Portal de Periódicos da CAPES

A Clearinghouse for Genome-Edited Crops and Field Testing

2020; Elsevier BV; Volume: 14; Issue: 1 Linguagem: Inglês

10.1016/j.molp.2020.12.010

1674-2052

Angela Joseph Fernando, Michael Gomez Selvaraj, Paúl Chavarriaga, Sandra Emma Carmona Valdés, Joe Tohmé,

Plant tissue culture and regeneration

Latin America was commonly called “sleeping giant” for its humid tropics and land base relative to its population size. The International Center for Tropical Agriculture (CIAT, by its Spanish acronym) was initiated in 1967 to serve three important zones—coastal plains, savannahs, and “hot, humid jungles.” In line, the research areas were organized to be fitted as appropriate into these important ecological zones. Over the 50 years, CIAT has been a forerunner in developing and disseminating improved crop varieties and agricultural technologies, including its pioneering approaches in the tropics. Rewinding the history of the Center's research accomplishments over the 50 years, partners and stakeholders' joint efforts have brought about $40 billion in economic benefits to Latin America, Africa, and Asia. In 2019, merging the two Consultative Group for International Agricultural Research (CGIAR) centers, each known for world-class research and development (the Alliance of Bioversity International and CIAT), was initiated. In addition to the alliance, the CGIAR centers are going through a dynamic reformulation leading to One-CGIAR to deliver research in a phased approach targeting the CGIAR's impact areas—food security and human welfare, such as climate change, on sustainable development goals by 2030. The CIAT's current leadership on CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), and co-leadership of the CGIAR Platform for Big Data in Agriculture, and the innovative plant breeding techniques, especially, CRISPR–Cas9-mediated genome editing (GEd), and decades-long record of CIAT for maintaining the world's largest and most diverse collections of tens of thousands of varieties of beans, cassava, rice, and tropical forages under Future Seeds leads to new CGIAR collaborations across the countries. Since the advent of CRISPR technology in 2012, the world of molecular biology was storming with the GEd technology. The CIAT's Advanced Breeding Platform (ABP) initiated its first testing on GEd for rice's genetic improvement in 2015, which was laid from a collaboration with Japan's National Institute of Agrobiological Sciences (NIAS) and the University of Melbourne, Australia. Here, we summarize the applications of the CRISPR technology in different widely grown rice varieties and other crops (Bean, Cassava, and Cocoa). The use of this technology in CIAT's ABP is not limited to these crops, but adaptable to Banana and many other crops. The CIAT's ABP has the potential to accelerate and disseminate the key targeted traits for biotic and abiotic stress tolerance, nutritional improvements, quality traits to meet the market demands, adding benefits to farmers and value chain actors on crops: Rice, Cassava, Beans, with emphasis on gene knockouts, or loss-of-function alleles, whose phenotypic consequences are functionally equivalent to total gene loss (Monroe et al., 2020Monroe J.G. Arciniegas J.P. Moreno J.L. Sanchez F. Sierra S. Valdes S. Torkamaneh D. Chavarriaga P. The lowest hanging fruit: Beneficial gene knockouts in past, present, and future crop evolution.Curr. Plant Biol. 2020; 24: 100185https://doi.org/10.1016/j.cpb.2020.100185Crossref Scopus (3) Google Scholar). To examine the feasibility of the CRISPR–Cas9-mediated GEd technology in rice, CIAT's ABP used the construct gDL-3 in the background of IR64, which causes the “drooping leaf” (DL) effect—the leaves appear droopy instead of upright. The effect of gene disruption was detected in the regenerated rice seedling through the DL effect, confirming the loss of function, which would be a visual indicator of the success of GEd technology (Alliance-CIAT Annual Report, 2018Alliance-CIAT Annual ReportBuilding a sustainable food future.https://ciat.cgiar.org/annual-report-2017-2018/Date: 2018Google