Genotype × environment interactions for grain iron and zinc content in rice.

BACKGROUND: Nutrient deficiency in humans, especially in children and lactating women, is a major concern. Increasing the micronutrient concentration in staple crops like rice is one way to overcome this. The micronutrient content in rice, especially the iron (Fe) and zinc (Zn) content, is highly variable. The identification of rice genotypes in which there are naturally high Fe and Zn concentrations across environments is an important target towards the production of biofortified rice. RESULTS: Phenotypic correlations between grain Fe and Zn content were positive and significant in all environments but a significant negative association was observed between grain yield and grain Fe and Zn. Promising breeding lines with higher Zn or Fe content, or both, were: IR 82475-110-2-2-1-2 (Zn: 20.24-37.33 mg kg-1 ; Fe: 7.47-14.65 mg kg-1 ); IR 83294-66-2-2-3-2 (Zn: 22-37-41.97 mg kg-1 ; Fe: 9.43-17.16); IR 83668-35-2-2-2 (Zn: 27.15-42.73 mg kg-1 ; Fe: 6.01-14.71); IR 68144-2B-2-2-3-1-166 (Zn: 23.53-40.30 mg kg-1 ; Fe: 10.53-17.80 mg kg-1 ) and RP Bio 5478-185M7 (Zn: 22.60-40.07 mg kg-1 ; Fe: 7.64-14.73 mg kg-1 ). Among these, IR82475-110-2-2-1-2 (Zn: 20.24-37.33 mg kg-1 ; Fe: 7.47-14.65 mg kg-1 ) is also high yielding with 3.75 t ha-1 . Kelhrie Cha (Zn: 17.76-36.45 mg kg-1 ; Fe: 7.17-14.77 mg kg-1 ), Dzuluorhe (Zn: 17.48-39.68 mg kg-1 ; Fe: 7.89-19.90 mg kg-1 ), Nedu (Zn: 18.97-43.55 mg kg-1 Fe: 8.01-19.51 mg kg-1 ), Kuhusoi-Ri-Sareku (Zn: 17.37-44.14 mg kg-1 ; Fe: 8.99-14.30 mg kg-1 ) and Mima (Zn: 17.10-45.64 mg kg-1 ; Fe: 9.97-17.40 mg kg-1 ) were traditional donor genotypes that possessed both high grain Fe and high Zn content. CONCLUSION: Significant genotype × location (G × L) effects were observed in all traits except Fe. Genetic variance was significant and was considerably larger than the variance of G × L for grain Zn and Fe content traits, except grain yield. The G × L × year variance component was significant in all cases. © 2020 Society of Chemical Industry.

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.

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.

Robust phenotyping strategies for evaluation of stem non-structural carbohydrates (NSC) in rice.

Rice plants (Oryza sativa) accumulate excess photoassimilates in the form of non-structural carbohydrates (NSCs) in their stems prior to heading that can later be mobilized to supplement photosynthate production during grain-filling. Despite longstanding interest in stem NSC for rice improvement, the dynamics of NSC accumulation, remobilization, and re-accumulation that have genetic potential for optimization have not been systematically investigated. Here we conducted three pilot experiments to lay the groundwork for large-scale diversity studies on rice stem NSC. We assessed the relationship of stem NSC components with 21 agronomic traits in large-scale, tropical yield trials using 33 breeder-nominated lines, established an appropriate experimental design for future genetic studies using a Bayesian framework to sample sub-datasets from highly replicated greenhouse data using 36 genetically diverse genotypes, and used 434 phenotypically divergent rice stem samples to develop two partial least-squares (PLS) models using near-infrared (NIR) spectra for accurate, rapid prediction of rice stem starch, sucrose, and total non-structural carbohydrates. We find evidence that stem reserves are most critical for short-duration varieties and suggest that pre-heading stem NSC is worthy of further experimentation for breeding early maturing rice.

Transition From Targeted Breeding to Mainstreaming of Biofortification Traits in Crop Improvement Programs.

Biofortification breeding for three important micronutrients for human health, namely, iron (Fe), zinc (Zn), and provitamin A (PVA), has gained momentum in recent years. HarvestPlus, along with its global consortium partners, enhances Fe, Zn, and PVA in staple crops. The strategic and applied research by HarvestPlus is driven by product-based impact pathway that integrates crop breeding, nutrition research, impact assessment, advocacy, and communication to implement country-specific crop delivery plans. Targeted breeding has resulted in 393 biofortified crop varieties by the end of 2020, which have been released or are in testing in 63 countries, potentially benefitting more than 48 million people. Nevertheless, to reach more than a billion people by 2030, future breeding lines that are being distributed by Consultative Group on International Agricultural Research (CGIAR) centers and submitted by National Agricultural Research System (NARS) to varietal release committees should be biofortified. It is envisaged that the mainstreaming of biofortification traits will be driven by high-throughput micronutrient phenotyping, genomic selection coupled with speed breeding for accelerating genetic gains. It is noteworthy that targeted breeding gradually leads to mainstreaming, as the latter capitalizes on the progress made in the former. Efficacy studies have revealed the nutritional significance of Fe, Zn, and PVA biofortified varieties over non-biofortified ones. Mainstreaming will ensure the integration of biofortified traits into competitive varieties and hybrids developed by private and public sectors. The mainstreaming strategy has just been initiated in select CGIAR centers, namely, International Maize and Wheat Improvement Center (CIMMYT), International Rice Research Institute (IRRI), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), International Institute of Tropical Agriculture (IITA), and International Center for Tropical Agriculture (CIAT). This review will present the key successes of targeted breeding and its relevance to the mainstreaming approaches to achieve scaling of biofortification to billions sustainably.

