Rice Breeding Innovations

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The drive to push rice science to the edge

“Operating in a restrained environment, where lockdowns are being implemented at certain periods, poses many challenges, especially in our day-to-day work commitments. However, we remain dedicated to our goal of delivering the best products for our stakeholders and this has been demonstrated as we maintain operational excellence and cost-effectiveness in our activities. The platform, while maintaining a strict skeletal workforce, has remained flexible and strategic towards these work restrictions from the laboratories to the screen houses and from genetic screening to seed processing.“

Dr. Hans Bhardwaj

Platform Leader

Rice Breeding Innovations

The COVID-19 pandemic has exacerbated unemployment and hunger all around the world. 2021 saw us needing to be further involved in helping our farmers provide nutritious and sufficient food, especially through a time when health, food security, and livelihood of the population are threatened. This challenge remains our guide in creating strategies for the Rice Breeding Innovations Platform.

Operating in a restrained environment, where lockdowns are being implemented at certain periods, posed many challenges, especially in our day-to-day work commitments. However, we remain dedicated to our goal of delivering the best products for our stakeholders - and this has been demonstrated as we maintain operational excellence and cost-effectiveness in our activities. The platform, while maintaining a strict skeletal workforce, has remained flexible and strategic towards these work restrictions from the laboratories to the screen houses, and from genetic screening to seed processing.

As we enter another year of uncertainty, one thing is clear: our goal is to continue our efforts in the development and deployment of breeding strategies, tools, and technologies that are responsive to the challenges of climate change, food security, and scarce resources through the use of genetic resources. Specifically in 2022, we aim to complete the deployment of major genetic materials, launch hybrid rice in Nepal, and pilot the arsenic-safe rice project, among many other projects that are in our platform’s pipeline.

These efforts, we hope, will not only be widely used in the regions where they are needed the most but will facilitate the recognition of rice germplasm as an important contributor to improving the lives of our farmers and consumers all around the world.

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Missions accomplished

Native trait resistance gene deployment

Incorporating genetic resistance into new crop varieties as a line of defense against plant pests and diseases is an important part of a breeding program. The advancements in molecular breeding methods have made it possible to utilize diverse sources of resistance genes.

Rice breeders at IRRI have been continuously searching for new sources of important resistance genes as part of the institute’s breeding strategies to achieve more durability of resistance in rice varieties to long-standing and emerging pests and pathogens as well as harsher environments caused by the climate crisis.

The deployment of rice yellow mottle virus (RYMV) resistance genes from African rice (Oryza glaberrima) has been completed. This represents the first time the RYMV genes have been available in an elite background in modern breeding programs. RYMV is a major disease of rice in Africa and these genes will be essential to achieving the continent’s food security targets.

The deployment and pyramiding of major blast and bacterial leaf blight resistance genes have been completed. This is also the first time these genes have been available in elite genomic backgrounds and, together as a pyramid, will help ensure robust resistance to diseases.

Rice is very sensitive to salinity stress, particularly at the early vegetative and reproductive stages. In rice production, salinity is the second most damaging environmental stress. In salt-affected agricultural lands, approximately 1 billion hectares around the world, rice yield is seriously affected with losses that may reach as much as 50%. A major QTL for vegetative stage salinity tolerance in an elite background has been verified and this discovery could significantly simplify the breeding for salinity tolerance in rice.

New japonica rice shows promise of higher income for Filipino farmers

Filipino farmers have the opportunity to tap the premium rice market and earn higher income based on successful field trials of new japonica rice varieties developed for tropical countries by the Germplasm Utilization Value Added (GUVA) Project.

Field trials at IRRI and the Philippine Rice Research Institute (PhilRice) showed that Japonica 7, the most recent variety developed by GUVA, produced 7 tons/hectare (t/ha), higher than some high-yielding indica varieties. In farmer participatory varietal selection conducted in Tarlac Province, Japonica 7 produced 4.7 t/ha, the highest among the GUVA japonica varieties tested.

GUVA japonica varieties also required less phosphorus and potassium than indica varieties. Additionally, most of the japonica varieties developed by GUVA exhibited intermediate resistance to certain diseases such as blast and bacterial leaf blight and insect pests such as stem borer and brown planthopper.

Preliminary market studies have shown that japonica rice can commands much higher prices than other Philippine premium varieties.

New collaborations

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Accelerating the impact of new rice varieties

Attaining food security does not end with developing new rice varieties that are high-yielding, tougher against pests and diseases, and more resilient to the impacts of climate change. New varieties must also reach farmers as quickly as possible.

The Network for Accelerated Rice Variety Impact (NARVI), a new membership-based elite germplasm sharing network for the private sector, was created in 2021 to speed up the transfer of technologies through IRRI-led multi-sectoral consortia that collaborate and network on key research and development areas.

The partnership program enables its 14 member companies to test new IRRI elite inbred rice for breeding in various countries. Each member receives access to 20 new elite inbred lines each year. Additionally, a user-friendly commercial licensing of the elite varieties will make it simpler for SMEs to develop and sell new varieties directly to farmers where the companies are based.

