Genetic Relationship of 22 Pigmented Rice from Central Java and East Java Based on Simple Sequence Repeat (SSR)

Yeni Avidhatul  Husnah; Turhadi  Turhadi; Anna  Safitri; Rista Nikmatu Rohmah; Fatchiyah Fatchiyah

doi:10.22146/jtbb.18676

Yeni Avidhatul Husnah Research Center of Smart Molecule of Natural Genetics Resources, Universitas Brawijaya, Jl. Veteran, Malang 65145, East Java, Indonesia; Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya, Jl. Veteran, Malang 65145, East Java, Indonesia
Turhadi Turhadi Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya, Jl. Veteran, Malang 65145, East Java, Indonesia https://orcid.org/0000-0003-4906-3769
Anna Safitri Research Center of Smart Molecule of Natural Genetics Resources, Universitas Brawijaya, Jl. Veteran, Malang 65145, East Java, Indonesia; Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya, Jl. Veteran, Malang 65145, East Java, Indonesia https://orcid.org/0000-0003-4262-8640
Rista Nikmatu Rohmah Research Center of Smart Molecule of Natural Genetics Resources, Universitas Brawijaya, Jl. Veteran, Malang 65145, East Java, Indonesia; Biosains Institute, Universitas Brawijaya, Malang 65123, Indonesia https://orcid.org/0000-0002-2452-3020
Fatchiyah Fatchiyah Research Center of Smart Molecule of Natural Genetics Resources, Universitas Brawijaya, Jl. Veteran, Malang 65145, East Java, Indonesia; Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya, Jl. Veteran, Malang 65145, East Java, Indonesia https://orcid.org/0000-0001-6241-9665

DOI: https://doi.org/10.22146/jtbb.18676

Keywords: Genetic relationship, Indonesia pigmented rice, Marker genes, Simple Sequence Repeat

Abstract

Pigmented rice contains distinct bioactive compounds compared to regular white rice. The study aimed to determine the genetic diversity of 22 pigmented local rice varieties originating from East Java and Central Java Province, Indonesia. This research used a PCR-based molecular marker approach utilizing plant pigment marker genes, namely Simple Sequence Repeat (SSR). The research commenced with planting and maintaining the rice plants, DNA isolation according to the cetyltrimethylammonium bromide (CTAB) method, DNA amplification, and PCR visualization, followed by phylogenetic tree construction using PAST 4.0 software. Based on the allele structure analysis, four main clusters of pigmented rice were identified. The identified polymorphisms and clustering patterns provide valuable insights for future plant evolution, breeding, and conservation research. In addition, genetic differentiation suggests a high level within the population. Based on allele structure analysis, black rice shares genetic characteristics with other rice colours, including red, brown, and white. In conclusion, black rice shows the most complex allele structure for colour-related genes among all rice colours.

References

Ahn, J.Y., Hong, K.N. & Lim, H.I., 2023. Genetic diversity and structure of Quercus variabilis populations in the Republic of Korea based on microsatellite markers. Journal of Forest Research, 28(5), pp.353–363. doi: 10.1080/13416979.2023.2213517.

Andarini, Y.N. et al., 2022. Genetic relationship of pigmented rice (Oryza sativa L.) collected from Eastern Indonesia based on morpho-agronomical traits and SSR markers. AIP Conference Proceedings, 2462, 020023. doi: 10.1063/5.0075706.

Ashraf, H. et al., 2016. SSR based genetic diversity of pigmented and aromatic rice (Oryza sativa L.) genotypes of the western Himalayan region of India. Physiology and Molecular Biology of Plants, 22(4), pp.547–555. doi: 10.1007/s12298-016-0377-8.

Basith, A., Noer, S.N. & Faizah, M., 2023. The Variation in anthocyanin content level in four local varieties of black rice (Oryza sativa L.) from Indonesia. Jurnal Pertanian, 14(1), pp.1–6. doi: 10.30997/jp.v14i1.7152.

