Sains Malaysiana 52(11)(2023): 3045-3059

http://doi.org/10.17576/jsm-2023-5211-03

Advances in Sago Palm Research: A Comprehensive Review of Recent Findings

(Kemajuan dalam Penyelidikan Pokok Sagu: Suatu Kajian Komprehensif Penemuan Terkini)

FIFI HAFIZZAH PENDI¹, WEI-JIE YAN¹, HASNAIN HUSSAIN^1,*, HAIRUL AZMAN ROSLAN¹ & NORZAINIZUL JULAIHI²

¹Centre for Sago Research, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia

²Land Custody and Development Authority, Level 4, 8 & 12, Wisma Satok, Jalan Satok, 93400 Kuching, Sarawak, Malaysia

Received: 3 July 2023/Accepted: 16 October 2023

Abstract

The sago palm (Metroxylon sagu Rottb.) is an indigenous plant in Papua New Guinea, Indonesia, Malaysia, and Thailand. It provides substantial needs to the locals, especially through the starch it produces in its trunk. Exhibiting remarkable adaptability, this palm can thrive in challenging environments like swamps and peat soils. This paper provides an overview of the molecular methods previously utilised to decipher the genes responsible conferring the characteristics of sago palm molecular techniques employed to investigate M. sagu molecular properties include molecular markers, genome walking, rapid amplification of cDNA ends (RACE), polymerase chain reaction (PCR) and sequencing. Additionally, this article presents other molecular techniques that can be applied to M. sagu for future crop breeding.

Keywords: Gene expression; genome assembly; Metroxylon sagu; non-trunking; trunking

Abstrak

Pokok sagu (Metroxylon saguRottb.) adalah tumbuhan asli di Papua New Guinea, Indonesia, Malaysia dan Thailand. Pokok sagu ini sangat berguna kepada masyarakat tempatan dengan menyediakan keperluan hidup terutamanya tepung sagu yang dihasilkan dalam batang tumbuhan unik ini. Memiliki daya penyesuaian yang tinggi, pokok sagu boleh hidup pada persekitaran yang mencabar seperti tanah paya dan tanah gambut. Kertas ini merumuskan teknik molekul yang pernah digunakan untuk mempelajari dan mentafsir gen yang bertanggungjawab terhadap ciri pokok sagu. Antara teknik molekul diaplikasikan ialah penitian genom; kandungan cDNA amplifikasi pantas (RACE); tindak balas berantai polimerase dan teknik penjujukan.

Kata kunci: Berbatang; himpunan genom; Metroxylon sagu; pengekspresan gen; tak berbatang

REFERENCES

Abbas, B. & Ehara, H. 2012. Assessment genetic variation and relationship of sago palm (Metroxylon sagu Rottb.) in Indonesia based on specific expression gene (Wx Genes) markers. African Journal of Plant Science 6(12): 314-320. https://doi.org/10.5897/AJPS12.015

Abbas, B., Renwarin, Y., Bintoro, M.H., Sudarsono, S., Surahman, M. & Ehara, H. 2010. Genetic diversity of sago palm in Indonesia based on chloroplast DNA (CpDNA) Markers. Biodiversitas Journal of Biological Diversity 11(3): 112-117. https://doi.org/10.13057/biodiv/d110302

Abbas, B., Bintoro, M.H., Sudarsono, Surahman, M. & Ehara, H. 2009. Genetic relationship of sago palm (Metroxylon sagu Rottb.) in Indonesia based on RAPD markers. Biodiversitas Journal of Biological Diversity 10(4): 168-174. https://doi.org/10.13057/biodiv/d100402

Abbas, B., Dailami, M., Santoso, B. & Munarti. 2017. Genetic variation of sago palm (Metroxylonsagu Rottb.) progenies with natural pollination by using RAPD markers. Natural Science 9(4): 104-109. https://doi.org/10.4236/ns.2017.94010