Scholar). Li et al., 2016Li M. Li X. Zhou Z. Wu P. Fang M. Pan X. Lin Q. Luo W. Wu G. Li H. Reassessment of the four yield-related genes Gn1a, DEP1, GS3, and IPA1 in rice using a CRISPR/Cas9 system.Front. Plant Sci. 2016; 7: 377https://doi.org/10.3389/fpls.2016.00377Crossref PubMed Scopus (175) Google Scholar reported enhanced grain yield parameters (grain number) by individually knockout Gn1a in rice. Likewise, the platform currently editing the Gn1a gene in the Llanura 11, an upland variety in Latin America, which leads to increased grain number per panicle by 25% (unpublished data) compared to wild types (Figure 1). CIAT's ABP is also using the CRISPR–Cas9 to validate the two genes resistance to rice hoja blanca disease (white leaf rice virus), a major disease affecting rice production in Latin America. CIAT has more than 50 years of experience in pioneering cassava research and delivering smallholder farmers' innovations to transition out of poverty, especially in rural areas. In the last 20 years, CIAT continued its biotechnological efforts in cassava to improve the targeted traits of interest, such as biofortification of roots and leaves, improving resistance for Sri Lankan cassava mosaic virus, and haploid induction (Chavarriaga-Aguirre et al., 2016Chavarriaga-Aguirre P. Brand A. Medina A. Prias M. Escobar R. Martinez J. Díaz P. López C. Roca W. Tohme J. The potential of using biotechnology to improve cassava: a review.In Vitro Cell Dev. Biol. Plant. 2016; 52: 461-478https://doi.org/10.1007/s11627-016-9776-3Crossref PubMed Scopus (36) Google Scholar). CIAT signed an agreement with a multinational starch company to develop high yielding amylose-free starch varieties for industrial use in addition to the value-added traits. Currently, the CIAT's ABP is editing waxy gene to reproduce amylose-free natural mutations in commercial cultivars released in Asia and Colombia. CIAT, with decades of experience in beans, has developed and released several varieties that are high yielding, improved high iron and zinc, pest and disease resistant, able to tolerate heat, drought, low soil fertility, and competent with the market demands in Africa and Latin America and the Caribbean. CIAT's ABP explores the use of GEd to make the beans more digestible from its naturally occurring compounds, such as polysaccharides that cannot be broken down quickly in the digestive tract. Therefore, ABP adopted a protocol used in editing genes in soybean to edit genes in common beans that do not produce the indigestible polysaccharides. CRISPR–Cas9 technology has been used to knockout raffinose synthase and stachyose synthase genes that synthesize complex sugars in the cultivars, namely Chaucha-Chuga, Ica Quimbaya, and Calima. Cocoa is an essential crop in Central America and the Caribbean, where thousands of families earn livelihoods from the crop. In recent times, the emerging challenge comes with the high levels of cadmium (Cd2+) uptake in the Andean region, which reduces the competitiveness and inclusiveness of these growing cocoa sectors, as the new European food safety regulation on cadmium in cocoa and chocolate has become effective in January 2019. CIAT's regional project, Clima-LoCa, will address the challenges faced in the cocoa-growing sectors—Colombia, Ecuador, and Peru, and foster the development and implementation of low cadmium production climate-relevant practices that fit the cocoa smallholders. Ullah et al., 2018Ullah I. Wang Y. Eide D.J. Dunwell J.M. Evolution, and functional analysis of Natural Resistance-Associated Macrophage Proteins (NRAMPs) from Theobroma cacao and their role in cadmium accumulation.Sci. Rep. 2018; 8: 1-15https://doi.org/10.1038/s41598-018-32819-yCrossref PubMed Scopus (26) Google Scholar, reported five Natural Resistance-Associated Macrophage Proteins (NRAMP) genes in cocoa which are responsible for the uptake of (Cd2+) cations in the yeast cells. CIAT's ABP uses CRISPR–Cas9 to knockout an NRAMP5 gene in Colombian commercial cocoa varieties to improve the farmers' value chains. The alliance had its first Biosafety guidelines in July 1991, which was reviewed