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

Abstract

Rice genetic improvement is a key component of achieving and maintaining food security in Asia and Africa in the face of growing populations and climate change. In this effort, the International Rice Research Institute (IRRI) continues to play a critical role in creating and disseminating rice varieties with higher productivity. Due to increasing demand for rice, especially in Africa, there is a strong need to accelerate the rate of genetic improvement for grain yield. In an effort to identify and characterize the elite breeding pool of IRRI’s irrigated rice breeding program, we analyzed 102 historical yield trials conducted in the Philippines during the period 2012–2016 and representing 15,286 breeding lines (including released varieties). A mixed model approach based on the pedigree relationship matrix was used to estimate breeding values for grain yield, which ranged from 2.12 to 6.27 t·ha−1. The rate of genetic gain for grain yield was estimated at 8.75 kg·ha−1 year−1 (0.23%) for crosses made in the period from 1964 to 2014. Reducing the data to only IRRI released varieties, the rate doubled to 17.36 kg·ha−1 year−1 (0.46%). Regressed against breeding cycle the rate of gain for grain yield was 185 kg·ha−1 cycle−1 (4.95%). We selected 72 top performing lines based on breeding values for grain yield to create an elite core panel (ECP) representing the genetic diversity in the breeding program with the highest heritable yield values from which new products can be derived. The ECP closely aligns with the indica 1B sub-group of Oryza sativa that includes most modern varieties for irrigated systems. Agronomic performance of the ECP under multiple environments in Asia and Africa confirmed its high yield potential. We found that the rate of genetic gain for grain yield found in this study was limited primarily by long cycle times and the direct introduction of non-improved material into the elite pool. Consequently, the current breeding scheme for irrigated rice at IRRI is based on rapid recurrent selection among highly elite lines. In this context, the ECP constitutes an important resource for IRRI and NAREs breeders to carefully characterize and manage that elite diversity.

Introgression of tsv1 improves tungro disease resistance of a rice variety BRRI dhan71

“…It is important to note that an elongation initiation factor (eIFG tsv1 ) has been identified as a candidate gene and allele specific SNPs have been identified for tsv1 36 . With the availability of 3 K genome sequence better haplotypes can be searched for tsv1 52 . Use of superior haplotypes and tightly linked gene specific markers can further improve the efficiency of MABB 53 .…”

Optimizing QTL introgression via stochastic simulations: an example of the IRRI rice breeding program

“…Modern breeding strategies focus on rapid-cycle recurrent selection achieved through intercrossing the best elite lines identified in each breeding cycle. A drawback often highlighted in this approach is that it produces (indeed relies on) a breeding program that is effectively closed; it is difficult to introduce new genetic variation from external sources, as these typically do not have equivalent performance with current elite cohorts (Juma et al 2021). This becomes a problem when the breeding program lacks key variations for major QTLs, such as major disease resistance or abiotic stress tolerance genes (Cobb et al 2019a).…”

“…A key limitation in the ability of breeding programs to leverage these benefits of major-gene markerassisted selection is the availability of those genes in appropriate elite germplasm (Bhatia et al 2016;Janaki Ramayya et al 2021). Studies on current breeding programs have shown that about half of the genes and QTLs that could be useful are not found in current elite material; a further 15% or so are present at very low levels (Cobb et al 2019b, a;Juma et al 2021). Furthermore, these genes are mostly only available from very poorlyperforming landraces or occasionally very old breeding material.…”

Climate change challenges, plant science solutions

“…The use of genes and QTLs through marker-assisted selection could shorten the breeding process. Although hundreds of stress-tolerance genes, QTLs, and physiological mechanisms have been identified, only a small number of these research outputs have been used in breeding ( Wissuwa et al, 2016 ; Cobb et al, 2019 ; Platten et al, 2019 ) and the frequency of known abiotic stress QTLs in the current elite breeding material remains low ( Juma et al, 2021 ). There is thus a need to bridge the gap between upstream science and breeding for adaptation to climate change so that valuable traits/genes/QTLs are more actively utilized in breeding pipelines.…”