Assessing the cadmium content of cacao crops in Arauca, Colombia

The district of Arauca is the second-largest producer of cacao in Colombia. However, despite its quality, it faces issues for export due to levels of cadmium (Cd) higher than the regulatory thresholds. A central question is how it may impact agricultural performance in the presence of Cd in cacao and chocolates. This study quantified Cd in cacao plantations from Arauca. Thus, 180 farms were assessed in the municipalities of Arauquita, Fortul, Saravena, and Tame. Five sample types (soil, irrigation channel sediment, soil litter, cacao seeds, and chocolates) were assessed for Cd. As a technological innovation, the new MXRF technology was used for Cd in chocolates. The sequence of Cd content was soil litter > chocolate > soils > cacao seeds > irrigation-channel sediment. A gradient north-south of Cd content in soil was observed, where highest content was found in farms near the Arauca River, and lower farther away. In irrigation channel sediment, Cd levels averaged 0.07 mg kg-1. The Cd content in cacao seeds was 0.78 mg kg-1 on average. Cd content in chocolates was above the threshold (1.10 mg kg-1 on average, including several cacao mass percentages). These artisanal chocolate bars produced by single farms were near the limit of Cd set by the European Union (up to 0.8 mg kg-1). Therefore, mixing beans from different farms could reduce their Cd content. The present study underscores the complexity of Cd distribution, emphasizing the importance of integrating soil, crop, and landscape features in managing and mitigating Cd levels in cacao.

Performance of Metarhizium rileyi Nm017: nutritional supplementation to improve production and quality conidia

This study aimed to analyze the effect of nutritional supplements on improving conidia production of Metarhizium rileyi Nm017 at laboratory scale (yields of conidia/substrate and biomass/substrate, and substrate consumption). Also, the influence on quality parameters were evaluated (germination at 36 and 48 h, enzymatic activity, and insecticidal activity on Helicoverpa zea). Six treatments (T1-T6) were assessed and all of them reached maximum conidia concentration after 7 days fermentation, a feasible production timetable. Yields from treatment T6 (yeast extract + V8 juice) were 1.5-threefold higher than the other treatments. Conidia from T6 reached germinations of 56% and 12% at 36 and 48 h, respectively, higher than T1 (without supplements), which had the lowest values found. M. rileyi conidia obtained from treatment T6 had the highest enzymatic activity (0.45 U chitinase g-1, 0.28 U lipase g-1, and 1.29 U protease g-1). However, treatments with the highest conidia yields and enzymatic activity were not positively correlated to the efficacy against H. zea. When M. rileyi was produced on T5 (yeast hydrolysate + V8 juice), conidia were 35% more virulent than treatment T6. The findings evidenced the noticeable impact of nutritional substrate amended for conidia production and quality. This work showed the relevance of insecticidal activity assessment as a selection criterion in the mass production development of a biocontrol agent.

Suppression of tomato wilt by cell-free supernatants of Acinetobacter baumannii isolates from wild cacao from the Colombian Amazon

Tomato vascular wilt caused by Fusarium oxysporum f. sp. lycopersici (Fol) is one of the most limiting diseases of this crop. The use of fungicides and varieties resistant to the pathogen has not provided adequate control of the disease. In this study, siderophore-producing bacteria isolated from wild cocoa trees from the Colombian Amazon were characterized to identify prominent strategies for plant protection. The isolates were taxonomically classified into five different genera. Eight of the fourteen were identified as bacteria of the Acinetobacter baumannii complex. Isolates CBIO024, CBIO086, CBIO117, CBIO123, and CBIO159 belonging to this complex showed the highest efficiency in siderophore synthesis, producing these molecules in a range of 91-129 µmol/L deferoxamine mesylate equivalents. A reduction in disease severity of up to 45% was obtained when plants were pretreated with CBIO117 siderophore-rich cell-free supernatant (SodSid). Regarding the mechanism of action that caused antagonistic activity against Fol, it was found that plants infected only with Fol and plants pretreated with SodSid CBIO117 and infected with Fol showed higher levels of PR1 and ERF1 gene expression than control plants. In contrast, MYC2 gene expression was not induced by the SodSid CBIO117 application. However, it was upregulated in plants infected with Fol and plants pretreated with SodSid CBIO117 and infected with the pathogen. In addition to the disease suppression exerted by SodSid CBIO117, the results suggest that the mechanism underlying this effect is related to an induction of systemic defense through the salicylic acid, ethylene, and priming defense via the jasmonic acid pathway.

