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Marker‐assisted simultaneous but stepwise backcross breeding (MASS‐BB) was utilized in the present study for pyramiding blast resistance genes, Piz5 and Pi54, from non‐Basmati donors, C101A51 and Tetep, respectively, into PRR78, an elite Basmati restorer line of rice hybrid, Pusa RH10. Marker‐assisted foreground selection coupled with stringent phenotypic selection and background analysis was carried out for hastening the recovery of recurrent parent phenome (RPP) and genome (RPG) in two separate backcross series to produce BC2F1 plants with individual blast resistance gene. The best BC2F1 plant from each backcross series was intercrossed, and the resultant F1 was selfed to pyramid both blast‐resistance genes into PRR78. The plants homozygous for both the genes in the F2 were advanced through pedigree selection to produce superior blast‐resistant F5 lines. Background analysis revealed that the RPG recovery was up to 91.6%. Improved versions of Pusa RH10 developed using the improved PRR78 lines (PRR78+Piz5+Pi54) performed on par with the original Pusa RH10 and showed resistance to blast disease both under artificial screening and at hot spot locations.

Background Climate extremes such as drought and flood have become major constraints to the sustainable rice crop productivity in rainfed environments. Availability of suitable climate-resilient varieties could help farmers to reduce the grain yield losses resulting from the climatic extremities. The present study was undertaken with an aim to develop high-yielding drought and submergence tolerant rice varieties using marker assisted introgression of qDTY 1.1 , qDTY 2.1 , qDTY 3.1 and Sub1. Performance of near isogenic lines (NILs) developed in the background of Swarna was evaluated across 60 multi-locations trials (MLTs). The selected promising lines from MLTs were nominated and evaluated in national trials across 18 locations in India and 6 locations in Nepal. Results Grain yield advantage of the NILs with qDTY 1.1 + qDTY 2.1 + qDTY 3.1 + Sub1 and qDTY 2.1 + qDTY 3.1 + Sub1 ranged from 76 to 2479 kg ha − 1 and 396 to 2376 kg ha − 1 under non-stress (NS) respectively and 292 to 1118 kg ha − 1 and 284 to 2086 kg ha − 1 under reproductive drought stress (RS), respectively. The NIL, IR96322–34-223-B-1-1-1-1 having qDTY 1.1 + qDTY 2.1 + qDTY 3.1 + Sub1 has been released as variety CR dhan 801 in India. IR 96321–1447-651-B-1-1-2 having qDTY 1.1 + qDTY 3.1 + Sub 1 and IR 94391–131–358-19-B-1-1-1 having qDTY 3.1 + Sub1 have been released as varieties Bahuguni dhan-1′ and ‘Bahuguni dhan-2’ respectively in Nepal. Background recovery of 94%, 93% and 98% was observed for IR 96322–34-223-B-1-1-1-1, IR 96321–1447-651-B-1-1-2 and IR 94391–131–358-19-B-1-1-1 respectively on 6 K SNP Infinium chip. Conclusion The drought and submergence tolerant rice varieties with pyramided multiple QTLs can ensure 0.2 to 1.7 t ha − 1 under reproductive stage drought stress and 0.1 to 1.0 t ha − 1 under submergence conditions with no yield penalty under non-stress to farmers irrespective of occurrence of drought and/or flood in the same or different seasons. Electronic supplementary material The online version of thi...

