Accurate nitrogen management in rice (Oryza sativa L.) is essential for optimizing both crop productivity and environmental sustainability. This study evaluated the potential of Near-Infrared Spectroscopy (NIRS) combined with chemometric modeling to classify leaf nitrogen content (LNC) in five rice genotypes (Nerica, Rufipogon, IR64, Ciherang, and Curinga) subjected to five nitrogen fertilization levels (0

Concerns about methane (CH4) emissions from rice, a staple sustaining over 3.5 billion people globally, are heightened due to its status as the second-largest contributor to greenhouse gases, driving climate change. Accurate quantification of CH4 emissions from rice fields is crucial for understanding gas concentrations. Leveraging technological advancements, we present a groundbreaking solution that integrates machine learning and remote sensing data, challenging traditional closed chamber methods. To achieve this, our methodology involves extensive data collection using drones equipped with a Micasense Altum camera and ground sensors, effectively reducing reliance on labor-intensive and costly field sampling. In this experimental project, our research delves into the intricate relationship between environmental variables, such as soil conditions and weather patterns, and CH4 emissions. We achieved remarkable results by utilizing unmanned aerial vehicles (UAV) and evaluating over 20 regression models, emphasizing an R2 value of 0.98 and 0.95 for the training and testing data, respectively. This outcome designates the random forest regressor as the most suitable model with superior predictive capabilities. Notably, phosphorus, GRVI median, and cumulative soil and water temperature emerged as the model’s fittest variables for predicting these values. Our findings underscore an innovative, cost-effective, and efficient alternative for quantifying CH4 emissions, marking a significant advancement in the technology-driven approach to evaluating rice growth parameters and vegetation indices, providing valuable insights for advancing gas emissions studies in rice paddies.

The primary transcript structure provides critical insights into protein diversity, transcriptional modification, and functions. Cassava transcript structures are highly diverse because of alternative splicing (AS) events and high heterozygosity. To precisely determine and characterize transcript structures, fully sequencing cloned transcripts is the most reliable method. However, cassava annotations were mainly determined according to fragmentation-based sequencing analyses (e.g., EST and short-read RNA-seq). In this study, we sequenced the cassava full-length cDNA library, which included rare transcripts. We obtained 8,628 non-redundant fully sequenced transcripts and detected 615 unannotated AS events and 421 unannotated loci. The different protein sequences resulting from the unannotated AS events tended to have diverse functional domains, implying that unannotated AS contributes to the truncation of functional domains. The unannotated loci tended to be derived from orphan genes, implying that the loci may be associated with cassava-specific traits. Unexpectedly, individual cassava transcripts were more likely to have multiple AS events than Arabidopsis transcripts, suggestive of the regulated interactions between cassava splicing-related complexes. We also observed that the unannotated loci and/or AS events were commonly in regions with abundant single nucleotide variations, insertions–deletions, and heterozygous sequences. These findings reflect the utility of completely sequenced FLcDNA clones for overcoming cassava-specific annotation-related problems to elucidate transcript structures. Our work provides researchers with transcript structural details that are useful for annotating highly diverse and unique transcripts and alternative splicing events. The complete sequencing of a cassava full-length cDNA library facilitates the annotation of unique transcript structures and alternative splicing events by avoiding cassava-specific issues affecting annotations, including extensive heterozygosity.

In the low fertility acid soils of the Orinoquian savannas of Colombia, Urochloa humidicola cv. Tully or Humidicola is one of the most widely planted tropical forage grasses for improving livestock productivity. Low nutritional quality of this grass limits sustainable livestock production in this region. In this study, we conducted a phenotypic evaluation under field and greenhouse conditions of one of the first hybrid populations of U. humidicola generated from the forage breeding program of CIAT. Our objective was to identify a set of new hybrids of U. humidicola that combine improved productivity and nutritional quality plus the biological nitrification inhibition (BNI) trait/ability to reduce nitrogen (N) losses via leaching and nitrous oxide (N2O) emissions. To this end, we tested 118 hybrids (planted in pots) in the greenhouse for over 6 months and measured potential nitrification rates (NR) using soil microcosm incubation. NR values observed ranged from 0.27 to 5.75 mg N-NO3- kg soil(-1) day(-1). Later, 12 hybrids with different levels of NR were selected and field-tested in the Orinoquia region over a 4 years period (2013-2017) for dry matter production, nutrition quality (crude protein, in vitro digestibility and fibres content) and NR in each year. In the rainy season of 2018, two hybrids with superior agronomic performance and contrasting field level NR (Uh08/1149 and 0450) were subjected to analysis of soil-borne N2O emissions after fertilization during 13 days. The NR values recorded were not directly correlated with the forage quality parameters evaluated, however, the two grasses with the lowest NR values were among those with the highest biomass production, crude protein content, and N uptake. The grass hybrid Uh08/1149 and the germplasm accession CIAT 16888 were found as materials with superior forage value, with production of 14.1 and 14.6 tons dry matter ha(-1) year(-1) (up to 8% higher than the cv. Tully), crude protein of 11.5 and 9.1% per cut (up to 20% higher than the cv. Tully), and N uptake of 31.6 and 25.7 kg N ha(-1) cut(-1) (up to 30% higher than the cv. Tully). Additionally, these two grasses are likely to exhibit high-BNI ability, with potential to improve N use efficiency in managed pastures.

