Rebecca Nelson - Academia.edu (original) (raw)
Papers by Rebecca Nelson
World Mycotoxin Journal
Spectroscopy is a rapid, non-destructive, and low-cost analytical technique that has the potentia... more Spectroscopy is a rapid, non-destructive, and low-cost analytical technique that has the potential to complement more resource-intensive analytical methods. We explored the use of spectral methods to differentiate maize genotypes and assess aflatoxin (AF) contamination in maize kernels. We compared the performance of two instruments: a research-grade ultraviolet-visible-near infrared (UV-Vis-NIR) spectrometer that measures reflectance from 304 -1,085 nm, and a miniaturised NIR spectrometer that measures reflectance from 740-1,070 nm. Both systems were used to predict AF levels in maize kernels from a single genotype and across 10 genotypes, and to predict genotype for the latter. A partial least square discriminant analysis model was trained on 70% of the kernels and tested on the remaining 30%. The classification accuracy for 10 maize genotypes was 71-72% using the UV-Vis-NIR instrument on 1,170 kernels, and 65-66% using the NIR device on 740 kernels. The classification accuracy fo...
The Plant Phenome Journal, 2019
Food Control
The spatiotemporal trends in aflatoxin B1 (AFB1), fumonisin B1 (FB1), and deoxynivalenol (DON) ac... more The spatiotemporal trends in aflatoxin B1 (AFB1), fumonisin B1 (FB1), and deoxynivalenol (DON) accumulation were analyzed in a range of food commodities (maize, groundnut, pearl millet, rice, and wheat) in village settings in Unnao, Uttar Pradesh, India. Samples (n = 1549) were collected across six communities and six time points spanning a calendar year and were analyzed for mycotoxins using enzyme-linked immunosorbent assays. AFB1 and FB1 were common across surveyed villages, with moderate to high detection rates (45–75%) observed across commodities. AFB1 levels in maize and groundnuts and FB1 levels in maize and pearl millet frequently exceeded regulatory threshold levels of 15 μg/kg (AFB1) and 2 μg/g (FB1). DON was analyzed in wheat, with 3% of samples yielding detectable levels and none exceeding 1 μg/g. In rice, AFB1 levels were highest in the bran and husk and lower in the kernel. Commodity type significantly influenced AFB1 detection status, while commodity type, season, and visual quality influenced samples’ legal status. Storage characteristics and household socioeconomic status indicators did not have significant effects on contamination. No significant effects of any variables on FB1 detection or legal status were observed. Data on mycotoxin contamination, combined with data on local dietary intake, were used to estimate spatiotemporal mycotoxin exposure profiles. Estimated seasonal per capita exposure levels for AFB1 (5.4–39.3 ng/kg body weight/day) and FB1 (~0–2.4 μg/kg body weight/day) exceeded provisional maximum tolerable daily intake levels (1 ng/kg body weight/day for AFB1 and 2 μg/kg body weight/day for FB1) in some seasons and locations. This study demonstrates substantial dietary mycotoxin exposure risk in Unnao food systems and serves as an evidentiary foundation for participatory food safety intervention in the region.
Food Control, 2017
Maize, a staple food in many African countries including Kenya, is often contaminated by toxic an... more Maize, a staple food in many African countries including Kenya, is often contaminated by toxic and carcinogenic fungal secondary metabolites such as aflatoxins and fumonisins. This study evaluated the potential use of a low-cost, multi-spectral sorter in identification and removal of aflatoxin-and fumonisin-contaminated single kernels from a bulk of mature maize kernels. The machine was calibrated by building a mathematical model relating reflectance at nine distinct wavelengths (470-1,550 nm) to mycotoxin levels of single kernels collected from small-scale maize traders in open-air markets and from inoculated maize field trials in Eastern Kenya. Due to the expected skewed distribution of mycotoxin contamination, visual assessment of putative risk factors such as discoloration, moldiness, breakage, and fluorescence under ultraviolet light (365 nm), was used to enrich for mycotoxin-positive kernels used for calibration. Discriminant analysis calibration using both infrared and visible spectra achieved 77% sensitivity and 83% specificity to identify kernels with aflatoxin > 10 ng g-1 and fumonisin > 1,000 ng g-1 , respectively (measured by ELISA or UHPLC). In subsequent sorting of 46 market maize samples previously tested for mycotoxins, 0-25% of sample mass was rejected from samples that previously tested toxin-positive and 0-1% was rejected for previously toxin-negative samples. In most cases where mycotoxins were detected in sorted maize streams, accepted maize had lower mycotoxin levels than the rejected maize (21/25 accepted maize streams had lower aflatoxin than rejected streams, 25/27 accepted maize streams had lower fumonisin than rejected streams). Reduction was statistically significant (p<0.001), achieving an 83% mean reduction in each toxin. With further development, this technology could be used to sort maize at local hammer mills to reduce human mycotoxin exposure in Kenya, and elsewhere in the world, while at once reducing food loss, and improving food safety and nutritional status.
