Joe Tohme

Colegio Bennett Cali Colombia, Santiago de Cali, Valle del Cauca, Colombia

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Publications (100)192.39 Total impact

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    ABSTRACT: More than two billion people are micronutrient deficient. Polished grains of popular rice varieties have concentration of approximately 2 μg g−1 iron (Fe) and 16 μg g−1 zinc (Zn). The HarvestPlus breeding programs for biofortified rice target 13 μg g−1 Fe and 28 μg g−1 Zn to reach approximately 30% of the estimated average requirement (EAR). Reports on engineering Fe content in rice have shown an increase up to 18 μg g−1 in glasshouse settings; in contrast, under field conditions, 4 μg g−1 was the highest reported concentration. Here, we report on selected transgenic events, field evaluated in two countries, showing 15 μg g−1 Fe and 45.7 μg g−1 Zn in polished grain. Rigorous selection was applied to 1,689 IR64 transgenic events for insert cleanliness and, trait and agronomic performances. Event NASFer-274 containing rice nicotianamine synthase (OsNAS2) and soybean ferritin (SferH-1) genes showed a single locus insertion without a yield penalty or altered grain quality. Endosperm Fe and Zn enrichment was visualized by X-ray fluorescence imaging. The Caco-2 cell assay indicated that Fe is bioavailable. No harmful heavy metals were detected in the grain. The trait remained stable in different genotype backgrounds.
    Full-text · Article · Jan 2016 · Scientific Reports
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    ABSTRACT: As global demand for livestock products (such as meat, milk, and eggs) is expected to double by 2050, necessary increases to future production must be reconciled with negative environmental impacts that livestock cause. This paper describes the LivestockPlus concept and demonstrates how the sowing of improved forages can lead to the sustainable intensification of mixed crop–forage–livestock–tree systems in the tropics by producing multiple social, economic, and environmental benefits. Sustainable intensification not only improves the productivity of tropical forage-based systems but also reduces the ecological footprint of livestock production and generates a diversity of ecosystem services (ES), such as improved soil quality and reduced erosion, sedimentation, and greenhouse gas (GHG) emissions. Integrating improved grass and legume forages into mixed production systems (crop–livestock, tree–livestock, crop–tree–livestock) can restore degraded lands and enhance system resilience to drought and waterlogging associated with climate change. When properly managed tropical forages accumulate large amounts of carbon in soil, fix atmospheric nitrogen (legumes), inhibit nitrification in soil and reduce nitrous oxide emissions (grasses), and reduce GHG emissions per unit livestock product. The LivestockPlus concept is defined as the sustainable intensification of forage-based systems, which is based on three interrelated intensification processes: genetic intensification – the development and use of superior grass and legume cultivars for increased livestock productivity; ecological intensification – the development and application of improved farm and natural resource management practices; and socioeconomic intensification – the improvement of local and national institutions and policies, which enable refinements of technologies and support their enduring use. Increases in livestock productivity will require coordinated efforts to develop supportive government, non-government organization, and private sector policies that foster investments and fair market compensation for both the products and ES provided. Effective research-for-development efforts that promote agricultural and environmental benefits of forage-based systems can contribute towards implemention of LivestockPlus across a variety of geographic, political, and socioeconomic contexts.
    Full-text · Technical Report · Oct 2015
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    ABSTRACT: Genomic selection (GS) is a promising strategy for enhancing genetic gain. We investigated the accuracy of genomic estimated breeding values (GEBV) in four inter-related synthetic populations that underwent several cycles of recurrent selection in an upland rice-breeding program. A total of 343 S2:4 lines extracted from those populations were phenotyped for flowering time, plant height, grain yield and panicle weight, and genotyped with an average density of one marker per 44.8 kb. The relative effect of the linkage disequilibrium (LD) and minor allele frequency (MAF) thresholds for selecting markers, the relative size of the training population (TP) and of the validation population (VP), the selected trait and the genomic prediction models (frequentist and Bayesian) on the accuracy of GEBVs was investigated in 540 cross validation experiments with 100 replicates. The effect of kinship between the training and validation populations was tested in an additional set of 840 cross validation experiments with a single genomic prediction model. LD was high (average r2 = 0.59 at 25 kb) and decreased slowly, distribution of allele frequencies at individual loci was markedly skewed toward unbalanced frequencies (MAF average value 15.2% and median 9.6%), and differentiation between the four synthetic populations was low (FST ≤0.06). The accuracy of GEBV across all cross validation experiments ranged from 0.12 to 0.54 with an average of 0.30. Significant differences in accuracy were observed among the different levels of each factor investigated. Phenotypic traits had the biggest effect, and the size of the incidence matrix had the smallest. Significant first degree interaction was observed for GEBV accuracy between traits and all the other factors studied, and between prediction models and LD, MAF and composition of the TP. The potential of GS to accelerate genetic gain and breeding options to increase the accuracy of predictions are discussed.
