Cold acclimation in cereal species is determined by complicated genetic and transcriptional interactions at the genome level. A controlled environment study that simulated the autumn natural field conditions at Saskatoon, Saskatchewan, Canada, was conducted utilizing Norstar (NO, cold tolerant) and Manitou (MA, cold tender) wheat and their near-isogenic lines (NILs), winter Manitou (WM) and spring Norstar (SN) with the growth habit VRN-A1 alleles swapped. MA, SN and WM reached the vegetative/reproductive transition (VRT) by 14, 21, and 60d, respectively, while NO was still in the vegetative stage at 70d. 96 RNA samples representing each line at 12 sampling dates during vernalization and cold acclimation were extracted from crown tissue and used for RNA sequencing that yielded 2,488,292,323 reads and a total of 176,581 genes. Number of differentially expressed genes (DEGs) peaked at 35d in MA and 49d in NO. MA responded to the decreasing temperatures faster than the other lines and 5,374, 2,106, 1,996, 2,630 unique DEGs were identified in MA, NO, SN and WM, respectively during the entire sampling period. Several gene clusters highly correlated with changes in LT50, sampling time, and day length were investigated to identify candidate genes for the adaptation to over winter stresses. Network comparisons revealed divergent and similar cold responses between the four NILs. Our study provides novel insights into the transcriptome reprogramming during phenological development and cold acclimation in wheat.