Instituto Nacional Of Innovacion Agraria Inia

Cusco, Peru

Instituto Nacional Of Innovacion Agraria Inia

Cusco, Peru
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Lozano I.,Agrobiodiversity Research Area AgBio | Leiva A.M.,Agrobiodiversity Research Area AgBio | Leiva A.M.,National University of Colombia | Jimenez J.,Agrobiodiversity Research Area AgBio | And 5 more authors.
Virus Research | Year: 2016

Several potexviruses (Family Alphaflexiviridae) have been reported infecting cassava (Manihot esculenta Crantz) in the Americas. They were isolated from severely diseased plants during the last 30-40 years and include: Cassava common mosaic virus (CsCMV), Cassava Caribbean mosaic virus (CsCaMV), Cassava Colombian symptomless virus (CsCSV) and Cassava virus X (CsVX). However, their definitive classification as distinct species remains unresolved for several reasons, including the lack of sequence data and unavailability of samples from original isolates. This complicates disease diagnostics, cassava germplasm exchange certification, evaluation of virus cleaning protocols and epidemiological studies. Furthermore, a recently detected novel alphaflexivirus, indicates that cassava-infecting potexviruses may be more diverse. To solve the identity of these viruses, we started indexing samples from different parts of Colombia using different sets of PCR primers, antisera available and inoculation to indicator plants. Results show that there are three major phylogenetic groups of potexviruses infecting cassava, and they correspond to CsCMV, CsVX and the newly identified Cassava new alphaflexivirus (CsNAV). Bioassays and sequence analysis established that isolates of CsNAV and CsVX cause latent infections in different cassava landraces, they are not efficiently transmitted to the indicator plant Nicotiana benthamiana and they lack the gene 3 of the conserved potexviral 'triple gene block' (TGB). In contrast, all isolates of CsCMV (which have a characteristic potexvirus genome arrangement) caused Cassava Common Mosaic Disease (CCMD) in single infections and were efficiently transmitted to N. benthamiana. Although phylogenetic analysis of the replicase sequence placed CsNAV and CsVX as members of the Potexvirus genus, their distinct genome arrangement and biological characteristics suggest they can be considered as members of a separate taxonomic group. © 2017.


Fernandez E.,Instituto Nacional Of Innovacion Agraria Inia | Espinoza I.,Trujillo National University | Lozano I.,Agrobiodiversity Research Area AgBio | Bolanos C.,Agrobiodiversity Research Area AgBio | And 2 more authors.
Plant Disease | Year: 2017

Cassava common mosaic disease (CCMD) can cause root yield losses of approximately 30% (Venturini et al. 2016) in cassava (Manihot esculenta Crantz) and it has already been reported in Brazil, Colombia, Paraguay, and Argentina (Calvert et al. 2012; Di Feo et al. 2015). Most of Peru’s cassava production is in the eastern side of the country (the rainforest region) and is mainly used for direct human consumption. Cultivated area in these regions is approximately 48.1 thousand hectares (MINAGRI 2015). CCMD is caused by Cassava common mosaic virus (CsCMV; Calvert et al. 1996), a mechanically transmitted potexvirus that can be disseminated via infected stem cuttings used for cassava propagation. Given the presence of the disease in neighboring countries, a field survey for virus diseases in cassava was organized during June 2016 in the province of Huaral, in the central coast of Peru, where typical leaf mosaic and leaf deformation symptoms associated to CCMD were observed in local cassava varieties. To verify the presence of CsCMV and CCMD in Peru, the youngest leaves of four plants showing virus-like symptoms and four plants not showing symptoms were collected from one of the affected fields and dried in silica gel for analysis. Double antibody sandwich (DAS)-ELISA tests using a polyclonal antiserum readily detected CsCMV in all symptomatic samples (Nolt et al. 1991). In addition, mechanical transmissions to the experimental host Nicotiana benthamiana induced typical systemic leaf mosaic. RT-PCR tests targeting the replicase region of CsCMV were carried out using primers CsCMV-3269-F: 5′-GAGGCTCTTCTCTGGGAAAC-3′ and CsCMV-3896-R: 5′-CTTGAGTCCAGTTTGATGTC-3′, designed using an alignment of CsCMV-related sequences available in GenBank. An expected PCR fragment of 627 bp was obtained only in samples showing symptoms of CCMD. RT-PCR tests for other cassava-infecting viruses reported in the Americas (Carvajal-Yepes et al. 2014) were negative in these samples. PCR products from two independent CsCMV-positive samples were sent for direct Sanger-sequencing (Macrogen, Korea). CsCMV sequence isolates from Peru (GenBank accession nos. KX964625 and KX964626) show a nucleotide identity of 88 to 93%, and an amino acid sequence identity of 99% with other CsCMV sequences available in GenBank, and phylogenetic analysis clustered Peruvian isolates with CsCMV sequences reported in cassava. These results stress the need to implement surveillance activities and quick diagnostic protocols, as the inadvertent propagation and accumulation of virus infections could cause an increasingly negative effect on cassava and other vegetatively propagated crops. © 2017, American Phytopathological Society. All rights reserved.


