DOI : https://doi.org/10.18517/ijaseit.14.3.19366

Application of SNP Markers to Identify Genetic Variation on Mutant Lines of Adan-Krayan, Special Local Rice from North Kalimantan

Joko Prasetiyono (1), Nurul Hidayatun (2), Tasliah (3), Etty Pratiwi (4), Selly Salma (5), Syakhril (6), Riyanto (7), Subandi (8), Mahrup (9), Sugiono Moeljopawiro (10)
(1) Research Center for Genetic Engineering, National Research and Innovation Agency, Indonesia
(2) Research Center for Food Crops, National Research and Innovation Agency, Indonesia
(3) Research Center for Genetic Engineering, National Research and Innovation Agency, Indonesia
(4) Research Center for Food Crops, National Research and Innovation Agency, Indonesia
(5) Research Center for Food Crops, National Research and Innovation Agency, Indonesia
(6) Faculty of Agriculture, Mulawarman University, East Kalimantan, Indonesia
(7) Local Government of East Kalimantan Province, West Kalimantan, Indonesia
(8) Local Government of Nunukan Regency, North Kalimantan Province, North Kalimantan, Indonesia
(9) Research Center for Genetic Engineering, National Research and Innovation Agency, Indonesia
(10) Ministry of Law and Human Rights, Jakarta, Indonesia
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How to cite (IJASEIT) :
Prasetiyono, Joko, et al. “Application of SNP Markers to Identify Genetic Variation on Mutant Lines of Adan-Krayan, Special Local Rice from North Kalimantan ”. International Journal on Advanced Science, Engineering and Information Technology, vol. 14, no. 3, June 2024, pp. 946-54, doi:10.18517/ijaseit.14.3.19366.
Citation Format :
Adan rice, a local rice from the Krayan highland of  North Kalimantan is marked by its fine taste that consumers like. However, this rice can only be planted once a year due to its long lifespan. Efforts have been made to develop a short-lived version of Adan, to enable it to be planted twice a year. Adan Kelabit was initially exposed to gamma radiation, which produced several mutants. Field selection identified eight mutants with shorter lifespans than the Adan.  In this study, these eight mutants were observed further. SNP markers were carried out to confirm the occurrence of mutations, while observations of agronomic characters and grain quality were carried out to determine the most promising lines. The molecular study showed mutations found in all chromosomes of the mutants and differentiated them from the original Adan, with the similarity level ranging from 0.746 to 0.843. However, this closeness is not correlated to the dosage of the gamma rays applied. The majority of the mutants have shorter plant height and higher yield potential. On average, the mutant is 11.5% shorter on heading date, 22.69% higher on tiller number, 27.14% higher on grain weight, and 26.64% higher on other parameters of yield potential. Apart from the shorter heading date, each mutant has its superiorities. The A25 and A28 mutant lines have much higher yield potential while maintaining the same level of amylose content as the Adan rice. These two mutants can be considered for further development or dissemination for farmer adoption.

F. Fauziah and M. Rizal, “Potensi Pengembangan Padi Adan di Kabupaten Nunukan,” Proceedings Series on Physical & Formal Sciences, vol. 4, pp. 90–94, Nov. 2022, doi: 10.30595/pspfs.v4i.488.

Rahmianti, “Beras Adan, si beras Krayan yang mendunia,” [Online]. Available: https://www.rri.co.id/daerah/468621/beras-adan-si-beras-krayan-yang-mendunia.

H. Wei, X. Wang, H. Xu, and L. Wang, “Molecular basis of heading date control in rice,” BIOTECH, vol. 1, no. 4. Springer, pp. 219–232, Oct. 01, 2020. doi: 10.1007/s42994-020-00019-w.

H. Kato, F. Li, and A. Shimizu, “The selection of gamma-ray irradiated higher yield rice mutants by directed evolution method,” Plants, vol. 9, no. 8, pp. 1–16, Aug. 2020, doi: 10.3390/plants9081004.

A. Abdelnour-Esquivel, J. Perez, M. Rojas, W. Vargas, and A. Gatica-Arias, “Use of gamma radiation to induce mutations in rice (Oryza sativa L.) and the selection of lines with tolerance to salinity and drought,” In Vitro Cellular and Developmental Biology - Plant, vol. 56, no. 1, pp. 88–97, Feb. 2020, doi: 10.1007/s11627-019-10015-5.

A. A. Ali, O. A. Galal, A. M. Elmoghazy, and M. M. Abd-Elrazek, “Using gamma rays for genetic improvement of rice resistance to blast disease,” Journal of Agricultural Chemistry and Biotechnology, vol. 13, no. 10, pp. 85–90, Oct. 2022, doi: 10.21608/jacb.2022.152986.1028.

B. Saragih, N. M. Naibaho, and B. Saragih, “Nutritional, functional properties, glycemic index and glycemic load of indigenous rice from North and East Borneo,” Food Res, vol. 3, no. 5, pp. 537–545, Oct. 2019, doi: 10.26656/fr.2017.3(5).035.

