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van Zonneveld M.,Bioversity International | van Zonneveld M.,Ghent University | Scheldeman X.,Bioversity International | Escribano P.,Institute Hortofruticultura Subtropical y Mediterranea | And 8 more authors.
PLoS ONE | Year: 2012

There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at province and department level in Ecuador and Peru, respectively. © 2012 van Zonneveld et al.


Carrillo Zenteno M.D.,Instituto Nacional Autonomo Of Investigaciones Agropecuarias Iniap | De Freitas R.C.A.,Federal University of Viçosa | Fernandes R.B.A.,Federal University of Viçosa | Fontes M.P.F.,Federal University of Viçosa | Jordao C.P.,Federal University of Viçosa
Water, Air, and Soil Pollution | Year: 2013

Although Cd concentrations in uncontaminated soils are usually low, pollution of soils by Cd from different sources of contamination pose problems. The application of soil amendments to increase plant production has been used as a viable alternative for recovery of soils contaminated with Cd. However, emphasis needs to be placed on the nature of Cd sorption processes in order that the amendments can be managed appropriately. A range of materials including vermicompost, sugarcane filter cake, palm kernel pie, lime, phosphate rock, and zeolite were used for the sorption studies. Total and nonspecific Cd sorption was estimated by batch experiments, and specific sorption was obtained by the difference between the former and the latter. Best adsorbents for specific Cd sorption from soil amendments were lime and zeolite. Langmuir adsorption isotherms fitted reasonably well in the experimental data, and their constants were evaluated, with R 2 values from 0.80 to 0.99. The maximum adsorption capacity of Cd(II) was higher for mineral amendments than for organic amendments and ranged from 0.89 to 10.86 g kg-1. The small value (0.08 L mg-1) of the constant related to the energy of adsorption indicated that Cd was bound weakly to the palm kernel pie. Thermodynamic parameter, the Gibbs free energy, was calculated for each system, and the negative values obtained confirm that the adsorption processes were spontaneous. The values of separation factor, R L, which has been used to predict affinity between adsorbate and adsorbent were between 0 and 1, indicating that sorption was very favorable for Cd(II). © 2013 Springer Science+Business Media Dordrecht.


Morillo E.,Instituto Nacional Autonomo Of Investigaciones Agropecuarias Iniap | Morillo E.,IRD Montpellier | Second G.,IRD Montpellier
Plant Genetic Resources: Characterisation and Utilisation | Year: 2016

Andean arracacha (Arracacia xanthorrhiza Bancr.) is a valuable but poorly known vegetatively reproduced root crop whose origin is still unresolved. Wild tuberous forms are present in the presumed areas of domestication and have a perennial or monocarpic life history. To elucidate the origin of the cultivated form, we surveyed a molecular analysis with amplified fragment length polymorphisms (AFLPs) in a representative sample of this crop and its wild relatives from Ecuador and Peru, the presumed areas of domestication. Wild species with tuberous and non-tuberous roots were included, as well as the perennial and monocarpic forms of the presumed wild ancestor. While the two wild varieties of A. xanthorrhiza were closest to the cultivars, they were distinguished by AFLPs. Unexpectedly, two clearly distinct groups were formed among the cultivars, one of which was significantly closer to the monocarpic wild form. However, the chloroplast DNA survey revealed greater similarity between all of the cultivars and the wild perennial A. xanthorrhiza. These results combined with the morphological and life history features, confirms the hypothesis that arracacha domestication started from the wild perennial form. We suggest this scenario of domestication followed by an unsuspected introgression in the cultivation, resulting in two cryptic genetic groups, well distinguished at the molecular level. This is an important revelation with implications in genetic resource conservation and breeding standpoints in this promissory crop. © NIAB 2016


Motamayor J.C.,Mars Incorporated | Mockaitis K.,Indiana University | Schmutz J.,Mars Incorporated | Schmutz J.,HudsonAlpha Institute for Biotechnology | And 30 more authors.
Genome Biology | Year: 2013

