Identification of Drought Tolerant Rice (Oryza Sativa L.) Genotypes with Asian and African Backgrounds.

Drought is among the major abiotic stresses on rice production that can cause yield losses of up to 100% under severe drought conditions. Neither of the rice varieties currently grown in Burundi can withstand very low and irregular precipitation. This study identified genotypes that have putative quantitative trait loci (QTLs) associated with drought tolerance and determined their performance in the field. Two hundred and fifteen genotypes were grown in the field under both drought and irrigated conditions. Genomic deoxyribonucleic acid (DNA) was extracted from rice leaves for further genotypic screening. The results revealed the presence of the QTLs qDTY12.1, qDTY3.1, qDTY2-2_1, and qDTY1.1 in 90%, 85%, 53%, and 22% of the evaluated genotypes, respectively. The results of the phenotypic evaluation showed a significant yield reduction due to drought stress. Yield components and other agronomic traits were also negatively affected by drought. Genotypes having high yield best linear unbiased predictions (BLUPs) with two or more major QTLs for drought tolerance, including IR 108044-B-B-B-3-B-B, IR 92522-45-3-1-4, and BRRI DHAN 55 are of great interest for breeding programs to improve the drought tolerance of lines or varieties with other preferred traits.

Multi-environment Genomic Selection in Rice Elite Breeding Lines.

BACKGROUND: Assessing the performance of elite lines in target environments is essential for breeding programs to select the most relevant genotypes. One of the main complexities in this task resides in accounting for the genotype by environment interactions. Genomic prediction models that integrate information from multi-environment trials and environmental covariates can be efficient tools in this context. The objective of this study was to assess the predictive ability of different genomic prediction models to optimize the use of multi-environment information. We used 111 elite breeding lines representing the diversity of the international rice research institute breeding program for irrigated ecosystems. The lines were evaluated for three traits (days to flowering, plant height, and grain yield) in 15 environments in Asia and Africa and genotyped with 882 SNP markers. We evaluated the efficiency of genomic prediction to predict untested environments using seven multi-environment models and three cross-validation scenarios. RESULTS: The elite lines were found to belong to the indica group and more specifically the indica-1B subgroup which gathered improved material originating from the Green Revolution. Phenotypic correlations between environments were high for days to flowering and plant height (33% and 54% of pairwise correlation greater than 0.5) but low for grain yield (lower than 0.2 in most cases). Clustering analyses based on environmental covariates separated Asia's and Africa's environments into different clusters or subclusters. The predictive abilities ranged from 0.06 to 0.79 for days to flowering, 0.25-0.88 for plant height, and - 0.29-0.62 for grain yield. We found that models integrating genotype-by-environment interaction effects did not perform significantly better than models integrating only main effects (genotypes and environment or environmental covariates). The different cross-validation scenarios showed that, in most cases, the use of all available environments gave better results than a subset. CONCLUSION: Multi-environment genomic prediction models with main effects were sufficient for accurate phenotypic prediction of elite lines in targeted environments. These results will help refine the testing strategy to update the genomic prediction models to improve predictive ability.

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

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.

Integrated Strategies for Durable Rice Blast Resistance in Sub-Saharan Africa.

Rice is a key food security crop in Africa. The importance of rice has led to increasing country-specific, regional, and multinational efforts to develop germplasm and policy initiatives to boost production for a more food-secure continent. Currently, this critically important cereal crop is predominantly cultivated by small-scale farmers under suboptimal conditions in most parts of sub-Saharan Africa (SSA). Rice blast disease, caused by the fungus Magnaporthe oryzae, represents one of the major biotic constraints to rice production under small-scale farming systems of Africa, and developing durable disease resistance is therefore of critical importance. In this review, we provide an overview of the major advances by a multinational collaborative research effort to enhance sustainable rice production across SSA and how it is affected by advances in regional policy. As part of the multinational effort, we highlight the importance of joint international partnerships in tackling multiple crop production constraints through integrated research and outreach programs. More specifically, we highlight recent progress in establishing international networks for rice blast disease surveillance, farmer engagement, monitoring pathogen virulence spectra, and the establishment of regionally based blast resistance breeding programs. To develop blast-resistant, high yielding rice varieties for Africa, we have established a breeding pipeline that utilizes real-time data of pathogen diversity and virulence spectra, to identify major and minor blast resistance genes for introgression into locally adapted rice cultivars. In addition, the project has developed a package to support sustainable rice production through regular stakeholder engagement, training of agricultural extension officers, and establishment of plant clinics.

