Agronomic performance evaluation and selection of doubled haploid rice lines in a lowland saline-prone area

i

This article has been updated. A Correction to this article was published on .

i

The Original Article was published on

i

The Original Article was published on

i

This article has been updated

i

This article was retracted on

i

This article has been updated

Abstract

Salinity stress is a major abiotic stress limiting rice productivity. The development of high-yielding and salinity-tolerant rice varieties is a key strategy for achieving global food security. Evaluation under contrasting saline field conditions is needed to validate salinity-tolerant rice genotypes. This study aimed to evaluate agronomic performance and select superior doubled haploid (DH) rice lines in yield trials in lowland saline-prone areas. The research was conducted during the 2025 dry season in two coastal areas in Indonesia-Subang (strongly saline: 1.61 dS/m) and Sidoarjo (saline: 0.62 dS/m)-using a randomized complete block design with one factor (genotypes) and three replications in Sidoarjo and two replications in Subang. The genetic materials consisted of 25 DH rice lines and three check varieties (Inpari 18, Inpari 30 Ciherang Sub1, Inpari 34 Salin Agritan). Observations were conducted on agronomic characters, including growth, phenological, yield components, and grain yield. The results showed that all observed traits were significantly influenced by genotype × environment interactions (p-values <0.01 and <0.05), indicating differential genotype responses across two environments. DH rice lines exhibited higher grain yield than the check varieties in Sidoarjo and comparable performance in Subang. Among them, GN12, GN18, and GN21 consistently outperformed the salinity-tolerant check variety, Inpari 34 Salin Agritan, across both locations. A weighted selection index enabled the identification of 14 DH lines with desirable agronomic performance in two lowland saline-prone environments, including a high number of productive tillers (23.8 tillers), a low number of unfilled grains (22.8 grains/panicle), and a high mean grain yield (6.96 t/ha) exceeding that of the check varieties. Those selected DH lines are promising candidates for salinity-tolerant rice breeding and should be further evaluated in multi-location yield trials for their yield stability and adaptability.

Keywords

abiotic stress / agronomic characters / index selection / salinity rice breeding

CHANGE HISTORY

A Correction to this paper has been published:
https://doi.org

The Retraction Note was updated to reflect reception of statements of disagreement from all authors.

This article has been retracted.Please see the Retraction Notice for more detail:
https://doi.org

References

[1] Fukagawa NK, Ziska LH (2019) Rice: importance for global nutrition. J Nutr Sci Vitaminol 65: S2-S3. https://doi.org/10.3177/jnsv.65.S2.

[2] Rahman ANMRB, Zhang J (2022) Trends in rice research: 2030 and beyond. Food Energy Secur 12: 1-17. https://doi.org/10.1002/fes3.390.

[3] Seck F, Covarrubias-Pazaran G, Gueye T, et al. (2023) Realized genetic gain in rice: achievements from breeding programs. Rice 16: 1-22. https://doi.org/10.1186/s12284-023-00677-6.

[4] Food and Agriculture Organization (2021) Global map of salt-affected soils.

[5] Krishnamurthy SL, Lokeshkumar BM, Rathor S, et al. (2022) Development of salt-tolerant rice varieties to enhancing productivity in salt-affected environments, The 2nd International Laayoune Forum on Biosaline Agriculture. 1-5.

[6] Aycan M (2026) Salinity stress in rice: mechanisms and molecular approaches to mitigation. Planta 263: 1-18. https://doi.org/10.1007/s00425-026-04964-6.

[7] Islam S (2025) Agriculture, food security, and sustainability: a review. Explor Foods Foodomics 3: 1-21. https://doi.org/10.37349/eff.2025.101082.

[8] Oelviani R, Adiyoga W, Suhendrata T, et al. (2024) Effects of soil salinity on rice production and technical efficiency: Evidence from the northern coastal region of Central Java, Indonesia. Case Stud Chem Environ Eng 10: 1-11. https://doi.org/10.1016/j.cscee.2024.101010.

[9] Tripathy SK (2018) Anther culture for double haploid breeding in rice-a way forward. Rice Genomics Genet 9: 1-6. https://doi.org/10.5376/rgg.2018.09.0001.