Nitrogen (N) is essential for amino acid synthesis in rice production, but its excessive use poses an environmental concern. This research aimed to improve rice agronomic nitrogen use efficiency (ANUE) by knockout (KO) of rice homologs of the two selected genes from Arabidopsis thaliana: AtAAP2, an amino acid permease involved in N transportation in shoots, and AtCRF4, a transcription factor participating in N uptake in roots. The homologs of these genes in rice were identified based on amino acid sequence similarity and knocked out using CRISPR/Cas9 mediated gene editing (GE). The AAP2-KO and CRF4-KO lines were subjected to agronomic evaluations with three N doses: 100% (180 kg ha-1), 50% (90 kg ha-1), and 0% (0 kg ha-1) and showed a 130-175% increase in dry biomass weight and a 183-313% increase in panicle number compared to wild type (WT) in the first experiment. These lines also had slower leaf senescence, the so-called “stay-green” trait, indicating the KO effect of target genes in N metabolism. However, neither AAP2-KO nor CRF4-KO showed better yield or ANUE than WT. This study demonstrated the usefulness of GE technology in gene evaluation and highlighted the effects of AtAAP2 and AtCRF4 genes in the plant N cycle.

Grassland pastures are crucial for the global food supply through their milk and meat production; hence, forage species monitoring is essential for cattle feed. Therefore, knowledge of pasture above-ground canopy features help understand the crop status. This paper finds how to construct machine learning models to predict above-ground canopy features in Brachiaria pasture from ground truth data (GTD) and remote sensing at larger (satellite data on the cloud) and smaller (unmanned aerial vehicles (UAV)) scales. First, we used above-ground biomass (AGB) data obtained from Brachiaria to evaluate the relationship between vegetation indices (VIs) with the dry matter (DM). Next, the performance of machine learning algorithms was used for predicting AGB based on VIs obtained from ground truth and satellite and UAV imagery. When comparing more than twenty-five machine learning models using an Auto Machine Learning Python API, the results show that the best algorithms were the Huber with R2 = 0.60, Linear with R2 = 0.54, and Extra Trees with R2 = 0.45 to large scales using satellite. On the other hand, short-scale best regressions are K Neighbors with an R2 of 0.76, Extra Trees with an R2 of 0.75, and Bayesian Ridge with an R2 of 0.70, demonstrating a high potential to predict AGB and DM. This study is the first prediction model approach that assesses the rotational grazing system and pasture above-ground canopy features to predict the quality and quantity of cattle feed to support pasture management in Colombia.

Status of the current outbreak of cassava mosaic disease (CMD) in Southeast Asia was reviewed. Healthy cassava seed production and dissemination systems have been established in Vietnam and Cambodia, along with integrated disease and pest management systems, to combat the outbreak. Cassava (Manihot esculenta Crantz) is one of the most important edible crops in tropical and subtropical regions. Recently, invasive insect pests and diseases have resulted in serious losses to cassava in Southeast Asia. In this review we discuss the current outbreak of cassava mosaic disease (CMD) caused by the Sri Lankan cassava mosaic virus (SLCMV) in Southeast Asia, and summarize similarities between SLCMV and other cassava mosaic begomoviruses. A SATREPS (Science and Technology Research Partnership for Sustainable Development) project “Development and dissemination of sustainable production systems based on invasive pest management of cassava in Vietnam, Cambodia and Thailand”, was launched in 2016, which has been funded by The Japan International Cooperation Agency (JICA) and The Japan Science and Technology Agency (JST), Japan. The objectives of SATREPS were to establish healthy seed production and dissemination systems for cassava in south Vietnam and Cambodia, and to develop management systems for plant diseases and insect pests of cassava. To achieve these goals, model systems of healthy seed production in Vietnam and Cambodia have been developed incorporating CMD-resistant planting materials through international networks with The International Center for Tropical Agriculture (CIAT) and The International Institute of Tropical Agriculture (IITA).

