Genome-wide association scan and transcriptome analysis reveal candidate genes for waterlogging tolerance in cultivated barley

Abstract

Waterlogging is the primary abiotic factor that destabilizes the yield and quality of barley (Hordeum vulgare L.). However, the genetic basis of waterlogging tolerance remains poorly understood. In this study, we conducted a genome-wide association study (GWAS) by involving 106,131 single-nucleotide polymorphisms (SNPs) with a waterlogging score (WLS) of 250 barley accessions in two years. Out of 72 SNPs that were found to be associated with WLS, 34 were detected in at least two environments. We further performed the transcriptome analysis in root samples from TX9425 (waterlogging tolerant) and Franklin (waterlogging sensitive), resulting in the identification of 5,693 and 8,462 differentially expressed genes (DEGs) in these genotypes, respectively. The identified DEGs included various transcription factor (TF) genes, primarily including AP2/ERF, bZIP and MYB. By combining GWAS and RNA-seq, we identified 27 candidate genes associated with waterlogging, of which three TFs (HvDnaJ, HvMADS and HvERF1) were detected in multiple treatments. Moreover, by overexpressing barley HvERF1 in Arabidopsis, the transgenic lines were detected with enhanced waterlogging tolerance. Altogether, our results provide new insights into the genetic mechanisms of waterlogging, which have implications in the molecular breeding of waterlogging-tolerant barley varieties.

Proteomic exploration reveals a metabolic rerouting due to low oxygen during controlled germination of malting barley (Hordeum vulgare L.)

“…In addition, attempts to aerate the water are inefficient due to the poor solubility of oxygen in water ( Kelly and Briggs, 1992 ). Therefore, we hypothesize that observed differences in IGB1467 and Flinders ( Figures 2 ; 3 , Supplementary Figure S3 ) are related to varied metabolic adaptations (‘tolerance’) during controlled germination to low-O 2 conditions with the regulation of previously reported submergence-responsive pathways ( Luan et al., 2018 ; Borrego-Benjumea et al., 2020 ; Luan et al., 2022 ). The observed difference in metabolic modulation of protein groups under low-O 2 enforced by submergence during controlled germination saw varied patterns between IGB1467 and Flinders related to signaling, protein synthesis, energy metabolism, including glycolysis, fermentation, and finally, the impacts of low-O 2 metabolic activity and generation of reactive oxygen species.…”

Transcriptional analysis in multiple barley varieties identifies signatures of waterlogging response

“…We next compared our RNA-seq results to two recently published RNA-seq datasets. Luan et al (2022) analyzed the transcriptomic response of four-leaf stage Franklin and TX9425 barley roots to waterlogging for 24 or 72 h. These were two-row spring varieties, with Franklin showing sensitivity and TX9425 showing tolerance to waterlogging (Luan et al, 2022). In addition, Borrego-Benjumea et al…”

Transcriptional signatures associated with waterlogging stress responses and aerenchyma formation in barley root tissue

“…The root system, as the first line of defence against soil waterlogging, undergoes metabolic and anatomical adaptations supporting survival of the whole plant, and therefore should be studied as a priority when early waterlogging stress responses are considered (Herzog et al, 2016; Langan et al, 2022). However, relatively limited resources are currently available in terms of transcriptomic (Borrego-Benjumea et al, 2020; Luan et al, 2023), proteomic or metabolomic datasets (Andrzejczak et al, 2020; Luan et al, 2018a; Luan et al, 2022) characterizing responses of barley root tissue to waterlogging stress or hypoxia. Here, we used a combination of plant phenotyping and transcriptomics (RNA-seq) to further our understanding of waterlogging responses in barely root tissue, with particular focus on elucidation of pathways and genes modulating formation of root aerenchyma, a key anatomical adaptation for waterlogging tolerance (Mustroph, 2018).…”

“…For example, Borrego-Benjumea et al (2020) carried out whole root tissue transcriptional profiling under waterlogging stress and a larger scale study examined waterlogging-induced root transcriptomic signatures in 21 barley cultivars that led to isolation of 98 core waterlogging response genes (Miricescu et al, 2023). Root transcriptome profiling (Luan et al, 2023), and combination of genome-wide association studies (GWAS) and root transcriptome profiling (Luan et al, 2022), also led to identification of several barley waterlogging associated genes that were further functionally validated in Arabidopsis thaliana .…”