Genome variation, expression divergence, phenotypic variation between BT×623 and Keller and their relationship. Functionally significant genome variations between BT×623 and Keller might be subjected into selection pressure during evolution and variety domestication. Variations in gene coding regions might lead to gene functional divergence. One of the divergences was in genes involved in programmed cell death, which might lead to divergent vascular systems between BT×623 and Keller. Another divergence is in DNA methylation, which might contribute to gene expression divergence. Variations in promoters, UTRs, introns, microRNAs etc. might also result in expression divergence. BT×623 and Keller exhibited significant divergence in gene expression, which might contribute to divergent sugar content and disease resistance.