    Full-text · Article · Aug 2015 · PLoS ONE
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    ABSTRACT: Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.
    Full-text · Article · Jul 2015 · Frontiers in Plant Science
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    ABSTRACT: As global demand for livestock products (such as meat, milk and eggs) is expected to double by 2050, necessary in- creases to future production must be reconciled with negative environmental impacts that livestock cause. This paper describes the LivestockPlus concept and demonstrates how the sowing of improved forages can lead to the sustainable intensification of mixed crop-forage-livestock-tree systems in the tropics by producing multiple social, economic and environmental benefits. Sustainable intensification not only improves the productivity of tropical forage-based systems but also reduces the ecological footprint of livestock production and generates a diversity of ecosystem services (ES) such as improved soil quality and reduced erosion, sedimentation and greenhouse gas (GHG) emissions. Integrating improved grass and legume forages into mixed production systems (crop-livestock, tree-livestock, crop-tree-livestock) can restore degraded lands and enhance system resilience to drought and waterlogging associated with climate change. When properly managed tropical forages accumulate large amounts of carbon in soil, fix atmospheric nitrogen (legumes), inhibit nitrification in soil and reduce nitrous oxide emissions (grasses), and reduce GHG emissions per unit livestock product. The LivestockPlus concept is defined as the sustainable intensification of forage-based systems, which is based on 3 interrelated intensification processes: genetic intensification - the development and use of superior grass and legume cultivars for increased livestock productivity; ecological intensification - the development and application of improved farm and natural resource management practices; and socio-economic intensification - the improvement of local and national institutions and policies, which enable refinements of technologies and support their enduring use. Increases in livestock productivity will require coordinated efforts to develop supportive government, non-government organization and private sector policies that foster investments and fair market compensation for both the products and ES provided. Effective research-for-development efforts that promote agricultural and environmental benefits of forage- based systems can contribute towards implemention of LivestockPlus across a variety of geographic, political and socio-economic contexts.
    Full-text · Article · Jun 2015
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    ABSTRACT: Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.
    Full-text · Article · Apr 2015 · PLoS ONE
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    ABSTRACT: As global demand for livestock products (such as meat, milk and eggs) is expected to double by 2050, necessary increases to future production must be reconciled with negative environmental impacts that livestock cause. This paper describes the LivestockPlus concept and demonstrates how the sowing of improved forages can lead to the sustainable intensification of mixed crop-forage-livestock-tree systems in the tropics by producing multiple social, economic and environmental benefits. Sustainable intensification not only improves the productivity of tropical forage-based systems but also reduces the ecological footprint of livestock production and generates a diversity of ecosystem services (ES) such as improved soil quality and reduced erosion, sedimentation and greenhouse gas (GHG) emissions. Integrating improved grass and legume forages into mixed production systems (crop-livestock, tree-livestock, crop-tree-livestock) can restore degraded lands and enhance system resilience to drought and waterlogging associated with climate change. When properly managed tropical forages accumulate large amounts of carbon in soil, fix atmospheric nitrogen (legumes), inhibit nitrification in soil and reduce nitrous oxide emissions (grasses), and reduce GHG emissions per unit livestock product. The LivestockPlus concept is defined as the sustainable intensification of forage-based systems, which is based on 3 interrelated intensification processes: genetic intensification - the development and use of superior grass and legume cultivars for increased livestock productivity; ecological intensification - the development and application of improved farm and natural resource management practices; and socio-economic intensification - the improvement of local and national institutions and policies, which enable refinements of technologies and support their enduring use. Increases in livestock productivity will require coordinated efforts to develop supportive government, non-government organization and private sector policies that foster investments and fair market compensation for both the products and ES provided. Effective research-for-development efforts that promote agricultural and environmental benefits of forage-based systems can contribute towards implemention of LivestockPlus across a variety of geographic, political and socio-economic contexts.
