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.