The global population is expected to increase by 10 billion by 2050,the demand for food and water is also likely to increase.Several factors intensify the growing water scarcity,such as inef-ficient water use in the food value chain and inadequate infra-structure to save water.The changing climate also exacerbates the rising temperature by making the drier areas drier and nega-tively impacting agriculture production in most parts of the world.A decrease in precipitation has been observed in the tropics and sub-tropics,such as the Sahel region of Southern Africa,the Mediterranean,South Asia,and the Southwest of US since 1970().

International Center for Tropical Agriculture (CIAT) has a long history of collaboration with Japanese institutions to develop improved crop varieties and adopt agricultural technologies with pioneering approaches for farmers' benefit. Since 1972, Japan has enjoyed a long history of successful cooperation with the CGIAR (formerly the Consultative Group on International Agricultural Research) after becoming its 22nd Member to meet global challenges such as climate change affecting agriculture and food systems in diplomacy through Japan's advanced science and technology. This long-standing collaboration adopts agricultural technologies developed in Japan and promotes agricultural innovation through cutting-edge technologies such as remote sensing for Internet of Things (IoT) and Artificial Intelligence (AI) that will provide novel solutions to the agriculture and food sectors in the tropics. Nowadays, it is presumed that this approach to data-driven agriculture realization will help establish a sustainable agroecosystem with increased agricultural productivity and sustainability by adapting or mitigating the effects of climate change and efficient use of natural resources and establishing a sustainable food value chain. This review highlights the research collaborations and new opportunities on advanced breeding technologies and digital innovations towards data-driven agriculture. In conjunction, we present a potential collaborative research between CIAT and Japan, prioritizing the current and future challenges in agriculture and food systems.

BackgroundIdentifying new sources of disease resistance and the corresponding underlying resistance mechanisms remains very challenging, particularly in Monocots. Moreover, the modification of most disease resistance pathways made so far is detrimental to tolerance to abiotic stresses such as drought. This is largely due to negative cross-talks between disease resistance and abiotic stress tolerance signaling pathways. We have previously described the role of the rice ZBED protein containing three Zn-finger BED domains in disease resistance against the fungal pathogen Magnaporthe oryzae. The molecular and biological functions of such BED domains in plant proteins remain elusive.ResultsUsing Nicotiana benthamiana as a heterologous system, we show that ZBED localizes in the nucleus, binds DNA, and triggers basal immunity. These activities require conserved cysteine residues of the Zn-finger BED domains that are involved in DNA binding. Interestingly, ZBED overexpressor rice lines show increased drought tolerance. More importantly, the disease resistance response conferred by ZBED is not compromised by drought-induced stress.ConclusionsTogether our data indicate that ZBED might represent a new type of transcriptional regulator playing simultaneously a positive role in both disease resistance and drought tolerance. We demonstrate that it is possible to provide disease resistance and drought resistance simultaneously.

Increasing drought resistance without sacrificing grain yield remains an ongoing challenge in crop improvement. In this study, we report that Oryza sativa CCCH-tandem zinc finger protein 5 (OsTZF5) can confer drought resistance and increase grain yield in transgenic rice plants. Expression of OsTZF5 was induced by abscisic acid, dehydration and cold stress. Upon stress, OsTZF5-GFP localized to the cytoplasm and cytoplasmic foci. Transgenic rice plants overexpressing OsTZF5 under the constitutive maize ubiquitin promoter exhibited improved survival under drought but also growth retardation. By introducing OsTZF5 behind the stress-responsive OsNAC6 promoter in two commercial upland cultivars, Curinga and NERICA4, we obtained transgenic plants that showed no growth retardation. Moreover, these plants exhibited significantly increased grain yield compared to non-transgenic cultivars in different confined field drought environments. Physiological analysis indicated that OsTZF5 promoted both drought tolerance and drought avoidance. Collectively, our results provide strong evidence that OsTZF5 is a useful biotechnological tool to minimize yield losses in rice grown under drought conditions.

