Genome-wide association study and transcriptome sequencing to identify candidate genes for waterlogging tolerance during germination in barley (Hordeum vulgare L.)

Abstract

Waterlogging stress is a significant abiotic stress that has a pronounced effect on both the yield and quality of barley. Despite this, there is a lack of comprehensive understanding regarding the molecular response mechanisms involved in barley germination under waterlogging stress. In this study, we investigated five root and shoot traits related to waterlogging tolerance across 250 barley accessions. Our findings indicate that the tolerant genotype displayed lower levels of starch degradation, electrical conductivity (EC), and malondialdehyde (MDA) content compared to the sensitive genotype under waterlogging conditions. Through genome-wide association study (GWAS) analysis, we identified 77 significant Single Nucleotide Polymorphisms (SNPs) associated with waterlogging tolerance during germination. Additionally, transcriptomic analysis (RNA-Seq) revealed 1776 and 839 differentially expressed genes (DEGs) in Liu Leng Zi Da Mai (waterlogging tolerant) and Naso Nijo (waterlogging sensitive), respectively. It is noteworthy that a considerable number of these DEGs were found to be associated with transcription factors, including AP2/ERF, HSF, WRKY, MYB, and MADS. Through the integration of GWAS and RNA-Seq data analysis, a total of 32 candidate genes were pinpointed, primarily linked to plant hormones and energy metabolism regulation such as ERF, HSF, AEC and LEA. In conclusion, these findings provide novel genetic resources and insights to enhance waterlogging tolerance at germination in future barley cultivars through genomic and marker-assisted selection. This results also lay the foundation for further functional analysis of the identified candidate genes.