Background: Theobroma cacao L. cultivar Matina 1-6 belongs to the most cultivated cacao type. The availability of its genome sequence and methods for identifying genes responsible for important cacao traits will aid cacao researchers and breeders.Results: We describe the sequencing and assembly of the genome of Theobroma cacao L. cultivar Matina. 1-6. The genome of the Matina 1-6 cultivar is 445 Mbp, which is significantly larger than a sequenced Criollo cultivar, and more typical of other cultivars. The chromosome-scale assembly, version 1.1, contains 711 scaffolds covering 346.0 Mbp, with a contig N50 of 84.4 kbp, a scaffold N50 of 34.4 Mbp, and an evidence-based gene set of 29,408 loci. Version 1.1 has 10x the scaffold N50 and 4x the contig N50 as Criollo, and includes 111 Mb more anchored sequence. The version 1.1 assembly has 4.4% gap sequence, while Criollo has 10.9%. Through a combination of haplotype, association mapping and gene expression analyses, we leverage this robust reference genome to identify a promising candidate gene responsible for pod color variation. We demonstrate that green/red pod color in cacao is likely regulated by the R2R3 MYB transcription factor TcMYB113, homologs of which determine pigmentation in Rosaceae, Solanaceae, and Brassicaceae. One SNP within the target site for a highly conserved trans-acting siRNA in dicots, found within TcMYB113, seems to affect transcript levels of this gene and therefore pod color variation.Conclusions: We report a high-quality sequence and annotation of Theobroma cacao L. and demonstrate its utility in identifying candidate genes regulating traits. © 2013 Motamayor et al.; licensee BioMed Central Ltd.


Zambrano J.L.,Ohio State University | Zambrano J.L.,Instituto Nacional Autonomo Of Investigaciones Agropecuarias Iniap | Jones M.W.,U.S. Department of Agriculture | Brenner E.,U.S. Department of Agriculture | And 3 more authors.
Theoretical and Applied Genetics | Year: 2014

Key message: Novel and previously known resistance loci for six phylogenetically diverse viruses were tightly clustered on chromosomes 2, 3, 6 and 10 in the multiply virus-resistant maize inbred line, Oh1VI. Virus diseases in maize can cause severe yield reductions that threaten crop production and food supplies in some regions of the world. Genetic resistance to different viruses has been characterized in maize populations in diverse environments using different screening techniques, and resistance loci have been mapped to all maize chromosomes. The maize inbred line, Oh1VI, is resistant to at least ten viruses, including viruses in five different families. To determine the genes and inheritance mechanisms responsible for the multiple virus resistance in this line, F1 hybrids, F2 progeny and a recombinant inbred line (RIL) population derived from a cross of Oh1VI and the virus-susceptible inbred line Oh28 were evaluated. Progeny were screened for their responses to Maize dwarf mosaic virus, Sugarcane mosaic virus, Wheat streak mosaic virus, Maize chlorotic dwarf virus, Maize fine streak virus, and Maize mosaic virus. Depending on the virus, dominant, recessive, or additive gene effects were responsible for the resistance observed in F1 plants. One to three gene models explained the observed segregation of resistance in the F2 generation for all six viruses. Composite interval mapping in the RIL population identified 17 resistance QTLs associated with the six viruses. Of these, 15 were clustered in specific regions of chr. 2, 3, 6, and 10. It is unknown whether these QTL clusters contain single or multiple virus resistance genes, but the coupling phase linkage of genes conferring resistance to multiple virus diseases in this population could facilitate breeding efforts to develop multi-virus resistant crops. © 2014 Springer-Verlag Berlin Heidelberg (outside the USA).


Delgado R.A.,Instituto Nacional Autonomo Of Investigaciones Agropecuarias Iniap | Delgado R.A.,Wageningen University | Monteros-Altamirano A.R.,Instituto Nacional Autonomo Of Investigaciones Agropecuarias Iniap | Monteros-Altamirano A.R.,Wageningen University | And 4 more authors.
Plant Pathology | Year: 2013

The population of Phytophthora infestans on potato landraces in three provinces (Carchi, Chimborazo and Loja) of Ecuador was analysed. All isolates (n = 66) were of the A1 mating type. Simple sequence repeats (SSR) were used to assess the genetic diversity of the isolates. The P. infestans isolates from the potato landraces grouped in a single clade together with reference isolates belonging to the clonal lineage EC-1. In the 66 SSR profiles obtained, 31 multilocus genotypes were identified. The 66 isolates constituted 49 different races according to the Solanum demissum differential set ( R1 to R11). The P. infestans population was complex and virulent on 4 to 11 R genes. Analysis showed that the subclonal variation in the Ecuadorian EC-1 clone is increasing over time and is much larger than clonal variation in lineages in the Netherlands and Nicaragua, suggesting high mutation rates and little or no selection in Ecuador. © 2013 British Society for Plant Pathology.