PubMed | Fundacion Promocion e Investigacion de Productos Andinos PROINPA, University of Wuppertal, Instituto Nacional Of Innovacion Agraria Inia, Bioversity International and Inter American Institute for Cooperation on Agriculture IICA
Type: Journal Article | Journal: PloS one | Year: 2015

For most crops, like Capsicum, their diversity remains under-researched for traits of interest for food, nutrition and other purposes. A small investment in screening this diversity for a wide range of traits is likely to reveal many traditional varieties with distinguished values. One objective of this study was to demonstrate, with Capsicum as model crop, the application of indicators of phenotypic and geographic diversity as effective criteria for selecting promising genebank accessions for multiple uses from crop centers of diversity. A second objective was to evaluate the expression of biochemical and agromorphological properties of the selected Capsicum accessions in different conditions. Four steps were involved: 1) Develop the necessary diversity by expanding genebank collections in Bolivia and Peru; 2) Establish representative subsets of ~100 accessions for biochemical screening of Capsicum fruits; 3) Select promising accessions for different uses after screening; and 4) Examine how these promising accessions express biochemical and agromorphological properties when grown in different environmental conditions. The Peruvian Capsicum collection now contains 712 accessions encompassing all five domesticated species (C. annuum, C. chinense, C. frutescens, C. baccatum, and C. pubescens). The collection in Bolivia now contains 487 accessions, representing all five domesticates plus four wild taxa (C. baccatum var. baccatum, C. caballeroi, C. cardenasii, and C. eximium). Following the biochemical screening, 44 Bolivian and 39 Peruvian accessions were selected as promising, representing wide variation in levels of antioxidant capacity, capsaicinoids, fat, flavonoids, polyphenols, quercetins, tocopherols, and color. In Peru, 23 promising accessions performed well in different environments, while each of the promising Bolivian accessions only performed well in a certain environment. Differences in Capsicum diversity and local contexts led to distinct outcomes in each country. In Peru, mild landraces with high values in health-related attributes were of interest to entrepreneurs. In Bolivia, wild Capsicum have high commercial demand.


Castro J.C.,National University of San Juan | Maddox J.D.,Pritzker Laboratory for Molecular Systematics and Evolution | Cobos M.,University Cientifica del Peru | Requena D.,Cayetano Heredia Peruvian University | And 5 more authors.
BMC Genomics | Year: 2015

