Transforming Rice Breeding: Re-Designing the Irrigated Breeding Pipeline at the International Rice Research Institute (IRRI)

Abstract

Rice breeding of inbred varieties in the public sector has hardly changed in decades. This has been a cause for concern given that the current rate of yield improvement from new varieties is not considered to be adequate to meet future global demands for rice. In this article, we describe major changes to the irrigated breeding program and former plant breeding division at the International Rice Research Institute (IRRI) headquarters by incorporating modern concepts in plant breeding and practices used in the private sector. These activities were conducted primarily within a five-year research program called "Transforming Rice Breeding" funded by the Bill and Melinda Gates Foundation. These changes were implemented with the specific objectives to increase the rate of genetic gain for yield and improve the effectiveness and efficiency of breeding operations. Key changes in the breeding program included implementing rapid generation advance, earlier multi-location trials, increased selection pressure for yield, an increase use of molecular breeding, and using variety product profiles. Regarding breeding operations, there was a concerted effort to streamline all processes and optimize logistics in order to make breeding like a "factory production line". The Plant Breeding, Genetics and Biotechnology Division was re-organised into variety

Strengthening Public Breeding Pipelines by Emphasizing Quantitative Genetics Principles and Open Source Data Management

“…A successful example of renewing a traditional breeding pipeline at the International Rice Research Institute (IRRI) has been described at by Collard et al (2019).…”

The Modern Plant Breeding Triangle: Optimizing the Use of Genomics, Phenomics, and Enviromics Data

“…Nevertheless, in the last two decades, a growing body of modern technologies has been developed and now awaits efficient integration into traditional breeding pipelines. This integration offers attractive benefits, yet comes with the challenges of making modifications in established and operational systems, a recent example of which is rice breeding (Collard et al, 2019). Newly available technologies, genomics rapid cycling (Crossa et al, 2017), high throughput phenotyping (HTP, phenomics) (Montesinos-López et al, 2017) and historical descriptions of environmental relatedness (enviromics) (Costa-Neto et al, 2020a,b;Resende et al, 2020;Rogers et al, 2021) are crucial to improving conventional breeding schemes and increasing genetic gain.…”

Identification of an Elite Core Panel as a Key Breeding Resource to Accelerate the Rate of Genetic Improvement for Irrigated Rice

“…With the acceleration of genotyping technologies through the early 21st century and the subsequent maturation of genomic selection-based breeding strategies, there has been a renewed interest in the application of quantitative genetics to plant breeding programs (Cobb et al 2019b;Bernardo 2020). To this end the irrigated rice breeding program at the International Rice Research Institute (IRRI) has spent signi cant effort to develop a modernized approach to rice breeding to substantially and sustainably increase response to selection (Collard et al 2019). In addition to implementing accelerated single seed descent strategies (Collard et al 2017), another major pillar of IRRI's effort to transform rice breeding is the deep characterization of the elite genetic base from which new products are derived.…”

“…The irrigated rice breeding program at IRRI has been a source of elite breeding germplasm for decades (Peng and Khush 2003;Mackill and Khush 2018;Collard et al 2019). This genetic diversity has been utilized in combination with landraces and local varieties to contribute substantially to the yield improvement achieved in Asia to date.…”

“…The objective of this study was twofold: i) estimate gains in breeding value for yield over the entire history of IRRI's breeding program for irrigated systems, and ii) identify and characterize a panel of elite lines from among the available germplasm that balances high breeding value for yield with su cient genetic variance to preserve long term gain from selection. To this end, we gathered historical data from 102 yield trials in the IRRI phenotypic database (Breeding4Results, 2021) spanning the years from 2012 to 2016 and combined it with pedigree data from the International Rice Information System (McLaren et al 2005;Collard et al 2019) to estimate breeding values for grain yield for all extant or recently extant lines. These trials included most of the existing advanced material of the breeding program as well as many replicated observations of IRRI released varieties, allowing us to estimate the rate of genetic gain over ve decades.…”