Plant Molecular Biology Reporter, 2007
Molecular Breeding, 1995
Rice blast, caused by Pyricularia grisea, is a major production constraint in many parts of the w... more Rice blast, caused by Pyricularia grisea, is a major production constraint in many parts of the world. The Korean rice variety Tongil showed high levels of resistance for about six years when widely planted under highly disease-conducive conditions, before becoming susceptible. Tongil was found to carry a single dominant gene, designated PilOt , conferring resistance to isolate 106 of the blast pathogen from the Philippines. We report here the use of bulked segregant RAPD analysis for rapid identification of DNA markers linked to PilOt. Pooled DNA extracts from five homozygous blast-resistant (RR) and five susceptible (rr) BC3F 2 plants, derived from a CO39 x Tongil cross, were analyzed by RFLP using 83 polymorphic probes and by RAPD using 468 random oligomers. We identified two RAPD markers linked to the PilOt locus: RRF6 (3.8 + 1.2 cM) and RRH18 (2.9 + 0.9 cM). Linkage of these markers with PilOt was verified using an F2 population segregating for PilOt. The two linked RAPD markers mapped 7 cM apart on chromosome 5. Chromosomal regions surrounding the Pi-10 t gene were examined with additional RFLP markers to define the segment introgressed from the donor genome. Pi-10t is likely to be a new blast-resistance locus, because no other known resistance gene has been mapped on chromosome 5. These tightly linked RAPD markers could facilitate early selection of the PilOt locus in rice breeding programmes.
Phytopathology, 2005
LATEBLIGHT, a mathematical model that simulates the effects of weather, host growth and resistanc... more LATEBLIGHT, a mathematical model that simulates the effects of weather, host growth and resistance, and fungicide use on asexual development and growth of Phytophthora infestans on potato foliage, was modified so that it can be used in the Andes and, eventually, worldwide. The modifications included (i) the incorporation of improved equations for the effect of temperature on lesion growth rate (LGR) and sporulation rate (SR); (ii) the incorporation of temperature-dependent latent period (LP); and (iii) the use of experimentally measured parameters of LGR, SR, and LP for specific potato cultivars and pathogen lineages. The model was parameterized for three Peruvian potato cultivars (Tomasa, Yungay, and Amarilis) infected with isolates of a new clonal lineage of P. infestans that is currently predominant in Ecuador and Peru (EC-1).
Applied and …, 1994
Several transposable elements were isolated from the genome of Xanthomonas oryzae pv. oryzae. The... more Several transposable elements were isolated from the genome of Xanthomonas oryzae pv. oryzae. These elements and an avirulence gene isolated from X. oryzae pv. oryzae were used as hybridization probes for a collection of X. oryzae pv. oryzae strains from the Philippines. Each of the sequences was present in multiple copies in all strains examined and showed distinct patterns of hybridizing bands. Phenograms were derived from the restriction fragment length polymorphism data obtained for each of the individual probes and for pooled data from multiple probes. The phenograms derived from the different probes differed in topology and, on the basis of bootstrap analysis, were not equally robust. For all of the probes, including the avirulence gene, some groups (even some haplotypes) consisted of multiple races. The strains were grouped into four major clusters on the basis of the two probes giving the highest bootstrap values. These groups were inferred to represent phylogenetic lineages. Three of the six races ofX. oryzae pv. oryzae appeared in more than one of the lineages, and another was present in two sublineages. For three of the races, strains representing different
Toxins
Fumonisin mycotoxins are a persistent challenge to human and livestock health in tropical and sub... more Fumonisin mycotoxins are a persistent challenge to human and livestock health in tropical and sub-tropical maize cropping systems, and more efficient methods are needed to reduce their presence in food systems. We constructed a novel, low-cost device for sorting grain, the “DropSort”, and tested its effectiveness on both plastic kernel models and fumonisin-contaminated maize. Sorting plastic kernels of known size and shape enabled us to optimize the sorting performance of the DropSort. The device sorted maize into three distinct fractions as measured by bulk density and 100-kernel weight. The level of fumonisin was lower in the heaviest fractions of maize compared to the unsorted samples. Based on correlations among fumonisin and bulk characteristics of each fraction, we found that light fraction 100-kernel weight could be an inexpensive proxy for unsorted fumonisin concentration. Single kernel analysis revealed significant relationships among kernel fumonisin content and physical c...
