Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.

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Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.

For over 50 years, host-plant resistance has been regarded as an efficient method to reduce yield losses to rice caused by delphacid and cicadelid hoppers. Already a number of resistant rice varieties have been developed and deployed throughout Asia. To date, over 70 hopper resistance genes have been identified in rice; however, less than 10 genes have been deliberately introduced to commercial rice varieties. Currently, due to recent brown planthopper (Nilaparvata lugens [Stal]) and whitebacked planthopper (Sogatella furcifera [Horvath]) outbreaks occurring at an unprecedented scale, researchers are working toward a second generation of resistant varieties using newly identified gene loci and applying new molecular breeding methods. This paper reviews advances in the identification of resistance genes and QTLs against hoppers in rice. It collates all published information on resistance loci and QTLs against the major rice planthoppers and leafhoppers and presents information on gene locations, genetic ma...

Rice Resistance to Planthoppers and Leafhoppers

With 3 figures and 5 tables

Abstract
To identify quantitative trait loci (QTL) controlling heat tolerance in rice, the progeny of BC1F1 and F2 populations derived from an IR64 × N22 cross were exposed to 38/24°C for 14 days at the flowering stage, and spikelet fertility was assessed. A custom 384-plex Illumina GoldenGate genotyping assay was used to genotype the F2 and selected BC1F1 plants. Four single nucleotide polymorphisms were associated with heat tolerance in the BC1F1 population using selective genotyping and single marker analysis, and four putative QTL were found to be associated with heat tolerance in the F2 population. Two major QTL were located on chromosome 1 (qHTSF1.1) and chromosome 4 (qHTSF4.1). These two major QTL could explain 12.6% (qHTSF1.1) and 17.6% (qHTSF4.1) of the variation in spikelet fertility under high temperature. Tolerant allele of qHTSF1.1 was from the susceptible parent IR64, and that of qHTSF4.1 was from tolerant parent N22. The effect of qHTSF4.1 on chromosome 4 was confirmed in selected BC2F2 progeny from the same IR64 × N22 cross, and the plants with qHTSF4.1 showed significantly higher spikelet fertility than other genotypes.

Mapping QTL for heat tolerance at flowering stage in rice using SNP markers

Rice is the most important food security crop and staple food of half of the world population. Major increases in rice production occurred during the past four decades of last century as a result of adoption of green revolution technology. Demand for rice continues to increase as a result of population increase and improvement in living standards particularly in Africa and Latin America. However, rate of increase of rice production has slowed down. It is estimated that we will have to produce 30% more rice in 2030. For this purpose we need rice varieties with higher yield potential and greater yield stability. Breakdown of blast resistance is the major cause of yield instability in several rice growing areas. Efforts are underway to develop rice varieties with durable blast resistance. More than 40 major genes as well as QTL for blast resistance have been identified. Monogenic resistance to blast is less stable but varieties with pyramided monogenes or QTLs are durably resistant. Rice research should focus on identifying more durably resistant genes, tagging of these genes with molecular markers and pyramiding these genes or QTLs through molecular marker-aided selection. Candidate gene identification through rice functional genomics has great potential for developing more durably resistant varieties.

Current Status and Future Prospects for Research on Blast Resistance in Rice ( Oryza sativa L.)

The major disease resistance gene Xa4 confers race-specific durable resistance against Xanthomonas oryzae pv. oryzae, which causes the most damaging bacterial disease in rice worldwide. Although Xa4 has been one of the most widely exploited resistance genes in rice production worldwide, its molecular nature remains unknown. Here we show that Xa4, encoding a cell wall-associated kinase, improves multiple traits of agronomic importance without compromising grain yield by strengthening the cell wall via promoting cellulose synthesis and suppressing cell wall loosening. Strengthening of the cell wall by Xa4 enhances resistance to bacterial infection, and also increases mechanical strength of the culm with slightly reduced plant height, which may improve lodging resistance of the rice plant. The simultaneous improvement of multiple agronomic traits conferred by Xa4 may account for its widespread and lasting utilization in rice breeding programmes globally. The rice resistance gene Xa4, which protects rice against Xanthomonas oryzae pv. oryzae, is widely used in global rice production. Now, a study reveals that Xa4 encodes a cell-wall-associated kinase that improves multiple agronomic traits by regulating cell wall strength.

P.S. Virk

Papers

IR varieties and their impact