Genome-Wide Association Study Reveals Genomic Regions Associated with Fusarium Wilt Resistance in Common Bean

Abstract

Fusarium wilt (Fusarium oxysporum f. sp. phaseoli, Fop) is one of the main fungal soil diseases in common bean. The aim of the present study was to identify genomic regions associated with Fop resistance through genome-wide association studies (GWAS) in a Mesoamerican Diversity Panel (MDP) and to identify potential common bean sources of Fop's resistance. The MDP was genotyped with BARCBean6K_3BeadChip and evaluated for Fop resistance with two different monosporic strains using the root-dip method. Disease severity rating (DSR) and the area under the disease progress curve (AUDPC), at 21 days after inoculation (DAI), were used for GWAS performed with FarmCPU model. The p-value of each SNP was determined by resampling method and Bonferroni test. For UFV01 strain, two significant single nucleotide polymorphisms (SNPs) were mapped on the Pv05 and Pv11 for AUDPC, and the same SNP (ss715648096) on Pv11 was associated with AUDPC and DSR. Another SNP, mapped on Pv03, showed significance for DSR. Regarding IAC18001 strain, significant SNPs on Pv03, Pv04, Pv05, Pv07 and on Pv01, Pv05, and Pv10 were observed. Putative candidate genes related to nucleotide-binding sites and carboxy-terminal leucine-rich repeats were identified. The markers may be important future tools for genomic selection to Fop disease resistance in beans.

Keywords: Fusarium oxysporum f. sp. phaseoli; Phaseolus vulgaris L.; SNP markers; disease resistance; molecular breeding.

Figure 1

The DSR was measured according to an adapted scale [56], with values ranging from 1 to 9: score 1 = absence of symptoms and discoloration in the hypocotyl; score 3 = chlorosis, wilt, and restricted necrosis of the first leaves of the plant, with slight discoloration in the hypocotyl; score 5 = chlorosis, wilt, and necrosis in the leaves below the pointer and intermediate discoloration in the hypocotyl; score 7 = severe symptoms of generalized wilting throughout the plant, and dwarfism and severe discoloration in the hypocotyl; and score 9 = dead plant.

Figure 2

Density of 2001 SNPs in the MDP with 205 Mesoamerican genotypes. The different colors represent different density levels, and “Chr” refers to common bean chromosomes.

Figure 3

Linkage disequilibrium (LD) decay determined by the LD measurements (r²) based on 2001 filtered common beans against the distance between SNPs (Mb) for the 11 chromosomes (Pv) adjusted according to the model proposed by Hill and Weir [66] controlled for relatedness and structure in the MDP with 205 Mesoamerican genotypes.

Figure 4

(A) Kinship plot of 205 common bean genotypes (MDP). (B) Principal component analysis calculated in the MDP with 205 genotypes and 2001 SNPs.

Figure 5

GWAS for Fop resistance in the MDP with 205 common bean genotypes with significant SNPs for the UFV01 strain using the DSR and AUDPC parameters and FarmCPU. (a) Manhattan plots and (b) Q-Q (Quantile-quantile) plots, with orange circles representing the p-values for DSR and blue circles the p-values for AUDPC. The dotted red line corresponds to the cut-offline obtained by the resampling method −log10(p) = 4.53 × 10⁻⁵, and the upper red line refers to the cut-offline obtained by the Bonferroni method (α = 0.05). (c,d) Histograms of the adjusted phenotypic means (BLUE) of AUDPC and DSR. (e–h) Boxplots of the relationship between the alleles and phenotype (Fop resistance) of each significant SNP for DSR and AUDPC.

Figure 6

GWAS for Fop resistance in the MDP with 205 common bean genotypes with significant SNPs for the IAC18001 strain using the DSR and the AUDPC parameters and FarmCPU. (a) Manhattan plots and (b) Q-Q (Quantile-quantile) plots, with orange circles representing the p-values for DSR and blue circles the p-values for AUDPC. The dotted red line corresponds to the cut-offline obtained by the resampling method −log10(p) = 4.48 × 10⁻⁵, and the upper red line refers to the cut-offline obtained by the Bonferroni method (α = 0.05). (c,d) Histograms of adjusted phenotypic means (BLUE) of AUDPC and DSR. (e–k) Boxplots of the relationship between the allele and phenotype (Fop resistance) of each significant SNP for DSR and AUDPC.