Comparative transcriptomic study of matured fruit and post-fruit developmental stages in Malaysian durian varieties

Poh, Keong Bun

Abstract

Durian (Durio zibethinus Murr.) is a famous tropical fruit in Malaysia and well-known for its sweet and creamy taste and unique strong aroma. Despite the differences, durian fruit undergo similar fruit developmental stages upon maturity. However, not much information related to metabolic changes at molecular level are available for fruit development in durian. Hence, the aim of this study was to identify and analyze fruit development transcriptomic changes on six commercial durian varieties (D24, D99, D160, D168, D197, and D200). The transcriptome analysis via RNA-seq assays generated 67 to 234 million raw reads, which are assembled into 49,601 genes with protein coding genes as the largest gene biotype, with a total of 35,832 genes (72.2%). All genes were annotated against Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). GO analysis revealed genes were highly linked to biological process, cellular components and molecular function, with the highest representation in cell wall, while the most common pathways identified by KEGG were carotenoid biosynthesis, fatty acid biosynthesis, starch and sucrose metabolism, phenylpropanoid biosynthesis and galactose metabolism. Important changes were found in abscisic acid and lignin accumulation, which associated with post-harvest response and concurrent colour change. Moreover, significant increase in butyric acid, palmitoyl-CoA and different forms of sugars were associated with buttery smell, creamy texture, and sweetness respectively. Thus, mass sequence data and expression profiling provide an insight into molecular mechanisms for durian fruit developmental process. This study aims to enhance comprehension of durian fruit development stages, including physiological, genetic, and molecular processes, to inform breeding, crop enhancement, and post-harvest strategies to meet consumer and agro-biotechnology demands. _ 2024 Elsevier B.V.

References

Boerjan, W., Ralph, J., & Baucher, M. (2003). Lignin Biosynthesis. Annual Review of Plant Biology, 54, 519-546. https://doi.org/10.1146/annurev.arplant.54.031902.134938.

Chabannes, M., Ruel, K., Yoshinaga, A., Chabbert, B., Jauneau, A., Joseleau, J. P., & Boudet, A. M. (2001). In situ analysis of lignins in transgenic tobacco reveals a differential impact of individual transformations on the spatial patterns of lignin deposition at the cellular and subcellular levels. The Plant Journal, 28(3), 271-282. https://doi.org/10.1046/j.1365-313X.2001.01159.x.

Charoenkiatkul, S., Thiyajai, P., & Judprasong, K. (2016). Nutrients and bioactive compounds in popular and indigenous durian (Durio zibethinus murr.). Food Chemistry, 193, 181. https://doi.org/10.1016/j.foodchem.2015.02.107.

Chevreul. (1815). Lettre de M. Chevreul a MM. les redacteurs des Annales de chimie [Letter from Mr. Chevreul to the editors of the Annals of Chemistry]. In Annales de chimie (pp. 73-79). https://books.google.com.my/books?id=tZU5AAAAcAAJ&pg=PA73&redir_esc=y#v=onepage&q&f=false.

Chin, S. T., Nazimah, S. A. H., Quek, S. Y., Man, Y. B. C., Rahman, R. A., & Hashim, D. M. (2007). Analysis of volatile compounds from Malaysian durians (Durio zibethinus) using headspace SPME coupled to fast GC-MS. Journal of Food Composition and Analysis, 20, 31-44. https://doi.org/10.1016/j.jfca.2006.04.011.

Department of Agriculture. (n.d.). Varieties Registered For National Crop List. DOA. Retrieved November 2, 2021, from http://pvpbkkt.doa.gov.my/.

Draghici, S. (2023). Pathway Analysis vs Gene Set Analysis: What is the Difference and When Should I Use Each? Advaita Bioinformatics. https://advaitabio.com/ipathwayguide/pathway-analysis-vs604 gene-set-analysis/.