BMC Research Notes
Objectives: Advanced tools and resources are needed to efficiently and sustainably produce food f... more Objectives: Advanced tools and resources are needed to efficiently and sustainably produce food for an increasing world population in the context of variable environmental conditions. The maize genomes to fields (G2F) initiative is a multi-institutional initiative effort that seeks to approach this challenge by developing a flexible and distributed infrastructure addressing emerging problems. G2F has generated large-scale phenotypic, genotypic, and environmental datasets using publicly available inbred lines and hybrids evaluated through a network of collaborators that are part of the G2F's genotype-by-environment (G × E) project. This report covers the public release of datasets for 2014-2017. Data description: Datasets include inbred genotypic information; phenotypic, climatic, and soil measurements and metadata information for each testing location across years. For a subset of inbreds in 2014 and 2015, yield component phenotypes were quantified by image analysis. Data released are accompanied by README descriptions. For genotypic and phenotypic data, both raw data and a version without outliers are reported. For climatic data, a version calibrated to the nearest airport weather station and a version without outliers are reported.
established in 1975, provides research-based policy solutions to sustainably reduce poverty and e... more established in 1975, provides research-based policy solutions to sustainably reduce poverty and end hunger and malnutrition. IFPRI's strategic research aims to foster a climate-resilient and sustainable food supply; promote healthy diets and nutrition for all; build inclusive and efficient markets, trade systems, and food industries; transform agricultural and rural economies; and strengthen institutions and governance. Gender is integrated in all the Institute's work. Partnerships, communications, capacity strengthening, and data and knowledge management are essential components to translate IFPRI's research from action to impact. The Institute's regional and country programs play a critical role in responding to demand for food policy research and in delivering holistic support for country-led development. IFPRI collaborates with partners around the world.
Remote Sensing
Plant disease poses a serious threat to global food security. Accurate, high-throughput methods o... more Plant disease poses a serious threat to global food security. Accurate, high-throughput methods of quantifying disease are needed by breeders to better develop resistant plant varieties and by researchers to better understand the mechanisms of plant resistance and pathogen virulence. Northern leaf blight (NLB) is a serious disease affecting maize and is responsible for significant yield losses. A Mask R-CNN model was trained to segment NLB disease lesions in unmanned aerial vehicle (UAV) images. The trained model was able to accurately detect and segment individual lesions in a hold-out test set. The mean intersect over union (IOU) between the ground truth and predicted lesions was 0.73, with an average precision of 0.96 at an IOU threshold of 0.50. Over a range of IOU thresholds (0.50 to 0.95), the average precision was 0.61. This work demonstrates the potential for combining UAV technology with a deep learning-based approach for instance segmentation to provide accurate, high-thro...
International Journal of Agricultural Sustainability
Lupin (Lupinus mutabilis) is a unique grain legume that can thrive in the adverse conditions of t... more Lupin (Lupinus mutabilis) is a unique grain legume that can thrive in the adverse conditions of the Andean mountains during the dry season, improve soils and provide a food with superior levels of protein and essential fats that are deficient in the Andean diet. Although it is a component of traditional Andean cropping systems, lupin is currently underutilized. This paper examines how research and market innovations can propel this environmentally and nutritionally beneficial crop from a marginal role into greater prominence in Andean crop rotations, livelihoods and diets. A comprehensive study that included farmer surveys, market analysis and a business case study were employed to examine lupin production and supply chains in Ecuador.
Toxins
The fungus Fusarium verticillioides can infect maize ears, causing Fusarium ear rot (FER) and con... more The fungus Fusarium verticillioides can infect maize ears, causing Fusarium ear rot (FER) and contaminating the grain with fumonisins (FUM), which are harmful to humans and animals. Breeding for resistance to FER and FUM and post-harvest sorting of grain are two strategies for reducing FUM in the food system. Kernel and cob tissues have been previously associated with differential FER and FUM. Four recombinant inbred line families from the maize nested associated mapping population were grown and inoculated with F. verticillioides across four environments, and we evaluated the kernels for external and internal infection severity as well as FUM contamination. We also employed publicly available phenotypes on innate ear morphology to explore genetic relationships between ear architecture and resistance to FER and FUM. The four families revealed wide variation in external symptomatology at the phenotypic level. Kernel bulk density under inoculation was an accurate indicator of FUM leve...