Background: Myrciaria dubia is an Amazonian fruit shrub that produces numerous bioactive phytochemicals, but is best known by its high L-ascorbic acid (AsA) content in fruits. Pronounced variation in AsA content has been observed both within and among individuals, but the genetic factors responsible for this variation are largely unknown. The goals of this research, therefore, were to assemble, characterize, and annotate the fruit transcriptome of M. dubia in order to reconstruct metabolic pathways and determine if multiple pathways contribute to AsA biosynthesis. Results: In total 24,551,882 high-quality sequence reads were de novo assembled into 70,048 unigenes (mean length = 1150 bp, N50 = 1775 bp). Assembled sequences were annotated using BLASTX against public databases such as TAIR, GR-protein, FB, MGI, RGD, ZFIN, SGN, WB, TIGR_CMR, and JCVI-CMR with 75.2 % of unigenes having annotations. Of the three core GO annotation categories, biological processes comprised 53.6 % of the total assigned annotations, whereas cellular components and molecular functions comprised 23.3 and 23.1 %, respectively. Based on the KEGG pathway assignment of the functionally annotated transcripts, five metabolic pathways for AsA biosynthesis were identified: animal-like pathway, myo-inositol pathway, L-gulose pathway, D-mannose/L-galactose pathway, and uronic acid pathway. All transcripts coding enzymes involved in the ascorbate-glutathione cycle were also identified. Finally, we used the assembly to identified 6314 genic microsatellites and 23,481 high quality SNPs. Conclusions: This study describes the first next-generation sequencing effort and transcriptome annotation of a non-model Amazonian plant that is relevant for AsA production and other bioactive phytochemicals. Genes encoding key enzymes were successfully identified and metabolic pathways involved in biosynthesis of AsA, anthocyanins, and other metabolic pathways have been reconstructed. The identification of these genes and pathways is in agreement with the empirically observed capability of M. dubia to synthesize and accumulate AsA and other important molecules, and adds to our current knowledge of the molecular biology and biochemistry of their production in plants. By providing insights into the mechanisms underpinning these metabolic processes, these results can be used to direct efforts to genetically manipulate this organism in order to enhance the production of these bioactive phytochemicals. The accumulation of AsA precursor and discovery of genes associated with their biosynthesis and metabolism in M. dubia is intriguing and worthy of further investigation. The sequences and pathways produced here present the genetic framework required for further studies. Quantitative transcriptomics in concert with studies of the genome, proteome, and metabolome under conditions that stimulate production and accumulation of AsA and their precursors are needed to provide a more comprehensive view of how these pathways for AsA metabolism are regulated and linked in this species. © 2015 Castro et al.


PubMed | Pritzker Laboratory for Molecular Systematics and Evolution, National University of San Juan, Virginia Polytechnic Institute and State University, Instituto Nacional Of Innovacion Agraria Inia and 2 more.
Type: | Journal: BMC genomics | Year: 2015

Myrciaria dubia is an Amazonian fruit shrub that produces numerous bioactive phytochemicals, but is best known by its high L-ascorbic acid (AsA) content in fruits. Pronounced variation in AsA content has been observed both within and among individuals, but the genetic factors responsible for this variation are largely unknown. The goals of this research, therefore, were to assemble, characterize, and annotate the fruit transcriptome of M. dubia in order to reconstruct metabolic pathways and determine if multiple pathways contribute to AsA biosynthesis.In total 24,551,882 high-quality sequence reads were de novo assembled into 70,048 unigenes (mean length = 1150 bp, N50 = 1775 bp). Assembled sequences were annotated using BLASTX against public databases such as TAIR, GR-protein, FB, MGI, RGD, ZFIN, SGN, WB, TIGR_CMR, and JCVI-CMR with 75.2 % of unigenes having annotations. Of the three core GO annotation categories, biological processes comprised 53.6 % of the total assigned annotations, whereas cellular components and molecular functions comprised 23.3 and 23.1 %, respectively. Based on the KEGG pathway assignment of the functionally annotated transcripts, five metabolic pathways for AsA biosynthesis were identified: animal-like pathway, myo-inositol pathway, L-gulose pathway, D-mannose/L-galactose pathway, and uronic acid pathway. All transcripts coding enzymes involved in the ascorbate-glutathione cycle were also identified. Finally, we used the assembly to identified 6314 genic microsatellites and 23,481 high quality SNPs.This study describes the first next-generation sequencing effort and transcriptome annotation of a non-model Amazonian plant that is relevant for AsA production and other bioactive phytochemicals. Genes encoding key enzymes were successfully identified and metabolic pathways involved in biosynthesis of AsA, anthocyanins, and other metabolic pathways have been reconstructed. The identification of these genes and pathways is in agreement with the empirically observed capability of M. dubia to synthesize and accumulate AsA and other important molecules, and adds to our current knowledge of the molecular biology and biochemistry of their production in plants. By providing insights into the mechanisms underpinning these metabolic processes, these results can be used to direct efforts to genetically manipulate this organism in order to enhance the production of these bioactive phytochemicals. The accumulation of AsA precursor and discovery of genes associated with their biosynthesis and metabolism in M. dubia is intriguing and worthy of further investigation. The sequences and pathways produced here present the genetic framework required for further studies. Quantitative transcriptomics in concert with studies of the genome, proteome, and metabolome under conditions that stimulate production and accumulation of AsA and their precursors are needed to provide a more comprehensive view of how these pathways for AsA metabolism are regulated and linked in this species.


