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

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....

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Autores principales:	López Hernández, Felipe, Burbano Erazo, Esteban, León Pacheco, Rommel Igor, Cordero Cordero, Carina Cecilia, Villanueva Mejía, Diego F., Tofiño Rivera, Adriana Patricia, Cortés, Andrés J.
Formato:	article
Lenguaje:	Inglés
Publicado:	Cold Sprimg Harbor Laboratory (CSH) 2024
Materias:	Cultivo - F01 Genoma Fríjol Rendimiento Hortalizas y plantas aromáticas http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_331566 http://aims.fao.org/aos/agrovoc/c_8488
Acceso en línea:	https://www.biorxiv.org/content/10.1101/2022.08.03.502649v1.full http://hdl.handle.net/20.500.12324/40335 https://doi.org/10.1101/2022.08.03.502649

id	RepoAGROSAVIA40335
record_format	dspace
institution	Corporación Colombiana de Investigación Agropecuaria
collection	Repositorio AGROSAVIA
language	Inglés
topic	Cultivo - F01 Genoma Fríjol Rendimiento Hortalizas y plantas aromáticas http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_331566 http://aims.fao.org/aos/agrovoc/c_8488
spellingShingle	Cultivo - F01 Genoma Fríjol Rendimiento Hortalizas y plantas aromáticas http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_331566 http://aims.fao.org/aos/agrovoc/c_8488 López Hernández, Felipe Burbano Erazo, Esteban León Pacheco, Rommel Igor Cordero Cordero, Carina Cecilia Villanueva Mejía, Diego F. Tofiño Rivera, Adriana Patricia Cortés, Andrés J. 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
description	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.) × 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.
format	article
author	López Hernández, Felipe Burbano Erazo, Esteban León Pacheco, Rommel Igor Cordero Cordero, Carina Cecilia Villanueva Mejía, Diego F. Tofiño Rivera, Adriana Patricia Cortés, Andrés J.
author_facet	López Hernández, Felipe Burbano Erazo, Esteban León Pacheco, Rommel Igor Cordero Cordero, Carina Cecilia Villanueva Mejía, Diego F. Tofiño Rivera, Adriana Patricia Cortés, Andrés J.
author_sort	López Hernández, Felipe
title	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
title_short	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
title_full	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
title_fullStr	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
title_full_unstemmed	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
title_sort	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
publisher	Cold Sprimg Harbor Laboratory (CSH)
publishDate	2024
url	https://www.biorxiv.org/content/10.1101/2022.08.03.502649v1.full http://hdl.handle.net/20.500.12324/40335 https://doi.org/10.1101/2022.08.03.502649
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spelling	RepoAGROSAVIA403352024-10-30T03:00:45Z 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 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, Felipe Burbano Erazo, Esteban León Pacheco, Rommel Igor Cordero Cordero, Carina Cecilia Villanueva Mejía, Diego F. Tofiño Rivera, Adriana Patricia Cortés, Andrés J. Cultivo - F01 Genoma Fríjol Rendimiento Hortalizas y plantas aromáticas http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_331566 http://aims.fao.org/aos/agrovoc/c_8488 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.) × 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. Korea-Latin America Food and Agriculture Cooperation Initiative - KoLFACI Corporación Colombiana de Investigación Agropecuaria - (AGROSAVIA) Fríjol-Phaseolus vulgaris 2024-10-29T20:13:35Z 2024-10-29T20:13:35Z 2022-08-05 2022 article Artículo científico http://purl.org/coar/resource_type/c_2df8fbb1 info:eu-repo/semantics/article https://purl.org/redcol/resource_type/ART http://purl.org/coar/version/c_970fb48d4fbd8a85 https://www.biorxiv.org/content/10.1101/2022.08.03.502649v1.full http://hdl.handle.net/20.500.12324/40335 https://doi.org/10.1101/2022.08.03.502649 reponame:Biblioteca Digital Agropecuaria de Colombia instname:Corporación colombiana de investigación agropecuaria AGROSAVIA eng BioRxiv 1 1 1 38 ↵Afgan, E., Baker, D., Batut, B., Van Den Beek, M., Bouvier, D., Ech, M., et al. (2018). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. 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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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