G3: Genes|Genomes|Genetics
Southern Leaf Blight (SLB), Northern Leaf Blight (NLB), and Gray Leaf Spot (GLS) caused by Cochli... more Southern Leaf Blight (SLB), Northern Leaf Blight (NLB), and Gray Leaf Spot (GLS) caused by Cochliobolus heterostrophus, Setosphaeria turcica, and Cercospora zeae-maydis respectively, are among the most important diseases of corn worldwide. Previously, moderately high and significantly positive genetic correlations between resistance levels to each of these diseases were identified in a panel of 253 diverse maize inbred lines. The goal of this study was to identify loci underlying disease resistance in some of the most multiple disease resistant (MDR) lines by the creation of chromosome segment substitution line (CSSL) populations in multiple disease susceptible (MDS) backgrounds. Four MDR lines (NC304, NC344, Ki3, NC262) were used as donor parents and two MDS lines (Oh7B, H100) were used as recurrent parents to produce eight BC 3 F 4:5 CSSL populations comprising 1,611 lines in total. Each population was genotyped and assessed for each disease in replicated trials in two environments. Moderate to high heritabilities on an entry mean basis were observed (0.32 to 0.83). Several lines in each population were significantly more resistant than the MDS parental lines for each disease. Multiple quantitative trait loci (QTL) for disease resistance were detected for each disease in most of the populations. Seventeen QTL were associated with variation in resistance to more than one disease (SLB/NLB: 2; SLB/GLS: 7; NLB/GLS: 2 and 6 to all three diseases). For most populations and most disease combinations, significant correlations were observed between disease scores and also between marker effects for each disease. The number of lines that were resistant to more than one disease was significantly higher than would be expected by chance. Using the results from individual QTL analyses, a composite statistic based on Mahalanobis distance (Md) was used to identify joint marker associations with multiple diseases. Across all populations and diseases, 246 markers had significant Md values. However further analysis revealed that most of these associations were due to strong QTL effects on a single disease. Together, these findings reinforce our previous conclusions that loci associated with resistance to different diseases are clustered in the genome more often than would be expected by chance. Nevertheless true MDR loci which have significant effects on more than one disease are still much rarer than loci with single disease effects. KEYWORDS Maize disease resistance Multiple disease resistance QTL Genetic resistance is the most cost-effective and environment-friendly method for reducing losses in yield and quality in agricultural crops caused by plant disease. Disease resistance is often described in the literature as being either qualitative or quantitative. Qualitative disease resistance typically confers high levels of resistance and is generally controlled by a single or a few genes with major effects (Bent and Mackey
Phytopathology, Jan 10, 2018
The fungus Fusarium verticillioides can infect maize ears, contaminating the grain with mycotoxin... more The fungus Fusarium verticillioides can infect maize ears, contaminating the grain with mycotoxins, including fumonisins. This global public health threat can be managed by breeding maize varieties that are resistant to colonization by F. verticillioides and by sorting grain after harvest to reduce fumonisin levels in food systems. Here we employed two F. verticillioides inoculation techniques representing distinct infection pathways to dissect ear symptomatology and morphological resistance mechanisms in a diverse panel of maize inbred lines. The "point" method involved penetrating the ear with a spore-coated toothpick, and the "inundative" method introduced a liquid spore suspension under the husk of the ear. We evaluated quantitative and qualitative indicators of external and internal symptom severity as low-cost proxies for fumonisin contamination, and found that kernel bulk density was predictive of fumonisin levels (78-84% sensitivity; 97-99% specificity). ...
BMC research notes, Jan 9, 2018
Crop improvement relies on analysis of phenotypic, genotypic, and environmental data. Given large... more Crop improvement relies on analysis of phenotypic, genotypic, and environmental data. Given large, well-integrated, multi-year datasets, diverse queries can be made: Which lines perform best in hot, dry environments? Which alleles of specific genes are required for optimal performance in each environment? Such datasets also can be leveraged to predict cultivar performance, even in uncharacterized environments. The maize Genomes to Fields (G2F) Initiative is a multi-institutional organization of scientists working to generate and analyze such datasets from existing, publicly available inbred lines and hybrids. G2F's genotype by environment project has released 2014 and 2015 datasets to the public, with 2016 and 2017 collected and soon to be made available. Datasets include DNA sequences; traditional phenotype descriptions, as well as detailed ear, cob, and kernel phenotypes quantified by image analysis; weather station measurements; and soil characterizations by site. Data are re...
Phytopathology, 2018
Generating effective and stable strategies for resistance breeding requires an understanding of t... more Generating effective and stable strategies for resistance breeding requires an understanding of the genetics of host-pathogen interactions and the implications for pathogen dynamics and evolution. Setosphaeria turcica causes northern leaf blight (NLB), an important disease of maize for which major resistance genes have been deployed. Little is known about the evolutionary dynamics of avirulence (AVR) genes in S. turcica. To test the hypothesis that there is a genetic association between avirulence and in vitro development traits, we (i) created a genetic map of S. turcica, (ii) located candidate AVRHt1 and AVRHt2 regions, and (iii) identified genetic regions associated with several in vitro development traits. A cross was generated between a race 1 and a race 23N strain, and 221 progeny were isolated. Genotyping by sequencing was used to score 2,078 single-nucleotide polymorphism markers. A genetic map spanning 1,981 centimorgans was constructed, consisting of 21 linkage groups. Gen...
