Daniel Ariza-Suárez
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View article: Association genetics and genomic prediction for resistance to root rot in a diverse collection of Pisum sativum L.
Association genetics and genomic prediction for resistance to root rot in a diverse collection of Pisum sativum L. Open
Background Root rot is one of the most threatening diseases to pea production. Root rot is caused by several interacting soil-borne pathogens which makes it challenging to manage. Breeding for resistance is a promising approach for sustain…
View article: EasyGeSe – a resource for benchmarking genomic prediction methods
EasyGeSe – a resource for benchmarking genomic prediction methods Open
Background Genomic prediction is a widely used method to predict phenotypes from genotypic data. Advances in both biological and computer science have enabled the generation of vast amounts of data and the development of new algorithms, sp…
View article: Holobiont-based genetic analysis reveals new plant and microbial markers for resistance against a root rot pathogen complex in pea
Holobiont-based genetic analysis reveals new plant and microbial markers for resistance against a root rot pathogen complex in pea Open
BACKGROUND: The pea root rot complex is caused by various soil-borne pathogens that likely reinforce each other, influencing the composition of the root microbiome and leading to significant yield reductions. Previous studies have shown va…
View article: Global genotype by environment prediction competition reveals that diverse modeling strategies can deliver satisfactory maize yield estimates
Global genotype by environment prediction competition reveals that diverse modeling strategies can deliver satisfactory maize yield estimates Open
Predicting phenotypes from a combination of genetic and environmental factors is a grand challenge of modern biology. Slight improvements in this area have the potential to save lives, improve food and fuel security, permit better care of …
View article: GWAS for Drought Resilience Traits in Red Clover (Trifolium pratense L.)
GWAS for Drought Resilience Traits in Red Clover (Trifolium pratense L.) Open
Red clover (Trifolium pratense L.) is a well-appreciated grassland crop in temperate climates but suffers from increasingly frequent and severe drought periods. Molecular markers for drought resilience (DR) would benefit breeding initiativ…
View article: Global Genotype by Environment Prediction Competition Reveals That Diverse Modeling Strategies Can Deliver Satisfactory Maize Yield Estimates
Global Genotype by Environment Prediction Competition Reveals That Diverse Modeling Strategies Can Deliver Satisfactory Maize Yield Estimates Open
Predicting phenotypes from a combination of genetic and environmental factors is a grand challenge of modern biology. Slight improvements in this area have the potential to save lives, improve food and fuel security, permit better care of …
View article: Association genetics and genomic prediction for resistance to root rot in a diverse collection of Pisum sativum L.
Association genetics and genomic prediction for resistance to root rot in a diverse collection of Pisum sativum L. Open
Root rot is one of the most threatening diseases to pea production. Root rot is caused by several interacting soil-borne pathogens, which makes it challenging to manage. Breeding for resistance is a promising approach for sustainable pea p…
View article: Mr.Bean: a comprehensive statistical and visualization application for modeling agricultural field trials data
Mr.Bean: a comprehensive statistical and visualization application for modeling agricultural field trials data Open
Crop improvement efforts have exploited new methods for modeling spatial trends using the arrangement of the experimental units in the field. These methods have shown improvement in predicting the genetic potential of evaluated genotypes. …
View article: ChromaX: a fast and scalable breeding program simulator
ChromaX: a fast and scalable breeding program simulator Open
Summary ChromaX is a Python library that enables the simulation of genetic recombination, genomic estimated breeding value calculations, and selection processes. By utilizing GPU processing, it can perform these simulations up to two order…
View article: ChromaX: a fast and scalable breeding program simulator
ChromaX: a fast and scalable breeding program simulator Open
Summary ChromaX is a Python library that enables the simulation of genetic recombination, genomic estimated breeding value calculations, and selection processes. By utilizing GPU processing, it can perform these simulations up to two order…
View article: Interspecific common bean population derived from Phaseolus acutifolius using a bridging genotype demonstrate useful adaptation to heat tolerance
Interspecific common bean population derived from Phaseolus acutifolius using a bridging genotype demonstrate useful adaptation to heat tolerance Open
Common bean ( Phaseolus vulgaris L.) is an important legume crop worldwide and is a major nutrient source in the tropics. Common bean reproductive development is strongly affected by heat stress, particularly overnight temperatures above 2…
View article: Genetic analysis of resistance to bean leaf crumple virus identifies a candidate <i>LRR‐RLK</i> gene
Genetic analysis of resistance to bean leaf crumple virus identifies a candidate <i>LRR‐RLK</i> gene Open
SUMMARY Bean leaf crumple virus (BLCrV) is a novel begomovirus (family Geminiviridae, genus Begomovirus ) infecting common bean ( Phaseolus vulgaris L.), threatening bean production in Latin America. Genetic resistance is required to ensur…
View article: Improving Association Studies and Genomic Predictions for Climbing Beans With Data From Bush Bean Populations
Improving Association Studies and Genomic Predictions for Climbing Beans With Data From Bush Bean Populations Open
Common bean ( Phaseolus vulgaris L.) has two major origins of domestication, Andean and Mesoamerican, which contribute to the high diversity of growth type, pod and seed characteristics. The climbing growth habit is associated with increas…
View article: Replication data for: Improving association studies and genomic predictions for climbing beans with data from bush bean populations
Replication data for: Improving association studies and genomic predictions for climbing beans with data from bush bean populations Open
Genomic predictions for climbing beans were established. The climbing bean panel (VEC) was phenotypically and genotypically characterized. To improve association studies and predictions, contrasting bush type bean data, i.e., publicly avai…
View article: Replication data for: Genetic analyses for the response to Bean Leaf Crumple Virus (BLCrV) identify a candidate LRR-RLK gene
Replication data for: Genetic analyses for the response to Bean Leaf Crumple Virus (BLCrV) identify a candidate LRR-RLK gene Open
These datasets contain phenotypic and genotypic data from three connected populations of common bean (Phaseolus vulgaris L.) that were used to identify the genomic regions controlling the phenotypic response to Bean Leaf Crumple Virus (BLC…
View article: Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa
Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa Open
Common bean ( Phaseolus vulgaris L.) is important in African diets for protein, iron (Fe), and zinc (Zn), but traditional cultivars have long cooking time (CKT), which increases the time, energy, and health costs of cooking. Genomic select…
View article: Correlation between genetic architecture of Fe and Zn accumulation and yield components in common bean (Phaseolus vulgaris L.)
