SNP Based Trait Characterization Detects Genetically Important and Stable Multiple Stress Tolerance Rice Genotypes in Salt-Stress Environments

Sanjoy K Debsharma; Mohammad Akhlasur Rahman; Mohammad Ruhul Quddus; Hasina Khatun; Ribed F Disha; Popy R Roy; Sharif Ahmed; Mohamed El-Sharnouby; Khandakar Md Iftekharuddaula; Salman Aloufi; Fahad M Alzuaibr; Mohammed Alqurashi; Mohamed I Sakran; Mohammad Shahjahan Kabir

doi:10.3390/plants11091150

SNP Based Trait Characterization Detects Genetically Important and Stable Multiple Stress Tolerance Rice Genotypes in Salt-Stress Environments

Plants (Basel). 2022 Apr 24;11(9):1150. doi: 10.3390/plants11091150.

Authors

Affiliations

¹ Bangladesh Rice Research Institute (BRRI), Gazipur 1701, Bangladesh.
² Seed Certification Agency, Ministry of Agriculture, The Peoples Republic of Bangladesh Government, Gazipur 1701, Bangladesh.
³ International Rice Research Institute, Bangladesh Office, Dhaka 1213, Bangladesh.
⁴ Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.
⁵ Department of Biotechnology, Faculty of Science, Taif University, Taif 21974, Saudi Arabia.
⁶ Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia.
⁷ Biochemistry Section, Chemistry Department, Faculty of Science, Tanta University, Tanta 31527, Egypt.
⁸ Biochemistry Department, Faculty of Science, University of Tabuk, Tabuk 47512, Saudi Arabia.

Abstract

Soil salinity is a major constraint to rice production in coastal areas around the globe, and modern high-yielding rice cultivars are more sensitive to high salt stress, which limits rice productivity. Traditional breeding programs find it challenging to develop stable salt-tolerant rice cultivars with other stress-tolerant for the saline environment in Bangladesh due to large yield variations caused by excessive salinity fluctuations during the dry (boro) season. We examined trait characterization of 18 advanced breeding lines using SNP genotyping and among them, we found line G6 (BR9621-B-1-2-11) (single breeding line with multiple-stress-tolerant QTL/genes) possessed 9 useful QTLs/genes, and two lines (G4:BR9620-2-7-1-1 and G14: IR 103854-8-3-AJY1) carried 7 QTLs/genes that control the desirable traits. To evaluate yield efficiency and stability of 18 rice breeding lines, two years of field experiment data were analyzed using AMMI (additive main effect and multiplicative interaction) and GGE (Genotype, Genotype Environment) biplot analysis. The AMMI analysis of variance demonstrated significant genotype, environment, and their interaction, accounting for 14.48%, 62.38%, and 19.70% of the total variation, respectively, and revealed that among the genotypes G1, G13, G14, G17, and G18 were shown to some extent promising. Genotype G13 (IR 104002-CMU 28-CMU 1-CMU 3) was the most stable yield based on the AMMI stability value. The GGE biplot analysis indicates 76% of the total variation (PC1 48.5% and PC2 27.5%) which is performed for revealing genotype × environment interactions. In the GGE biplot analysis, genotypes were checked thoroughly in two mega-environments (ME). Genotype G14 (IR103854-8-3-AJY1) was the winning genotype in ME I, whereas G1 (BR9627-1-3-1-10) in ME II. Because of the salinity and stability factors, as well as the highest averages of grain yield, the GGE and AMMI biplot model can explain that G1 and G13 are the best genotypes. These (G1, G6, G13, G14, G17, and G18) improved multiple-stress-tolerant breeding lines with stable grain yield could be included in the variety release system in Bangladesh and be used as elite donor parents for the future breeding program as well as for commercial purposes with sustainable production.

Keywords: Oryza sativa; advanced breeding lines; multiple stress; salinity stress; stable yield; trait genotyping.