S. G. Hwang et al., “Resequencing of a core rice mutant population induced by gamma-ray irradiation and its application in a genome-wide association study,” Journal of Plant Biology, vol. 63, no. 6, pp. 463–472, Dec. 2020, doi: 10.1007/s12374-020-09266-2.

C. Lee et al., “Development and application of a target capture sequencing SNP-genotyping platform in rice. ,” Genes , vol. 13, no. 794, Apr. 2022, doi: 10.3390/genes13050794.

K. Y. Morales et al., “An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies,” PLoS One, vol. 15, no. 5, May 2020, doi: 10.1371/journal.pone.0232479.

C. Zhang et al., “Rice3K56 is a high-quality SNP array for genome-based genetic studies and breeding in rice (Oryza sativa L.),” Crop Journal, vol. 11, no. 3, pp. 800–807, Jun. 2023, doi: 10.1016/j.cj.2023.02.006.

K. W. Kim, B. Nawade, J. Nam, S. H. Chu, J. Ha, and Y. J. Park, “Development of an inclusive 580K SNP array and its application for genomic selection and genome-wide association studies in rice,” Front Plant Sci, vol. 13, 1036177, Oct. 2022, doi: 10.3389/fpls.2022.1036177.

P. M. Babu et al., “Stable SNP allele associations with high grain zinc content in polished rice (Oryza sativa L.) identified based on ddRAD sequencing,” Front Genet, vol. 11, Aug. 2020, doi: 10.3389/fgene.2020.00763.

J. W. Lee, J. S. Oh, and S. C. Yoo, “Development of SNP marker set to select varieties tolerant to multiple abiotic stresses in rice,” Plant Breed Biotechnol, vol. 11, no. 3, pp. 208–219, 2023, doi: 10.9787/PBB.2023.11.3.208.

E. Sales, J. García-Romeral, and C. Domingo, “Bioinformatics approach for developing a minimum set of SNP markers for identification of temperate japonica rice varieties cultivated in Spain,” PLoS One, vol. 18, no. 6, e0286839, June, Jun. 2023, doi: 10.1371/journal.pone.0286839.

C. Winarti et al., “Nutrient composition of Indonesian specialty cereals: rice, corn, and sorghum as alternatives to combat malnutrition,” Prev Nutr Food Sci, vol. 28, no. 4, pp. 471–482, Dec. 2023, doi: 10.3746/pnf.2023.28.4.471.

BSN, Standar Nasional Indonesia (SNI): Beras (= National Standard Bureau: Rice). Jakarta: Badan Standardisasi Nasional, 2015.

A. N. M. R. Bin Rahman and J. Zhang, “Trends in rice research: 2030 and beyond,” Food and Energy Security, vol. 12, no. 2, John Wiley and Sons Inc, Mar. 01, 2023. doi: 10.1002/fes3.390.

D. Gong et al., “Genetic improvements in rice grain quality: A review of elite genes and their applications in molecular breeding,” Agronomy, vol. 13, no. 5, 1375, MDPI, May 01, 2023. doi: 10.3390/agronomy13051375.

M. J. Thomson et al., “Large-scale deployment of a rice 6K SNP array for genetics and breeding applications,” Rice, vol. 10, no. 40, Dec. 2017, doi: 10.1186/s12284-017-0181-2.

S. L. Dellaporta, J. Wood, and J. B. Hicks, “A plant DNA minipreparation: Version II,” Plant Mol Biol Report, vol. 1, no. 4, pp. 19–21, 1983.

Y. Du et al., “Frequency and spectrum of mutations induced by gamma rays revealed by phenotype screening and whole-genome re-sequencing in Arabidopsis thaliana,” Int J Mol Sci, vol. 23, no. 654, Jan. 2022, doi: 10.3390/ijms23020654.

L. Ma, F. Kong, K. Sun, T. Wang, and T. Guo, “From classical radiation to modern radiation: Past, present, and future of radiation mutation breeding,” Frontiers in Public Health, vol. 9, :768071, Frontiers Media S.A., Dec. 21, 2021. doi: 10.3389/fpubh.2021.768071.

R. Baadu, K. P. Chong, J. A. Gansau, M. R. M. Zin, and J. Dayou, “A systematic review on physical mutagens in rice breeding in Southeast Asia,” PeerJ, vol. 11, no. 5, e15682 2023, doi: 10.7717/peerj.15682.

A. Jadhav et al., “Assessment of genetic variability in gamma rays induced mutants of rice (Oryza sativa L.),” vol. 12, no. 6, pp. 4417–4422, 2023, [Online]. Available: www.thepharmajournal.com

J. Prasetiyono, T. Rafsanjani, T. Aminingsih, Tasliah, and S. Moeljaopawiro, “Genetic variation of Adan, a Krayan local rice mutant, using microsatellite markers,” in The Second International Conference on Genetic Resources and Biotechnology, Harnessing Technology for Conservation and Sustainable Use of Genetic Resources for Food and Agriculture, I. Tasma, D. Utami, I. Roostika, Y. Suryadi, Chaerani, E. Riyanti, P. Lestari, T. Hadiarto, Reflinur, J. Prasetiyono, Fatimah, S. Diantina, T. Priyatno, K. Kusumanegara, W. Enggarini, R. Terryana, and D. Satyawan, Eds., Jakarta: AIP Conference Proceedings 2462, 2022, doi: 10.1063/5.0075660.