[10] Chen X, Li S, Zha W, et al. (2025) Advances in anther culture-based rice breeding in China. Plants 14: 1-16. https://doi.org/10.3390/plants14111586.

[11] Anshori MF, Purwoko BS, Dewi IS, et al. (2022) Salinity tolerance selection of doubled-haploid rice lines based on selection index and factor analysis. AIMS Agric Food 7: 520-535. https://doi.org/10.3934/agrfood.2022032.

[12] Khan NA, Owens L, Nuñez MA, et al. (2025) Complexity of combined abiotic stresses to crop plants. Plant Stress 17: 1-19. https://doi.org/10.1016/j.stress.2025.100926.

[13] Ramadhani SU, Rokhmatuloh R, Wibowo A (2022) The rice production of paddy field and relationship with elevation using sentinel-1a sar in Subang regency. IOP Conf Ser: Earth Environ Sci 1089: 1-9. https://doi.org/10.1088/1755-1315/1089/1/012029.

[14] Putra AN, Martiana A, Alberth FS, et al. (2021) Response macronutrient content of saline-resistant paddy to the saline source distance. J Trop Soils 26: 63-74. https://doi.org/10.5400/jts.2021.v26i2.63-74.

[15] Ministry of Agriculture of the Republic of Indonesia(2019) Ministerial decree no. 681/HK.540/C/11/2019 on standard operating procedures for variety evaluation for release of food crop varieties, In: Ministry of Agriculture of the Republic of Indonesia, Jakarta.

[16] Li R, Li M, Ashraf U, et al. (2019) Exploring the relationships between yield and yield-related traits for rice varieties released in China from 1978 to 2017. Front Plant Sci 10: 1-12. https://doi.org/10.3389/fpls.2019.00543.

[17] Xu Y, Bu W, Xu Y, et al. (2024) Effects of salt stress on physiological and agronomic traits of rice genotypes with contrasting salt tolerance. Plants 13: 1-18. https://doi.org/10.3390/plants13081157.

[18] Yuana HW, Purwoko BS, Suwarno WB, et al. (2025) Yield trial of doubled-haploid rice lines with multiple abiotic stress tolerance. Caraka Tani J Sustain Agric 40: 390-403. https://doi.org/10.20961/carakatani.v40i3.94856.

[19] Gunarsih C(2022) Multiple tolerance to abiotic stress in doubled haploid rice lines derived from anther culture, Bogor: IPB University.

[20] Supriyati, Tjahjono B, Effendy S (2018) Analysis of rainfall pattern for lahar mitigation at sinabung volcano. J Ilmu Tanam Lingkung 20: 95-100. https://doi.org/10.29244/jitl.20.2.95-100.

[21] Ismayilov AI, Mamedov AI, Fujimaki H, et al. (2021) Soil salinity type effects on the relationship between the electrical conductivity and salt content for 1: 5 soil-to-water extract. Sustainability 13: 1-11. https://doi.org/10.3390/su13063395.

[22] Fehr WR, Fehr EL, Jessen HJ (1987) Principles of cultivar development: Theory and technique, Macmillan.

[23] Singh RK, Chaudhary BD (1985) xBiometrical methods in quantitative genetics analysis, Kalyani Publishers.

[24] Falconer DS (1989) Introduction to quantitative genetics, Longman.

[25] Walpole R(1982) Introduction of statistics, 3 Eds., New York: Macmillan Publishing Company, Inc.

[26] Bakare MA, Kayondo SI, Aghogho CI, et al. (2022) Exploring genotype by environment interaction on cassava yield and yield related traits using classical statistical methods. PLoS One 17: 1-24. https://doi.org/10.1371/journal.pone.0268189.

[27] Mondal KK, Akhter MAE, Mallik MAK (2025) Seasonal variability in soil salinity and its climatic drivers in Khulna, Bangladesh. Forum Geogr 39: 307-317. https://doi.org/10.23917/forgeo.v39i3.9038.

[28] Kawser U, Nath B, Hoque A (2022) Observing the influences of climatic and environmental variability over soil salinity changes in the Noakhali Coastal Regions of Bangladesh using geospatial and statistical techniques. Environ Chall 6: 1-17. https://doi.org/10.1016/j.envc.2021.100429.

