Allele frequencies in the VRN-A1, VRN-B1 and VRN-D1 vernalization response and PPD-B1 and PPD-D1 photoperiod sensitivity genes, and their effects on heading in a diverse set of wheat cultivars (Triticum aestivum L.)

Tibor Kiss 0 1 2 Krisztina Balla 0 1 2 Otto Veisz 0 1 2 Laszl o La ng 0 1 2 Zoltan Bedo} 0 1 2 Simon Griffiths 0 1 2 Peter Isaac 0 1 2 Ildiko Karsai 0 1 2 0 P. Isaac IDna Genetics Ltd, Norwich Research Park , Norwich NR4 7UH, UK 1 S. Griffiths John Innes Centre, Norwich Research Park , Norwich NR4 7UH, UK 2 T. Kiss (&) K. Balla O. Veisz L. Lang Z. Bedo} I. Karsai Centre for Agricultural Research, Agricultural Institute, Hungarian Academy of Sciences , Martonvasar 2462, Hungary Heading of cereals is determined by complex genetic and environmental factors in which genes responsible for vernalization and photoperiod sensitivity play a decisive role. Our aim was to use diagnostic molecular markers to determine the main allele types in VRN-A1, VRN-B1, VRN-D1, PPD-B1 and PPD-D1 in a worldwide wheat collection of 683 genotypes and to investigate the effect of these alleles on heading in the field. The dominant VRN-A1, VRNB1 and VRN-D1 alleles were present at a low frequency. The PPD-D1a photoperiod-insensitive allele was carried by 57 % of the cultivars and was most frequent in Asian and European cultivars. The PPD-B1 photoperiod-insensitive allele was carried by 22 % of the genotypes from Asia, America and Europe. Nine versions of the PPD-B1-insensitive allele were identified based on gene copy number and intercopy structure. The allele compositions in PPD-D1, PPD-B1 and VRN-D1 significantly influenced heading and together explained 37.5 % of the phenotypic variance. The role of gene model increased to 39.1 % when PPD-B1 intercopy structure was taken into account instead of overall PPD-B1 type (sensitive vs. insensitive). As a single component, PPD-D1 had the most important role (28.0 % of the phenotypic variance), followed by PPD-B1 (12.3 % for PPDB1_overall, and 15.1 % for PPD-B1_intercopy) and VRN-D1 (2.2 %). Significant gene interactions were identified between the marker alleles within PPD-B1 and between VRN-D1 and the two PPD1 genes. The earliest heading genotypes were those with the photoperiod-insensitive allele in PPD-D1 and PPD-B1, and with the spring allele for VRN-D1 and the winter alleles for VRN-A1 and VRN-B1. This combination could only be detected in genotypes from Southern Europe and Asia. Late-heading genotypes had the sensitivity alleles for both PPD1 genes, regardless of the allelic composition of the VRN1 genes. There was a 10-day difference in heading between the earliest and latest groups under field conditions. - Bread wheat is grown approximately between latitudes 60 N and 40 S in the temperate zone (Nuttonson 1955). These regions exhibit considerable differences in macro- and microclimate, requiring a wide range of genetic diversity if the crops are to be capable of acclimatization. Detailed knowledge of the physiological and genetic factors influencing the start and length of the flowering period could contribute to the successful breeding of genotypes better able to adapt to present and future changes in the environment. The molecular basis of the complex genetic regulation of the flowering period has largely been clarified in wheat and barley (Cockram et al. 2007; Distelfeld et al. 2009), but there is still much uncertainty about the adaptation of these species to a wide range of environmental factors and about the molecular and genetic processes taking place in the plants due to interactions between these factors. One of the most important components of adaptation is flowering time, which is determined to a great extent by gene groups that regulate the vernalization requirement, i.e. the cold period that induces the transition from the vegetative to the generative phase (VRN genes), and the photoperiod sensitivity (PPD genes) (Worland 1996; Dubcovsky et al. 1998; Worland et al. 1998). In the case of wheat, several gene families are involved in the genetic regulation of the vernalization response. Those with the greatest effect are VRN-A1, VRN-B1 and VRN-D1, which are located on the long arm of the homologous chromosomes 5A, 5B and 5D (Pugsley 1971; Law et al. 1975; Galiba et al. 1995; Worland 1996; Barrett et al. 2002; Yan et al. 2003). Depending on the ratio of dominant and recessive alleles in the VRN genes in the three genomes of hexaploid wheat, it is possible to distinguish cultivars with winter (recessive) or spring (dominant) seasonal growth habit, while genotypes with the facultative habit have various combinations of dominant and recessive alleles. Numerous polymorphisms have been found in the promoter, exon and intron regions of the VRNA1 gene, which include duplications and deletions. The basic allele types of spring/winter habit are associated with various sequence differences detected in the promoter region and with relatively large insertions or deletions in the intron1 region (Yan et al. 2004; Fu et al. 2005), based on which several haplotypes have been identified. Thus, the promoter region of the VRN-A1a allele is duplicated, while the VRN-A1b allele differs from the vrn-A1 (recessive) allele in a 20-bp deletion in the TC-repetitive elements of the 50 untranslated region. The alleles vrn-A1c (a 7,222-bp deletion in the intron1 region), Vrn-A1d (a 32-bp deletion in the promoter region) and Vrn-A1e (a 54-bp deletion in the promoter region) have been described in tetraploid wheat (Yan et al. 2004; Fu et al. 2005). The VRN-A1a and VRN-A1b alleles have been found to be associated with the dominant VRN-A1 haplotypes, and the vrn-A1c allele with the recessive haplotype (Sherman et al. 2004). To date, the correlation between the VRN-A1d and VRN-A1e alleles and spring (dominant) habit has not been proven experimentally (Yan et al. 2004; Fu et al. 2005). A much smaller extent of polymorphism has been demonstrated for the VRN-B1 and VRN-D1 genes, and for these two genes the spring/winter type can basically be attributed to an insertion/deletion in the intron1 region (Fu et al. 2005; Milec et al. 2013). The dominant VRNA1a allele has the most pronounced genetic effect in the development of spring habit. Plants bearing this allele require no cold treatment at all to flower. By contrast, the dominant VRN-B1 and VRN-D1 genes only partially eliminate the need for cold treatment before the generative phase begins (Pugsley 1971, 1972; Kato et al. 2001; Loukoianov et al. 2005). In wheat the most important genes regulating photoperiod sensitivity are PPD-A1, PPD-B1 and PPD-D1, which are located on the homologous chromosomes 2A, 2B and 2D, respectively (Law et al. 1978; Borner et al. 1993). Based on the distribution of the alleles of these genes, temperate zone cereals can be divided into photoperiod-sensitive and -insensitive groups. The heading of genotypes carrying the photoperiod-insensitive allele is rapid regardless of whether they are exposed to short-day or long-day illumination. The presence of the photoperiod-sensitive allele, however, substantially delays heading in the case of short days. From the point of view of functional poly (...truncated)