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.

Multi-environment Genomic Selection in Rice Elite Breeding Lines

“…This information allows the breeder to drive the breeding population in the desired direction while making efficient use of the available genetic diversity. In the framework of IRRI breeding programs for irrigated systems, a panel representing the elite diversity of the program was constituted in 2018 and then enriched with recent parental lines (Juma et al 2021 ). In this study, we took advantage of the ECP and evaluated it in 15 environments in Asia and Africa.…”

“…The plant material consisted of 111 elite lines from the IRRI breeding program for irrigated systems (Additional file 1 : Table S1), hereafter referred to as the elite core panel (ECP). The ECP represents the elite diversity of the parental lines used in IRRI’s breeding program for irrigated systems and is derived mostly from the breeding efforts that were conducted at IRRI since the 1960s (Juma et al 2021 ). The population included recent varieties such as IRRI 154, IRRI 156, IRRI 174, IRRI 180, IRRI 186, and IRRI 193 as well as current parental lines.…”

Multi-environment genomic selection in rice elite breeding lines

“…The plant material consisted of 111 elite lines from the IRRI breeding program for irrigated systems (Additional le 1: Table S1), hereafter referred to as the elite core panel (ECP). The ECP represents the elite diversity of the parental lines used in IRRI's breeding program for irrigated systems and is derived mostly from the breeding efforts that were conducted at IRRI since the 1960s (Juma et al, 2021). The population included recent varieties such as IRRI 154, IRRI 156, IRRI 174, IRRI 180, IRRI 186, and IRRI 193 as well as current parental lines.…”

“…This information allows the breeder to drive the breeding population in the desired direction while making e cient use of the available genetic diversity. In the framework of IRRI breeding programs for irrigated systems, a panel representing the elite diversity of the program was constituted in 2018 and then enriched with recent parental lines (Juma et al, 2021). In this study, we took advantage of the ECP and evaluated it in 15 environments in Asia and Africa.…”

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 .…”