[29] Corwin DL, Yemoto K (2020) Salinity: electrical conductivity and total dissolved solids. Soil Sci Soc Am J 2: 1442-1461. https://doi.org/10.1002/saj2.20154.

[30] Yang M, Zhou D, Hang H, et al. (2024) Effects of balancing exchangeable cations Ca, Mg, and K on the growth of tomato seedlings (Solanum lycopersicum L.) based on increased soil cation exchange capacity. Agronomy 14: 1-13. https://doi.org/10.3390/agronomy14030629.

[31] Cucci G, Lacolla G (2013) Irrigation with saline-sodic water: effects on two clay soils. Ital J Agron 8: 94-101. https://doi.org/10.4081/ija.2013.e13.

[32] Dey G, Banerjee P, Sharma RK, et al. (2021) Management of phosphorus in salinity-stressed agriculture for sustainable crop production by salt-tolerant phosphate-solubilizing bacteria-a review. Agronomy 11: 1-27. https://doi.org/10.3390/agronomy11081552.

[33] Amanat MA, Naeem MK, Algwaiz HIM, et al. (2022) Evaluation of green super rice lines for agronomic and physiological traits under salinity stress. Plants 11: 1-19. https://doi.org/10.3390/plants11111461.

[34] Crossa J (2012) From genotype × environment interaction to gene × environment interaction. Curr Genomics 13: 225-244. https://doi.org/10.2174/138920212800543066.

[35] Gomez KA, Gomez AA (1984) Statistical procedures for agricultural research, New York: John Wiley & Sons.

[36] Teressa T, Zigale S, Tamirat B (2021) Multi environments and genetic-environmental interaction (GxE) in plant breeding and its challenges: a review article. Int J Res Stud Agric Sci 7: 10-18. https://doi.org/10.20431/2454-6224.0704002.

[37] Limbongan Y, Sjahril R,Pata'dungan AM, et al. (2024) Genetic performance, heritability, and correlation of traits in new plant type of rice lines for highland ecosystem. Reprod Breed 4: 203-211. https://doi.org/10.1016/j.repbre.2024.08.002.

[38] Steinsaltz D, Dahl A, Wachter KW (2020) On negative heritability and negative estimates of heritability. Genetics 215: 343-357. https://doi.org/10.1534/genetics.120.303161.

[39] Khanna A, Anumalla M, Ramos J, et al. (2024) Genetic gains in IRRI’s rice salinity breeding and elite panel development as a future breeding resource. Theor Appl Genet 137: 1-14. https://doi.org/10.1007/s00122-024-04545-9.

[40] Simmonds NW (1979) Principles of crop improvement, London: Longman.

[41] Chacko A, Jayalekshmy V, Shahiba A (2023) Studies on pcv, gcv, heritability, and genetic advance in rice genotypes for yield and yield components. Int J Plant Soil Sci 35: 324-330. https://doi.org/10.9734/ijpss/2023/v35i163266.

[42] Modarresi M (2026) Genetic variability, heritability and genetic advance in Iranian local rice genotypes for yield, and some agronomic traits. Reprod Breed 6: 9-20. https://doi.org/10.1016/j.repbre.2025.12.003.

[43] Tiwari U, Singh L, Kumar S, et al. (2025) Evaluation of genetic variability, gcv and pcv in F₁ and F₂ populations of pea (Pisum sativum L.). J Sci Res Rep 31: 310-320. https://doi.org/10.9734/jsrr/2025/v31i123777.

[44] Anshori MF, Purwoko BS, Dewi IS, et al. (2019) Selection index based on multivariate analysis for selecting doubled-haploid rice lines in lowland saline prone area. SABRAO J Breed Genet 51: 161-174.

[45] International Rice Research Institute (2013) Standard evaluation system for rice, Manila: International Rice Research Institute.

[46] Puvanitha S, Mahendran S (2017) Effect of salinity on plant height, shoot and root dry weight of selected rice cultivars. Sch J Agric Vet Sci 4: 126-131. https://doi.org/10.36347/sjavs.2017.v04i04.001.

