publications

2026

1. Strengthening national genebanks through genomics and regional collaboration: Lessons from Latin America and the Caribbean

   Carvajal-Yepes, M., Petroli, C., Correa, M., Breseghello, F., Tapia, G., Salazar, E., Chassaigne, A., Ferreyra, M.,  Reyes-Herrera, P.H., Guzmán, M., Mendoza, A., Vidal, R., Condón, F., de Almeida, N., Fernandez, E., Rodríguez, L., Solano, W., Morales, A.J., Velásquez-Flores, B.L., Soto, J., Robles, R., Ledesma, A., Aragón, M., Castillo, D., Roa, C., López Noriega, I., Wenzl, P., and Sansaloni, C.

   Global Food Security 2026

   Abs

   Latin America and the Caribbean (LAC) is a center of origin and domestication for globally important crops such as cassava, common bean, maize, and potato, all of which are key to food and nutrition security worldwide. Despite this strategic role, many national genebanks in the region face technical, financial, and policy barriers that limit the use of genomic tools for characterization and conservation. These genebanks safeguard the genetic diversity needed to enhance crop yields, climate-change resilience, nutritional quality, and pest and disease resistance. In 2022, CGIAR Centers and partners established the “Community of Practice (CoP) of national genebanks in LAC” to strengthen regional capacity for generating and interpreting digital sequence information (DSI), facilitate collaboration, and promote sustainable management of plant genetic resources. Through coordinated capacity-building activities, joint crop-based analyses, and shared learning, the CoP has connected 17 institutions across 13 countries. Members have begun generating and interpreting DSI for common bean, maize, and potato, while addressing gaps in data sharing, interoperability, and policy frameworks. Looking ahead, the CoP seeks to conduct diversity analysis, establish regional core collections, integrate existing global data portals, and advocate for policy alignment to sustain genomic characterization and access to diversity. This CoP initiative provides a model applicable in other regions to strengthen genebank operations through collaborative innovation and coordinated action, contributing to resilient and equitable global food systems.

2025

1. Evidence of long-distance clonal spreading and low genomic diversity of Kikuyu grass from highland livestock farms after a century of intentional introduction in Colombia

   Cerón-Souza, Ivania, Castillo-Sierra, Javier, Reyes-Herrera, Paula H., Berdugo-Cely, Jhon A., Parra-Salazar, Andrea, Lozano-Arce, Daniela, Duitama, Jorge, Avellaneda, Yesid, and Vargas-Martínez, Juan de Jesús

   Crop Science 2025

   Abs

   Abstract Kikuyu grass was introduced to Colombia in 1928 as livestock forage at high altitudes. Despite its low genetic diversity, it exhibits substantial phenotypic variation in Colombia, the United States, and Australia. Therefore, it remains unclear whether improvements in livestock productivity in the Colombian highlands should include selection programs. To address this gap, we analyzed diversity using a reduced-representation genome library of 146 samples from livestock farms across six localities at three distinct altitudes. We identified 514 and 41 single nucleotide polymorphisms (SNPs) through SNP calling based on the tetraploid whole genome using a de novo strategy and the haploid reference genome of the chloroplast, respectively. The data indicated long-distance clonality, nonsignificant genomic diversity within groups, and low genetic differentiation among groups unrelated to the sampling locations, which ranged from one to five clusters, depending on the SNP calling strategy and missing data thresholds. We concluded that this low diversity pattern aligns with the reported history of farmers progressively dispersing Kikuyu grass samples over long distances, preventing local isolation 96 years after arrival and masking the effects of sexual reproduction. As Colombian law prohibits importing foreign varieties, selection programs should focus on broadening genetic diversity based on a deeper understanding of reproductive strategies using modern omics techniques and developing optimized management strategies.

2. Colombia Gene Bank

   Cañar, Dubert Yamil, Socorro Cerón, Maria, Cerón-Souza, Ivania, Enriquez, Ayda Lilia, González, Carolina, Guzmán, Manuel Alejandro, Jiménez, Hugo, Reyes-Herrera, Paula Helena, Torres, Rosa Tulia, Villa, Alba Lucı́a, and others,

   Crop Science 2025

2024

1. Chromosome-scale genome assembly and annotation of the tetraploid potato cultivar Diacol Capiro adapted to the Andean region

   Reyes-Herrera, Paula H, Delgadillo-Duran, Diego A, Flores-Gonzalez, Mirella, Mueller, Lukas A, Cristancho, Marco A, and Barrero, Luz Stella

   G3: Genes, Genomes, Genetics 2024
2. Wild relatives of potato (Solanum L. sec. Petota) poorly sampled and unprotected in Colombia

   González-Orozco, Carlos E., Reyes-Herrera, Paula H., Sosa, Chrystian C., Torres, Rosa T., Manrique-Carpintero, Norma C., Lasso-Paredes, Zahara, Cerón-Souza, Ivania, and Yockteng, Roxana

   Crop Science 2024

   Abs

   Abstract Wild potato relatives (Solanum L. sec. Petota) play a vital role in crop improvement, understanding crop evolution, and conserving potato diversity. However, these invaluable resources are often neglected and underutilized and are susceptible to threats such as climate change, urbanization, and agricultural expansion. Little is known about the diversity, conservation status, and distribution of wild potato species in Colombia. To address this gap, we assessed the conservation status of five wild potato relatives conserved in the ex situ Colombian Central Collection. Five species were analyzed for their spatial patterns of biodiversity, conservation status, and conservation gaps. Colombia was found to have six centers of species richness, four areas of endemism, and six biogeographical regions. Of the five native species, only one was classified as adequately conserved for ex situ conservation, while the other four were considered low priority. In contrast, for in situ conservation, three species showed high priority, one was classified as medium priority, and one as low priority. In light of these findings, we propose three conservation strategies: (1) conducting collection missions to increase accessions in the national germplasm bank, prioritizing high-priority species; (2) identifying and protecting unprotected natural habitats and engaging stakeholders to enhance in situ conservation efforts; and (3) establishing regional community genebanks to ensure localized conservation efforts.