    Full-text · Article · Jan 2015 · Tropical Grasslands
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    ABSTRACT: Many areas critical to agricultural production and research, such as the breeding and trait mapping in plants and livestock, require robust and scalable genotyping platforms. Genotyping-by-sequencing (GBS) is a one such method highly suited to non-human organisms. In the GBS protocol, genomic DNA is fractionated via restriction digest, then reduced representation is achieved through size selection. Since many restriction sites are conserved across a species, the sequenced portion of the genome is highly consistent within a population. This makes the GBS protocol highly suited for experiments that require surveying large numbers of markers within a population, such as those involving genetic mapping, breeding, and population genomics. We have modified the GBS technology in a number of ways. Custom, enzyme specific adaptors have been replaced with standard Illumina adaptors compatible with blunt-end restriction enzymes. Multiplexing is achieved through a dual barcoding system, and bead-based library preparation protocols allows for in-solution size selection and eliminates the need for columns and gels. A panel of eight restriction enzymes was selected for testing on B73 maize and Nipponbare rice genomic DNA. Quality of the data was demonstrated by identifying that the vast majority of reads from each enzyme aligned to restriction sites predicted in silico. The link between enzyme parameters and experimental outcome was demonstrated by showing that the sequenced portion of the genome was adaptable by selecting enzymes based on motif length, complexity, and methylation sensitivity. The utility of the new GBS protocol was demonstrated by correctly mapping several in a maize F2 population resulting from a B73 × Country Gentleman test cross. This technology is readily adaptable to different genomes, highly amenable to multiplexing and compatible with over forty commercially available restriction enzymes. These advancements represent a major improvement in genotyping technology by providing a highly flexible and scalable GBS that is readily implemented for studies on genome-wide variation.
    Full-text · Article · Nov 2014 · BMC Genomics
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    ABSTRACT: Rice breeding has made important contributions to Latin America. More than 400 cultivars were released from 1975 to 2012, which helped to raise total production to >27 million tonnes obtained from 5.7 million hectares (average for 2010-2012). Rice production provides ∼US$8.8 billion for thousands of farmers in Latin America and the Caribbean (LAC). The result of higher yields in the irrigated sector was to triple rice production in LAC while area did not grow, thus preserving more fragile environments. Several estimates on genetic gains for grain yield have been carried out in LAC. In temperate irrigated rice, the estimates are around 1.5-2.6% per year. In the tropical irrigated, it is ∼1% and in the upland rice the estimate is ∼1.4% per year. Different breeding strategies, including pedigree, modified bulk, recurrent selection methods, anther culture, interspecific crosses, composite populations, quantitative trait loci (QTL) introgression, and recombinant inbred lines, accompanied by shuttle breeding schemes, direct seeding, and evaluation/selection in hot spots for main diseases are being used by CIAT and NARES in the region. In this process, methods for screening for diseases and other stresses were established. Networking has been a cornerstone for success and several networks such as INGER, FLAR, and HIAAL were created. Looking forward, as farmers' yields are approaching the genetic yield potential exhibited by current cultivars, as a result of improved agronomic management, a new breakthrough is needed in terms of more productive cultivars. To achieve this goal, a strategy is needed that includes strong pipelines focused on specific environments and markets; better product profiling; integration between discovery, development, and delivery; and new breeding strategies using cutting-edge technologies and new breeding methods to accelerate genetic gains.