Eunyoung, J., Lee, S., Lee, S., Han, S. O., Yoon, Y. J., & Lee, J. (2012). Improved Production of Long606 Chain Fatty Acid in Escherichia coli by an Engineering Elongation Cycle During Fatty Acid Synthesis (FAS) Through Genetic Manipulation. Journal of Microbiology and Biotechnology, 22(7), 990-999. https://doi.org/10.4014/jmb.1112.12057.

Foster, D. W. (2012). Malonyl-CoA: The regulator of fatty acid synthesis and oxidation. The Journal of Clinical Investigation, 122(6), 1958-1959. https://doi.org/10.1172/JCI63967.

Frey, A., Effroy, D., Lefebvre, V. rie, Seo, M., Perreau, F., Berger, A., Sechet, J., To, A., North, H. M., & Marion-Poll, A. (2012). Epoxycarotenoid cleavage by NCED5 fine-tunes ABA accumulation and affects seed dormancy and drought tolerance with other NCED family members. The Plant Journal, 70, 501-512. https://doi.org/doi: 10.1111/j.1365-313X.2011.04887.x.

Hanover, L. M., & White, J. S. (1993). Manufacturing, composition, and applications of fructose. The American Journal of Clinical Nutrition, 58(5), 724S-732S.

Happe, R. P., & Gambelli, L. (2015). Infant formula. In Specialty Oils and Fats in Food and Nutrition. Elsevier Ltd. https://doi.org/10.1016/B978-1-78242-376-8.00012-0.

Haruenkit, R., Poovarodom, S., Vearasilp, S., Namiesnik, J., Sliwka-Kaszynska, M., Park, Y. S., Heo, B. G., Cho, J. Y., Jang, H. G., & Gorinstein, S. (2010). Comparison of bioactive compounds, antioxidant and antiproliferative activities of Mon Thong durian during ripening. Food Chemistry, 118(3), 540-547. https://doi.org/10.1016/j.foodchem.2009.05.029.

Hofman, D. L., Buul, V. J. Van, & Brouns, F. J. P. H. (2016). Nutrition, Health, and Regulatory Aspects of Digestible Maltodextrins. Critical Reviews in Food Science and Nutrition, 56(12), 2091-2100. https://doi.org/10.1080/10408398.2014.940415.

Jantan, S. Z., Poh, K. B., & Ginibun, F. C. (2022). Morphological Observation of Six Durian Varieties 627 in Malaysia (Durio zibethinus). 5th International Plant Breeding Conference 2022, 121.

Ji, F., Wu, J., & Zhang, Z. (2023). Identification and Characterization of CCD Gene Family in Rose (Rosa chinensis Jacq . ' Old Blush ') and Gene Co-Expression Network in Biosynthesis of Flower Scent. Horticulturae, 9(1), 1-15. https://doi.org/https://doi.org/10.3390/horticulturae9010115.

Ketsa, S., Wisutiamonkul, A., Palapol, Y., & Paull, R. E. (2020). The Durian: Botany, Horticulture, and Utilization. In Horticultural Reviews (Vol. 47, pp. 125-211). John Wiley & Sons, Inc. https://doi.org/10.1002/9781119625407.ch4.

Kukurba, K. R., & Montgomery, S. B. (2015). RNA sequencing and analysis. Cold Spring Harbor Protocols, 1-19. https://doi.org/10.1101/pdb.top084970.

Li, J.-X., Schieberle, P., & Steinhaus, M. (2012). Characterization of the Major Odor-Active Compounds in Thai Durian (Durio zibethinus L. 'Monthong') by Aroma Extract Dilution Analysis and Headspace Gas Chromatography-Olfactometry. Journal of Agricultural and Food Chemistry, 60(45), 11253-11262. https://doi.org/10.1021/jf303881k.

Lu, M., Ma, W.-T., Liu, Y.-Q., An, H.-M., & Ludlow, R. A. (2020). Transcriptome Analysis Reveals Candidate Lignin-Related Genes and Transcription Factors in Rosa roxburghii During Fruit Ripening. Plant Molecular Biology Reporter, 38, 331-342. https://doi.org/https://doi.org/10.1007/s11105-020-01193-3.