KEY MESSAGE:The field survey in this article showed in 'KU50', a popular variety and late-branching type of cassava in Southeast Asia, that flowering rarely occurs in normal-field conditions in Southeast Asia but is strongly induced in the dry season in the mountainous region. Flowering time is correlated with the expression patterns of MeFT1 and homologs of Arabidopsis GI, PHYA, and NF-Ys. Cassava (Manihot esculenta Crantz) is a tropical crop that is propagated vegetatively rather than sexually by seed. Flowering rarely occurs in the erect-type variety grown in Southeast Asia, but it is known that cassava produces flowers every year in mountainous regions. Data pertaining to the effect of environmental factors on flowering time and gene expression in cassava, however, is limited. The aim of the present study was to determine the kinds of environmental conditions that regulate flowering time in cassava and the underlying molecular mechanisms. The flowering status of KU50, a popular variety in Southeast Asia and late-branching type of cassava, was monitored in six fields in Vietnam and Cambodia. At non-flowering and flowering field locations in North Vietnam, the two FLOWERING LOCUS T (FT)-like genes, MeFT1 and MeFT2, were characterized by qPCR, and the pattern of expression of flowering-related genes and genes responsive to environmental signals were analyzed by using RNA sequencing data from time-series samples. Results indicate that cassava flowering was induced in the dry season in the mountain region, and that flowering time was correlated with the expression of MeFT1, and homologs of Arabidopsis GI, PHYA, and NF-Ys. Based upon these data, we hypothesize that floral induction in cassava is triggered by some conditions present in the mountain regions during the dry season.

In Asia, cassava (Manihot esculenta) is cultivated by more than 8 million farmers, driving the rural economy of many countries. The International Center for Tropical Agriculture (CIAT), in partnership with national agricultural research institutes (NARIS), instigated breeding and agronomic research in Asia, 1983. The breeding program has successfully released high-yielding cultivars resulting in an average yield increase from 13.0 t ha(-1) in 1996 to 21.3 t ha(-1) in 2016, with significant economic benefits. Following the success in increasing yields, cassava breeding has turned its focus to higher-value traits, such as waxy cassava, to reach new market niches. More recently, building resistance to invasive pests and diseases has become a top priority due to the emergent threat of cassava mosaic disease (CMD). The agronomic research involves driving profitability with advanced technologies focusing on better agronomic management practices thereby maintaining sustainable production systems. Remote sensing technologies are being tested for trait discovery and large-scale field evaluation of cassava. In summary, cassava breeding in Asia is driven by a combination of food and market demand with technological innovations to increase the productivity. Further, exploration in the potential of data-driven agriculture is needed to empower researchers and producers for sustainable advancement.

Cassava (Manihot esculenta Crantz) is a root crop grown in tropical and subtropical regions. Cassava production faces an increasing number of new diseases and arthropod pests, especially in Southeast Asia, where its area and trade have expanded. An efficient plant-multiplication system is required to provide disease-free plants to farmers to sustain production. Cassava is generally propagated vegetatively by planting properly lignified stem cuttings in soil. Vegetative multiplication is a simple approach and has the advantage of producing vigorous plants. The generation of new plants from seed, however, is not a common practice. Notably, properly lignified stems, rather than young and non-lignified stems, are required for successful vegetative propagation. On average, it takes approximately 8–12 months to produce lignified stems of sufficient size to establish an efficient and cost-effective propagation system. In the present study, an aeroponic culture system for producing cassava was developed, which is simple, low-cost, and enables the use of young stems (4–6 weeks old) for propagation. Additionally, we have demonstrated that the survival ratio and plant growth are improved in comparison with general propagation in soil. We propose that aeroponic culture can serve as an efficient method for producing disease-free cassava planting material.

BackgroundThe apomictic reproductive mode of Brachiaria (syn. Urochloa) forage species allows breeders to faithfully propagate heterozygous genotypes through seed over multiple generations. In Brachiaria, reproductive mode segregates as single dominant locus, the apospory-specific genomic region (ASGR). The AGSR has been mapped to an area of reduced recombination on Brachiaria decumbens chromosome 5. A primer pair designed within ASGR-BABY BOOM-like (BBML), the candidate gene for the parthenogenesis component of apomixis in Pennisetum squamulatum, was diagnostic for reproductive mode in the closely related species B. ruziziensis, B. brizantha, and B. decumbens. In this study, we used a mapping population of the distantly related commercial species B. humidicola to map the ASGR and test for conservation of ASGR-BBML sequences across Brachiaria species.ResultsDense genetic maps were constructed for the maternal and paternal genomes of a hexaploid (2n=6x=36) B. humidicola F-1 mapping population (n=102) using genotyping-by-sequencing, simple sequence repeat, amplified fragment length polymorphism, and transcriptome derived single nucleotide polymorphism markers. Comparative genomics with Setaria italica provided confirmation for x=6 as the base chromosome number of B. humidicola. High resolution molecular karyotyping indicated that the six homologous chromosomes of the sexual female parent paired at random, whereas preferential pairing of subgenomes was observed in the apomictic male parent. Furthermore, evidence for compensated aneuploidy was found in the apomictic parent, with only five homologous linkage groups identified for chromosome 5 and seven homologous linkage groups of chromosome 6. The ASGR mapped to B. humidicola chromosome 1, a region syntenic with chromosomes 1 and 7 of S. italica. The ASGR-BBML specific PCR product cosegregated with the ASGR in the F-1 mapping population, despite its location on a different carrier chromosome than B. decumbens.ConclusionsThe first dense molecular maps of B. humidicola provide strong support for cytogenetic evidence indicating a base chromosome number of six in this species. Furthermore, these results show conservation of the ASGR across the Paniceae in different chromosomal backgrounds and support postulation of the ASGR-BBML as candidate genes for the parthenogenesis component of apomixis.