Genealogical structure of the Colombian Romosinuano Creole cattle

The Romosinuano cattle breed is one of the most important Creole genetic resources in Colombia, and interesting traits like adaptation or reproductive efficiency have promoted its use in different countries in America. To consolidate the genealogical historical records, the review of very first yield records in this population was used to reconstruct the genealogy of the breed since the first animals incorporated to the in vivo germplasm bank and estimate different demographic parameters. The complete genealogy comprises 17,136 animals with 5.8 years of generation interval for two pathways. The estimated average inbreeding for the population and inbred animals was 2.53% and 6.32% respectively, with a progressive increase of inbred animals across the generations. Almost 48% of the total animals presented some level of consanguinity. Effective population size (Ne) based on the inbreeding rate estimated by regression in all generations was 120 animals whereas Ne estimated by equivalent generations was 69 animals. Effective number of founders (Fe), effective number of ancestors (Fa), and ancestors explaining 50% of variability were 75, 48, and 22, respectively. The relation between Fa/Fe of 64% indicates a genetic bottleneck effect in the population studied.

Use of near-infrared reflectance spectroscopy on feces to estimate digestibility and dry matter intake of dietary nutritional characteristics under grazing conditions in Colombian creole steers

Digestibility and intake are parameters difficult and expensive to estimate under grazing conditions; therefore, the aim of this study was to develop near-infrared reflectance spectroscopy (NIRS) calibrations applied to feces (F-NIRS) and evaluate their accuracy to predict dry matter digestibility (DMD) and dry matter intake (DMI) of Colombian creole cattle. Five digestibility trials using creole steers were conducted; indigestible neutral detergent fiber (iNDF) was used as internal marker and Cr₂O₃ and TiO₂ as external markers. A total of 249 forage and 396 fecal samples from individual animals were collected, dried, and grinded for conventional chemical analysis. For spectral analysis, fecal samples were pooled across collection periods (77 samples). Chemometric analysis was performed using WinISI V4.10 software applying the modified partial least squares method. Cross-validation was performed to avoid overfitting the models. The goodness-of-fit statistics considered were the coefficient of determination in cross-validation and prediction sets (R²cv and r², respectively) and the ratio performance deviation (RPD). Fecal NIRS calibrations developed for forage and supplement DMD showed a satisfactory fit (R²cv =0.87 and RPD=2.77 and R²cv=0.92 and RPD=3.50, respectively). The accuracy of fecal output equations using chromium (Cr) and titanium (Ti) was similar in terms of R²cv (0.92) and RPD (3.63 vs. 3.57). Total DMI equations using Ti performed better compared to Cr (R²cv = 0.82 vs. 0.78; RPD=2.41 vs. 2.17, respectively). The F-NIRS models were validated using a completely independent set of fecal samples showing a moderate fit (r²>0.8 and RPD>2.0). This study showed that F-NIRS is a feasible tool to predict DMD and DMI of creole steers under grazing conditions. However, previous to socialization, this requires an improvement in accuracy of the calibrated equations related to grazing animals in different production contexts.

Study on the insecticidal activity of entomopathogenic fungi for the control of the fruit fly (Anastrepha obliqua), the main pest in mango crop in Colombia

The aim of this study was to evaluate and select entomopathogenic fungi that produces insecticidal compounds for the control of adults of Anastrepha obliqua Macquart (Diptera: tephritidae) that are the main pest of mango (Mangifera indica L. Bark) in Colombia. Nine entomopathogenic fungi isolates were evaluated, five belonging to the genus Metarhizium and four belonging to the genus Beauveria. One strain of the species Metarhizium robertsii with insecticidal activity was selected. By column fractionation, an active fraction was obtained, which caused mortalities higher than 90% after 48 h of exposure. Through HPLC it was determined that the active fraction is composed of more than 22 metabolites. Identification of the metabolites by UHPLC MS/MS revealed the presence of destruxin in E, D, A and B groups (destruxin E-diol, destruxin D, destruxin D1, destruxin D2, destruxin A2, destruxin A, destruxin A3, dihydrodestruxin A, desmB, destruxin B2, destruxin B and destruxin B1). The evaluation of the insecticidal capacity of the organic fractions obtained by HPLC indicated that the extract obtained from the isolate M. robertsii had a compound with high activity on adults of A. obliqua (destruxin A) causing massive mortality of up to 100%, after 48 h of the treatment administration. Furthermore, two other compounds with medium activity were found (destruxin A2 and destruxin B), showing mortalities between 60.0 and 81.3%, respectively. The extract of the isolate MT008 of M. robertsii showed higher insecticidal activity and a potential source for the control of A. obliqua.

