Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions
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 c...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer
2020
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/110291 |
| _version_ | 1855529132537937920 |
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| author | Díaz, Santiago Ariza-Suárez, Daniel Izquierdo, Paulo Lobaton, Juan David Hoz, Juan Fernando de la Acevedo, Fernando Duitama, Jorge Guerrero, Alberto F. Cajiao V., César Hernando Mayor, Victor Beebe, Stephen E. Raatz, Bodo |
| author_browse | Acevedo, Fernando Ariza-Suárez, Daniel Beebe, Stephen E. Cajiao V., César Hernando Duitama, Jorge Díaz, Santiago Guerrero, Alberto F. Hoz, Juan Fernando de la Izquierdo, Paulo Lobaton, Juan David Mayor, Victor Raatz, Bodo |
| author_facet | Díaz, Santiago Ariza-Suárez, Daniel Izquierdo, Paulo Lobaton, Juan David Hoz, Juan Fernando de la Acevedo, Fernando Duitama, Jorge Guerrero, Alberto F. Cajiao V., César Hernando Mayor, Victor Beebe, Stephen E. Raatz, Bodo |
| author_sort | Díaz, Santiago |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace110291 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1102912025-11-12T05:56:37Z Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions Díaz, Santiago Ariza-Suárez, Daniel Izquierdo, Paulo Lobaton, Juan David Hoz, Juan Fernando de la Acevedo, Fernando Duitama, Jorge Guerrero, Alberto F. Cajiao V., César Hernando Mayor, Victor Beebe, Stephen E. Raatz, Bodo genotypes genomes drought agronomic characters quantitative trait loci sequence experiments genotipos genomas sequía 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. 2020-12 2020-11-25T14:13:59Z 2020-11-25T14:13:59Z Journal Article https://hdl.handle.net/10568/110291 en Open Access application/pdf Springer Diaz, S.; Ariza-Suarez, D.; Izquierdo, P.; Lobaton, J.D.; de la Hoz, J.F.; Acevedo, F.; Duitama, J.; Guerrero, A.F.; Cajiao, C.; Mayor, V.; Beebe, S.E.; Raatz, B. (2020) Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions. BMC Genomics 21: 799 20 p. ISSN: 1471-2164 |
| spellingShingle | genotypes genomes drought agronomic characters quantitative trait loci sequence experiments genotipos genomas sequía Díaz, Santiago Ariza-Suárez, Daniel Izquierdo, Paulo Lobaton, Juan David Hoz, Juan Fernando de la Acevedo, Fernando Duitama, Jorge Guerrero, Alberto F. Cajiao V., César Hernando Mayor, Victor Beebe, Stephen E. Raatz, Bodo Genetic mapping for agronomic traits in a MAGIC population of common bean (Phaseolus vulgaris L.) under drought conditions |
| 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 | genotypes genomes drought agronomic characters quantitative trait loci sequence experiments genotipos genomas sequía |
| url | https://hdl.handle.net/10568/110291 |
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