Abstract：Phytochrome B (PHYB) is one of key factors regulating photoperiod-dependent flowering in plant. At present study, whole genomic sequences of PHYB, which were isolated from extremely late- and early-bolting Chinese cabbage (Brassica rapa L. ssp. pekinensis) inbred lines 06-247 and He102, were analyzed bioinformatically. The results revealed that the total length of PHYB in both lines were 5 986 and 5 528 bp respectively. And the sequences of both were not completely identical to that of Chiifu-401 from BRAD (Brassica Database), thus they were all mutants of wild type PHYB and named as BraphyB1(GenBank No. KJ866947) (from 06-247) and BraphyB2 (GenBank No. KJ866948)(from He102). There were 476 Inserts/Deletions(InDels) and 57 SNPs, among which 473 InDels and 31 SNPs located in promotor and 3 InDels and 26 SNPs located in coding region. InDels appeared 445, 18 and 3 bp deletions in phyB2 promoter, 5'UTR and coding region, respectively, among which 445 bp deletion in promotor containing two TATABOX4, two MYB-like transcription factors biding sites and one GA-responsive element; 18 bp deletion in 5'UTR might influence secondary structure of mature mRNA and then the scanning of pre-initiation complex and translation efficiency; 3 bp deletion in coding region of phyB2 caused an amino acid deletion. Furtermore, among 26 SNPs in coding region, 3 were nonsynonymous mutations which caused amino acid subtitutions between phyB1 and phyB2. A set of codorminant markers relating to large fragment InDel in promotor were developed and named as phyB1-762/phyB2-317. A segregating F2 population derived from 06-247 and He102 was detected with the markers. Association analysis between markers and flowering time revealed that phyB1-762 and phyB2-317 were significantly (P<0.05) related to late and early flowering respectively. Real-time quantitative RT-PCR analysis revealed that the relative mRNA level in tissues of He102 were evidantly lower than that in 06-247, the difference was statistically the most significant (P<0.01) at all development stages tested. Thus the large fragment deletion mutation in promotor was one of the most important factors causing low level phyB2 expresson and early flowering in He102. The results provide clues for research on molecular mechanism which influences Chinese cabbage flowering time by PHYB mutation at the level of trancription, translation and protein structure.
