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.)

Abstract

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, VRN-B1 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 PPD-B1_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.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-014-0034-2) contains supplementary material, which is available to authorized users.

Allelic variation and differential expression of VRN‐A1 in durum wheat genotypes varying in the vernalization response

“…A recent study carried out on ~700 T. aestivum cultivars from different geographical origins reported that only 7% of the samples analysed carried spring alleles in VRN‐A1 (Kiss et al. ). Our analysis of 30 durum wheat accessions with specific molecular markers demonstrated a clear preponderance of spring dominant alleles at the VRN‐A1 locus (93% of accessions).…”

Effects of ambient temperature in association with photoperiod on phenology and on the expressions of major plant developmental genes in wheat (Triticum aestivum L.)

“…The major allele types of the 19 wheat cultivars in the VRN and the PPD genes (Table 1) were determined using gene allele specific primers as listed in Kiss et al (2014). In addition, they were subjected to the 15K Illumina SNP platform (TraitGenetics Ltd, Gatersleben, Germany), which resulted in 4971 polymorphic markers after leaving out those with any missing values, being monomorphic, or rare alleles (characteristic to only one genotype) or showing complete linkage within the same genetic distance in the consensus marker map provided by the company.…”

“…In wheat, the photoperiod insensitivity alleles in the PPD1 genes result in rapid heading irrespective of the photoperiod. While the role of PPD‐A1 is not significant in Triticum aestivum , several functional polymorphisms were identified in PPD‐B1 and PPD‐D1 leading to significant variations in heading date (Beales et al ; Diaz et al 2012; Kiss et al ). The basis of insensitivity is the increased gene copy number in the PPD‐B1 locus, while in the case of PPD‐D1 gene, it is a large deletion of 2089 bp in the promoter region leading to overexpression (Beales et al .…”

Effect of VRN‐1 and PPD‐D1 genes on heading time in European bread wheat cultivars

“…Recently, a diverse set of predominantly winter wheat cultivars from Europe was screened for vernalization and photoperiod alleles (Kiss et al. ). European wheat cultivars with spring type of growth have not been studied systematically in this regard.…”