World Mycotoxin Journal
Spectroscopy is a rapid, non-destructive, and low-cost analytical technique that has the potentia... more Spectroscopy is a rapid, non-destructive, and low-cost analytical technique that has the potential to complement more resource-intensive analytical methods. We explored the use of spectral methods to differentiate maize genotypes and assess aflatoxin (AF) contamination in maize kernels. We compared the performance of two instruments: a research-grade ultraviolet-visible-near infrared (UV-Vis-NIR) spectrometer that measures reflectance from 304 -1,085 nm, and a miniaturised NIR spectrometer that measures reflectance from 740-1,070 nm. Both systems were used to predict AF levels in maize kernels from a single genotype and across 10 genotypes, and to predict genotype for the latter. A partial least square discriminant analysis model was trained on 70% of the kernels and tested on the remaining 30%. The classification accuracy for 10 maize genotypes was 71-72% using the UV-Vis-NIR instrument on 1,170 kernels, and 65-66% using the NIR device on 740 kernels. The classification accuracy fo...
The Plant Phenome Journal, 2019
Food Control
The spatiotemporal trends in aflatoxin B1 (AFB1), fumonisin B1 (FB1), and deoxynivalenol (DON) ac... more The spatiotemporal trends in aflatoxin B1 (AFB1), fumonisin B1 (FB1), and deoxynivalenol (DON) accumulation were analyzed in a range of food commodities (maize, groundnut, pearl millet, rice, and wheat) in village settings in Unnao, Uttar Pradesh, India. Samples (n = 1549) were collected across six communities and six time points spanning a calendar year and were analyzed for mycotoxins using enzyme-linked immunosorbent assays. AFB1 and FB1 were common across surveyed villages, with moderate to high detection rates (45–75%) observed across commodities. AFB1 levels in maize and groundnuts and FB1 levels in maize and pearl millet frequently exceeded regulatory threshold levels of 15 μg/kg (AFB1) and 2 μg/g (FB1). DON was analyzed in wheat, with 3% of samples yielding detectable levels and none exceeding 1 μg/g. In rice, AFB1 levels were highest in the bran and husk and lower in the kernel. Commodity type significantly influenced AFB1 detection status, while commodity type, season, and visual quality influenced samples’ legal status. Storage characteristics and household socioeconomic status indicators did not have significant effects on contamination. No significant effects of any variables on FB1 detection or legal status were observed. Data on mycotoxin contamination, combined with data on local dietary intake, were used to estimate spatiotemporal mycotoxin exposure profiles. Estimated seasonal per capita exposure levels for AFB1 (5.4–39.3 ng/kg body weight/day) and FB1 (~0–2.4 μg/kg body weight/day) exceeded provisional maximum tolerable daily intake levels (1 ng/kg body weight/day for AFB1 and 2 μg/kg body weight/day for FB1) in some seasons and locations. This study demonstrates substantial dietary mycotoxin exposure risk in Unnao food systems and serves as an evidentiary foundation for participatory food safety intervention in the region.
Food Control, 2017
Maize, a staple food in many African countries including Kenya, is often contaminated by toxic an... more Maize, a staple food in many African countries including Kenya, is often contaminated by toxic and carcinogenic fungal secondary metabolites such as aflatoxins and fumonisins. This study evaluated the potential use of a low-cost, multi-spectral sorter in identification and removal of aflatoxin-and fumonisin-contaminated single kernels from a bulk of mature maize kernels. The machine was calibrated by building a mathematical model relating reflectance at nine distinct wavelengths (470-1,550 nm) to mycotoxin levels of single kernels collected from small-scale maize traders in open-air markets and from inoculated maize field trials in Eastern Kenya. Due to the expected skewed distribution of mycotoxin contamination, visual assessment of putative risk factors such as discoloration, moldiness, breakage, and fluorescence under ultraviolet light (365 nm), was used to enrich for mycotoxin-positive kernels used for calibration. Discriminant analysis calibration using both infrared and visible spectra achieved 77% sensitivity and 83% specificity to identify kernels with aflatoxin > 10 ng g-1 and fumonisin > 1,000 ng g-1 , respectively (measured by ELISA or UHPLC). In subsequent sorting of 46 market maize samples previously tested for mycotoxins, 0-25% of sample mass was rejected from samples that previously tested toxin-positive and 0-1% was rejected for previously toxin-negative samples. In most cases where mycotoxins were detected in sorted maize streams, accepted maize had lower mycotoxin levels than the rejected maize (21/25 accepted maize streams had lower aflatoxin than rejected streams, 25/27 accepted maize streams had lower fumonisin than rejected streams). Reduction was statistically significant (p<0.001), achieving an 83% mean reduction in each toxin. With further development, this technology could be used to sort maize at local hammer mills to reduce human mycotoxin exposure in Kenya, and elsewhere in the world, while at once reducing food loss, and improving food safety and nutritional status.