Abbas, B., Tjolli, I. & Munarti. 2019. Genetic diversity of sago palm (Metroxylon sagu) accessions based on plastid CpDNA MatK gene as DNA barcoding. Biodiversitas Journal of Biological Diversity 21(1): 219-225. https://doi.org/10.13057/biodiv/d210128

Abbas, B., Tjolli, I., Dailami, M. & Munarti. 2019. Phylogenetic of sago palm (Metroxylon sagu) and others monocotyledon based on mitochondrial Nad2 gene markers. Biodiversitas Journal of Biological Diversity 20(8): 2249-2256. https://doi.org/10.13057/biodiv/d200820

Abbas, T., Zahir, Z.A., Naveed, M. & Kremer, R.J. 2018. Limitations of existing weed control practices necessitate development of alternative techniques based on biological approaches. Advances in Agronomy 147: 239-280. https://doi.org/10.1016/bs.agron.2017.10.005

Ahmad, M.N., Awang Adeni, D.S., Suhaili, N. & Bujang, K. 2022. Optimisation of pre-harvest sago frond sap for the production of L-lactic acid using Lactococcus lactis IO-1. Biocatalysis and Agricultural Biotechnology 43: 102435. https://doi.org/10.1016/j.bcab.2022.102435

Al-Mssallem, I. S., Hu, S., Zhang, X., Lin, Q., Liu, W., Tan, J., Yu, X., Liu, J., Pan, L., Zhang, T., Yin, Y., Xin, C., Wu, H., Zhang, G., Ba Abdullah, M. M., Huang, D., Fang, Y., Alnakhli, Y. O., Jia, S., Yin, A., Alhuzimi, E., Alsaihati, B., Al-Owayyed, S., Zhao, D., Zhang, S., Al-Otaibi, N., Sun, G., Majrashi, M., Li, F., Tala, Wang, J., Yun, Q., Alnassar, N. A., Wang, L., Yang, M., Al-Jelaify, R. F., Liu, K., Gao, S., Chen, K., Alkhaldi, S. R., Liu, G., Zhang, M., Guo, H. & Yu, J. 2013. Genome sequence of the date palm Phoenix dactylifera L. Nature Communications 4(1): 1-9. https://doi.org/10.1038/ncomms3274

Beccari, O. 1918. Asiatic Palms-Lepidocaryeae: part 3: The species of the genera Ceratolobus, Calospatha, Plectocomia, Plectocomiopsis, Myrialepis, Zalacca, Pigafettia, Korthalsia, Metroxylon and Eugeissona. Annals of the Royal Botanic Garden, Calcutta 12: 156-195.

Benz, B.R., Rhode, J.M. & Cruzan, M.B. 2007. Aerenchyma development and elevated alcohol dehyrogenase activity as alternative responses to hypoxic soils in Piriqueta caroliniana complex. American Journal of Botany 94(4): 542-550.

Bintoro, M.H., Iqbal Nurulhaq, M., Pratama, A.J., Ahmad, F. & Ayulia, L. 2018. Growing area of sago palm and its environment. In Sago Palm Multiple Contributions to Food Security and Sustainable Livelihoods, edited by Ehara, H., Toyoda, Y. & Johnson, D.V. Singapore: Springer Nature. pp. 17-30.

Boocock, J., Chagné, D., Merriman, T.R. & Black, M.A. 2015. The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus x domestica Borkh. BMC Genomics 16: 848. https://doi.org/10.1186/s12864-015-2096-x

Boonsermsuk, S., Anai, T., Hasegawa, K. & Hisajima, S. 1997. Variation in random polymorphic DNA of sago palm (Metroxylon Spp.) in Thailand. Japanese Journal of Tropical Agriculture 41(2): 89-92.

Bujang, K. 2018. Production, purification, and health benefits of sago sugar. In Sago Palm: Multiple Contributions to Food Security and Sustainable Livelihoods, 1st ed., edited by Ehara, H. Johnson, D.V. & Toyoda, Y. Singapore: Springer Nature. 1: 229-308.

