Rice production needs to increase in the future in order to meet increasing demands. The development of new improved and higher yielding varieties more quickly will be needed to meet this demand. However, most rice breeding programmes in the world have not changed in several decades. In this article, we revisit the evidence in favour of using rapid generation advance (RGA) as a routine breeding method. We describe preliminary activities at the International Rice Research Institute (IRRI) to re-establish RGA on a large scale as the main breeding method for irrigated rice breeding. We also describe experiences from the early adoption at the Bangladesh Rice Research Institute. Evaluation of RGA breeding lines at IRRI for yield, flowering time and plant height indicated transgressive segregation for all traits. Some RGA lines were also higher yielding than the check varieties. The cost advantages of using RGA compared to the pedigree method were also empirically determined by performing an economic analysis. This indicated that RGA is several times more cost effective and advantages will be realized after 1 year even if facilities need to be built. Based on our experience, and previous independent research empirically testing the RGA method in rice, we recommend that this method should be implemented for routine rice breeding in order to improve breeding efficiency.

A first set of 25 NILs carrying ten BPH resistance genes and their pyramids was developed in the background of indica variety IR24 for insect resistance breeding in rice. Brown planthopper (Nilaparvata lugens Stal.) is one of the most destructive insect pests in rice. Development of near-isogenic lines (NILs) is an important strategy for genetic analysis of brown planthopper (BPH) resistance (R) genes and their deployment against diverse BPH populations. A set of 25 NILs with 9 single R genes and 16 multiple R gene combinations consisting of 11 two-gene pyramids and 5 three-gene pyramids in the genetic background of the susceptible indica rice cultivar IR24 was developed through marker-assisted selection. The linked DNA markers for each of the R genes were used for foreground selection and confirming the introgressed regions of the BPH R genes. Modified seed box screening and feeding rate of BPH were used to evaluate the spectrum of resistance. BPH reaction of each of the NILs carrying different single genes was variable at the antibiosis level with the four BPH populations of the Philippines. The NILs with two- to three-pyramided genes showed a stronger level of antibiosis (49.3-99.0%) against BPH populations compared with NILs with a single R gene NILs (42.0-83.5%) and IR24 (10.0%). Background genotyping by high-density SNPs markers revealed that most of the chromosome regions of the NILs (BCF) had IR24 genome recovery of 82.0-94.2%. Six major agronomic data of the NILs showed a phenotypically comparable agronomic performance with IR24. These newly developed NILs will be useful as new genetic resources for BPH resistance breeding and are valuable sources of genes in monitoring against the emerging BPH biotypes in different rice-growing countries.

The brown planthopper (BPH: Nilaparvata lugens Stål.) is a major pest of rice, Oryza sativa, in Asia. Host plant resistance has tremendous potential to reduce the damage caused to rice by the planthopper. However, the effectiveness of resistance genes varies spatially and temporally according to BPH virulence. Understanding patterns in BPH virulence against resistance genes is necessary to efficiently and sustainably deploy resistant rice varieties. To survey BPH virulence patterns, seven near-isogenic lines (NILs), each with a single BPH resistance gene (BPH2-NIL, BPH3-NIL, BPH17-NIL, BPH20-NIL, BPH21-NIL, BPH32-NIL and BPH17-ptb-NIL) and fifteen pyramided lines (PYLs) carrying multiple resistance genes were developed with the genetic background of the japonica rice variety, Taichung 65 (T65), and assessed for resistance levels against two BPH populations (Hadano-66 and Koshi-2013 collected in Japan in 1966 and 2013, respectively). Many of the NILs and PYLs were resistant against the Hadano-66 population but were less effective against the Koshi-2013 population. Among PYLs, BPH20+BPH32-PYL and BPH2+BPH3+BPH17-PYL granted relatively high BPH resistance against Koshi-2013. The NILs and PYLs developed in this research will be useful to monitor BPH virulence prior to deploying resistant rice varieties and improve rice’s resistance to BPH in the context of regionally increasing levels of virulence.

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.

In the last decade, association mapping (AM) has become a well-established method to detect genes and quantitative trait loci (QTLs) associated with agronomically important traits. The identification of a large number of single nucleotide polymorphisms (SNPs) from genome sequencing and concurrent development of high-throughput genotyping platforms has led to AM being widely used for a range of crops. These technologies have been used in rice (Oryza sativa) to explore the abundant diversity and there is enormous potential to identify novel QTLs for traits of interest. Due to the availability of cost-effective high-throughput SNP genotyping methods and rapid developments in rice genomics, it is inevitable that these AM approaches will become more popular in the future, especially in the context of genome-wide association studies (GWASs). In this paper, we review the fundamental concepts, critical considerations and limitations of AM focusing on rice, and reiterate the importance of accurate phenotypic data. We also include a section about connecting GWAS to molecular breeding, covering practical consideration for breeders, which is required to use GWAS results in actual rice molecular breeding programs and which has not received adequate attention in the scientific literature.