Genetic control of pod morphological traits and pod edibility in a common bean RIL population

Abstract

QTL mapping, association analysis, and colocation study with previously reported QTL revealed three main regions controlling pod morphological traits and two loci for edible pod characteristics on the common bean chromosomes Pv01 and Pv06. Bean pod phenotype is a complex characteristic defined by the combination of different traits that determine the potential use of a genotype as a snap bean. In this study, the TUM RIL population derived from a cross between 'TU' (dry) and 'Musica' (snap) was used to investigate the genetic control of pod phenotype. The character was dissected into pod morphological traits (PMTs) and edible pod characteristics (EPC). The results revealed 35 QTL for PMTs located on seven chromosomes, suggesting a strong QTL colocation on chromosomes Pv01 and Pv06. Some QTL were colocated with previously reported QTL, leading to the mapping of 15 consensus regions associated with bean PMTs. Analysis of EPC of cooked beans revealed that two major loci with epistatic effect, located on chromosomes Pv01 and Pv06, are involved in the genetic control of this trait. An association study using a subset of the Spanish Diversity Panel (snap vs. non-snap) detected 23 genomic regions, with three regions being mapped at a position similar to those of two loci identified in the TUM population. The results demonstrated the relevant roles of Pv01 and Pv06 in the modulation of bean pod phenotype. Gene ontology enrichment analysis revealed a significant overrepresentation of genes regulating the phenylpropanoid metabolic process and auxin response in regions associated with PMTs and EPC, respectively. Both biological functions converged in the lignin biosynthetic pathway, suggesting the key role of the pathway in the genetic control of bean pod phenotype.

Fig. 1

Phenotypic frequency distribution of adjusted means of the six PMTs evaluated in the TUM population. Black arrows indicate the mean phenotype values of the corresponding parent lines. The solid red line represents the normal distribution curve. The results of the normality test (Kolmogorov–Smirnov) are displayed to the right of each histogram

Fig. 2

Location of QTL associated with PMTs and genomic regions involved in the control of EPC (EDIBILITY) on the TUM linkage map. QTL are presented as vertical bars on the right of the chromosome. The regions associated with the edible-pod character are indicated as vertical bars of asterisk. The grey boxes indicate the regions with overlapping QTL for PMTs

Fig. 3

A Manhattan and B QQ plots of GWAS scan for EPC (‘snap’ vs. ‘non-snap’) on a subset of the SDP using MLM model in Tassel v5.1 (Bradbury et al. 2007). The red line represents the significant threshold (− Log10(P) values = 3), which was determined from FDR. Detailed information about the SNP-trait association is shown in the supplementary Table S5