Campos, E.V.R., Ratko, J., Bidyarani, N., Takeshita, V. & Fraceto, L.F. 2023. Nature-based herbicides and micro-/nanotechnology fostering sustainable agriculture. ACS Sustainable Chemistry & Engineering 11(27): 9900-9917. https://doi.org/10.1021/acssuschemeng.3c02282

Dolatabadian, A., Patel, D.A., Edwards, D. & Batley, J. 2017. Copy number variation and disease resistance in plants. Theoretical and Applied Genetics 130(1): 2479-2490.

Ehara, H., Yamamoto, T., Tsuchiya, T., Hitoshi, N., Dowe, J.L., McClatchey, W.C., Mishima, T., Itaya, A., Mizota, C., Pasolon, Y.B., Ala, P., Tuiwawa, M., Naikatini, A., Rounds, I.A., Foliga, T., Lui, S. & Kwan, S. 2019. Phylogenetic study of metroxylon palms in Southeast Asia and Oceania based on 5S NrDNA spacer sequence data. Sago Palm 26(2): 37-43.

Ellen, R. 2006. Local knowledge and management of sago palm (Metroxylon sagu Rottboel) diversity in South Central Seram, Maluku, Eastern Indonesia. Journal of Ethnobiology 26(2): 258-298.

Enguito, R.Z.C. & Novero, A.U. 2018. Genetic variation of sago palm (Metroxylon sagu Rottb.) samples from Mindanao, Philippines using internal transcribed spacer analysis. Malaysian Applied Biology 47(3): 39-48.

Flach, M. 1997. Sago Palm: Metroxylon sagu Rottb.: Promoting the Conservation and Use of Underutilized and Neglected Crops. 1st ed. Vol. 13. Rome: International Plant Genetic Resources Institute.

Fukazawa, J., Miyamoto, C., Ando, H., Mori, K. & Takahashi, Y. 2021. DELLA-GAF1 complex is involved in tissue-specific expression and gibberellin feedback regulation of GA20ox1 in Arabidopsis. Plant Molecular Biology 107(3): 147-158.

Hirao, K., Kondo, T., Kainuma, K. & Takahashi, S. 2018. Starch properties and uses as food for human heatlh and welfare. In Sago Palm: Multiple Contributions to Food Security and Sustainable Livelihoods, 1st ed., edited by Ehara, H., Johnson, D.V. & Toyoda, Y. 1: 285-288. Singapore: Springer Nature.

Hussain, H., Edward-Atit, A.S., Julaihi, N., Tommy, R., Nisar, M., Hamdan, N. & Ehara, H. 2022. Identification of differentially expressed transcripts for trunk formation in sago palm using annealing control primer genefishing technique. Journal Pf Applied Biology and Biotechnology 10(2): 2-4.

Hussain, H., Mustafa Kamal, M., Al-Obaidi, J.R., Hamdin, N.E., Ngaini, Z. & Mohd-Yusuf, Y. 2020. Proteomics of sago palm towards identifying contributory proteins in stress-tolerant cultivar. Protein Journal 39(1): 62-72. https://doi.org/10.1007/s10930-019-09878-9

Hussain, H., Yan, W-J., Ngaini, Z., Julaihi, N., Tommy, R. & Ahmad Bhawani, S. 2020. Differential metabolites markers from trunking and stressed non-trunking sago palm (Metroxylon sagu Rottb.). Current Chemical Biology 14(4): 262-278. https://doi.org/10.2174/2212796814999200930120925

Ibrahim, E.R., Hossain, M.A. & Roslan, H.A. 2014. Genetic transformation of Metroxylon sagu (Rottb.) cultures via Agrobacterium -Mediated and particle bombardment. BioMed Research International 2014: 348140. https://doi.org/10.1155/2014/348140

Jamel, B., Hussain, M.H., Salleh, M.A. & Busri, N. 2011. Isolation and characterization of the GA 20-Oxidase CDNA from sago palm (Metroxylon sagu Rottb.). Asia-Pacific Journal of Molecular Biology and Biotechnology 19(2): 83-93.

