Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties.

Haplotype-based breeding is an emerging and innovative concept that enables the development of designer crop varieties by exploiting and exploring superior alleles/haplotypes among target genes to create new traits in breeding programs. In this regard, whole-genome re-sequencing of 399 genotypes (landraces and breeding lines) from the 3000 rice genomes panel (3K-RG) is mined to identify the superior haplotypes for 95 drought-responsive candidate genes. Candidate gene-based association analysis reveals 69 marker-trait associations (MTAs) in 16 genes for single plant yield (SPY) under drought stress. Haplo-pheno analysis of these 16 genes identifies superior haplotypes for seven genes associated with the higher SPY under drought stress. Our study reveals that the performance of lines possessing superior haplotypes is significantly higher (p ≤ 0.05) as measured by single plant yield (SPY), for the OsGSK1-H4, OsDSR2-H3, OsDIL1-H22, OsDREB1C-H3, ASR3-H88, DSM3-H4 and ZFP182-H4 genes as compared to lines without the superior haplotypes. The validation results indicate that a superior haplotype for the DREB transcription factor (OsDREB1C) is present in all the drought-tolerant rice varieties, while it was notably absent in all susceptible varieties. These lines carrying the superior haplotypes can be used as potential donors in haplotype-based breeding to develop high-yielding drought-tolerant rice varieties.

Marker-assisted forward and backcross breeding for improvement of elite Indian rice variety Naveen for multiple biotic and abiotic stress tolerance.

The elite Indian rice variety, Naveen is highly susceptible to major biotic and abiotic stresses such as blast, bacterial blight (BB), gall midge (GM) and drought which limit its productivity in rainfed areas. In the present study, a combined approach of marker-assisted forward (MAFB) and back cross (MABC) breeding was followed to introgress three major genes, viz., Pi9 for blast, Xa21 for bacterial blight (BB), and Gm8 for gall midge (GM) and three major QTLs, viz., qDTY1.1, qDTY2.2 and qDTY4.1 conferring increased yield under drought in the background of Naveen. At each stage of advancement, gene-based/linked markers were used for the foreground selection of biotic and abiotic stress tolerant genes/QTLs. Intensive phenotype-based selections were performed in the field for identification of lines with high level of resistance against blast, BB, GM and drought tolerance without yield penalty under non-stress situation. A set of 8 MAFB lines and 12 MABC lines with 3 to 6 genes/QTLs and possessing resistance/tolerance against biotic stresses and reproductive stage drought stress with better yield performance compared to Naveen were developed. Lines developed through combined MAFB and MABC performed better than lines developed only through MAFB. This study exemplifies the utility of the combined approach of marker-assisted forward and backcrosses breeding for targeted improvement of multiple biotic and abiotic stress resistance in the background of popular mega varieties.

Characterization of a Nagina22 rice mutant for heat tolerance and mapping of yield traits.

BACKGROUND: Heat is one of the major factors that considerably limit rice production. Nagina 22 (N22) is a deep-rooted, drought and heat tolerant aus rice cultivar. This study reports the characterization of a previously isolated dark green leaf mutant N22-H-dgl219 (NH219) which showed reduced accumulation of reactive oxygen species in leaf under 40°C heat conditions.The mutant was characterized for several traits in field under ambient (38°C) and heat stress (44°C) conditions by raising temperature artificially from flowering stage till maturity by covering plants with polythene sheets during dry season 2011. Yield traits were mapped in 70 F2 segregants of IR64 × NH219 and 36 F2 segregants of its reciprocal cross. RESULTS: Leaf proteome analysis using two-dimensional gel electrophoresis from N22 and NH219 showed distinct constitutive expression of ribulose bisphosphate carboxylase large chain precursor (EC 4.1.1.39) in NH219 under ambient growth condition. Heat stress resulted in reduction of all 11 traits except plant height in both N22 and NH219. The extent of reduction was more in N22 than in NH219. Both pollen viability and spikelet fertility were not reduced significantly in N22 and NH219 but reduced by 20% in IR64. CONCLUSION: NH219 is more tolerant to heat stress than wild type N22 as its percent yield reduction is lesser than N22. Single marker analysis showed significant association of RM1089 with number of tillers and yield per plant, RM423 with leaf senescence, RM584 with leaf width and RM229 with yield per plant.