Plant Molecular Biology Reporter, 2007
Molecular Breeding, 1995
Rice blast, caused by Pyricularia grisea, is a major production constraint in many parts of the w... more Rice blast, caused by Pyricularia grisea, is a major production constraint in many parts of the world. The Korean rice variety Tongil showed high levels of resistance for about six years when widely planted under highly disease-conducive conditions, before becoming susceptible. Tongil was found to carry a single dominant gene, designated PilOt , conferring resistance to isolate 106 of the blast pathogen from the Philippines. We report here the use of bulked segregant RAPD analysis for rapid identification of DNA markers linked to PilOt. Pooled DNA extracts from five homozygous blast-resistant (RR) and five susceptible (rr) BC3F 2 plants, derived from a CO39 x Tongil cross, were analyzed by RFLP using 83 polymorphic probes and by RAPD using 468 random oligomers. We identified two RAPD markers linked to the PilOt locus: RRF6 (3.8 + 1.2 cM) and RRH18 (2.9 + 0.9 cM). Linkage of these markers with PilOt was verified using an F2 population segregating for PilOt. The two linked RAPD markers mapped 7 cM apart on chromosome 5. Chromosomal regions surrounding the Pi-10 t gene were examined with additional RFLP markers to define the segment introgressed from the donor genome. Pi-10t is likely to be a new blast-resistance locus, because no other known resistance gene has been mapped on chromosome 5. These tightly linked RAPD markers could facilitate early selection of the PilOt locus in rice breeding programmes.
Phytopathology, 2005
LATEBLIGHT, a mathematical model that simulates the effects of weather, host growth and resistanc... more LATEBLIGHT, a mathematical model that simulates the effects of weather, host growth and resistance, and fungicide use on asexual development and growth of Phytophthora infestans on potato foliage, was modified so that it can be used in the Andes and, eventually, worldwide. The modifications included (i) the incorporation of improved equations for the effect of temperature on lesion growth rate (LGR) and sporulation rate (SR); (ii) the incorporation of temperature-dependent latent period (LP); and (iii) the use of experimentally measured parameters of LGR, SR, and LP for specific potato cultivars and pathogen lineages. The model was parameterized for three Peruvian potato cultivars (Tomasa, Yungay, and Amarilis) infected with isolates of a new clonal lineage of P. infestans that is currently predominant in Ecuador and Peru (EC-1).
Applied and …, 1994
Several transposable elements were isolated from the genome of Xanthomonas oryzae pv. oryzae. The... more Several transposable elements were isolated from the genome of Xanthomonas oryzae pv. oryzae. These elements and an avirulence gene isolated from X. oryzae pv. oryzae were used as hybridization probes for a collection of X. oryzae pv. oryzae strains from the Philippines. Each of the sequences was present in multiple copies in all strains examined and showed distinct patterns of hybridizing bands. Phenograms were derived from the restriction fragment length polymorphism data obtained for each of the individual probes and for pooled data from multiple probes. The phenograms derived from the different probes differed in topology and, on the basis of bootstrap analysis, were not equally robust. For all of the probes, including the avirulence gene, some groups (even some haplotypes) consisted of multiple races. The strains were grouped into four major clusters on the basis of the two probes giving the highest bootstrap values. These groups were inferred to represent phylogenetic lineages. Three of the six races ofX. oryzae pv. oryzae appeared in more than one of the lineages, and another was present in two sublineages. For three of the races, strains representing different
Toxins
Fumonisin mycotoxins are a persistent challenge to human and livestock health in tropical and sub... more Fumonisin mycotoxins are a persistent challenge to human and livestock health in tropical and sub-tropical maize cropping systems, and more efficient methods are needed to reduce their presence in food systems. We constructed a novel, low-cost device for sorting grain, the “DropSort”, and tested its effectiveness on both plastic kernel models and fumonisin-contaminated maize. Sorting plastic kernels of known size and shape enabled us to optimize the sorting performance of the DropSort. The device sorted maize into three distinct fractions as measured by bulk density and 100-kernel weight. The level of fumonisin was lower in the heaviest fractions of maize compared to the unsorted samples. Based on correlations among fumonisin and bulk characteristics of each fraction, we found that light fraction 100-kernel weight could be an inexpensive proxy for unsorted fumonisin concentration. Single kernel analysis revealed significant relationships among kernel fumonisin content and physical c...