    Full-text · Book · Nov 2014
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    Full-text · Book · Oct 2014
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    ABSTRACT: Cassava, originally from South America, is the fourth most important source of calories in the developing world after the cereal crops wheat,maize, and rice.Worldwide, it feeds an estimated 700 million people directly or indirectly. Cassava production has increased steadily for the last 50 years, with 242 MT harvested in 2012. The increase is likely to continue as farmers in more than 105 countries come to recognize the crop’s advantages. A semi-perennial root crop, cassava can stay in the ground for up to 3 years. This makes it an excellent food security crop: when all other crops have been exhausted, cassava roots can still be harvested. It is naturally drought resistant and resilient to climatic changes, high temperatures, and poor soils, and in addition, cassava responds extremely well to high CO2 concentrations, making it a very important crop for the 21st century. Africa alone accounts for more than 55 % of the world’s production, and cassava is the first food crop in fresh tonnage before maize and plantain in sub-Saharan Africa. Cassava is also an important source of income, especially for women in sub-Saharan Africa (SSA). Furthermore, cassava is the second most important source of starch in the world. Cassava is thus a highly valuable crop for the world today and in the future. It is critical that it should not be compromised by viral diseases.
    Full-text · Article · May 2014 · Food Security
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    ABSTRACT: Since their initial discovery, transposons have been widely used as mutagens for forward and reverse genetic screens in a range of organisms. The problems of high copy number and sequence divergence among related transposons have often limited the efficiency at which tagged genes can be identified. A method was developed to identity the locations of Mutator (Mu) transposons in the Zea mays genome using a simple enrichment method combined with genome resequencing to identify transposon junction fragments. The sequencing library was prepared from genomic DNA by digesting with a restriction enzyme that cuts within a perfectly conserved motif of the Mu terminal inverted repeats (TIR). Paired-end reads containing Mu TIR sequences were computationally identified and chromosomal sequences flanking the transposon were mapped to the maize reference genome. This method has been used to identify Mu insertions in a number of alleles and to isolate the previously unidentified lazy plant1 (la1) gene. The la1 gene is required for the negatively gravitropic response of shoots and mutant plants lack the ability to sense gravity. Using bioinformatic and fluorescence microscopy approaches, we show that the la1 gene encodes a cell membrane and nuclear localized protein. Our Mu-Taq method is readily adaptable to identify the genomic locations of any insertion of a known sequence in any organism using any sequencing platform.
    Full-text · Article · Jan 2014 · PLoS ONE
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    ABSTRACT: Recent advances in high-throughput sequencing (HTS) technologies and computing capacity have produced unprecedented amounts of genomic data that have unraveled the genetics of phenotypic variability in several species. However, operating and integrating current software tools for data analysis still require important investments in highly skilled personnel. Developing accurate, efficient and user-friendly software packages for HTS data analysis will lead to a more rapid discovery of genomic elements relevant to medical, agricultural and industrial applications. We therefore developed Next-Generation Sequencing Eclipse Plug-in (NGSEP), a new software tool for integrated, efficient and user-friendly detection of single nucleotide variants (SNVs), indels and copy number variants (CNVs). NGSEP includes modules for read alignment, sorting, merging, functional annotation of variants, filtering and quality statistics. Analysis of sequencing experiments in yeast, rice and human samples shows that NGSEP has superior accuracy and efficiency, compared with currently available packages for variants detection. We also show that only a comprehensive and accurate identification of repeat regions and CNVs allows researchers to properly separate SNVs from differences between copies of repeat elements. We expect that NGSEP will become a strong support tool to empower the analysis of sequencing data in a wide range of research projects on different species.
    Full-text · Article · Jan 2014 · Nucleic Acids Research
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    Full-text · Article · Jan 2014 · Tropical Grasslands
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    ABSTRACT: Micronutrient malnutrition—also known as hidden hunger—is a growing public health concern that affects especially women and children in the developing world. Worldwide, at least 2 billion people suffer from vitamin A, iron, and zinc deficiencies. Here we review recent advances in the application of genomic approaches for biofortification of staple crops to enhance their nutritional quality and thus reduce ‘hidden hunger’. The application of genomic tools such as marker-assisted selection in conventional breeding or genetic modification offers sustainable and cost-effective ways to provide essential micronutrients (here provitamin A or iron) to people in developing countries. To maximize the benefits of genomic approaches for biofortification, we need to extend our understanding of the genetic control mechanisms and relative contribution from different rate-limiting steps for both provitamin A and iron accumulation in edible plant parts.