Arias N.,University of Veterinary Medicine Vienna | Arias N.,Cayetano Heredia Peruvian University | Requena M.,Instituto Nacional Of Innovacion Agraria Inia | Palme R.,University of Veterinary Medicine Vienna
Animal Welfare | Year: 2013

The welfare and productivity of South American camelids may be affected by stressful events. The purpose of this study was to validate a non-invasive method for stress monitoring using faecal samples and to apply it to evaluate a stressful event, such as confinement. For physiological validation, nine alpacas (Vicugna pacos) and six llamas (Lama glama) were subjected to pharmacological stimulation of their adrenal cortex. Serial faecal samples were collected during 48 h before and after stimulation. During confinement, faecal samples from six llamas were collected twice per day during six consecutive days. Faeces belonging to 18 vicuñas (Vicugna vicugna) were collected before and one day after their capture for confinement (Chacu). Faecal cortisol metabolites (FCM) were extracted from each sample and quantified by an 11- oxoaetiocholanolone enzyme immunoassay. Thirty-three and 28 h (median) after ACTH stimulation, FCM concentrations peaked with a ten- and eight-fold increase (median) above baseline in alpacas and llamas, respectively. There were no significant differences in FCM concentrations between sexes. In llamas, FCM concentrations peaked (4.7 times higher than baseline) after five days of confinement in females and after three days (2.7 times) in males. In vicuñas, three times higher FCM levels were observed the day after the start of confinement (in comparison to the starting values). Based on our findings, this non-invasive method is well suited to measure adrenocortical activity in alpacas, llamas and vicuñas. Thus, this method could help to improve management, handling and welfare in wild and domesticated South American camelids. © 2013 Universities Federation for Animal Welfare.


Meckelmann S.W.,University of Wuppertal | Jansen C.,University of Wuppertal | Riegel D.W.,University of Wuppertal | van Zonneveld M.,Tropical Agriculture Research and Higher Education Center | And 5 more authors.
European Food Research and Technology | Year: 2015

Peru is considered a hotspot with maybe the highest diversity of domesticated chili peppers. Capsicum pubescens is the least explored domesticated chili pepper, especially with regard to its chemical composition. Thirty-two different C. pubescens (Rocoto) accessions, out of the national Peruvian Capsicum germplasm collection at the Instituto Nacional de Innovación Agraria, were selected for investigating the phytochemical content and its variability. After drying and milling, the fruits were analyzed for the three major capsaicinoids (capsaicin, dihydrocapsaicin and nordihydrocapsaicin), flavonoid aglycons (quercetin, kaempferol, luteolin, apigenin), total polyphenol content, antioxidant capacity, tocopherol (α-, β- and γ-) content, fat content, ascorbic acid content, surface color and extractable color. The concentrations for selected traits ranged as follows: total capsaicinoids from 55 to 410 mg/100 g (corresponding to ca. 8400–60,000 SHU), total polyphenols from 1.8 to 2.5 g gallic acid equivalents/100 g, antioxidant capacity from 2.4 to 4.6 mmol Trolox/100 g and tocopherols from 6.8 to 18.4 mg/100 g. Only very few of the accessions contained detectable amounts of the major chili flavonoid quercetin. The results indicate that C. pubescens is generally less diverse and exhibits a lower content of almost all analyzed traits when compared to 147 Peruvian chili pepper accessions belonging to the other four domesticated species. © 2015, Springer-Verlag Berlin Heidelberg.