BMC Research Notes
Objectives: Advanced tools and resources are needed to efficiently and sustainably produce food f... more Objectives: Advanced tools and resources are needed to efficiently and sustainably produce food for an increasing world population in the context of variable environmental conditions. The maize genomes to fields (G2F) initiative is a multi-institutional initiative effort that seeks to approach this challenge by developing a flexible and distributed infrastructure addressing emerging problems. G2F has generated large-scale phenotypic, genotypic, and environmental datasets using publicly available inbred lines and hybrids evaluated through a network of collaborators that are part of the G2F's genotype-by-environment (G × E) project. This report covers the public release of datasets for 2014-2017. Data description: Datasets include inbred genotypic information; phenotypic, climatic, and soil measurements and metadata information for each testing location across years. For a subset of inbreds in 2014 and 2015, yield component phenotypes were quantified by image analysis. Data released are accompanied by README descriptions. For genotypic and phenotypic data, both raw data and a version without outliers are reported. For climatic data, a version calibrated to the nearest airport weather station and a version without outliers are reported.
established in 1975, provides research-based policy solutions to sustainably reduce poverty and e... more established in 1975, provides research-based policy solutions to sustainably reduce poverty and end hunger and malnutrition. IFPRI's strategic research aims to foster a climate-resilient and sustainable food supply; promote healthy diets and nutrition for all; build inclusive and efficient markets, trade systems, and food industries; transform agricultural and rural economies; and strengthen institutions and governance. Gender is integrated in all the Institute's work. Partnerships, communications, capacity strengthening, and data and knowledge management are essential components to translate IFPRI's research from action to impact. The Institute's regional and country programs play a critical role in responding to demand for food policy research and in delivering holistic support for country-led development. IFPRI collaborates with partners around the world.
Remote Sensing
Plant disease poses a serious threat to global food security. Accurate, high-throughput methods o... more Plant disease poses a serious threat to global food security. Accurate, high-throughput methods of quantifying disease are needed by breeders to better develop resistant plant varieties and by researchers to better understand the mechanisms of plant resistance and pathogen virulence. Northern leaf blight (NLB) is a serious disease affecting maize and is responsible for significant yield losses. A Mask R-CNN model was trained to segment NLB disease lesions in unmanned aerial vehicle (UAV) images. The trained model was able to accurately detect and segment individual lesions in a hold-out test set. The mean intersect over union (IOU) between the ground truth and predicted lesions was 0.73, with an average precision of 0.96 at an IOU threshold of 0.50. Over a range of IOU thresholds (0.50 to 0.95), the average precision was 0.61. This work demonstrates the potential for combining UAV technology with a deep learning-based approach for instance segmentation to provide accurate, high-thro...
International Journal of Agricultural Sustainability
Lupin (Lupinus mutabilis) is a unique grain legume that can thrive in the adverse conditions of t... more Lupin (Lupinus mutabilis) is a unique grain legume that can thrive in the adverse conditions of the Andean mountains during the dry season, improve soils and provide a food with superior levels of protein and essential fats that are deficient in the Andean diet. Although it is a component of traditional Andean cropping systems, lupin is currently underutilized. This paper examines how research and market innovations can propel this environmentally and nutritionally beneficial crop from a marginal role into greater prominence in Andean crop rotations, livelihoods and diets. A comprehensive study that included farmer surveys, market analysis and a business case study were employed to examine lupin production and supply chains in Ecuador.
Toxins
The fungus Fusarium verticillioides can infect maize ears, causing Fusarium ear rot (FER) and con... more The fungus Fusarium verticillioides can infect maize ears, causing Fusarium ear rot (FER) and contaminating the grain with fumonisins (FUM), which are harmful to humans and animals. Breeding for resistance to FER and FUM and post-harvest sorting of grain are two strategies for reducing FUM in the food system. Kernel and cob tissues have been previously associated with differential FER and FUM. Four recombinant inbred line families from the maize nested associated mapping population were grown and inoculated with F. verticillioides across four environments, and we evaluated the kernels for external and internal infection severity as well as FUM contamination. We also employed publicly available phenotypes on innate ear morphology to explore genetic relationships between ear architecture and resistance to FER and FUM. The four families revealed wide variation in external symptomatology at the phenotypic level. Kernel bulk density under inoculation was an accurate indicator of FUM leve...