Correlation between genetic architecture of Fe and Zn accumulation and yield components in common bean (Phaseolus vulgaris L.) Open
These datasets contain phenotypic and genotypic data of three biparental Mesoamerican biofortified populations of common bean (SCR16 x SMC40, SMC44 x SCR9 and SMC33 x SCR16). The main goal of these populations is to be used for genetic ana…
View article: Using Bean populations derived from P. acutifolius to advance toward generation of new bean varieties and discerning the traits and genetic base associated to heat tolerance
Using Bean populations derived from P. acutifolius to advance toward generation of new bean varieties and discerning the traits and genetic base associated to heat tolerance Open
This dataset contains phenotypic and genotypic data of an interspecific genetic mapping population between P. vulgaris and P. acutifolius using the bridge genotype VAP 1. The population is composed by 14 crosses including five Mesoamerican…
View article: Genetic Analyses and Genomic Predictions of Root Rot Resistance in Common Bean Across Trials and Populations
Genetic Analyses and Genomic Predictions of Root Rot Resistance in Common Bean Across Trials and Populations Open
Root rot in common bean is a disease that causes serious damage to grain production, particularly in the upland areas of Eastern and Central Africa where significant losses occur in susceptible bean varieties. Pythium spp. and Fusarium spp…
View article: Genetic Architecture and Genomic Prediction of Cooking Time in Common Bean (Phaseolus vulgaris L.)
Genetic Architecture and Genomic Prediction of Cooking Time in Common Bean (Phaseolus vulgaris L.) Open
Cooking time of the common bean is an important trait for consumer preference, with implications for nutrition, health, and environment. For efficient germplasm improvement, breeders need more information on the genetics to identify fast c…
View article: Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions
Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions Open
Background Common bean is an important staple crop in the tropics of Africa, Asia and the Americas. Particularly smallholder farmers rely on bean as a source for calories, protein and micronutrients. Drought is a major production constrain…
View article: Genetic architecture and genomic prediction of cooking time in common bean (Phaseolus vulgaris L.)
Genetic architecture and genomic prediction of cooking time in common bean (Phaseolus vulgaris L.) Open
These datasets contain phenotypic and genotypic data of a MAGIC population, DOR364 x G19833 biparental population, VEF panel and MIP panel. The main goal for these populations is to be used for genetic analysis and applications in breeding…
View article: Genetic improvement through genomic prediction for Pythium spp in lines common bean
Genetic improvement through genomic prediction for Pythium spp in lines common bean Open
Phenotypic and genotypic data for bean root disease and Pythium in common bean
View article: Genomic Prediction of Agronomic Traits in Common Bean (Phaseolus vulgaris L.) Under Environmental Stress
Genomic Prediction of Agronomic Traits in Common Bean (Phaseolus vulgaris L.) Under Environmental Stress Open
In plant and animal breeding, genomic prediction models are established to select new lines based on genomic data, without the need for laborious phenotyping. Prediction models can be trained on recent or historic phenotypic data and incre…
View article: Replication Data for: Genomic prediction of agronomic traits in common bean under environmental stress
Replication Data for: Genomic prediction of agronomic traits in common bean under environmental stress Open
These datasets contain phenotypic and genotypic data of a panel of elite Andean breeding lines of common bean (Phaseolus vulgaris L.) from CIAT. This population has been tested in twelve yield trials carried out in Palmira and Darien (Colo…
View article: Additional file 13 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions
Additional file 13 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions Open
Additional file 13. Phenotypic performance of top 10 RILs of the common bean MAGIC population and their genotypes at 12 major QTL. Phenotypic values for each of the top ten MAGIC RIL lines are shown for each trial, color coded from desirab…
View article: VEF_raw_phenotypic_data.tab
VEF_raw_phenotypic_data.tab Open
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View article: VEF_raw_phenotypic_data_dictionary.tab
VEF_raw_phenotypic_data_dictionary.tab Open
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View article: Additional file 7 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions
Additional file 7 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions Open
Additional file 7. Haplotype composition of the MAGIC lines. The parental source, the length and genomic construction of each haplotype in each MAGIC line is shown, using the method proposed by Kover et al. [10].
View article: Additional file 3 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions
Additional file 3 of Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions Open
Additional file 3. Phenotypic variability, least significant difference (LSD) and broad-sense heritability (H2) for best linear unbiased predictors (BLUPs) of the evaluated traits in the trials of 2013, 2014 and 2016 of the MAGIC populatio…