W. Aesomnuk et al., “Estimation of the genetic diversity and population structure of thailand’s rice landraces using snp markers,” Agronomy, vol. 11, no. 995, 2021, doi: 10.3390/agronomy11050995.

D. R. Choudhury et al., “SSR and SNP marker-based investigation of Indian rice landraces in relation to their genetic diversity, population structure, and geographical isolation,” Agriculture (Switzerland), vol. 13, no. 4, 823, Apr. 2023, doi: 10.3390/agriculture13040823.

P. Huang et al., “Genetic analysis of a collection of rice germplasm (Oryza sativa L.) through high-density SNP array provides useful information for further breeding practices,” Genes (Basel), vol. 13, no. 830, May 2022, doi: 10.3390/genes13050830.

J. Jankowicz-Cieslak et al., “Spectrum and density of gamma and X-ray induced mutations in a non-model rice cultivar,” Plants, vol. 11, no. 23, 3232, Dec. 2022, doi: 10.3390/plants11233232.

R. Sao, P. K. Sahu, R. S. Patel, B. K. Das, L. Jankuloski, and D. Sharma, “Genetic improvement in plant architecture, maturity duration and agronomic traits of three traditional rice landraces through gamma ray-based induced mutagenesis,” Plants, vol. 11, no. 3448, Dec. 2022, doi: 10.3390/plants11243448.

M. T. Andrew-Peter-Leon, S. Ramchander, K. K. Kumar, M. Muthamilarasan, and M. A. Pillai, “Assessment of efficacy of mutagenesis of gamma-irradiation in plant height and days to maturity through expression analysis in rice,” PLoS One, vol. 16, no. 1, e0245603, Jan. 2021, doi: 10.1371/journal.pone.0245603.

Lekha P. S., A. J. Shridevi, Nachiketha T. K., D. Kumar, B. Halingali I., and Jayashree S., “Genetic analysis of M5 generation of gamma irradiated red rice (Oryza sativa L.) mutant lines,” International Journal of Environment and Climate Change, vol. 14, no. 3, pp. 355–363, Mar. 2024, doi: 10.9734/ijecc/2024/v14i34047.

W. N. Hanifah, Parjanto, S. Hartati, and A. Yunus, “The performances of M4 generation of mentik susu rice mutants irradiated with gamma-ray,” Biodiversitas, vol. 21, no. 9, pp. 4041–4046, Sep. 2020, doi: 10.13057/biodiv/d210915.

A. Zhang et al., “Genetic analysis for cooking and eating quality of super rice and fine mapping of a novel locus qGC10 for gel consistency,” Front Plant Sci, vol. 11, no. 342, pp. 1–9, March 2020, doi: 10.3389/fpls.2020.00342.

L. Huang et al., “Improving rice eating and cooking quality by coordinated expression of the major starch synthesis-related genes, SSII and Wx, in endosperm,” Plant Mol Biol, vol. 106, no. 4–5, pp. 419–432, Jul. 2021, doi: 10.1007/s11103-021-01162-8.

M. S. Kim et al., “Breeding of high cooking and eating quality in rice by marker-assisted backcrossing (Mabc) using kasp markers,” Plants, vol. 10, no. 4, pp. 1–18, 2021, doi: 10.3390/plants10040804.

C. X. Wang et al., “Grain quality and starch physicochemical properties of chalky rice mutant,” Agronomy, vol. 11, no. 8, Aug. 2021, doi: 10.3390/agronomy11081575.

R. P. Bachtari, S. Listyawati, and Sutarno, “ Starch, amylose and amylopectin levels of M5 and M6 generations of black rice irradiated by gamma Co 60 ray ,” J Phys Conf Ser, vol. 1436, p. 012116, Jan. 2020, doi: 10.1088/1742-6596/1436/1/012116.

M. E. Ronie, A. H. Abdul Aziz, N. Q. I. Mohd Noor, F. Yahya, and H. Mamat, “Characterisation of Bario rice flour varieties: Nutritional compositions and physicochemical properties,” Applied Sciences (Switzerland), vol. 12, no. 18, Sep. 2022, doi: 10.3390/app12189064.

S. Sultana, M. Faruque, and M. R. Islam, “Rice grain quality parameters and determination tools: a review on the current developments and future prospects,” International Journal of Food Properties, vol. 25, no. 1. Taylor and Francis Ltd., pp. 1063–1078, 2022. doi: 10.1080/10942912.2022.2071295.

Z. Lu et al., “Grain quality characteristics analysis and application on breeding of Yuenongsimiao, a high-yielding and disease-resistant rice variety,” Sci Rep, vol. 13, no. 1, Dec. 2023, doi: 10.1038/s41598-022-21030-9.

K. Khaerunnisa et al., “Is agricultural institutions affect the sustainability of local Adan rice farming?,” Indigenous Agriculture, vol. 1, no. 1, pp. 18–28, Mar. 2023, doi: 10.20956/ia.v1i1.25785.

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