Genetic gains in IRRI's rice salinity breeding and elite panel development as a future breeding resource.

Estimating genetic gains and formulating a future salinity elite breeding panel for rice pave the way for developing better high-yielding salinity tolerant lines with enhanced genetic gains. Genetic gain is a crucial parameter to check the breeding program's success and help optimize future breeding strategies for enhanced genetic gains. To estimate the genetic gains in IRRI's salinity breeding program and identify the best genotypes based on high breeding values for grain yield (kg/ha), we analyzed the historical data from the trials conducted in the IRRI, Philippines and Bangladesh.

Optimizing predictions in IRRI's rice drought breeding program by leveraging 17 years of historical data and pedigree information.

Prediction models based on pedigree and/or molecular marker information are now an inextricable part of the crop breeding programs and have led to increased genetic gains in many crops. Optimization of IRRI's rice drought breeding program is crucial for better implementation of selections based on predictions. Historical datasets with precise and robust pedigree information have been a great resource to help optimize the prediction models in the breeding programs.

Genetic Dissection of Epistatic Interactions Contributing Grain Yield Variability in Rice under Drought.

Aims: The aim of the present study was to evaluate the performance of 'high'-'low' yielding pyramided lines (PLs), having the same combinations of in Samba Mahsuri, MR219 and IR64-Sub1 genetic backgrounds, and to understand the genetic interactions among QTL and/with genetic background affecting grain yield.

Background: Epistasis regulates the expression of traits governed by several major/minor genes/QTL. Multiple pyramided lines (PLs) with the same grain yield QTL () combinations but possessing grain yield variability under different levels of reproductive stage drought stress were identified in different rice genetic backgrounds at International Rice Research Institute (IRRI).

Genetic Trends Estimation in IRRIs Rice Drought Breeding Program and Identification of High Yielding Drought-Tolerant Lines.

Estimating genetic trends using historical data is an important parameter to check the success of the breeding programs. The estimated genetic trends can act as a guideline to target the appropriate breeding strategies and optimize the breeding program for improved genetic gains. In this study, 17 years of historical data from IRRI's rice drought breeding program was used to estimate the genetic trends and assess the breeding program's success.

Open-source analytical pipeline for robust data analysis, visualizations and sharing in crop breeding.

Background: Developing a systematic phenotypic data analysis pipeline, creating enhanced visualizations, and interpreting the results is crucial to extract meaningful insights from data in making better breeding decisions. Here, we provide an overview of how the Rainfed Rice Breeding (RRB) program at IRRI has leveraged R computational power with open-source resource tools like R Markdown, plotly, LaTeX, and HTML to develop an open-source and end-to-end data analysis workflow and pipeline, and re-designed it to a reproducible document for better interpretations, visualizations and easy sharing with collaborators.

Results: We reported the state-of-the-art implementation of the phenotypic data analysis pipeline and workflow embedded into a well-descriptive document.

DECUSSATE network with flowering genes explains the variable effects of qDTY12.1 to rice yield under drought across genetic backgrounds.

The impact of qDTY12.1 in maintaining yield under drought has not been consistent across genetic backgrounds. We hypothesized that synergism or antagonism with additive-effect peripheral genes across the background genome either enhances or undermines its full potential.

Laboratory phenomics predicts field performance and identifies superior indica haplotypes for early seedling vigour in dry direct-seeded rice.

Seedling vigour is an important agronomic trait and is gaining attention in Asian rice (Oryza sativa) as cultivation practices shift from transplanting to forms of direct seeding. To understand the genetic control of rice seedling vigour in dry direct seeded (aerobic) conditions we measured multiple seedling traits in 684 accessions from the 3000 Rice Genomes (3K-RG) population in both the laboratory and field at three planting depths. Our data show that phenotyping of mesocotyl length in laboratory conditions is a good predictor of field performance.

Developing Climate-Resilient, Direct-Seeded, Adapted Multiple-Stress-Tolerant Rice Applying Genomics-Assisted Breeding.

There is an urgent need to breed dry direct-seeded adapted rice varieties in order to address the emerging scenario of water-labor shortage. The aim of this study was to develop high-yielding, direct-seeded adapted varieties utilizing biparental to multiparental crosses involving as many as six different parents in conventional breeding programs and 12 parents in genomics-assisted breeding programs. The rigorous single plant selections were followed from the F generation onwards utilizing phenotypic selection and quantitative trait locus (QTL)/gene-based/linked markers for tracking the presence of desirable alleles of targeted QTL/genes.

Genomics-assisted breeding for successful development of multiple-stress-tolerant, climate-smart rice for southern and southeastern Asia.

Rice (Oryza sativa L.) in rainfed marginal environments is prone to multiple abiotic and biotic stresses, which can occur in combination in a single cropping season and adversely affect rice growth and yield. The present study was undertaken to develop high-yielding, climate-resilient rice that can provide tolerance to multiple biotic and abiotic stresses.

Genotyping-by-sequencing based QTL mapping for rice grain yield under reproductive stage drought stress tolerance.

QTLs for rice grain yield under reproductive stage drought stress (qDTY) identified earlier with low density markers have shown linkage drag and need to be fine mapped before their utilization in breeding programs. In this study, genotyping-by-sequencing (GBS) based high-density linkage map of rice was developed using two BCF mapping populations namely Swarna*2/Dular (3929 SNPs covering 1454.68 cM) and IR11N121*2/Aus196 (1191 SNPs covering 1399.

Evaluating the Performance of Rice Genotypes for Improving Yield and Adaptability Under Direct Seeded Aerobic Cultivation Conditions.

With the changing climatic conditions and reducing labor-water availability, the potential contribution of aerobic rice varieties and cultivation system to develop a sustainable rice based agri-food system has never been more important than today. Keeping in mind the goal of identifying high-yielding aerobic rice varieties for wider adaptation, a set of aerobic rice breeding lines were developed and evaluated for grain yield, plant height, and days to 50% flowering in 23 experiments conducted across different location in Philippines, India, Bangladesh, Nepal, and Lao-PDR between 2014 and 2017 in both wet and dry seasons. The heritability for grain yield ranged from 0.

Positive interactions of major-effect QTLs with genetic background that enhances rice yield under drought.

To improve the grain yield of the lowland-adapted popular rice variety Samba Mahsuri under reproductive-stage drought (RS) and to understand the interactions between drought QTLs, two mapping populations were developed using marker-assisted selection (MAS) and marker-assisted recurrent selection (MARS). The mean grain yield of pyramided lines (PLs) with qDTY  + qDTY in MAS is significantly higher under RS and irrigated control than lines with single QTLs. Among MARS PLs, lines with four qDTYs (qDTY  + qDTY  + qDTY  + qDTY ) and two QTLs (qDTY  + qDTY ) yielded higher than PLs with other qDTY combinations.

Genetic Loci Governing Grain Yield and Root Development under Variable Rice Cultivation Conditions.

Drought is the major abiotic stress to rice grain yield under unpredictable changing climatic scenarios. The widely grown, high yielding but drought susceptible rice varieties need to be improved by unraveling the genomic regions controlling traits enhancing drought tolerance. The present study was conducted with the aim to identify quantitative trait loci (QTLs) for grain yield and root development traits under irrigated non-stress and reproductive-stage drought stress in both lowland and upland situations.