2023

1. Pleistocene-dated genomic divergence of avocado trees supports cryptic diversity in the Colombian germplasm

   Berdugo-Cely, Jhon A, Cortés, Andrés J, López-Hernández, Felipe, Delgadillo-Durán, Paola, Cerón-Souza, Ivania, Reyes-Herrera, Paula H, Navas-Arboleda, Alejandro A, and Yockteng, Roxana

   Tree Genetics & Genomes 2023
2. Genome Sequence Data Reveal at Least Two Distinct Incursions of the Tropical Race 4 Variant of Fusarium Wilt into South America

   Reyes-Herrera, Paula H., Torres-Bedoya, Eliana, Lopez-Alvarez, Diana, Burbano-David, Diana, Carmona, Sandra L., Bebber, Daniel P., Studholme, David J., Betancourt, Monica, and Soto-Suarez, Mauricio

   Phytopathology® 2023

2022

1. Prioritizing Colombian plant genetic resources for investment in research using indicators about the geographic origin, vulnerability status, economic benefits, and food security importance

   Cerón-Souza, Ivania, Delgadillo-Duran, Diego A, Polo-Murcia, Sonia M, Sarmiento-Naizaque, Zaida X, and Reyes-Herrera, Paula H

   2022
2. Robust and efficient software for reference-free genomic diversity analysis of genotyping-by-sequencing data on diploid and polyploid species

   Parra-Salazar, Andrea, Gomez, Jorge, Lozano-Arce, Daniela, Reyes-Herrera, Paula H, and Duitama, Jorge

   Molecular Ecology Resources 2022
3. Vis–NIR spectroscopy and machine learning methods to diagnose chemical properties in Colombian sugarcane soils

   Delgadillo-Duran, Diego A., Vargas-García, Cesar A., Varón-Ramírez, Viviana M., Calderón, Francisco, Montenegro, Andrea C., and Reyes-Herrera, Paula H.

   Geoderma Regional 2022

2021

1. MultiGWAS: An integrative tool for Genome Wide Association Studies in tetraploid organisms

   Garreta, Luis, Cerón-Souza, Ivania, Palacio, Manfred Ricardo, and Reyes-Herrera, Paula H

   Ecology and Evolution 2021

2020

1. Inheritance of rootstock effects in avocado (Persea americana Mill.) cv. Hass

   Reyes-Herrera, Paula H, Muñoz-Baena, Laura, Velásquez-Zapata, Valeria, Patiño, Laura, Delgado-Paz, Oscar A, Dı́az-Diez, Cipriano A, Navas-Arboleda, Alejandro A, and Cortés, Andrés J

   Frontiers in plant science 2020
2. Robust and efficient software for reference-free genomic diversity analysis of GBS data on diploid and polyploid species

   Parra-Salazar, Andrea, Gomez, Jorge, Lozano-Arce, Daniela, Reyes-Herrera, Paula H, and Duitama, Jorge

   bioRxiv 2020

2015

1. Predicting RAD-seq marker numbers across the eukaryotic tree of life

   Herrera, Santiago, Reyes-Herrera, Paula H, and Shank, Timothy M

   Genome Biology and Evolution 2015
2. BackCLIP: a tool to identify common background presence in PAR-CLIP datasets

   Reyes-Herrera, Paula Helena, Speck-Hernandez, CA, Sierra, CA, and Herrera, S

   Bioinformatics 2015
3. Predicting genome sizes and restriction enzyme recognition-sequence probabilities across the eukaryotic tree of life

   Herrera, Santiago, Reyes-Herrera, Paula H, and Shank, Timothy M

   bioRxiv 2015

2014

1. Computational methods for CLIP-seq data processing

   Reyes-Herrera, Paula H, and Ficarra, Elisa

   Bioinformatics and Biology insights 2014
2. Genome-wide predictability of restriction sites across the eukaryotic tree of life

   Herrera, Santiago, Reyes-Herrera, Paula H, and Shank, Timothy M

   bioRxiv 2014

2011

1. miREE: miRNA recognition elements ensemble

   Reyes-Herrera, Paula H, Ficarra, Elisa, Acquaviva, Andrea, and Macii, Enrico

   Bmc Bioinformatics 2011

2010

1. MicroRNA Target Prediction and Exploration through Candidate Binding Sites Generation

   Reyes-Herrera, Paula Helena, Acquaviva, Andrea, Ficarra, Elisa, and Macii, Enrico

   In 2010 International Conference on Complex, Intelligent and Software Intensive Systems 2010

2009

1. Novel Method for MicroRNA Target Prediction Using a Genetic Algorithm

   Reyes Herrera, Paula Helena, Acquaviva, Andrea, Ficarra, Elisa, and Macii, Enrico

   In 7th Rocky Mountain Bioinformatics Conference 2009