Zambrano J.L.,Ohio State University | Zambrano J.L.,Instituto Nacional Autonomo Of Investigaciones Agropecuarias Iniap | Jones M.W.,U.S. Department of Agriculture | Francis D.M.,Ohio State University | And 2 more authors.
Molecular Breeding | Year: 2014

Maize rayado fino virus (MRFV) causes one of the most important virus diseases of maize in regions of Mexico, Central and South America, where it causes moderate to severe yield losses. The virus is found from the southern USA to northern Argentina where its vector, the maize leafhopper Dalbulus maidis, is present. Although resistance to MRFV has been identified in tropical maize lines, little was known about genes or quantitative trait locus (QTL) conferring resistance to MRFV. In order to identify the location of genes conferring resistance to MRFV, two recombinant inbred line mapping populations that segregated for MRFV resistance were inoculated using viruliferous leafhoppers, and their responses to virus inoculation were evaluated under greenhouse conditions 7, 14 and 21 days post inoculation. A QTL explaining up to 23 % of the total phenotypic variance was mapped on chromosome 10 in both populations, with similar genetic and physical positions identified in the two populations. The magnitude of the QTL effect and the validation in two independent populations suggests that resistance to MFRV could be transferred into elite breeding lines to develop resistant cultivars. © 2014, Springer Science+Business Media Dordrecht (outside the USA).


Zambrano J.L.,Ohio State University | Zambrano J.L.,Instituto Nacional Autonomo Of Investigaciones Agropecuarias Iniap | Francis D.M.,OSU OARDC | Redinbaugh M.G.,U.S. Department of Agriculture
Plant Disease | Year: 2013

Maize rayado fino virus (MRFV) causes one of the most important virus diseases of maize in America. Severe yield losses, ranging from 10 to 50% in landraces to nearly 100% in contemporary cultivars, have been reported. Resistance has been reported in maize populations, but few resistant inbred lines have been identified. Maize inbred lines representing the range of diversity in the cultivated types and selected lines known to be resistant to other viruses were evaluated to identify novel sources of resistance to MRFV. The virus was transmitted to maize seedlings using the vector Dalbulus maidis, and disease incidence and severity were evaluated beginning 7 days postinoculation. Most of the 36 lines tested were susceptible to MRFV, with mean disease incidence ranging from 21 to 96%, and severity from 1.0 to 4.3 (using a 0 to 5 severity scale). A few genotypes, including CML333 and Ki11, showed intermediate levels of resistance, with 14 and 10% incidence, respectively. Novel sources of resistance, with incidence of less than 5% and severity ratings of 0.4 or less, included the inbred lines Oh1VI, CML287, and Cuba. In Oh1VI, resistance appeared to be dominant, and segregation of resistance in F2 plants was consistent with one or two resistance genes. The discovery of novel sources of resistance in maize inbred lines will facilitate the identification of virus resistance genes and their incorporation into breeding programs.


Redinbaugh M.G.,Ohio State University | Zambrano J.L.,Instituto Nacional Autonomo Of Investigaciones Agropecuarias Iniap
Advances in Virus Research | Year: 2014

Diseases caused by viruses are found throughout the maize-growing regions of the world and can cause significant losses for producers. In this review, virus diseases of maize and the pathogens that cause them are discussed. Factors leading to the spread of disease and measures for disease control are reviewed, as is our current knowledge of the genetics of virus resistance in this important crop. © 2014.


PubMed | Ohio State University and Instituto Nacional Autonomo Of Investigaciones Agropecuarias Iniap
Type: | Journal: Advances in virus research | Year: 2014

Diseases caused by viruses are found throughout the maize-growing regions of the world and can cause significant losses for producers. In this review, virus diseases of maize and the pathogens that cause them are discussed. Factors leading to the spread of disease and measures for disease control are reviewed, as is our current knowledge of the genetics of virus resistance in this important crop.

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