Journal Article

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

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

2020

Overview

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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Accumulation / Africa / Agronomy / Animal Genetics and Genomics / Asia / Beans / Biomedical and Life Sciences / Botanical research / Calories / Chromosome Mapping / Chromosomes / Climate change / Cloning / Common beans / Confidence / Developing countries / Drought / Droughts / Gene mapping / Gene sequencing / Genes / Genetic aspects / Genetic research / Genetic resources / Genome-wide association study (GWAS) / Genomes / Genomics / Genotyping / Genotyping-by-sequencing (GBS) / Haplotypes / Harvesting / Iron / LDCs / Legumes / Life Sciences / Microarrays / Microbial Genetics and Genomics / Micronutrients / Multiparent advanced generation inter-crosses (MAGIC) / Phaseolus - genetics / Phaseolus vulgaris / Phenology / Phenotype / Phenotypes / Phenotypic variations / Physiology / Plant Breeding / Plant Genetics and Genomics / Plant genomics / Plant hardiness / Population / Population genetics / Population structure / Properties / Proteomics / Quantitative Trait Loci / Quantitative trait loci (QTL) / Rain / Research Article / Small farms / Tropical environments / Whole genome sequencing / Whole genome sequencing (WGS)