Rice Biofortification With Zinc and Selenium: A Transcriptomic Approach to Understand Mineral Accumulation in Flag Leaves.

Human malnutrition due to micronutrient deficiencies, particularly with regards to Zinc (Zn) and Selenium (Se), affects millions of people around the world, and the enrichment of staple foods through biofortification has been successfully used to fight hidden hunger. Rice (Oryza sativa L.) is one of the staple foods most consumed in countries with high levels of malnutrition. However, it is poor in micronutrients, which are often removed during grain processing. In this study, we have analyzed the transcriptome of rice flag leaves biofortified with Zn (900 g ha-1), Se (500 g ha-1), and Zn-Se. Flag leaves play an important role in plant photosynthesis and provide sources of metal remobilization for developing grains. A total of 3170 differentially expressed genes (DEGs) were identified. The expression patterns and gene ontology of DEGs varied among the three sets of biofortified plants and were limited to specific metabolic pathways related to micronutrient mobilization and to the specific functions of Zn (i.e., its enzymatic co-factor/coenzyme function in the biosynthesis of nitrogenous compounds, carboxylic acids, organic acids, and amino acids) and Se (vitamin biosynthesis and ion homeostasis). The success of this approach should be followed in future studies to understand how landraces and other cultivars respond to biofortification.

Putrescine differently influences the effect of salt stress on polyamine metabolism and ethylene synthesis in rice cultivars differing in salt resistance.

Effects of salt stress on polyamine metabolism and ethylene production were examined in two rice (Oryza sativa L.) cultivars [I Kong Pao (IKP), salt sensitive; and Pokkali, salt resistant] grown for 5 d and 12 d in nutrient solution in the presence or absence of putrescine (1 mM) and 0, 50, and 100 mM NaCl. The salt-sensitive (IKP) and salt-resistant (Pokkali) cultivars differ not only in their mean levels of putrescine, but also in the physiological functions assumed by this molecule in stressed tissues. Salt stress increased the proportion of conjugated putrescine in salt-resistant Pokkali and decreased it in the salt-sensitive IKP, suggesting a possible protective function in response to NaCl. Activities of the enzymes ornithine decarboxylase (ODC; EC 4.1.1.17) and arginine decarboxylase (ADC; EC 4.1.1.19) involved in putrescine synthesis were higher in salt-resistant Pokkali than in salt-sensitive IKP. Both enzymes were involved in the response to salt stress. Salt stress also increased diamine oxidase (DAO; 1.4.3.6) and polyamine oxidase (PAO EC 1.5.3.11) activities in the roots of salt-resistant Pokkali and in the shoots of salt-sensitive IKP. Gene expression followed by reverse transcription-PCR suggested that putrescine could have a post-translational impact on genes coding for ADC (ADCa) and ODC (ODCa and ODCb) but could induce a transcriptional activation of genes coding for PAO (PAOb) mainly in the shoot of salt-stressed plants. The salt-resistant cultivar Pokkali produced higher amounts of ethylene than the salt-sensitive cultivar IKP, and exogenous putrescine increased ethylene synthesis in both cultivars, suggesting no direct antagonism between polyamine and ethylene pathways in rice.

Do exogenous polyamines have an impact on the response of a salt-sensitive rice cultivar to NaCl?

In order to analyze the putative impact of polyamines (PAs) on the plant response to salt, seedlings from the salt-sensitive rice cultivar I Kong Pao (IKP) were exposed for 5, 12 and 19 days to 0, 50 or 100 mM NaCl in the absence, or in the presence of exogenous PAs (putrescine (Put), spermidine (Spd) or spermine (Spm) 1mM) or inhibitors of PA synthesis (methylglyoxalbis-guanyl hydrazone (MGBG) 1mM, cyclohexylammonium (CHA) 5mM and D-arginine (D-Arg) 5mM). The addition of PAs in nutritive solution reduced plant growth in the absence of NaCl and did not afford protection in the presence of salt. PA-treated plants exhibited a higher K+/Na+ ratio in the shoots, suggesting an improved discrimination among monovalent cations at the root level, especially at the sites of xylem loading. The diamine Put induced a decrease in the shoot water content in the presence of NaCl, while Spd and Spm had no effects on the plant water status. In contrast to Spd, Spm was efficiently translocated to the shoots. Both PAs (Spd and Spm) induced a decrease in cell membrane stability as suggested by a strong increase in malondialdehyde content of PA-treated plants exposed to NaCl. These results are discussed in relation to the putative functions of PAs in stressed plant metabolism.