G3: Genes|Genomes|Genetics
Southern Leaf Blight (SLB), Northern Leaf Blight (NLB), and Gray Leaf Spot (GLS) caused by Cochli... more Southern Leaf Blight (SLB), Northern Leaf Blight (NLB), and Gray Leaf Spot (GLS) caused by Cochliobolus heterostrophus, Setosphaeria turcica, and Cercospora zeae-maydis respectively, are among the most important diseases of corn worldwide. Previously, moderately high and significantly positive genetic correlations between resistance levels to each of these diseases were identified in a panel of 253 diverse maize inbred lines. The goal of this study was to identify loci underlying disease resistance in some of the most multiple disease resistant (MDR) lines by the creation of chromosome segment substitution line (CSSL) populations in multiple disease susceptible (MDS) backgrounds. Four MDR lines (NC304, NC344, Ki3, NC262) were used as donor parents and two MDS lines (Oh7B, H100) were used as recurrent parents to produce eight BC 3 F 4:5 CSSL populations comprising 1,611 lines in total. Each population was genotyped and assessed for each disease in replicated trials in two environments. Moderate to high heritabilities on an entry mean basis were observed (0.32 to 0.83). Several lines in each population were significantly more resistant than the MDS parental lines for each disease. Multiple quantitative trait loci (QTL) for disease resistance were detected for each disease in most of the populations. Seventeen QTL were associated with variation in resistance to more than one disease (SLB/NLB: 2; SLB/GLS: 7; NLB/GLS: 2 and 6 to all three diseases). For most populations and most disease combinations, significant correlations were observed between disease scores and also between marker effects for each disease. The number of lines that were resistant to more than one disease was significantly higher than would be expected by chance. Using the results from individual QTL analyses, a composite statistic based on Mahalanobis distance (Md) was used to identify joint marker associations with multiple diseases. Across all populations and diseases, 246 markers had significant Md values. However further analysis revealed that most of these associations were due to strong QTL effects on a single disease. Together, these findings reinforce our previous conclusions that loci associated with resistance to different diseases are clustered in the genome more often than would be expected by chance. Nevertheless true MDR loci which have significant effects on more than one disease are still much rarer than loci with single disease effects. KEYWORDS Maize disease resistance Multiple disease resistance QTL Genetic resistance is the most cost-effective and environment-friendly method for reducing losses in yield and quality in agricultural crops caused by plant disease. Disease resistance is often described in the literature as being either qualitative or quantitative. Qualitative disease resistance typically confers high levels of resistance and is generally controlled by a single or a few genes with major effects (Bent and Mackey
Phytopathology, Jan 10, 2018
The fungus Fusarium verticillioides can infect maize ears, contaminating the grain with mycotoxin... more The fungus Fusarium verticillioides can infect maize ears, contaminating the grain with mycotoxins, including fumonisins. This global public health threat can be managed by breeding maize varieties that are resistant to colonization by F. verticillioides and by sorting grain after harvest to reduce fumonisin levels in food systems. Here we employed two F. verticillioides inoculation techniques representing distinct infection pathways to dissect ear symptomatology and morphological resistance mechanisms in a diverse panel of maize inbred lines. The "point" method involved penetrating the ear with a spore-coated toothpick, and the "inundative" method introduced a liquid spore suspension under the husk of the ear. We evaluated quantitative and qualitative indicators of external and internal symptom severity as low-cost proxies for fumonisin contamination, and found that kernel bulk density was predictive of fumonisin levels (78-84% sensitivity; 97-99% specificity). ...
BMC research notes, Jan 9, 2018
Crop improvement relies on analysis of phenotypic, genotypic, and environmental data. Given large... more Crop improvement relies on analysis of phenotypic, genotypic, and environmental data. Given large, well-integrated, multi-year datasets, diverse queries can be made: Which lines perform best in hot, dry environments? Which alleles of specific genes are required for optimal performance in each environment? Such datasets also can be leveraged to predict cultivar performance, even in uncharacterized environments. The maize Genomes to Fields (G2F) Initiative is a multi-institutional organization of scientists working to generate and analyze such datasets from existing, publicly available inbred lines and hybrids. G2F's genotype by environment project has released 2014 and 2015 datasets to the public, with 2016 and 2017 collected and soon to be made available. Datasets include DNA sequences; traditional phenotype descriptions, as well as detailed ear, cob, and kernel phenotypes quantified by image analysis; weather station measurements; and soil characterizations by site. Data are re...
Phytopathology, 2018
Generating effective and stable strategies for resistance breeding requires an understanding of t... more Generating effective and stable strategies for resistance breeding requires an understanding of the genetics of host-pathogen interactions and the implications for pathogen dynamics and evolution. Setosphaeria turcica causes northern leaf blight (NLB), an important disease of maize for which major resistance genes have been deployed. Little is known about the evolutionary dynamics of avirulence (AVR) genes in S. turcica. To test the hypothesis that there is a genetic association between avirulence and in vitro development traits, we (i) created a genetic map of S. turcica, (ii) located candidate AVRHt1 and AVRHt2 regions, and (iii) identified genetic regions associated with several in vitro development traits. A cross was generated between a race 1 and a race 23N strain, and 221 progeny were isolated. Genotyping by sequencing was used to score 2,078 single-nucleotide polymorphism markers. A genetic map spanning 1,981 centimorgans was constructed, consisting of 21 linkage groups. Gen...