Diverse gene regulatory strategies in response to heavy metal
stress
To investigate whether the selective genes function stably in response
to abiotic stress across different hybrid populations, we treated two
genotypes with a series of cadmium and conducted a comprehensive
transcriptomic analysis. PCA of the RNAseq dataset showed the first
principal component (PC1) accounted for 72% of the variance, while the
second principal component (PC2) accounted for 20% of the variations.
The transcriptomes of the Heze and Panjin genotypes were clearly
separated along PC1. Minimal variation was observed among the Panjin
individuals, regardless of Cd treatments, suggesting this genotype is
less sensitive to cadmium exposure. In contrast, PC2 separated the gene
expression profiles of the Heze control group from those of the
treatment groups. One sample treated with a high cadmium concentration
grouped with the control genotypes. Although most samples had more than
92% of reads mapped to the reference genome, this particular sample
showed a lower mapping rate of 86%, indicating that the individual may
not have been in optimal condition during sampling (Fig. 3a ).
As a result, we excluded this genotype from subsequent analyses. In the
Panjin genotype, compared to the Heze genotype, 2,078 genes were
upregulated and 1,492 genes were downregulated (seeSupplementary Fig. S2 ). Among these, 14 selective genes were
found to be upregulated, while nine selective genes were downregulated
(Supplementary Table S5 ).
The upregulated genes are predominantly involved in biological processes
such as responses to external biotic stimuli, defense against bacteria
and oomycetes, cell surface receptor signaling pathways, responses to
salicylic acid, intracellular water homeostasis, and phosphorylation.
Regarding cellular components, these genes mainly impact the plasma
membrane and contribute to protein serine/threonine kinase activity, ADP
binding, phosphotransferase activity involving alcohol group acceptors,
cyclase activity, and transmembrane signaling receptor activity. In
contrast, the downregulated genes did not show any significantly
enriched Gene Ontology (GO) terms.
The coefficient of variation (CVa) analysis is essential for assessing
the variability in gene expression across different treatment conditions
relative to the mean expression levels. The Heze genotype under
treatment conditions exhibited the highest median CVa among all groups,
with a value of 1.53 (Fig. 3b ; Supplementary Table
S6 ). In contrast, the control groups of the Heze and Panjin genotypes
displayed similar CVa values, with 0.983 and 0.920, respectively. The
adaptive genes that were upregulated in the Panjin C vs Heze C
comparison, showed the highest CVa values in Panjin HL treatment group.
Conversely, downregulated genes in the Panjin C vs Heze C comparison
exhibited the highest CVa values in the Heze HL cadmium groups
(Supplementary Figure S3, S4 ). Nonetheless, all the selective
genes showed higher CVa values than the median CVa of all genes
(Supplementary Table S7 ). This suggests that Heze genotype
showed higher response to the cadmium stress, and the adaptive genes
have played a special role with independent regulatory pathways in each
genotype.