We developed and modified a precise, rapid, and reproducible protocol isolating high‐quality RNA from tissues of multiple varieties of cassava plants (Manihot esculenta Crantz). The resulting method is suitable for use in mini, midi, and maxi preparations and rapidly achieves high total RNA yields (170–600 μg·g−1) using low‐cost chemicals and consumables and with minimal contamination from polysaccharides, polyphenols, proteins, and other secondary metabolites. In particular, A260 : A280 ratios were > 2.0 for RNA from various tissues, and all of the present RNA samples yielded ribosomal integrity number values of greater than six. The resulting high purity and quality of isolated RNA will facilitate downstream applications (quantitative reverse transcriptase‐polymerase chain reaction or RNA sequencing) in cassava molecular breeding.

The burgeoning demand for rice in Latin America and Caribbean (LAC) exceeds supply, resulting in a rice deficit. To overcome this challenge, rice production should be increased, albeit sustainably. However, since rice production is associated with increases in the atmospheric concentration of two greenhouse gases (GHGs), namely methane (CH4) and nitrous oxide (N2O), the challenge is on ensuring that production increases are not associated with an increase in GHG emissions and thus do not cause an increase in GHG emission intensities. Based on current understanding of drivers of CH4 and N2O production, we provide here insights on the potential climate change mitigation benefits of management and technological options (i.e., seeding, tillage, irrigation, residue management) pursued in the LAC region. Studies conducted in the LAC region show intermittent irrigation or alternate wetting and drying of rice fields to reduce CH4 emissions by 25–70% without increasing N2O emissions. Results on yield changes associated with intermittent irrigation remain inconclusive. Compared to conventional tillage, no-tillage and anticipated tillage (i.e., fall tillage) cause a 21% and 25% reduction in CH4 emissions, respectively. From existing literature, it was unambiguous that the mitigation potential of most management strategies pursued in the LAC region need to be quantified while acknowledging country-specific conditions. While breeding high yielding and low emitting rice varieties may represent the most promising and possibly sustainable approach for achieving GHG emission reductions without demanding major changes in on-farm management practices, this is rather idealistic. We contend that a more realistic approach for realizing low GHG emitting rice production systems is to focus on increasing rice yields, for obvious food security reasons, which, while not reducing absolute emissions, should translate to a reduction in GHG emission intensities. Moreover, there is need to explore creative ways of incentivizing the adoption of promising combinations of management and technological options.

Cassava is an important tropical starch crop that provides food security, income generation and industrial application in tropical countries. We have developed cassava research platform towards advancing molecular breeding and understanding biological phenomena by the international collaborations between Japan, Vietnam, Thailand, and Colombia. The platform provides: a) 20,000 full-length cDNA resources, b) Omic analyses, c) integrative database, d) transformation system and e) CRISPR/Cas9-mediated mutagenesis. We optimized the system for induction of friable embryonic calli in cassava. Using the improved protocol, we have produced several transgenic cassava plants to improve cassava biomass quantitatively and qualitatively. We also have analyzed the molecular mechanisms of various biological phenomena, such as tuberization, disease resistance, drought and high-salinity stress response by integrative Omic analyses. Furthermore, we have analyzed the effects of environmental factors on the developmental phenotypes in the fields of Vietnam and Cambodia. RIKEN group has educated young Asian researchers cutting-edge plant science. We hope that our approach using the cutting-edge research platform and ICT will advance the molecular breeding of useful cassava plants, such as high-yield, increased stress tolerance and beneficial modifications of starch quality and contribute to solve the SDGs.