Jiao, Y., Zhao, H., Ren, L., Song, W., Zeng, B., Guo, J., Wang, B., Liu, Z., Chen, J., Li, W., Zhang, M., Xie, S. & Lai, J. 2012. Genome-wide genetic changes during modern breeding of maize. Nature Genetics 44(7): 812-815. https://doi.org/10.1038/ng.2312

Kjær, A., Barfod, A.S., Asmussen, C.B. & Seberg, O. 2004. Investigation of genetic and morphological variation in the sago palm (Metroxylon sagu; Arecaceae) in Papua New Guinea. Annals of Botany 94(1): 109-117. https://doi.org/10.1093/aob/mch112

Kumar, R.A., Oldenburg, D.J. & Bendich, A.J. 2014. Changes in DNA damage, molecular integrity, and copy number for plastid DNA and mitochondrial DNA during maize development. Journal of Experimental Botany 65(22): 6425-6439. https://doi.org/10.1093/jxb/eru359

Lam, H-M., Xu, X., Liu, X., Chen, W., Yang, G., Wong, F-L., Li, M-W., He, W., Qin, N., Wang, B., Li, J., Jian, M., Wang, J., Shao, G., Wang, J., Sun, S.S.M. & Zhang, G. 2010. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nature Genetics 42(12): 1053-1059. https://doi.org/10.1038/ng.715

Lim, H., Kobayashi, M.J., Marsoem, S.N., Irawati, D., Kosugi, A., Kondo, T. & Tani, N. 2023. Transcriptomic responses of oil palm (Elaeis guineensis) stem to waterlogging at plantation in relation to precipitation seasonality. Frontiers in Plant Science 14: 1213496. https://doi.org/10.3389/fpls.2023.1213496

Lim, L.W.K., Chung, H.H. & Hussain, H. 2020a. Complete chloroplast genome sequencing of sago palm (Metroxylon sagu Rottb.): Molecular structures, comparative analysis and evolutionary significance. Gene Reports 19: 100662. https://doi.org/10.1016/j.genrep.2020.100662

Lim, L.W.K., Chung, H.H. & Hussain, H. 2020b. Organellar genome copy number variations and integrity across different organs, growth stages, phenotypes and main localities of sago palm (Metroxylon sagu Rottboll) in Sarawak, Malaysia. Gene Reports 21: 100808. https://doi.org/10.1016/j.genrep.2020.100808

Lim, L.W.K., Chung, H.H., Hussain, H. & Gan, H.M. 2021. Genome survey of sago palm (Metroxylon sagu Rottboll). Plant Gene 28: 100341. https://doi.org/10.1016/j.plgene.2021.100341

Lim, L.W.K., Lau, M.M.L., Chung, H.H., Hussain, H. & Gan, H.M. 2022. First high-quality genome assembly data of sago palm (Metroxylon sagu Rottboll). Data in Brief 40: 107800. https://doi.org/10.1016/j.dib.2022.107800

Mace, E.S., Tai, S., Gilding, E.K., Li, Y., Prentis, P.J., Bian, L., Campbell, B.C., Hu, W., Innes, D.J., Han, X., Cruickshank, A., Dai, C., Frère, C., Zhang, H., Hunt, C.H., Wang, X., Shatte, T., Wang, M., Su, Z., Li, J., Lin, X., Godwin, I.D., Jordan, D.R. & Wang, J. 2013. Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum. Nature Communications 4(1): 2320. https://doi.org/10.1038/ncomms3320

Mahmoud, A. 2021. Genome Sequence of Oil Palm. In Oil Crop Genomics edited by Tombuloglu, H., Unver, T., Tombuloglu, G., Hakeem, K.R. Springer, Cham. https://doi.org/10.1007/978-3-030-70420-9_6

Miao, H., Jiang, B., Chen, S., Zhang, S., Chen, F., Fang, W., Teng, N. & Guan, Z. 2010. Isolation of a Gibberellin 20-Oxidase CDNA from and characterization of its expression in chrysanthemum. Plant Breeding 129(6): 707-714. https://doi.org/10.1111/j.1439-0523.2009.01736.x