Meckelmann S.W.,University of Wuppertal | Riegel D.W.,University of Wuppertal | van Zonneveld M.,Tropical Agriculture Research and Higher Education Center | Rios L.,Instituto Nacional Of Innovacion Agraria Inia | And 3 more authors.
European Food Research and Technology | Year: 2014

Twenty-three Peruvian chili pepper accessions, belonging to the four domesticated species Capsicum annuum, Capsicum baccatum, Capsicum chinense and Capsicum frutescens, were grown under different meteorological conditions and agricultural practices in three Peruvian locations (Chiclayo, Piura and Pucallpa). Results are reported for powdered oven-dried bulk samples of each accession and each location by important quality attributes (capsaicinoids, flavonoids, tocopherols, antioxidant capacity, total polyphenols, extractable color (ASTA 20.1) and surface color). Multivariate data evaluation by principle component analysis and partial least square discriminant analysis did not show any underlying structure. Moreover, a high influence of the environment on the analyzed traits could be demonstrated by analysis of variance. Significant differences (p ≤ 0.001) between the accessions and all locations were observed for all traits. Besides, significant interaction between accessions and locations indicated that the accessions responded differently to changes of the locations. The calculation of an environmental impact factor allowed differing between chili peppers provided consistent phytochemical levels widely independent of the location or those that provided exceptional high levels for a specific trait at one of the locations. © 2014, Springer-Verlag Berlin Heidelberg.


de Haan S.,International Potato Center | Burgos G.,International Potato Center | Arcos J.,Instituto Nacional Of Innovacion Agraria Inia | Ccanto R.,Grupo Yanapai | And 3 more authors.
Economic Botany | Year: 2010

Traditional Processing of Black and White Chuño in the Peruvian Andes: Regional Variants and Effect on the Mineral Content of Native Potato Cultivars. Farmers in the high Andes of central to southern Peru and Bolivia typically freeze-dry potatoes to obtain chuño. Processing of so-called black chuño follows tending, treading, freezing, and drying. The making of white chuño is generally more complex and involves exposure of tubers to water. Regional variants exist for each of these processes, yet their influence on the nutritional composition of native potato cultivars is little known. Tubers belonging to four distinct cultivars and produced in a replicated trial under uniform conditions were processed into four types of chuño following standard traditional procedures (farmer-managed). These regional variants were documented, and the dry matter, iron, zinc, calcium, potassium, phosphorus, magnesium, and sodium content of the four resulting different types of boiled chuño determined at the International Potato Center's Quality and Nutrition Laboratory (Lima, Peru). Content values were compared with those of boiled (unprocessed) tubers from the same experiment. Regional variants of processing are to a large extent determined by tradition, environmental condition, and market demand. The zinc, potassium, phosphorus, and magnesium content of all types of chuño decreases in comparison with unprocessed tubers. Concentrations of these same minerals decrease more drastically for white as compared to black chuño. The effect of the four regional variants of freeze-drying on the dry matter, iron, calcium, and sodium content of chuño differs by process and/or cultivar. © 2010 The New York Botanical Garden.


Gomez J.C.C.,National University of San Juan | Reategui A.D.C.E.,National University of San Juan | Flores J.T.,National University of San Juan | Saavedra R.R.,National University of San Juan | And 2 more authors.
Preparative Biochemistry and Biotechnology | Year: 2013

Myrciaria dubia is a main source of vitamin C for people in the Amazon region. Molecular studies of M. dubia require high-quality total RNA from different tissues. So far, no protocols have been reported for total RNA isolation from leaves of this species. The objective of this research was to develop protocols for extracting high-quality total RNA from leaves of M. dubia. Total RNA was purified following two modified protocols developed for leaves of other species (by Zeng and Yang, and by Reid et al.) and one modified protocol developed for fruits of the studied species (by Silva). Quantity and quality of purified total RNA were assessed by spectrophotometric and electrophoretic analysis. Additionally, quality of total RNA was evaluated with reverse-transcription polymerase chain reaction (RT-PCR). With these three modified protocols we were able to isolate high-quality RNA (A 260nm/A280nm > 1.9 and A260nm/A 230nm > 2.0). Highest yield was produced with the Zeng and Yang modified protocol (384 ± 46 g ARN/g fresh weight). Furthermore, electrophoretic analysis showed the integrity of isolated RNA and the absence of DNA. Another proof of the high quality of our purified RNA was the successful cDNA synthesis and amplification of a segment of the M. dubia actin 1 gene. We report three modified protocols for isolation total RNA from leaves of M. dubia. The modified protocols are easy, rapid, low in cost, and effective for high-quality and quantity total RNA isolation suitable for cDNA synthesis and polymerase chain reaction. © 2013 Taylor & Francis Group, LLC.

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