    No preview · Chapter · Jan 2014
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    Full-text · Article · Jan 2014 · Tropical Grasslands
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    ABSTRACT: Seed sterility and grain discoloration limit rice production in Colombia and several Central American countries. In samples of discolored rice seed grown in Colombian fields, the species Burkholderia glumae and B. gladioli were isolated, and field isolates were compared phenotypically. An artificial inoculation assay was used to determine that while both bacterial species cause symptoms on rice grains, B. glumae is a more aggressive pathogen, causing yield reduction and higher levels of grain sterility. To identify putative virulence genes differing between B. glumae and B. gladioli, four previously sequenced genomes of Asian and US strains of the two pathogens were compared with each other and with two draft genomes of Colombian B. glumae and B. gladioli isolates generated for this study. While previously characterized Burkholderia virulence factors are highly conserved between the two species, B. glumae and B. gladioli strains are predicted to encode distinct groups of genes encoding type VI secretion systems, transcriptional regulators, and membrane sensing proteins. This study shows that both B. glumae and B. gladioli can threaten grain quality although only one species affects yield. Furthermore, genotypic differences between the two strains are identified that could contribute to disease phenotypic differences.
    Full-text · Article · Nov 2013 · Phytopathology
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    ABSTRACT: The study of microRNAs (miRNAs) in plants has gained significant attention in recent years due to their regulatory role during development and in response to biotic and abiotic stresses. Although cassava (Manihot esculenta Crantz) is tolerant to drought and other adverse conditions, most cassava miRNAs have been predicted using bioinformatics alone or through sequencing of plants challenged by biotic stress. Here, we use high-throughput sequencing and different bioinformatics methods to identify potential cassava miRNAs expressed in different tissues subject to heat and drought conditions. We identified 60 miRNAs conserved in other plant species and 821 potential cassava-specific miRNAs. We also predicted 134 and 1002 potential target genes for these two sets of sequences. Using real time PCR, we verified the condition-specific expression of 5 cassava small RNAs relative to a non-stress control. We also found, using publicly available expression data, a significantly lower expression of the predicted target genes of conserved and nonconserved miRNAs under drought stress compared to other cassava genes. Gene Ontology enrichment analysis along with condition specific expression of predicted miRNA targets, allowed us to identify several interesting miRNAs which may play a role in stress-induced posttranscriptional regulation in cassava and other plants.
    Full-text · Article · Nov 2013 · International Journal of Genomics
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    ABSTRACT: DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates.Mol. Mar. Biol. Biotechnol. 3: 294-297. GILBERTSON, R. L.; ROJAS, M.R.; RUSSELL, D.; MAXWELL, D. P. 1991. The use of the asymmetric polymerase chain reaction and DNA sequencing to determinate genetic variability among isolates of bean golden mosaic geminivirus in the Dominican Republic. J. Gen. Virol. 72: 2843-2848. KATTAN, G. H.; FRANCO, P.; ROJAS, V.; MORALES, G. 2004. Biological diversification in a complex región: a spatial analysis of faunistic diversity and biogeography of the Andes of Colombia.
    Full-text · Conference Paper · Oct 2013

  • No preview · Article · Jan 2013

Publication Stats

2k Citations
192.39 Total Impact Points

Institutions

  • 2005-2015
    • Colegio Bennett Cali Colombia
      Santiago de Cali, Valle del Cauca, Colombia
    • International Atomic Energy Agency (IAEA)
      • FAO/IAEA Agriculture and Biotechnology Laboratories
      Vienna, Vienna, Austria
  • 2013
    • Michigan State University
      • Department of Plant Biology
      Ист-Лансинг, Michigan, United States
  • 2001
    • University of Nottingham
      • Division of Plant and Crop Sciences
      Nottigham, England, United Kingdom
  • 1999
    • University of Georgia
      Атина, Georgia, United States