The Development and Characterization of Near-Isogenic and Pyramided Lines Carrying Resistance Genes to Brown Planthopper with the Genetic Background of Japonica Rice (Oryza sativa L.).

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.

Introgression of a functional epigenetic OsSPL14WFP allele into elite indica rice genomes greatly improved panicle traits and grain yield.

Rice yield potential has been stagnant since the Green Revolution in the late 1960s, especially in tropical rice cultivars. We evaluated the effect of two major genes that regulate grain number, Gn1a/OsCKX2 and IPA1/WFP/OsSPL14, in elite indica cultivar backgrounds. The yield-positive Gn1a-type 3 and OsSPL14WFP alleles were introgressed respectively through marker-assisted selection (MAS). The grain numbers per panicle (GNPP) were compared between the recipient allele and the donor allele groups using segregating plants in BC3F2 and BC3F3 generations. There was no significant difference in GNPP between the two Gn1a alleles, suggesting that the Gn1a-type 3 allele was not effective in indica cultivars. However, the OsSPL14WFP allele dramatically increased GNPP by 10.6-59.3% in all four different backgrounds across cropping seasons and generations, indicating that this allele provides strong genetic gain to elite indica cultivars. Eventually, five high-yielding breeding lines were bred using the OsSPL14WFP allele by MAS with a conventional breeding approach that showed increased grain yield by 28.4-83.5% (7.87-12.89 t/ha) vis-à-vis the recipient cultivars and exhibited higher yield (~64.7%) than the top-yielding check cultivar, IRRI 156 (7.82 t/ha). We demonstrated a strong possibility to increase the genetic yield potential of indica rice varieties through allele mining and its application.

Nonenzymatic ß-Carotene Degradation in Provitamin A-Biofortified Crop Plants.

Provitamin A biofortification, the provision of provitamin A carotenoids through agriculture, is regarded as an effective and sustainable intervention to defeat vitamin A deficiency, representing a global health problem. This food-based intervention has been questioned in conjunction with negative outcomes for smokers and asbestos-exposed populations of the CARET and ATBC trials in which very high doses of ß-carotene were supplemented. The current notion that ß-carotene cleavage products (apocarotenoids) represented the harmful agents is the basis of the here-presented research. We quantitatively analyzed numerous plant food items and concluded that neither the amounts of apocarotenoids nor ß-carotene provided by plant tissues, be they conventional or provitamin A-biofortified, pose an increased risk. We also investigated ß-carotene degradation pathways over time. This reveals a substantial nonenzymatic proportion of carotene decay and corroborates the quantitative relevance of highly oxidized ß-carotene polymers that form in all plant tissues investigated.

Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.

BACKGROUND: Rice is one of the major staple foods in the world, especially in the developing countries of Asia. Its consumption as a dietary source is also increasing in Africa. To meet the demand for rice to feed the increasing human population, increasing rice yield is essential. Improving the genetic yield potential of rice is one ideal solution. It is imperative to introduce the identified yield-enhancing gene(s) into modern rice cultivars for the rapid improvement of yield potential through marker-assisted breeding. RESULTS: We report the development of PCR-gel-based markers for eight yield-related functional genes (Gn1a, OsSPL14, SCM2, Ghd7, DEP1, SPIKE, GS5, and TGW6) to introduce yield-positive alleles from the donor lines. Six rice cultivars, including three each of donor and recipient lines, respectively, were sequenced by next-generation whole-genome sequencing to detect DNA polymorphisms between the genotypes. Additionally, PCR products containing functional nucleotide polymorphism (FNP) or putative FNPs for yield-related genes were sequenced. DNA polymorphisms discriminating yield-positive alleles and non-target alleles for each gene were selected through sequence analysis and the allele-specific PCR-gel-based markers were developed. The markers were validated with our intermediate breeding lines produced from crosses between the donors and 12 elite indica rice cultivars as recipients. Automated capillary electrophoresis was tested and fluorescence-labeled SNP genotyping markers (Fluidigm SNP genotyping platform) for Gn1a, OsSPL14, Ghd7, GS5, and GS3 genes were developed for high-throughput genotyping. CONCLUSIONS: The SNP/indel markers linked to yield related genes functioned properly in our marker-assisted breeding program with identified high yield potential lines. These markers can be utilized in local favorite rice cultivars for yield enhancement. The marker designing strategy using both next generation sequencing and Sanger sequencing methods can be used for suitable marker development of other genes associated with useful agronomic traits.

Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa).

Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.

Rice molecular breeding laboratories in the genomics era: Current status and future considerations.

Using DNA markers in plant breeding with marker-assisted selection (MAS) could greatly improve the precision and efficiency of selection, leading to the accelerated development of new crop varieties. The numerous examples of MAS in rice have prompted many breeding institutes to establish molecular breeding labs. The last decade has produced an enormous amount of genomics research in rice, including the identification of thousands of QTLs for agronomically important traits, the generation of large amounts of gene expression data, and cloning and characterization of new genes, including the detection of single nucleotide polymorphisms. The pinnacle of genomics research has been the completion and annotation of genome sequences for indica and japonica rice. This information-coupled with the development of new genotyping methodologies and platforms, and the development of bioinformatics databases and software tools-provides even more exciting opportunities for rice molecular breeding in the 21st century. However, the great challenge for molecular breeders is to apply genomics data in actual breeding programs. Here, we review the current status of MAS in rice, current genomics projects and promising new genotyping methodologies, and evaluate the probable impact of genomics research. We also identify critical research areas to "bridge the application gap" between QTL identification and applied breeding that need to be addressed to realize the full potential of MAS, and propose ideas and guidelines for establishing rice molecular breeding labs in the postgenome sequence era to integrate molecular breeding within the context of overall rice breeding and research programs.