Bhat, F.M. et al., 2020. Status of Bioactive Compounds from Bran of Pigmented Traditional Rice Varieties and Their Scope in Production of Medicinal Food with Nutraceutical Importance. Agronomy, 10(11), 1817. doi: 10.3390/agronomy10111817.

Budiman, L.F. et al., 2019. Genetic diversity analysis of Tenera × Tenera and Tenera × Pisifera Crosses and D self of oil palm (Elaeis guineensis) parental populations originating from Cameroon. Biodiversitas Journal of Biological Diversity, 20(4), pp.937–949. doi: 10.13057/biodiv/d200402.

Chen, C. et al., 2017. Molecular characterization and genetic diversity of different genotypes of Oryza sativa and Oryza glaberrima. Electronic Journal of Biotechnology, 30, pp.48–57. doi: 10.1016/j.ejbt.2017.08.001.

Debsharma, S.K. et al., 2022. Harnessing on Genetic Variability and Diversity of Rice (Oryza sativa L.) Genotypes Based on Quantitative and Qualitative Traits for Desirable Crossing Materials. Genes, 14(1), 10. doi: 10.3390/genes14010010.

Dwiwibangga, Y., Safitri, A. & Fatchiyah, F., 2022. Profiling of Phytochemical Compounds of East Java Red Rice Bran Has the High-Value Biological Activities as Antioxidant and Antidiabetic. Indonesian Journal of Chemistry, 22(5), pp.1304–1320. doi: 10.22146/ijc.73432.

Fatchiyah et al., 2011. Biologi Molekular : prinsip Dasar Analisis, Jakarta: Penerbit Erlangga.

Fatchiyah, F. et al., 2020. Phytochemical Compound and Nutritional Value in Black Rice from Java Island, Indonesia. Systematic Reviews in Pharmacy, 11(7), pp.414–421. doi: 10.31838/srp.2020.7.61.

Fatchiyah, F. et al., 2023. Bioactive compound profile and their biological activities of endogenous black rice from Java and East Nusa Tenggara. CyTA - Journal of Food, 21(1), pp.159–170. doi: 10.1080/19476337.2023.2173306.

Gao, J. et al., 2019. Mapping and Identifying a Candidate Gene Plr4, a Recessive Gene Regulating Purple Leaf in Rice, by Using Bulked Segregant and Transcriptome Analysis with Next-Generation Sequencing. International Journal of Molecular Sciences, 20(18), 4335. doi: 10.3390/ijms20184335.

Hamidah, H. et al., 2024. Genetic diversity and cluster analysis of local pigmented rice from East and North Kalimantan, Indonesia based on quantitative and qualitative characters. Biodiversitas Journal of Biological Diversity, 25(5), pp.1938–1945. doi: 10.13057/biodiv/d250510.

Husnah, Y.A. et al., 2024. Morphoagronomical Evaluation of Several Indonesian Pigmented Rice ( Oryza sativa L.) Accessions from East Java and Central Java, Indonesia. Plant Breeding and Biotechnology, 12, pp.122–137. doi: 10.9787/PBB.2024.12.122.

Kusumardani, H.D., Yuwono, T. & Rachmawati, D., 2022. Growth and Physiological Attributes of Rice by the Inoculation of Osmotolerant Rhizobacteria (Enterobacter flavescens) under Drought Condition. Journal of Tropical Biodiversity and Biotechnology, 7(2), jtbb67359. doi: 10.22146/jtbb.67359.

Manzo-Sánchez, G. et al., 2021. Genetic Diversity of Fusarium Wilt Disease of Banana. In Genetic Variation. IntechOpen. doi: 10.5772/intechopen.94158.

Mbanjo, E.G.N. et al., 2020. The Genetic Basis and Nutritional Benefits of Pigmented Rice Grain. Frontiers in Genetics, 11, 229. doi: 10.3389/fgene.2020.00229.

McFarlane, S.E. et al., 2020. Increased genetic marker density reveals high levels of admixture between red deer and introduced Japanese sika in Kintyre, Scotland. Evolutionary Applications, 13(2), pp.432–441. doi: 10.1111/eva.12880.

