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Swarna (MTU7029), an Indian mega-variety of rice, is cultivated on an estimated 8Mha of land. There is a pressing need to address yield stagnation and wider adaptability to irrigated lowland and rainfed ecologies as a result of the negative consequences of climate change and population growth. The present study was aimed at improving Swarna for two yield-related traits through marker-assisted backcross breeding strategy by introgression of OsSPL14 (panicle branching) and SCM2 (stronger culm). Foreground and background selection was carried out at each generation. Homozygous BC2F2 plants harbouring both yield-enhancing genes were identified and advanced through pedigree selection till BC2F5 and evaluated in station trials. Three promising lines possessing higher yield over recurrent parent were identified, and a single line, IET 27661 exhibited superior yield in multi-location trials of the All India Coordinated Rice Improvement Programme (AICRIP) and was found to be promising.

From a ship-to-mouth existence at the time of its Independence, India became a food sufficient country due to the research and policy interventions during the green revolution era and in the last six decades. The country witnessed a phenomenal increase in the production and productivity of rice and wheat and presently the country is exporting significant quantities of rice. However, there are multiple challenges in ensuring food and nutritional security through rice in the coming decades including a rapidly changing climate and a plateauing of rice yields has been witnessed in the last two decades in many rice growing countries across the world including India. It is therefore imperative to enhance rice productivity and production through application of modern tools of science. This review traces the developments related to rice research and yield improvement over the last six decades and discusses about the conventional and modern approaches to enhance grain yield in rice. These approaches include pre-breeding, wide-hybridization, new plant type/ideotype breeding, heterosis breeding, marker and genomics-assisted breeding, haplotype-based breeding, transgenic breeding and genome editing.

Drought stress has become more important abiotic factor affecting rice yield under present changing climate conditions. IR58025B is a maintainer line of widely used WA CMS line IR58025A and widely used in commercial rice hybrids production in India. Most of the rice hybrids are released for the irrigated ecosystem consequently, these derived hybrids suffer drastic yield decline under moisture stress conditions. To facilitate the efficient use of complex polygenic traits in hybrid rice molecular breeding research, we undertook development of introgression lines in background of IR58025B with tolerance to moisture stress by introgression of major QTL qDTY3.1 controlling grain yield under moisture stress. The present study reports the development and evaluation of 230 introgression lines (BC2F2) lines in IR58025B background for improvement of grain yield under moisture stress condition. Among 230 ILs, 24 introgression lines were found positive for qDTY3.1 and negative for fertility restoration (rf4 & rf3).Promising BILs exhibited earliness of 7 days under moisture stress with grain yield advantage of 8.54g to 10.78g in comparison to the recurrent parent. This suggested that the efficacy of introgressed drought tolerant QTL qDTY3.1 in enhancing grain yield under moisture stress conditions. Further, breeding lines of IR58025B possessing qDTY3.1 could also serve as good donors for development of drought tolerant rice hybrids for unfavorable ecologies.

Additional file 3. Table S2A: Estimation of Na and K in the introgressed lines of ISM with respect to recurrent and donor parents (stressed). Table S2B: Estimation of Na and K in the introgressed lines of ISM with respect to recurrent and donor parents (unstressed).

Additional file 9. Table S5: Summary of yield (kg/ha) data of Zone wise Advanced varietal trails (AVT NIL) for Kharif 2019 and 2020 (June to Nov)

Additional file 2. Table S1: List of SSR markers used for background analysis.

Additional file 7. Table S7: Distribution of variants (SNPs, Insertions and Deletions) across the chromosomes in the rice lines including Pokkali, FL478, ISM, and DRR Dhan 58.

Additional file 8: Table S8: Distribution of variants based on the location in the genome of the rice lines and their consequences.

Additional file 1. Figure S1: Marker assisted backcross breeding strategy used in the present study. Figure S2: Analysis of donor parent genome introgression associated with Salinity tolerance QTL, Saltol locus using GGT version (2.0), a segment of 1.0 Mb was introgressed at the proximal end, 1.5Mb at the distal end from the donor parent genome in the best BC3F2 plant (i.e., RP6287-188-45-12-88), thus, in total, a segment of 2.5Mb was introgressed from the donor parent with respect to the genomic region in the vicinity of Saltol. The position of the polymorphic SSR markers in Mb on Chr. 1 is given in parenthesis adjacent to each marker. Figure S3: Screening for seedling stage salinity tolerance. (A) Uprooted seedlings of checks (ISM and FL478) and improved lines of ISM possessing Saltol QTL (IL1 to IL4), (B) Root morphology of checks ISM and FL478 along with introgressed lines IL-1(RP6287-88), IL-2 (RP6287-43), IL-3 (RP6287-12) and IL-4 (RP6287-178). Figure S4: (A): Improved bacterial blight and Salinity tolerance lines of ISM (B): Improved Salinity tolerance lines with better grain and panicle number; IL-1(RP6287-88), IL-2 (RP6287-43), IL-3 (RP6287-12) -Introgressed lines of ISM. Figure S5: Map depicting the salinity effected areas in the coastal regions of India (AICRIP centres). Map depicts the centres -Zone wise where the AICRIP trials were conducted and each zone was indicated in different colours. Figure S6: Frequency of the variants (SNPs, Insertions, and Deletions) per Mb that are present in the rice lines including Pokkali, FL478, ISM, and DRR Dhan 58 (IET28784). Figure S7: Neighbor-joining dendrograms showing the relatedness among the rice lines at the (A) Saltol locus (~0.9 Mb interval) and (B) the OsSKC1 gene based on the variants data. The data indicates no considerable difference in the relatedness among the rice lines ta the Saltol locus but a clear relatedness among the salt-tolerant lines at the OsSKC1 gene locus. The numbers on the branches indicate the distance between the rice lines (DRR Dhan58 is the line IET28784).

Additional file 5. Table S4: Site characterization of tested location data during Kharif 2019 and 2020

Additional file 4. Table S3: Station trial data of promising entries during wet season 2018 (June to Nov).