Nisar, M. & Hussain, H. 2022. Assessment of the genetic variations of sago palm Metroxylon Sagu in three regions of Sarawak, Malaysia using amplified fragment length polymorphism (AFLP) marker. Chemical and Biological Technologies in Agriculture 9: 46. https://doi.org/10.1186/s40538-022-00315-1

Nishimura, Y. 2018. Sago Starch: Transformation of extraction and consumption processes in traditional Indonesian societies. In Sago Palm: Multiple Contributions to Food Security and Sustainable Livelihoods, 1st ed., edited by Ehara, H., Johnson, D.V. & Toyoda, Y. Singapore: Spinger Nature. 1: 221-230.

Novero, A. 2012. Recent advances in sago palm (Metroxylon sagu Rottboell) micropropagation. In Frontiers on Recent Developments in Plant Science, edited by Goyal, A. & Maheshwari, P. Lethbridge, Canada: Bentham Science Publishers. pp. 60-66. https://doi.org/10.2174/978160805403911201010060

Pati, P., Gupta, M.K., Gouda, G. & Rathore, S.K. 2021. Conservation of rice germplasm by bioinformatics strategy. In Applications of Bioinformatics in Rice Research, edited by Gupta, M.K. & Behera, L. Singapore: Springer. pp. 315-332. https://doi.org/10.1007/978-981-16-3997-5_15

Phillips, A.L., Ward, D.A., Uknes, S., Appleford, N.E.J., Lange, T., Huttly, A.K., Gaskin, P., Graebe, J.E. & Hedden, P. 1995. Isolation and expression of three Gibberellin 20-Oxidase CDNA clones from Arabidopsis. Plant Physiology 108(3): 1049-1057. https://doi.org/10.1104/pp.108.3.1049

Prunier, J., Giguère, I., Ryan, N., Guy, R., Soolanayakanahally, R., Isabel, N., MacKay, J. & Porth, I. 2019. Gene copy number variations involved in balsam poplar (Populus balsamifera L.) adaptive variations. Molecular Ecology 28(6): 1476-1490. https://doi.org/10.1111/mec.14836

Purwoko, D., Cartealy, I.C., Tajuddin, T., Dinarti, D. & Sudarsono. 2019. SSR Identification and marker development for sago palm based on NGS genome data. Breeding Science 69(1): 1-10. https://doi.org/10.1270/jsbbs.18061

Roslan, H.A. & Anji, S.B. 2011. Characterization of inflorescence-predominant chitinase gene in Metroxylon sagu via differential display. 3 Biotech 1(1): 27-33. https://doi.org/10.1007/s13205-011-0004-x

Roslan, H.A., Hossain, M.A. & Gerunsin, J. 2017. Molecular and 3D-structural characterization of fructose-1,6-bisphosphate aldolase derived from Metroxylon sagu. Brazilian Archives of Biology and Technology 60(0): e17160108. https://doi.org/10.1590/1678-4324-2017160108

Roslan, H.A., Hossain, M.A., Ngieng, N.S. & Hussaini A. 2020. Sago palm genome size estimation via real-time quantitative PCR. Current Applied Science and Technology 20(2): 208-216.

Shi, H., Liu, W., Yao, Y., Wei, Y. & Chan, Z. 2017. Alcohol dehydrogenase 1 (ADH1) confers both abiotic and biotic stress resistance in Arabidopsis. Plant Science 262: 24-31. https://doi.org/10.1016/j.plantsci.2017.05.013

Sieber, A.N., Longin, C.F.H., Leiser, W.L. & Würschum, T. 2016. Copy number variation of CBF-A14 at the Fr-A2 locus determines frost tolerance in winter durum wheat. Theoretical and Applied Genetics 129(6): 1087-1097.

Tan, K. 1983. The Swamp-Sago Industry in West Malaysia: A Study of the Sungei Batu Pahat Floodplain. Pasir Panjang, Singapore: Institute of Southeast Asian Studies.