In the face of global water scarcity, a successful transition of rice cultivation from puddled to dry direct-seeded rice (DDSR) is a future need. A genome-wide association study was performed on a complex mapping population for 39 traits: 9 seedling-establishment traits, 14 root and nutrient-uptake traits, 5 plant morphological traits, 4 lodging resistance traits, and 7 yield and yield-contributing traits. A total of 10 significant marker-trait associations (MTAs) were found along with 25 QTLs associated with 25 traits. The percent phenotypic variance explained by SNPs ranged from 8% to 84%. Grain yield was found to be significantly and positively correlated with seedling-establishment traits, root morphological traits, nutrient uptake-related traits, and grain yield-contributing traits. The genomic colocation of different root morphological traits, nutrient uptake-related traits, and grain-yield-contributing traits further supports the role of root morphological traits in improving nutrient uptake and grain yield under DDSR. The QTLs/candidate genes underlying the significant MTAs were identified. The identified promising progenies carrying these QTLs may serve as potential donors to be exploited in genomics-assisted breeding programs for improving grain yield and adaptability under DDSR.

Epistatic interactions of QTLs with the genetic background and QTL-QTL interaction plays an important role in the phenotypic performance of introgression lines developed through genomic-assisted breeding (GAB). In this context, NIL pairs developed with various drought QTL ( qDTY ) combinations in the genetic background of IR64, TDK1- Sub1 and Savitri backgrounds were utilized to study the interactions. Multi-season phenotyping of NIL pairs harboring similar qDTY combinations provided contrasting performance for grain yield under drought (RS) (classified as high and low yielding NILs) but nearly similar performance under non-stress(NS) conditions. Genome wide genotyping data revealed a total of 16, 5 and 6 digenic interactions were detected under RS conditions in low yielding NILs of IR64, TDK1- Sub1 and Savitri respectively while no significant interaction was found in high yielding NILs under RS and NS conditions in any of the genetic backgrounds used in this study. It is evident from this study that existence of epistatic interactions between QTLs with genetic background, QTL-QTL interaction and interactions among background markers loci itself on different chromosomes influences the expression of a complex trait such as grain yield under drought. The generated information will be useful in all the GAB program of across the crops for precise breeding.

Background Puddled transplanted system of rice cultivation despite having several benefits, is a highly labor, water and energy intensive system. In the face of changing climatic conditions, a successful transition from puddled to dry direct seeded rice (DDSR) cultivation system looks must in future. Genome-wide association study was performed for traits including, roots and nutrient uptake (14 traits), plant-morphological (5 traits), lodging-resistance (4 traits) and yield and yield attributing traits (7 traits) with the aim to identify significant marker-trait associations (MTAs) for traits enhancing rice adaptability to dry direct-seeded rice (DDSR) system. Results Study identified a total of 37 highly significant MTAs for 20 traits. The false discovery rate (FDR) ranged from 0.264 to 3.69 × 10 − 4 , 0.0330 to 1.25 × 10 − 4 , and 0.0534 to 4.60 × 10 − 6 in 2015WS, 2016DS and combined analysis, respectively. The percent phenotypic variance (PV) explained by SNPs ranged from 9 to 92%. Among the identified significant MTAs, 15 MTAs associated with the traits including nodal root, root hair length, root length density, stem and culm diameter, plant height and grain yield were reported to be located in the proximity of earlier identified candidate gene. The significant positive correlation of grain-yield with seedling establishment traits, root morphological and nutrient-uptake related traits and grain yield attributing traits pointing towards combining target traits to increase rice yield and adaptability under DDSR. Seven promising progenies with better root morphology, nutrient-uptake and higher grain yield were identified that can further be used in genomics assisted breeding for DDSR varietal development. Conclusions Once validated, the identified MTAs and the SNPs linked with trait of interest could be of direct use in genomic assisted breeding (GAB) to improve grain yield and adaptability of rice under DDSR. Electronic supplementary material The online version of this article (10.1186/s12864-019-5840-9) contains supplementary material, which is available to authorized users.

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Highlights Genetic gain for rice grain yield for International Rice Research Institute drought breeding program was estimated. Positive trend of 0.68 %, 0.87 %, 1.9 % under irrigated control, moderate and severe drought achieved. Superiority of new rice varieties over currently grown demonstrated on farmers’ fields. International Rice Research Institute developed rice varieties can protect farmers from crop losses under drought conditions.