Genomic regions associated with physiological, biochemical and yield-related responses under water deficit in diploid potato at the tuber initiation stage revealed by GWAS

Abstract

Water deficit, which is increasing with climate change, is a serious threat to agricultural sustainability worldwide. Dissection of the genetic architecture of water deficit responses is highly desirable for developing water-deficit tolerant potato cultivars and enhancing the resilience of existing cultivars. This study examined genetic variation in response to water deficit in a panel of diploid potato and identified the QTL governing this trait via a genome-wide association study (GWAS). A panel of 104 diploid potato accessions were evaluated under both well-watered and water deficit treatments at tuber initiation stage. Drought stress index (DTI) was calculated to assess tolerance of the diploid potato genotypes to water deficit. The GWAS was conducted using a matrix of 47K single nucleotide polymorphisms (SNP), recently available for this population. We are reporting 38 QTL, seven for well-watered conditions, twenty-two for water deficit conditions and nine for DTI which explain between 12.6% and 44.1% of the phenotypic variance. A set of 6 QTL were found to be associated with more than one variable. Marker WDP-9.21 was found associated with tuber fresh weigh under WD and gene annotation analysis revealed co-localization with the Glucan/water dikinase (GWD) gene. Of the nine QTL detected from DTI on chromosomes 2,3,5,8,10 and 12, three candidate genes with a feasible role in water deficit response were identified. The findings of this study can be used in marker-assisted selection (MAS) for water- deficit tolerance breeding in potato.

Fig 1. Histogram of phenotypic values distribution analysis of the studied variables in 104 diploid genotypes under well-watered and water deficit conditions.

a.) Sucrose (Suc), b.) Glucose (Glc), c.) Fructose (Fru), d.) the maximum quantum efficiency of PSII (F_v/F_m), e.) Relative chlorophyll content (CC), f.) Tuber number (TN), g.) Tuber fresh weight per plant (TW) and h.) Relative water content (RWC). The vertical lines in the histograms show population mean values in well-watered condition (green) and water-deficit conditions (red) conditions, and values in parentheses represent the significant percentage change (+, increase;–, decrease) in water-deficit conditions over the well-watered. Levels of significance for genotype (G), water conditions (WC), and their interaction (G*WC) effects from ANOVA are given in the histograms (*** p ≤ 0.0001; ** p ≤ 0.001; * p ≤ 0.05; ns, p > 0.05.

Fig 2. Spearman’s correlation matrix between physiological, biochemical and yield-related variables.

The color and size squares represent the correlation between pairwise comparisons. * significant at p <0.05 level, **significant at <0.01 level, ***significant at <0.001 level, blank for non-significant.

Fig 3. Principal component analysis biplot with clusters defined from physiological, biochemical and yield-related variables of a diversity panel of Solanum tuberosum group Phureja genotypes grouping.

a.) water deficit conditions, b.) well-watered conditions and c.) drought stress index (DTI). The axes present the percentage of variance accounted in the first two principal components. The color of triangles represents the 104 genotypes from the Work Collection of Potato Breeding program at the Universidad Nacional de Colombia and denote the clusters from genotypes. Sucrose content (Suc), Glucose content (Glc), Fructose content (Fru), the maximum quantum efficiency of PSII (F_v/F_m), the relative chlorophyll content (CC), tuber number (TN), tuber fresh weight per plant (TW) and relative water content (RWC).

Fig 4. SNPs identified and mapped in the potato chromosomes of Group Phureja.

Genomic distances are given in Mbp according to the PGSC V4.03 pseudomolecules [15]. In red are presented the QTL detected in the phenotypic response for water deficit condition, black presented those detected for well- watered conditions, in green are presented those detected for DTI. In black are presented the markers that limit each chromosome in the potato genome. Diagram plotted using MapChart software.

Fig 5

Boxplots showing the allele effects of six significant QTL: a.) relative chlorophyll content (CC)- well-watered condition (WW), b.) relative chlorophyll content (CC)- water deficit condition (WD), c.) tuber fresh weigh per plant (TW)-water deficit condition (WD), d-f.) glucose (Glc)-water deficit condition (WD) and e.) the maximum quantum efficiency of PSII (F_v/F_m). Y-axis: values for variables. X-axis: SNP genotypic classes. The gene annotation is presented in italic.