Replication Data for: Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

Diaz, Santiago; Ariza-Suárez, Daniel; Izquierdo, Paulo; Lobaton, Juan David; Hoz, Juan De la; Acevedo, Fernando; Duitama, Jorge; Guerrero, Alberto F.; Cajiao, César; Mayor, Victor; Beebe, Stephen E.; Raatz, Bodo

doi:10.7910/dvn/jr4x4c

Cited by 4 publications

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“…The variant calling was carried out using NGSEP, filtering SNPs with a genotype quality below 40, minor allele frequency (MAF) below 0.05, and removing SNPs with less than 60% of genotype calls, which yielded a matrix with 20% of missing data. The imputation of the missing data was performed with Beagle v.5.0 (Browning et al, 2018 ) using 100 as an effective population size and using the genetic map reported by Diaz et al ( 2019 ). The SNP calling was carried out once on the VEC separately and once on all five panels together.…”

Section: Methodsmentioning

confidence: 99%

Improving Association Studies and Genomic Predictions for Climbing Beans With Data From Bush Bean Populations

et al. 2022

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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 increased days to flowering (DF), seed iron concentration (SdFe), nitrogen fixation, and yield. However, breeding efforts in climbing beans have been limited and independent from bush type beans. To advance climbing bean breeding, we carried out genome-wide association studies and genomic predictions using 1,869 common bean lines belonging to five breeding panels representing both gene pools and all growth types. The phenotypic data were collected from 17 field trials and were complemented with 16 previously published trials. Overall, 38 significant marker-trait associations were identified for growth habit, 14 for DF, 13 for 100 seed weight, three for SdFe, and one for yield. Except for DF, the results suggest a common genetic basis for traits across all panels and growth types. Seven QTL associated with growth habits were confirmed from earlier studies and four plausible candidate genes for SdFe and 100 seed weight were newly identified. Furthermore, the genomic prediction accuracy for SdFe and yield in climbing beans improved up to 8.8% when bush-type bean lines were included in the training population. In conclusion, a large population from different gene pools and growth types across multiple breeding panels increased the power of genomic analyses and provides a solid and diverse germplasm base for genetic improvement of common bean.

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Section: Methodsmentioning

confidence: 99%

Improving Association Studies and Genomic Predictions for Climbing Beans With Data From Bush Bean Populations

et al. 2022

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“…GWAS analyses in common bean using Andean and Mesoamerican germplasm collections offered a broad perspective on common bean diversity and the genetic basis of multiple traits such as growth habit, seed size, and drought tolerance ( Hoyos-Villegas et al., 2017 ; Diaz et al., 2020 ; Valdisser et al., 2020 ). We used the method FarmCPU to perform the GWAS analyses, this method uses a fixed effect model (FEM) to test the association one marker at time using as covariates a multiple associated marker set (also named pseudo QTNs) to control false positives.…”

Section: Discussionmentioning

confidence: 99%

“…Green cells represent the minor allele (less frequent allele among the population). Villegas et al, 2017;Diaz et al, 2020;Valdisser et al, 2020). We used the method FarmCPU to perform the GWAS analyses, this method uses a fixed effect model (FEM) to test the association one marker at time using as covariates a multiple associated marker set (also named pseudo QTNs) to control false positives.…”

Section: Gwas Analysismentioning

confidence: 99%

“…To overcome this, we used the Bonferroni threshold to differentiate the true positives from false positives, this threshold is considered the most conservative method and depends on genotype density and the desired significance level (Kaler & Purcell, 2019). Genotype density reported in other studies that used GBS and the RE ApeK1 produced between 20 -30k SNPs (Diaz et al, 2020;Garcıá-Fernańdez et al, 2021). Exist other GBS protocols that use different RE enzymes or dual digest with MseI and TaqaI that could increase in 3.8 to 12.5-fold the number of SNPs compared to ApeK1 (Schröder et al, 2016).…”

