Crop development with data-driven approach towards sustainable agriculture: Lifting the achievements and opportunities of collaborative research between CIAT and Japan

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

Expression of the CCCH-tandem zinc finger protein gene OsTZF5 under a stress-inducible promoter mitigates the effect of drought stress on rice grain yield under field conditions

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

Construction and EST sequencing of full-length, drought stress cDNA libraries for common beans (Phaseolus vulgaris L.)

<p>Abstract</p> <p>Background</p> <p>Common bean is an important legume crop with only a moderate number of short expressed sequence tags (ESTs) made with traditional methods. The goal of this research was to use full-length cDNA technology to develop ESTs that would overlap with the beginning of open reading frames and therefore be useful for gene annotation of genomic sequences. The library was also constructed to represent genes expressed under drought, low soil phosphorus and high soil aluminum toxicity. We also undertook comparisons of the full-length cDNA library to two previous non-full clone EST sets for common bean.</p> <p>Results</p> <p>Two full-length cDNA libraries were constructed: one for the drought tolerant Mesoamerican genotype BAT477 and the other one for the acid-soil tolerant Andean genotype G19833 which has been selected for genome sequencing. Plants were grown in three soil types using deep rooting cylinders subjected to drought and non-drought stress and tissues were collected from both roots and above ground parts. A total of 20,000 clones were selected robotically, half from each library. Then, nearly 10,000 clones from the G19833 library were sequenced with an average read length of 850 nucleotides. A total of 4,219 unigenes were identified consisting of 2,981 contigs and 1,238 singletons. These were functionally annotated with gene ontology terms and placed into KEGG pathways. Compared to other EST sequencing efforts in common bean, about half of the sequences were novel or represented the 5' ends of known genes.</p> <p>Conclusions</p> <p>The present full-length cDNA libraries add to the technological toolbox available for common bean and our sequencing of these clones substantially increases the number of unique EST sequences available for the common bean genome. All of this should be useful for both functional gene annotation, analysis of splice site variants and intron/exon boundary determination by comparison to soybean genes or with common bean whole-genome sequences. In addition the library has a large number of transcription factors and will be interesting for discovery and validation of drought or abiotic stress related genes in common bean.</p

Expression of the Aeluropus littoralis AlSAP gene enhances rice yield under field drought at the reproductive stage

We evaluated the yields of Oryza sativa L. 'Nipponbare' rice lines expressing a gene encoding an A20/AN1 domain stress-associated protein, AlSAP, from the halophyte grass Aeluropus littoralis under the control of different promoters. Three independent field trials were conducted, with drought imposed at the reproductive stage. In all trials, the two transgenic lines, RN5 and RN6, consistently out-performed non-transgenic (NT) and wild-type (WT) controls, providing 50–90% increases in grain yield (GY). Enhancement of tillering and panicle fertility contributed to this improved GY under drought. In contrast with physiological records collected during previous greenhouse dry-down experiments, where drought was imposed at the early tillering stage, we did not observe significant differences in photosynthetic parameters, leaf water potential, or accumulation of antioxidants in flag leaves of AlSAP-lines subjected to drought at flowering. However, AlSAP expression alleviated leaf rolling and leaf drying induced by drought, resulting in increased accumulation of green biomass. Therefore, the observed enhanced performance of the AlSAP-lines subjected to drought at the reproductive stage can be tentatively ascribed to a primed status of the transgenic plants, resulting from a higher accumulation of biomass during vegetative growth, allowing reserve remobilization and maintenance of productive tillering and grain filling. Under irrigated conditions, the overall performance of AlSAP-lines was comparable with, or even significantly better than, the NT and WT controls. Thus, AlSAP expression inflicted no penalty on rice yields under optimal growth conditions. Our results support the use of AlSAP transgenics to reduce rice GY losses under drought conditions. (Résumé d'auteur

Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response

<p>Abstract</p> <p>Background</p> <p>Cassava, an allotetraploid known for its remarkable tolerance to abiotic stresses is an important source of energy for humans and animals and a raw material for many industrial processes. A full-length cDNA library of cassava plants under normal, heat, drought, aluminum and post harvest physiological deterioration conditions was built; 19968 clones were sequence-characterized using expressed sequence tags (ESTs).</p> <p>Results</p> <p>The ESTs were assembled into 6355 contigs and 9026 singletons that were further grouped into 10577 scaffolds; we found 4621 new cassava sequences and 1521 sequences with no significant similarity to plant protein databases. Transcripts of 7796 distinct genes were captured and we were able to assign a functional classification to 78% of them while finding more than half of the enzymes annotated in metabolic pathways in Arabidopsis. The annotation of sequences that were not paired to transcripts of other species included many stress-related functional categories showing that our library is enriched with stress-induced genes. Finally, we detected 230 putative gene duplications that include key enzymes in reactive oxygen species signaling pathways and could play a role in cassava stress response features.</p> <p>Conclusion</p> <p>The cassava full-length cDNA library here presented contains transcripts of genes involved in stress response as well as genes important for different areas of cassava research. This library will be an important resource for gene discovery, characterization and cloning; in the near future it will aid the annotation of the cassava genome.</p

Establishment of drought screening protocols for rice under field conditions

Protocols were established for screening rice genotypes for tolerance to water-limited conditions under field conditions. These protocols were successfully used to select the best genotypes for further experiments. Rice genotypes responded differently when subjected to water-limited conditions. Experiments conducted under field conditions indicated that rice genotypes Curinga and CT6241 performed much better in terms of grain yield under water-limited conditions than varieties Azucena, Nerica, CICA8 and Palmar. Curinga, CT6241, CICA8 and Palmar were selected for further studies. The first two genotypes are tolerant and whereas the last two are susceptible to water stress.Se estableció un protocolo para la selección de genotipos de arroz tolerantes a déficit hídrico bajo condiciones de campo. El protocolo desarrollado permitió la separación de los genotipos evaluados por su tolerancia a estrés hídrico, los cuales respondieron en forma diferente. En condiciones limitantes de agua, los genotipos Curinga y CT6241 presentaron mejor comportamiento en términos de rendimiento que las variedades Azucena, CICA8, Nerica y Palmar. Curinga, CT6241, CICA8 y Palmar fueron seleccionados para estudios futuros. Los dos primeros como genotipos tolerantes y los dos últimos como susceptibles al estrés hídrico