NARVI will support the goals of IRRI and CGIAR of a data-driven variety release and ensure improved varieties will also reach the farmers.

Achieving food security in Nepal through hybrid rice technology

Nepal’s food security depends on the production of rice which is the country’s primary staple cereal crop. Rice is grown on almost 1.5 million hectares in Nepal with average productivity of 3.5 tons per hectare. To meet local demand, Nepal imports rice.

Theoretically, rice still has a great yield potential to be tapped and there are several ways to increase rice yield. Based on successful experiences in China, the most effective and economical means is by developing hybrid rice.

If half of the rice-growing areas in the world are replaced with hybrid rice varieties with a 2 tons per hectare yield advantage, it is estimated that total global rice production would increase by another 150 million tons annually, according to the late Longping Yuan, the father of hybrid rice. This could feed 400‒500 million more people each year. This would truly be a significant contribution to ensuring food security and peace all over the world, Prof. Yuan added.

Nepal is focusing on reducing its rice importation by increasing domestic rice production. To this end, the Nepal Government and IRRI launched the project, Achieving Rice Self-sufficiency in Nepal through Systematic Development and Use of Hybrid Technology on 16 July 2021.

Linking IRRI’s valuable upstream discovery research with breeding pipelines

In 2021, we held a series of Trait Advancement Workshops with the aim of linking IRRI’s valuable upstream discovery research with breeding pipelines. All trait scientists shared their ongoing work, which includes pathology, grain quality, nutrition, and physiology.

Each trait was “mapped” to the Trait Development Pipeline. The Trait Development Pipeline is a framework that provides clear guidelines for taking the next steps in our work on the identification of key traits/genes/QTLs that are needed by rice farmers and consumers.

The workshop involved fruitful discussions on the myriad ways that discovery research can contribute to breeding, from identifying new sources of stress resistance to helping breeders prioritize which breeding lines to use in their crossing work.

By better designing our discovery experiments, the Trait Development Pipeline is helping us become more efficient in generating research outputs that lead to impact. The strategy laid out in IRRI’s Trait Development Pipeline is now used as an example across the CG system. It promises to increase the efficiency and impact of upstream work across multiple crop species.

Dr. John Damien Platten
Breeding Innovations and Informatics Research Unit
Leader

Dr. Amelia Henry
Stress Physiology and Research Unit Leader
Traits for Challenged Environments

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Research milestones

Discovery of traditional rice varieties with strong anti-cancer properties

A team of researchers, headed by Dr. Nese Sreenivasulu from IRRI, in collaboration with Dr. Alisdair Fernie and Dr. Yariv Brotman from the Max Planck Institute of Molecular Plant Physiology, and Dr. Glenn Oyong from De La Salle University, looked into the identification of traditional rice varieties harboring the genetic basis of natural variation in secondary metabolites and their vital role in human nutrition.

The study, The genetics underlying metabolic signatures in a brown rice diversity panel and their vital role in human nutrition published in The Plant Journal, found rare traditional rice varieties with the genetic traits of higher catechin levels, elevated total flavonoid contents, heightened antioxidant activity in the whole grain, and exhibiting anti-cancer properties. In addition, the genetic variations were also linked to a low glycemic index (GI), which is ideal for rice consumers with type II diabetes.

Although the importance of brown rice as a nutritionally dense food staple has long been established, the study now provides genetic links to the production of plant metabolites important to human health.

A breeding breakthrough for rice varieties with an extremely low GI

Rice breeders aiming to develop rice varieties with a very low GI are now closer to that reality with the important scientific breakthrough on lowering GI in high-yielding varieties.

Published in Plant Biotechnology Journal, the study, OsTPR boosts the superior grains through increase in upper secondary rachis branches without incurring a grain quality penalty, found a way to increase the yield of a rice mutant with an extremely low GI.

By combining a low-GI trait mediated by the mutation in starch branching enzyme IIb with a superior haplotype of OsTPR increases the upper secondary rachis branches of the rice plant which increases superior grain production.

“We were able to overcome the yield barrier of an extremely low-GI mutant by developing recombinant inbred lines (RILs) in the Samba Mahsuri background,” said Dr. Nese Sreenivasulu, “These superior RILs exhibit optimum yield with an extremely low GI of 38, while
many of the popular varieties of rice are high-GI in nature ranging from 70-92.”

Initial peer-reviewed publications of Golden Rice biosafety data completed

The first series of peer-reviewed publications on the GR2E Golden Rice field trial data are now available in Nature Scientific Reports and Frontiers in Plant Science journals. These articles focus on the agronomic performance of Golden Rice varieties developed in the
Philippines and Bangladesh.

These publications were authored by scientists and researchers of the Healthier Rice Program at IRRI, in collaboration with colleagues at the Department of Agriculture-PhilRice and Bangladesh Rice Research Institute.

Key findings indicate that agronomy, yield, and grain qualities are comparable to the conventional inbred rice counterparts: IR64, PSBRc82, and BRRI dhan 29. Data show that the Golden Rice breeding lines developed in the genetic backgrounds of different
local varieties contain enough beta-carotene to provide more than the 30% estimated average requirement for vitamin A in young children.

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