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

Research article Open Access Published: 05 December 2013 Molecular characterization of vernalization and response genes in bread wheat from the Yellow and Huai Valley of China Feng Chen1,2,3, Manxia Gao1, Jianghua Zhang1, Aihui Zuo1, Xiaoli Shang1 & Dangqun Cui1,2,3  BMC Plant Biology volume 13, Article number: 199 (2013) | Download Citation Article metrics 5229 Accesses 35 Citations Abstract 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. Background The grain yield of wheat is determined not only by the genes directly controlling yield and yield components, but also by the genes controlling plant development and maturity [1]. Vernalization and photoperiod responses, which determine flowering and heading times, have a significant influence on the adaptability of wheat plants to a set of environmental conditions. The vernalization requirement of winter wheat cultivars (a prolonged exposure to low temperatures to accelerate flowering) protects the sensitive floral meristems from frost damage by cold temperatures. Differences in photoperiod sensitivity are also widely used in wheat breeding to provide adaptation to diverse agronomic environments. Major vernalization response (Vrn) loci, which determine flowering and maturity times, have been mapped to the middle of the long arms of chromosomes 5 [2–5]. Moreover, vernalization response is actually controlled by 3 distinct Vrn loci in bread wheat. Vrn-1 genes, directly influencing flowering and maturity times, are located on chromosomes 5AL, 5BL and 5DL [6, 7] and were the first vernalization genes cloned in polyploid wheat by map-based cloning techniques [8]. Subsequently, Vrn-2 and Vrn-3 genes were cloned in wheat and barley by map-based cloning [9, 10]. However, Vrn-2 affected wheat growth habit as an indirect repressor of expression level of Vrn-A1 by repressing Vrn-3[11]. Loss-of-function Vrn-2 natural mutations or deletions result in the spring growth of bread wheat, which does not require vernalization to flower. The Vrn-3 gene, a homolog of the Arabidopsis FT gene [10, 12], exhibits increased expression if its dominant allele is present, resulting in accelerated flowering and a bypass of the vernalization requirement [10]. Therefore, the growth habits and vernalization requirements of cereal plants are mainly determined by 3 genes Vrn-1, Vrn-2 and Vrn-3. Photoperiod response is another important factor that influences the flowering and maturity of wheat plants. Photoperiod insensitivity is widespread in bread wheat production areas globally and is particularly prevalent in regions where the crop is grown during short days or where crop maturity is required before the onset of high summer temperatures [13]. Based on several previous reports [14–16], photoperiod response in bread wheat is mainly controlled by the Ppd-1 loci on the short arms of chromosomes 2D, 2B, and 2A. The Ppd-D1 allele for photoperiod insensitivity is generally considered the most potent, followed by Ppd-B1 and Ppd-A1[17, 18], though this view is still controversial due to conflicting results showing that Ppd-B1a could be as strong as Ppd-D1[19]. However, in the same type of wheat cultivars with winter or spring growth habits, there were still several-day differences among heading and flowering times. This difference mainly resulted from allelic variation in vernalization and photoperiod response genes at one or more loci. Therefore, identification of the vernalization and photoperiod response alleles will enhance the selection of cultivars with wide adaptability to a set of environments. Several vernalization and photoperiod response alleles have been identified in polyploidy wheat cultivars from different countries, subsequently leading to the development of a series of molecular markers for improved efficiency in identifying different vernalization and photoperiod response alleles [9, 15, 20–23]. Fu et al. [20] indicated that the Argentine and Californian spring wheat cultivars showed a lower frequency of the dominant Vrn-A1 allele and a higher frequency of the dominant Vrn-D1 allele relative to the worldwide collection, though the dominant Vrn-A1 allele was the most popular genotype at the Vrn-A1 locus. Iqbal et al. [21] developed new molecular marker for identifying Vrn-A1 alleles and found that the dominant Vrn-A1a allele was the most prevalent while the dominant Vrn-D1 allele was absent in the Canadian spring wheat surveyed. Zhang et al. [24] found that the dominant Vrn-D1 allele showed the highest frequency in Chinese popular wheat cultivars (37.8%), followed by the dominant Vrn-A1, Vrn-B1, and Vrn-B3 alleles. They also (...truncated)