The integration of quantitative trait locus mapping and transcriptome studies reveals candidate genes for water stress response in St. Augustinegrass

Abstract

Background: Drought resistance is an increasingly important trait for many plants-including St. Augustinegrass, a major warm-season turfgrass-as more municipalities impose restrictions on frequency and amount of irrigation. Breeding efforts have focused on breeding for drought resistance, and several drought-related quantitative trait loci (QTL) have been identified for St. Augustinegrass in previous studies. However, the molecular basis of this trait remains poorly understood, posing a significant roadblock to the genetic improvement of the species.

Results: This study sought to validate those QTL regions in an independent biparental population developed from two sibling lines, XSA10098 and XSA10127. The drought evaluation in two greenhouse trials showed significant genotype variation for drought stress traits including leaf wilting, percent green cover, relative water content, percent recovery, and the area under the leaf wilting-, percent green cover-, and percent recovery- curves. A linkage map was constructed using 12,269 SNPs, representing the densest St. Augustinegrass linkage map to date. A multiple QTL mapping approach identified 24 QTL including overlapping regions on linkage groups 3, 4, 6, and 9 between this study and previous St. Augustinegrass drought resistance studies. At the transcriptome level, 1965 and 1005 differentially expressed genes were identified in the drought sensitive and tolerant genotypes, respectively. Gene Ontology and KEGG analysis found different mechanisms adopted by the two genotypes in response to drought stress. Integrating QTL and transcriptomics analyses revealed several candidate genes which are involved in processes including cell wall organization, photorespiration, zinc ion transport, regulation of reactive oxygen species, channel activity, and regulation in response to abiotic stress.

Conclusions: By innovatively integrating QTL and transcriptomics, our study advances the understanding of the genetic control of water stress response in St. Augustinegrass, providing a foundation for targeted drought resistance breeding.

Keywords: Drought stress; QTL mapping; St. Augustinegrass; Transcriptome.

Fig. 1

Histograms of best linear unbiased estimators (BLUEs) for each trait across the two years of evaluation. White triangles indicate the XSA10098 maternal value while black triangles indicate the XSA10127 paternal value. GH = greenhouse, PGC = percent green cover, LW = leaf wilting, PR = percent recovery, RWC = relative water content, AULWC = area under leaf wilting curve, AUPGCC = area under percent green cover curve, AUPRC = area under percent recovery curve

Fig. 2

Pearson correlations for all traits across two years. PGC = percent green cover, LW = leaf wilting, PR = percent recovery, RWC = relative water content, AULWC = area under leaf wilting curve, AUPGCC = area under percent green cover curve, AUPRC = area under percent recovery curve. Color bar indicates correlation coefficient (r). *** indicates p-value < 0.001

Fig. 3

QTL overlap between the current study and previously identified QTL for drought resistance and morphological characteristics. For black regions from current study: PGC = percent green cover, LW = leaf wilting, PR = percent recovery, RWC = relative water content, AULWC = area under leaf wilting curve, AUPGCC = area under percent green cover curve, AUPRC = area under percent recovery curve. For blue regions from Yu et al. (2019): RWC = relative water content, CC = chlorophyll content, LF = leaf firing, LW = leaf wilting, GC = green cover, NDVI = normalized difference vegetative index. For red regions from Yu et al. (2022): LW = leaf blade width, LL = leaf blade length, CD = canopy density, SGO = shoot growth orientation

Fig. 4

Differentially expressed genes (DEGs) in St. Augustinegrass in response to water stress. (A): Number of DEGs identified in the drought sensitive and tolerant genotypes. (B): Venn diagram of DEGs, showing the unique and overlapping genes expressed among comparison groups. SW vs. SD: normal watered vs. drought stress in sensitive genotype; TW vs. TD: normal watered vs. drought stress in tolerant genotype. Groups A-H indicate different DEGs expression pattern groups

Fig. 5

Gene Ontology (GO) classification of the up-regulated DEGs (A) and down-regulated DEGs (B) identified in both genotypes. DEGs were annotated in three categories: biological process, cellular component, and molecular function. Hit% is calculated as the ratio of the input number of DEGs and the number of total annotated genes in this category

Fig. 6

KEGG pathway enrichment of the up-regulated DEGs identified in the S genotype (A) and the T genotype (C) and the down-regulated DEGs identified in the S genotype (B) and the T genotype (D). Hit% is calculated as ratio of input number of DEGs and number of total annotated genes in this pathway

Fig. 7

Expression pattern of differentially expressed genes co-localized in overlapped QTL regions across the present study

Fig. 8

Leaf wilting rating scale for St. Augustinegrass experiencing drought stress. A score of 5 indicates healthy, symptom-free turf while a score of 1 indicates desiccated turf that has lost all its green color