[47] Quan R,Wang J,Qin H,et al. (2025) Improving grain yield and salt tolerance by optimizing plant height with beneficial haplotypes in rice (Oryza sativa). J Adv Res 76: 17-32. https://doi.org/10.1016/j.jare.2024.12.007.

[48] Akbar MR, Purwoko BS, Dewi IS, et al. (2021) Agronomic and yield selection of doubled haploid lines of rainfed lowland rice in advanced yield trials. Biodiversitas 22: 3006-3012. https://doi.org/10.13057/biodiv/d220754.

[49] Hussain S, Zhang JH, Zhong C, et al. (2017) Effects of salt stress on rice growth, development characteristics, and the regulating ways: A review. J Integr Agric 16: 2357-2374. https://doi.org/10.1016/s2095-3119(16)61608-8.

[50] Radanielson AM, Gaydon DS, Khan MMR, et al. (2018) Varietal improvement options for higher rice productivity in salt affected areas using crop modelling. Field Crops Res 229: 27-36. https://doi.org/10.1016/j.fcr.2018.08.020.

[51] Wei HH, Zhang X, Zhu W, et al. (2024) Effects of salinity stress on grain-filling characteristics and yield of rice. Acta Agron Sin 50: 734-746. https://doi.org/10.3724/sp.J.1006.2024.32021.

[52] Rusliani A, Nasrudin, Ramadhan RAM, et al. (2026) Source-sink dynamics and grain yield formation of rice under single and dual salinity-drought stresses. Curr Appl Sci Technol e0269229: 1-18. https://doi.org/10.55003/cast.2026.269229.

[53] Vieira RA, Nogueira APO, Fritsche-Neto R (2025) Optimizing the selection of quantitative traits in plant breeding using simulation. Front Plant Sci 16: 1-19. https://doi.org/10.3389/fpls.2025.1495662.

[54] Anshori MF, Purwoko BS, Dewi IS, et al. (2023) Systematic selection to adaptive doubled haploid rice lines under different environments of submergence screening methods. J Agric Food Res 14: 1-9. https://doi.org/10.1016/j.jafr.2023.100775.

[55] Mahmud A, Islam MN, Islam AKMA, et al. (2024) Evaluation of yield-attributing parameters in Aus rice for enhancing productivity. Plant Genet Resour-C 22: 368-377. https://doi.org/10.1017/s1479262124000364.

[56] Blancon J, Buet C, Dubreuil P, et al. (2024) Maize green leaf area index dynamics: Genetic basis of a new secondary trait for grain yield in optimal and drought conditions. Theor Appl Genet 137: 1-20. https://doi.org/10.1007/s00122-024-04572-6.

[57] Guimarães PHR, Melo PGS, Cordeiro ACC, et al. (2021) Index selection can improve the selection efficiency in a rice recurrent selection population. Euphytica 217: 1-16. https://doi.org/10.1007/s10681-021-02819-7.

[58] Cobos F, Reyes W, Perez-Almeida I, et al. (2025) Response of advanced rice lines from inter and intraspecific backgrounds to saline stress conditions. AGRIVITA J Agric Sci 47: 199-213. https://doi.org/10.17503/agrivita.v47i2.4466.

[59] Khatun T, Khatun SM, Naim J, et al. (2024) Advanced mutant line developed from fatemadhan shows salinity tolerance at both seedling and reproductive stages. Plant Sci Today 11: 316-328. https://doi.org/10.14719/pst.2917.

[60] Zayed BA, Anis GB, Abdel-Fattah AFG, et al. (2025) Validation and detection of some new rice hybrids to salt stress using various statistical Analysis Methods. Trends Appl Sci Res 20: 1-13. https://doi.org/10.3923/tasr.2025.01.13.

[61] Hadianto W, Purwoko BS, Dewi IS, et al. (2023) Agronomic performance, yield stability and selection of doubled haploid rice lines in advanced yield trials. AIMS Agric Food 8: 1010-1027. https://doi.org/10.3934/agrfood.2023054.

[62] Biodiversity International,International Rice Research Institute,Africa Rice Center(2007) Descriptors for wild and cultivated Rice (Oryza spp.), Rome: Bioversity International.