Varshney, R.K., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., Srivastava, R.K., Chitikineni, A., Fan, G., Bajaj, P., Punnuri, S., Gupta, S.K., Wang, H., Jiang, Y., Couderc, M., Katta, M.A.V.S.K., Paudel, D.R., Mungra, K.D., Chen, W., Harris-Shultz, K.R., Garg, V., Desai, N., Doddamani, D., Kane, N.A., Conner, J.A., Ghatak, A., Chaturvedi, P., Subramaniam, S., Yadav, O.P., Berthouly-Salazar, C., Hamidou, F., Wang, J., Liang, X., Clotault, J., Upadhyaya, H.D., Cubry, P., Rhoné, B., Gueye, M.C., Sunkar, R., Dupuy, C., Sparvoli, F., Cheng, S., Mahala, R.S., Singh, B., Yadav, R.S., Lyons, E., Datta, S.K., Hash, C.T., Devos, K.M., Buckler, E., Bennetzen, J.L., Paterson, A.H., Ozias-Akins, P., Grando, S., Wang, J., Mohapatra, T.,  Weckwerth, W., Reif, J.C., Liu, X., Vigouroux, Y. & Xu, X. 2017. Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nature Biotechnology 35: 969-976. https://doi.org/10.1038/nbt.3943

Ventura, I., Brunello, L., Iacopino, S., Valeri, M.C., Novi, G., Dornbusch, T., Perata, P. & Loreti, E. 2020. Arabidopsis phenotyping reveals the importance of alcohol dehydrogenase and pyruvate decarboxylase for aerobic plant growth. Scientific Reports 10: 16669. https://doi.org/10.1038/s41598-020-73704-x

Wang, Wensheng, Ramil Mauleon, Zhiqiang Hu, Dmytro Chebotarov, Shuaishuai Tai, Zhichao Wu, Min Li, et al. 2018. “Genomic Variation in 3,010 Diverse Accessions of Asian Cultivated Rice.” Nature 557 (7703): 43–49. https://doi.org/10.1038/s41586-018-0063-9.

Wee, C.C. & Roslan, H.A. 2012. Isolation of alcohol dehydrogenase CDNA and basal regulatory region from Metroxylon sagu. International Scholarly Research Network Molecular Biology 2012: 839427. https://doi.org/10.5402/2012/839427

Wei, C., Chen, J. & Kuang, H. 2016. Dramatic number variation of R genes in solanaceae species accounted for by a few R gene subfamilies. PLoS ONE 11(2): e0148708. https://doi.org/10.1371/journal.pone.0148708

Withanage, S.P., Hossain, M.A., Kumar, M.S., Roslan, H.A., Abdullah, M.P., Napis, S.B. & Ab Shukor, N.A. 2015. Overexpression of Arabidopsis thaliana gibberellic acid 20 oxidase (AtGa20ox) gene enhance the vegetative growth and fiber quality in kenaf (Hibiscus cannabinus L.) plants. Breeding Science 65(3): 177-191. https://doi.org/10.1270/jsbbs.65.177

Yong, C.M.R., Sobeng, Y., Zaini, F. & Busri, N. 2018. Suitability of peat swamps areas for commercial production of sago palms: The Sarawak experience. In Sago Palm: Multiple Contributions to Food Security and Sustainable Livelihoods, edited by Ehara, H., Toyoda, Y. & Johnson, D.V. Singapore: Springer Nature. pp. 91-108.

Zhang, M., Ma, Y., Zheng, X., Tan, B., Ye, X., Wang, W., Zhang, L., Li, J., Li, Z., Cheng, J. & Feng, J. 2022. The distribution of bioactive gibberellins along peach annual shoots is closely associated with PpGA20ox and PpGA2ox expression profiles. BMC Genomics 23(1): 730. https://doi.org/10.1186/s12864-022-08943-5

Zhou, Y. & Underhill, S.J.R. 2015. Breadfruit (Artocarpus altilis) gibberellin 20-oxidase genes: Sequence variants, stem elongation and abiotic stress response. Tree Genetics and Genomes 11: 84. https://doi.org/10.1007/s11295-015-0909-3

*Corresponding author; email: hhasnain@unimas.my