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 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.

Genetic Architecture and Genomic Prediction of Cooking Time in Common Bean (Phaseolus vulgaris L.)

“…The genetic map previously reported for the MAGIC population was used for QTL analyses ( Diaz et al, 2020 ; Supplementary Table 3 ). Five QTL were mapped in the MAGIC population using the haplotype-based interval mapping, four QTL for CKT, and one for WAC ( Table 3 ).…”

“…The DxG population was advanced by a modified single-seed descent (SSD) to F 9:11 generation. (2) A multiparent advanced-generation intercross (MAGIC) population previously described by Diaz et al (2020) . This population used a set of eight Mesoamerican breeding lines from CIAT as founders.…”

“…The DxG population and its parental lines were established in the field following a randomized complete block design with three replicates for each RIL in 2011. The MAGIC population and its eight founders were planted in 2013 in an alpha-lattice incomplete-block design with three replicates as described by Diaz et al (2020) . A subset of 223 MAGIC lines and its eight founders were phenotyped for cooking time.…”

“…Genotyping of the MAGIC population and its founders (629 RIL + 8 lines), the VEF panel (330 lines), the MIP panel (210 lines), and each founder genotype of the DxG population was obtained using the Ape KI-based genotyping-by-sequencing (GBS) protocol ( Elshire et al, 2011 ), as previously described ( Perea et al, 2016 ; Gil et al, 2019 ; Keller et al, 2020 ; Diaz et al, 2020 ). Briefly, DNA was extracted using the urea buffer-based DNA extraction midi prep protocol.…”

“…The construction of the genetic map of the MAGIC population was described in detail by Diaz et al (2020) using the method for haplotype prediction reported in an Arabidopsis thaliana MAGIC population ( Kover et al, 2009 ). Briefly, the inferred haplotypes were used to transform the GBS matrix with allele information into a matrix with founders’ source information for each marker.…”