Statistical analyses
For the hypothesis testing, the Wald test was used in DEseq2 to evaluate
genes that are significantly differently expressed among the haplotypes
and treatments with Bonferroni correction. Then, the differentially
expressed genes were used to infer the associated gene ontology and
Kyoto Encyclopedia of Genes and Genomes (KEGG) terms using Fisher’s
exact test with Bonferroni multiple correction. ANOVA was conducted to
compare the physiological traits including net photosynthetic rate,
chlorophyll content, actual quantum efficiency of PSⅡ, maximum quantum
efficiency of PSⅡ, electron transfer efficiency, ion leakage rate across
haplotypes and treatments, followed by Turkey’s post-hoc HSD test for
multiple corrections.