and complemented with the Center's Bio policy and approved by the board in December 2002. The Colombian Agricultural Institute (ICA), the equivalent of USDA, has granted CIAT a generic permit to generate, test transgenic and GEd plants for research in 2008. This authorization enables CIAT to conduct and evaluate transgenic plants' research in the laboratory and biosafety greenhouse upon reporting to the Colombian Biosafety authorities. Recently, CIAT is testing the agronomic performance and yield penalty of 20 GEd rice lines produced at the International Rice Research Institute (IRRI) through confined field testing in Colombia, and IRRI, Philippines. The field trials showed that the tested GEd rice lines did not show any significant yield reductions compared to wild type. CIAT's long experience in conducting confined field testing in Colombia and its strict biosafety protocols made the ICA declared that these GEd rice lines are equivalent to conventional cultivars, as in this case, they did not contain any foreign DNA. This approval will encourage the researchers in Colombia and its region to contemplate GEd crops use for smallholder farmers with a safe and affordable option. With phenomics is entering the “Big Data era” (Zhao et al., 2019Zhao C. Zhang Y. Du J. Guo X. Wen W. Gu S. Wang J. Fan J. Crop phenomics: current status and perspectives.Front. Plant Sci. 2019; 10: 714https://doi.org/10.3389/fpls.2019.00714Crossref PubMed Scopus (86) Google Scholar), crop physiologists need to exploit the wealth of GEd through high-throughput phenotyping technologies to interpret the gene function accurately. Therefore, characterizing the large set of genotypes in multiple timing points using non-invasive sensors and advanced computational platforms is very much needed. CIAT's field phenomics platform is a state-of-art high-throughput facility equipped with automated rain-out shelters and pheno-towers integrated with multispectral cameras and a terrestrial laser scanning system screening crops for water-use- and nitrogen-use-efficiency. The unmanned aerial vehicles, together with the automated system, allows repeated image capture at multiple time points and performs multi-parametric analysis of small and medium-sized plots. With the advancement in root phenomics technologies and extensive collaborations, CIAT uses ground-penetrating radar, a non-invasive technology, to study the growth dynamics of cassava storage root directly in the ield, which helps to predict the root biomass and early root bulking at real time (Delgado et al., 2017Delgado A. Hays D.B. Bruton R.K. Ceballos H. Novo A. Boi E. Selvaraj M.G. Ground penetrating radar: a case study for estimating root bulking rate in cassava (Manihot esculenta Crantz).Plant Methods. 2017; 13: 65https://doi.org/10.1186/s13007-017-0216-0Crossref PubMed Scopus (34) Google Scholar). The combination of CIAT's high-throughput phenotyping facilities—drones, satellites, field robotics (yet to come) machine learning, spatial data and analytics, cloud-based data and analysis platform (Pheno-i) (Selvaraj et al., 2020Selvaraj M.G. Valderrama M. Guzman D. Valencia M. Ruiz H. Acharjee A. Machine learning for high-throughput field phenotyping and image processing provides insight into the association of above and below-ground traits in cassava (Manihot esculenta Crantz).Plant Methods. 2020; 16: 87https://doi.org/10.1186/s13007-020-00625-1Crossref PubMed Scopus (11) Google Scholar), and GEd will help advance and speed up the development of high yielding crop varieties. We thank the Japanese National Institute of Agrobiological Sciences (NIAS) under National Agriculture and Food Research Organization (NARO), for bringing the genome editing technology to the Alliance of Bioversity International and CIAT. We thank ICA , Colombia, for their continuous guidance for the biosafety regulations in Colombia, and IICA for their support on genome editing communication and training in Latin America. A special thanks to the Alliance of Bioversity International and CIAT programs on Beans, Cassava, and Rice for including genome editing as a tool for breeding.