Population-level transcriptomes reveal gene expression and splicing underlying cadmium accumulation in barley

Area of Science:

• Plant Genetics
• Environmental Stress Response
• Food Safety

Background:

• Genetic variation significantly impacts gene transcription and phenotypic diversity.
• Understanding genetic control of gene expression and splicing in response to cadmium (Cd) is vital for food safety and human health.
• Cadmium accumulation in crops is a significant concern.

Purpose of the Study:

• To investigate population-level transcriptome variation in barley under Cd exposure.
• To identify genetic variants controlling gene expression and alternative splicing related to Cd accumulation.
• To elucidate the mechanisms underlying Cd accumulation in plants.

Main Methods:

• Genome-wide association study (GWAS) on barley core accessions.
• Analysis of transcriptome variation under Cd exposure.
• Identification of expression quantitative trait loci (eQTLs) and splicing quantitative trait loci (sQTLs).

Main Results:

• Marked transcriptomic changes in barley in response to Cd exposure, largely tissue-independent.
• Identification of 59,498 eQTLs and 23,854 sQTLs, forming a network covering 66.6% of expressed genes, including metal transporters.
• Co-localization of 34.5% of GWAS QTLs for Cd accumulation traits with eQTLs and sQTLs, suggesting a role in phenotypic plasticity.

Conclusions:

• Genetic variants significantly influence gene expression and alternative splicing in barley under Cd stress.
• Distal and proximal genetic effects play a role in phenotypic plasticity related to Cd accumulation.
• The findings provide insights into the genetic basis of Cd accumulation, aiding in developing strategies for safer crops.