A Genome-Wide Association Study To Understand the Effect of Fusarium verticillioides Infection on Seedlings of a Maize Diversity Panel

Abstract

Fusarium verticillioides, which causes ear, kernel and stem rots, has been reported as the most prevalent species on maize worldwide. Kernel infection by F. verticillioides results in reduced seed yield and quality as well as fumonisin contamination, and may affect seedling traits like germination rate, entire plant seedling length and weight. Maize resistance to Fusarium is a quantitative and complex trait controlled by numerous genes with small effects. In the present work, a Genome Wide Association Study (GWAS) of traits related to Fusarium seedling rot was carried out in 230 lines of a maize association population using 226,446 SNP markers. Phenotypes were scored on artificially infected kernels applying the rolled towel assay screening method and three traits related to disease response were measured in inoculated and not-inoculated seedlings: plant seedling length (PL), plant seedling weight (PW) and germination rate (GERM). Overall, GWAS resulted in 42 SNPs significantly associated with the examined traits. Two and eleven SNPs were associated with PL in inoculated and not-inoculated samples, respectively. Additionally, six and one SNPs were associated with PW and GERM traits in not-inoculated kernels, and further nine and thirteen SNPs were associated to the same traits in inoculated kernels. Five genes containing the significant SNPs or physically closed to them were proposed for Fusarium resistance, and 18 out of 25 genes containing or adjacent to significant SNPs identified by GWAS in the current research co-localized within QTL regions previously reported for resistance to Fusarium seed rot, Fusarium ear rot and fumonisin accumulation. Furthermore, linkage disequilibrium analysis revealed an additional gene not directly observed by GWAS analysis. These findings could aid to better understand the complex interaction between maize and F. verticillioides.

Keywords: Artificial inoculation; Fusarium verticillioides; GWAS; Maize; SNPs.

Figure 1

Effect of inoculation with Fusarium verticillioides on germination percentage compared to control, in kernels of selected maize lines.

Figure 2

Correlation among disease severity (SEV; Stagnati et al. 2019), plant length (PL), plant weight (PW), germination percentage (G) traits measured in the control (C) or inoculated (I) plants. The distribution of each trait is shown on the diagonal. On the bottom of the diagonal the bivariate scatter plots with a fitted line are displayed. On the top of the diagonal the value of the correlation plus the significance level are reported as stars (*** p-value 0.001).

Figure 3

Manhattan plots of the traits PL_C (A), PL_I (B), PW_C (C), PW_I (D), GERM_C (E) and GERM_I (F). SNPs significantly associated to the traits are indicated by green dots.

Figure 4

Localization of QTL and genes containing or adjacent to SNPs identified by GWAS on chromosomes 1, 2 and 3. Genes associated with different traits (PL_C; PL_I; PW_C; PW_I; GERM_C; GERM_I) from this study are indicated by the black arrow. Candidate genes from Zila et al. (2013) are indicated by the orange arrow. Horizontal lines of different colors represent different QTL intervals for resistance to Fusarium and fumonisin accumulation identified by previous reports: pink and gray (Fusarium ear rot and fumonisins from Lanubile et al. 2014b and Maschietto et al. 2017, respectively); green (Fusarium seed rot from Ju et al. 2017); blue (Fusarium seedling rot, plant length and weight from Septiani et al. 2019). The centromere is indicated by a red label on the chromosome.

Figure 5

Localization of QTL and genes containing or adjacent to SNPs identified by GWAS on chromosomes 4, 5 and 6. Genes associated with different traits (PL_C; PL_I; PW_C; PW_I; GERM_C; GERM_I) from this study are indicated by the black arrow. Candidate genes from Zila et al. (2013) are indicated by the orange arrow. Horizontal lines of different colors represent different QTL intervals for resistance to Fusarium and fumonisin accumulation identified by previous reports: pink and gray (Fusarium ear rot and fumonisins from Lanubile et al. 2014b and Maschietto et al. 2017, respectively); green (Fusarium seed rot from Ju et al. 2017); blue (Fusarium seedling rot, plant length and weight from Septiani et al. 2019). The centromere is indicated by a red label on the chromosome.

Figure 6

Localization of QTL and genes containing or adjacent to SNPs identified by GWAS on chromosomes 8 and 9. Genes associated with different traits (PL_C; PL_I; PW_C; PW_I; GERM_C; GERM_I) from this study are indicated by the black arrow. Candidate genes from Zila et al. (2013) are indicated by the orange arrow. Horizontal lines of different colors represent different QTL intervals for resistance to Fusarium and fumonisin accumulation identified by previous reports: pink and gray (Fusarium ear rot and fumonisins from Lanubile et al. 2014b and Maschietto et al. 2017, respectively); green (Fusarium seed rot from Ju et al. 2017); blue (Fusarium seedling rot, plant length and weight from Septiani et al. 2019). The centromere is indicated by a red label on the chromosome.