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Background  Flowering time greatly influences the adaptation of wheat cultivars to diverse environmental conditions and is mainly controlled by vernalization and photoperiod genes. In wheat cultivars from the Yellow and Huai Valleys, which represent 60%-70% of the total wheat production in China, the large-scale genotyping of wheat germplasms has not yet been performed in terms of vernalization and photoperiod response alleles, limiting the use of Chinese wheat germplasms to a certain extent.    Results  In this study, 173 winter wheat cultivars and 51 spring wheat cultivars from China were used to identify allelic variations of vernalization and photoperiod genes as well as copy number variations of  Ppd-B1  and  Vrn-A1 . Two new co-dominant markers were developed in order to more precisely examine  Vrn-A1b ,  Vrn-B1a , and  Vrn-B1b . Two novel alleles at the  Vrn-B3  locus were discovered and were designated  Vrn-B3b  and  Vrn-B3c. Vrn-B3b  had an 890-bp insertion in the promoter region of the recessive  vrn-B3  allele, and  Vrn-B3c  allele had 2 deletions (a 20-bp deletion and a 4-bp deletion) in the promoter region of the dominant  Vrn-B3a  allele. Cultivar Hemai 26 lacked the  Vrn-A1  gene. RT-PCR indicated that the 890-bp insertion in the  Vrn-B3b  allele significantly reduced the transcription of the  Vrn-B3  gene. Cultivars Chadianhong with the  Vrn-B3b  allele and Hemai 26 with a  Vrn-A1 -null allele possessed relatively later heading and flowering times compared to those of Yanzhan 4110, which harbored recessive  vrn-B3  and  vrn-A1  alleles. Through identification of photoperiod genes, 2 new polymorphism combinations were found in 6 winter wheat cultivars and were designated  Hapl-VII  and  Hapl-VIII , respectively. Distribution of the vernalization and photoperiod genes indicated that all recessive alleles at the 4 vernalization response loci, truncated “Chinese Spring”  Ppd-B1  allele at  Ppd-B1  locus and  Hapl-I  at the  Ppd-D1  locus were predominant in Chinese winter wheat cultivars.    Conclusion  This study illustrated the distribution of vernalization and photoperiod genes and identified 2 new  Vrn-B3  alleles, 1  Vrn-A1 -null allele, and two new  Ppd-D1  polymorphism combinations, using developed functional markers. Results of this study have the potential to provide useful information for screening relatively superior wheat cultivars for better adaptability and maturity.

Molecular characterization of vernalization and response genes in bread wheat from the Yellow and Huai Valley of China