Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions
Abstract 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 constraint for common bean, a situation that will be aggravat...
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| Format: | Article |
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BMC
2020-11-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-020-07213-6 |
| _version_ | 1818410065177083904 |
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| author | Santiago Diaz Daniel Ariza-Suarez Paulo Izquierdo Juan David Lobaton Juan Fernando de la Hoz Fernando Acevedo Jorge Duitama Alberto F. Guerrero Cesar Cajiao Victor Mayor Stephen E. Beebe Bodo Raatz |
| author_facet | Santiago Diaz Daniel Ariza-Suarez Paulo Izquierdo Juan David Lobaton Juan Fernando de la Hoz Fernando Acevedo Jorge Duitama Alberto F. Guerrero Cesar Cajiao Victor Mayor Stephen E. Beebe Bodo Raatz |
| author_sort | Santiago Diaz |
| collection | DOAJ |
| description | Abstract 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 constraint for common bean, a situation that will be aggravated with current climate change scenarios. In this context, new tools designed to understand the genetic basis governing the phenotypic responses to abiotic stress are required to improve transfer of desirable traits into cultivated beans. Results A multiparent advanced generation intercross (MAGIC) population of common bean was generated from eight Mesoamerican breeding lines representing the phenotypic and genotypic diversity of the CIAT Mesoamerican breeding program. This population was assessed under drought conditions in two field trials for yield, 100 seed weight, iron and zinc accumulation, phenology and pod harvest index. Transgressive segregation was observed for most of these traits. Yield was positively correlated with yield components and pod harvest index (PHI), and negative correlations were found with phenology traits and micromineral contents. Founder haplotypes in the population were identified using Genotyping by Sequencing (GBS). No major population structure was observed in the population. Whole Genome Sequencing (WGS) data from the founder lines was used to impute genotyping data for GWAS. Genetic mapping was carried out with two methods, using association mapping with GWAS, and linkage mapping with haplotype-based interval screening. Thirteen high confidence QTL were identified using both methods and several QTL hotspots were found controlling multiple traits. A major QTL hotspot located on chromosome Pv01 for phenology traits and yield was identified. Further hotspots affecting several traits were observed on chromosomes Pv03 and Pv08. A major QTL for seed Fe content was contributed by MIB778, the founder line with highest micromineral accumulation. Based on imputed WGS data, candidate genes are reported for the identified major QTL, and sequence changes were identified that could cause the phenotypic variation. Conclusions This work demonstrates the importance of this common bean MAGIC population for genetic mapping of agronomic traits, to identify trait associations for molecular breeding tool design and as a new genetic resource for the bean research community. |
| first_indexed | 2024-12-14T10:09:35Z |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-14T10:09:35Z |
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| series | BMC Genomics |
| spelling | doaj.art-bc2dd40668e74b81b586a8359ab8fefb2022-12-21T23:07:01ZengBMCBMC Genomics1471-21642020-11-0121112010.1186/s12864-020-07213-6Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditionsSantiago Diaz0Daniel Ariza-Suarez1Paulo Izquierdo2Juan David Lobaton3Juan Fernando de la Hoz4Fernando Acevedo5Jorge Duitama6Alberto F. Guerrero7Cesar Cajiao8Victor Mayor9Stephen E. Beebe10Bodo Raatz11Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT)Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT)Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT)Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT)Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT)Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT)Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT)Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT)Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT)Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT)Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT)Bean Program, Agrobiodiversity Area, International Center for Tropical Agriculture (CIAT)Abstract 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 constraint for common bean, a situation that will be aggravated with current climate change scenarios. In this context, new tools designed to understand the genetic basis governing the phenotypic responses to abiotic stress are required to improve transfer of desirable traits into cultivated beans. Results A multiparent advanced generation intercross (MAGIC) population of common bean was generated from eight Mesoamerican breeding lines representing the phenotypic and genotypic diversity of the CIAT Mesoamerican breeding program. This population was assessed under drought conditions in two field trials for yield, 100 seed weight, iron and zinc accumulation, phenology and pod harvest index. Transgressive segregation was observed for most of these traits. Yield was positively correlated with yield components and pod harvest index (PHI), and negative correlations were found with phenology traits and micromineral contents. Founder haplotypes in the population were identified using Genotyping by Sequencing (GBS). No major population structure was observed in the population. Whole Genome Sequencing (WGS) data from the founder lines was used to impute genotyping data for GWAS. Genetic mapping was carried out with two methods, using association mapping with GWAS, and linkage mapping with haplotype-based interval screening. Thirteen high confidence QTL were identified using both methods and several QTL hotspots were found controlling multiple traits. A major QTL hotspot located on chromosome Pv01 for phenology traits and yield was identified. Further hotspots affecting several traits were observed on chromosomes Pv03 and Pv08. A major QTL for seed Fe content was contributed by MIB778, the founder line with highest micromineral accumulation. Based on imputed WGS data, candidate genes are reported for the identified major QTL, and sequence changes were identified that could cause the phenotypic variation. Conclusions This work demonstrates the importance of this common bean MAGIC population for genetic mapping of agronomic traits, to identify trait associations for molecular breeding tool design and as a new genetic resource for the bean research community.http://link.springer.com/article/10.1186/s12864-020-07213-6Genotyping-by-sequencing (GBS)Genome-wide association study (GWAS)Multiparent advanced generation inter-crosses (MAGIC)Quantitative trait loci (QTL)Whole genome sequencing (WGS) |
| spellingShingle | Santiago Diaz Daniel Ariza-Suarez Paulo Izquierdo Juan David Lobaton Juan Fernando de la Hoz Fernando Acevedo Jorge Duitama Alberto F. Guerrero Cesar Cajiao Victor Mayor Stephen E. Beebe Bodo Raatz Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions BMC Genomics Genotyping-by-sequencing (GBS) Genome-wide association study (GWAS) Multiparent advanced generation inter-crosses (MAGIC) Quantitative trait loci (QTL) Whole genome sequencing (WGS) |
| title | Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions |
| title_full | Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions |
| title_fullStr | Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions |
| title_full_unstemmed | Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions |
| title_short | Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions |
| title_sort | genetic mapping for agronomic traits in a magic population of common bean phaseolus vulgaris l under drought conditions |
| topic | Genotyping-by-sequencing (GBS) Genome-wide association study (GWAS) Multiparent advanced generation inter-crosses (MAGIC) Quantitative trait loci (QTL) Whole genome sequencing (WGS) |
| url | http://link.springer.com/article/10.1186/s12864-020-07213-6 |
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