Occurrence and molecular characterization of cyst nematode species (Globodera spp.) associated with potato crops in Colombia

Potato cyst nematodes (PCN) from the genus Globodera spp. cause major losses in the potato (Solanum tuberosum) industry worldwide. Despite their importance, at present little is known about the status of this plant pathogen in cultivated potatoes in Colombia. In this study, a total of 589 samples collected from 75 geographic localities in nine potato producing regions of Colombia (Cundinamarca, Boyacá, Antioquia, Nariño, Santander, Norte de Santander, Tolima, Caldas and Cauca) were assayed for the presence of potato cyst nematodes. Fifty-seven percent of samples tested positive for PCN. Based on phylogenetic analysis of the internal transcribed spacer region (ITS1-5.8S-ITS2) of the rRNA gene and D2-D3 expansion segments of the 28S rRNA gene, all populations but one were identified as Globodera pallida. Sequences of G. pallida from Colombia formed a monophyletic group closely related to Peruvian populations, with the lowest average number of nucleotide substitutions per site (Dxy = 0.002) and net nucleotide substitutions per site (Da = 0.001), when compared to G. pallida populations from Europe, South and North America. A single sample formed a well-supported subclade along with G. rostochiensis and G. tabacum from Japan, USA and Argentina. To our knowledge this is the first comprehensive survey of Globodera populations from Colombia that includes genetic data. Our findings on species diversity and phylogenetic relationships of Globodera populations from Colombia may help elucidate the status and distribution of Globodera species, and lead to the development of accurate management strategies for the potato cyst nematodes.

Optimization of the genotyping-by-sequencing SNP calling for diversity analysis in cape gooseberry (Physalis peruviana L.) and related taxa

A robust Genotyping-By-Sequencing (GBS) pipeline platform was examined to provide accurate discovery of Single Nucleotide Polymorphisms (SNPs) in a cape gooseberry (Physalis peruviana L.) and related taxa germplasm collection. A total of 176 accessions representing, wild, weedy, and commercial cultivars as well as related taxa from the Colombian germplasm bank and other world repositories were screened using GBS. The pipeline parameters mnLCov of 0.5 and a mnScov of 0.7, tomato and potato genomes, and cape gooseberry transcriptome for read alignments, were selected to better assess diversity and population structure in cape gooseberry and related taxa. A total of 7,425 SNPs, derived from P. peruviana common tags (unique 64 bp sequences shared between selected species), were used. Within P. peruviana, five subpopulations with a high genetic diversity and allele fixation (H_E: 0.35 to 0.36 and F_IS: -0.11 to -0.01, respectively) were detected. Conversely, low genetic differentiation (F_ST: 0.01 to 0.05) was also observed, indicating a high gene flow among subpopulations. These results contribute to the establishment of adequate conservation and breeding strategies for Cape gooseberry and closely related Physalis species.

Genome-wide association study (GWAS) for morphological and yield-related traits in an oil palm hybrid (Elaeis oleifera x Elaeis guineensis) population

BACKGROUND

The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. This work provides to our knowledge, the first association mapping study in an interspecific OxG oil palm population, which shows tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production.

RESULTS

Using genotyping-by-sequencing (GBS), we identified a total of 3776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrid population for 10 agronomic traits. Twelve genomic regions (SNPs) were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes.

CONCLUSIONS

We provide new insights on genomic regions that mapped on candidate genes involved in plant architecture and yield. These potential candidate genes need to be confirmed for future targeted functional analyses. Associated markers to the traits of interest may be valuable resources for the development of marker-assisted selection in oil palm breeding.

Genetic diversity and association mapping in the Colombian Central Collection of Solanum tuberosum L. Andigenum group using SNPs markers

The potato (Solanum tuberosum L.) is the fourth most important crop food in the world and Colombia has one of the most important collections of potato germplasm in the world (the Colombian Central Collection-CCC). Little is known about its potential as a source of genetic diversity for molecular breeding programs. In this study, we analyzed 809 Andigenum group accessions from the CCC using 5968 SNPs to determine: 1) the genetic diversity and population structure of the Andigenum germplasm and 2) the usefulness of this collection to map qualitative traits across the potato genome. The genetic structure analysis based on principal components, cluster analyses, and Bayesian inference revealed that the CCC can be subdivided into two main groups associated with their ploidy level: Phureja (diploid) and Andigena (tetraploid). The Andigena population was more genetically diverse but less genetically substructured than the Phureja population (three vs. five subpopulations, respectively). The association mapping analysis of qualitative morphological data using 4666 SNPs showed 23 markers significantly associated with nine morphological traits. The present study showed that the CCC is a highly diverse germplasm collection genetically and phenotypically, useful to implement association mapping in order to identify genes related to traits of interest and to assist future potato genetic breeding programs.