Section: Gwas Analysismentioning

confidence: 99%

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Interspecific common bean population derived from Phaseolus acutifolius using a bridging genotype demonstrate useful adaptation to heat tolerance

et al. 2023

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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 20°C. The desert Tepary bean (Phaseolus acutifolius A. Gray) offers a promising source of adaptative genes due to its natural acclimation to arid conditions. Hybridization between both species is challenging, requiring in vitro embryo rescue and multiple backcrossing cycles to restore fertility. This labor-intensive process constrains developing mapping populations necessary for studying heat tolerance. Here we show the development of an interspecific mapping population using a novel technique based on a bridging genotype derived from P. vulgaris, P. Acutifolius and P. parvifolius named VAP1 and is compatible with both common and tepary bean. The population was based on two wild P. acutifolius accessions, repeatedly crossed with Mesoamerican elite common bush bean breeding lines. The population was genotyped through genotyping-by-sequencing and evaluated for heat tolerance by genome-wide association studies. We found that the population harbored 59.8% introgressions from wild tepary, but also genetic regions from Phaseolus parvifolius, a relative represented in some early bridging crosses. We found 27 significative quantitative trait loci, nine located inside tepary introgressed segments exhibiting allelic effects that reduced seed weight, and increased the number of empty pods, seeds per pod, stem production and yield under high temperature conditions. Our results demonstrate that the bridging genotype VAP1 can intercross common bean with tepary bean and positively influence the physiology of derived interspecific lines, which displayed useful variance for heat tolerance.

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“…For instance, the exploring of genetic architecture of abiotic stress in common beans as drought (Cortés and Blair, 2018) and heat (López-Hernández and Cortés, 2019) under GEA paradigm. Also, several GWAS works have studied breeding attributes in beans such as: agronomic traits (Diaz et al, 2020), mineral concentration (Wu et al, 2020), or aluminum toxicity tolerance (Ambachew and Blair, 2021).…”

Section: Introductionmentioning

confidence: 99%

Multi-environment Genome Wide Association Studies of Yield Traits in Common Bean (Phaseolus vulgaris L.) × Tepary Bean (P. acutifolius A. Gray) Interspecific Advanced Lines at the Humid and Dry Colombian Caribbean Subregions

López-Hernández

Burbano-Erazo

León-Pacheco

et al. 2022

Preprint

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Genome Wide Associations Studies GWAS are a powerful strategy for the exploration adaptive genetic variation to drought stress in advanced lines in common bean with interspecific genotypes, yet they still lack behind in the use of arid multi-environments as the subregions of the Colombian Caribbean. In order to bridge this gap, we couple an advanced genotypes panel integrated with Common Bean (Phaseolus vulgaris L.) x Tepary Bean (P. acutifolius A. Gray) interspecific lines with GWAS algorithms to identify novel sources of drought tolerance across the subregions of Colombian Caribbean. One of the most important challenges in agriculture is to achieve food security in environments vulnerable to climate change which worsens with the passing of the years. The common bean, a key product of the food basket of vulnerable regions of the Caribbean is affected by the reduction in yield under drought stress. A total of 87 advanced accessions with interspecific lines were genotyped by sequencing (GBS), leading to the discovery of 15,645 single-nucleotide polymorphism (SNP) markers. Five yield traits were developed for each accession and inputted in GWAS algorithms (i.e. FarmCPU, and BLINK) to identify putative associated loci in drought stress. Best-fit models revealed 47 significantly associated alleles distributed in all 11 common bean chromosomes. Flanking candidate genes were identified using 1-kb genomic windows centered in each associated SNP marker. A pathways enriched analysis was carried out using the mapped output in the GWAS step for each yield traits indices. Some of these genes were directly linked to response mechanisms of drought stress to level morphological, physiological, metabolic, signal transduction, and fatty acid and phospholipid metabolism. This work offers putative associated loci for marker-assisted and genomic selection for drought tolerance in common bean. It also demonstrates that it is feasible to identify genome-wide associations with an interspecific panel of genotypes and modern GWAS algorithms in multiples environments.

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Replication Data for: Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions

Cited by 4 publications

References 0 publications

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

Interspecific common bean population derived from Phaseolus acutifolius using a bridging genotype demonstrate useful adaptation to heat tolerance

Multi-environment Genome Wide Association Studies of Yield Traits in Common Bean (Phaseolus vulgaris L.) × Tepary Bean (P. acutifolius A. Gray) Interspecific Advanced Lines at the Humid and Dry Colombian Caribbean Subregions

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