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

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.

QTLs and Genes for Salt Stress Tolerance: A Journey from Seed to Seed Continued

“…SNP genotyping was used for 18 advanced breeding lines, wherein a single line had multiple stress tolerance QTLs/genes. Those lines were used for the evaluation of yield stability and efficiency with additive main effect and multiplicative interaction (AMMI) and genotype/genotype–environment (GGE) biplot analysis [ 107 ]. Using a reciprocal population developed from salt-tolerant Horkuch and IR29, a major QTL was identified using SNP for leaf total potassium and grain weight [ 108 ].…”

Developing climate-resilient rice varieties (BRRI dhan97 and BRRI dhan99) suitable for salt-stress environments in Bangladesh

“…The ASVs were derived from the AMMI, and their estimates were based on Yield stability index (YSI) for individual genotypes which combines both mean grains yield and ASV index was estimated as YSI = RASVi + RYi. Here, the rank of the AMMI stability value for the ith genotype is RASVi, while the rank of the mean grain yield for the ith genotype across environments is RYi [18].…”

“…Both the salt-afflicted areas and the human population are steadily expanding day by day. To feed the gradually increasing people in Bangladesh, coastal saline areas should be converted to paddy cultivation to ensure the country's food security and sustainability [16][17][18].…”

Recent advances in population improvement through RGA under Irrigated Boro rice breeding program in Bangladesh

“…In LST trial, genotyping was done to figure out the favourable alleles for all desired traits in the breeding population of FBR and CTR. However, SNP-based trait genotyping has showed remarkable efficiency in identifying genetically important lines with multiple stress tolerance including seedling stress salt tolerance, blast resistance and gall midge resistance (Debsharma et al, 2022). In the breeding population designed for irrigated Boro rice, trait marker profiles were considered mainly for amylose, BLB, Blast and BPH resistance.…”