Mohidem, N.A. et al., 2022. Rice for Food Security: Revisiting Its Production, Diversity, Rice Milling Process and Nutrient Content. Agriculture, 12(6), pp.741–768. doi: 10.3390/agriculture12060741.

Mukta, S. et al., 2024. Assessment of genetic diversity in Bangladeshi rice (Oryza sativa L.) varieties utilizing SSR markers. Gene Reports, 37, 102051. doi: 10.1016/j.genrep.2024.102051.

Panwar, S. et al., 2018. DNA fingerprinting in African marigold ( Tagetes erecta L.) genotypes using ISSR and URP markers. Indian Journal of Horticulture, 75(1), 105. doi: 10.5958/0974-0112.2018.00018.X.

Pathaichindachote, W. et al., 2019. Genetic Diversity and Allelic Frequency of Selected Thai and Exotic Rice Germplasm Using SSR Markers. Rice Science, 26(6), pp.393–403. doi: 10.1016/j.rsci.2018.11.002.

Peakall, R. & Smouse, P.E., 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics, 28(19), pp.2537–2539. doi: 10.1093/bioinformatics/bts460.

Pritchard, J.K., Stephens, M. & Donnelly, P., 2000. Inference of Population Structure Using Multilocus Genotype Data. Genetics, 155(2), pp.945–959. doi: 10.1093/genetics/155.2.945.

Salem, K.F.M. & Sallam, A., 2015. Analysis of population structure and genetic diversity of Egyptian and exotic rice (Oryza sativa L.) genotypes. Comptes Rendus. Biologies, 339(1), pp.1–9. doi: 10.1016/j.crvi.2015.11.003.

Samyor, D., Das, A.B. & Deka, S.C., 2017. Pigmented rice a potential source of bioactive compounds: a review. International Journal of Food Science & Technology, 52(5), pp.1073–1081. doi: 10.1111/ijfs.13378.

Sari, D.R.T. et al., 2021. Black rice cultivar from Java Island of Indonesia revealed genomic, proteomic, and anthocyanin nutritional value. Acta Biochimica Polonica, 68(1), pp.55–63. doi: 10.18388/abp.2020_5386.

Sarif, H.M. et al., 2020. Genetic diversity and variability among pigmented rice germplasm using molecular marker and morphological traits. Biotechnology & Biotechnological Equipment, 34(1), pp.747–762. doi: 10.1080/13102818.2020.1804451.

Serrote, C.M.L. et al., 2020. Determining the Polymorphism Information Content of a molecular marker. Gene, 726, 144175. doi: 10.1016/j.gene.2019.144175.

Shinta, S., Indriyani, S. & Arisoesilaningsih, E., 2014. Morphological Variation of Six Pigmented Rice Local Varieties Grown in Organic Rice Field at Sengguruh Village, Kepanjen Subdistrict, Malang District. Journal of Tropical Life Science, 4(2), pp.149–160. doi: 10.11594/jtls.04.02.12.

Susiyanti et al., 2021. Genetic diversity of Some Indonesian Local Rice Varieties based on Simple Sequence Repeat (SSR) marker related to Aromatic Genes. IOP Conference Series: Earth and Environmental Science, 715(1), 012046. doi: 10.1088/1755-1315/715/1/012046.

Wang, J. et al., 2020. Transcription Factors Rc and OsVP1 Coordinately Regulate Preharvest Sprouting Tolerance in Red Pericarp Rice. Journal of Agricultural and Food Chemistry, 68(50), pp.14748–14757. doi: 10.1021/acs.jafc.0c04748.

Wijayanti, E.D. et al., 2021. Antimicrobial Activity of Ferulic Acid in Indonesian Purple Rice through Toll-like Receptor Signaling. Makara Journal of Science, 25(4), pp.247–257. doi: 10.7454/mss.v25i4.1266.

Zulfahmi, Z. et al., 2021. Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia. Biodiversitas Journal of Biological Diversity, 22(10), pp.4431-4439. doi: 10.13057/biodiv/d221036.