oilseeds. - BMC Plant Biol. 18: 247, 2018.
Go to original source... - Yanik H., Turktas M., Dundar E. et al.: Genome-wide identification of alternate bearing-associated microRNAs (miRNAs) in olive (Olea europaea L.). - BMC Plant Biol. 13: 10, 2013.
Go to original source... - Ye Z.C., Yu J., Yan W.P. et al.: Integrative iTRAQ-based proteomic and transcriptomic analysis reveals the accumulation patterns of key metabolites associated with oil quality during seed ripening of Camellia oleifera. - Hortic. Res. 8: 157, 2021.
Go to original source... - Yeboah A., Lu J.N., Yang T. et al.: Genome-wide association study identifies loci, beneficial alleles, and candidate genes for cadmium tolerance in castor (Ricinus communis L.). - Ind. Crop. Prod. 171: 113842, 2021.
Go to original source... - Zeng L.P., Zhang N., Zhang Q. et al.: Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets. - New Phytol. 214: 1338-1354, 2017.
Go to original source... - Zhang S.L., Tian L., Zhang Y.Q. et al.: De novo transcriptome assembly of the fresh-cut white husk of Juglans cathayensis Dode: Insights for enzymatic browning mechanism of fresh-cut husk of walnut. - Sci. Hortic.-Amsterdam 257: 108654, 2019.
Go to original source... - Zhang X., Li J., Pan B.Z. et al.: Extended mining of the oil biosynthesis pathway in biofuel plant Jatropha curcas by combined analysis of transcriptome and gene interactome data. - BMC Bioinformatics 22: 409, 2021.
Go to original source... - Zheng Y.S., Chen C.J., Liang Y.X. et al.: Genome-wide association analysis of the lipid and fatty acid metabolism regulatory network in the mesocarp of oil palm (Elaeis guineensis Jacq.) based on small noncoding RNA sequencing. - Tree Physiol. 39: 356-371, 2019.
Go to original source...



