Copy Number Variation Affecting the Photoperiod-B1 and Vernalization-A1 Genes Is Associated with Altered Flowering Time in Wheat (Triticum aestivum)

Abstract

The timing of flowering during the year is an important adaptive character affecting reproductive success in plants and is critical to crop yield. Flowering time has been extensively manipulated in crops such as wheat ( Triticum aestivum L.) during domestication, and this enables them to grow productively in a wide range of environments. Several major genes controlling flowering time have been identified in wheat with mutant alleles having sequence changes such as insertions, deletions or point mutations. We investigated genetic variants in commercial varieties of wheat that regulate flowering by altering photoperiod response ( Ppd-B1 alleles) or vernalization requirement ( Vrn-A1 alleles) and for which no candidate mutation was found within the gene sequence. Genetic and genomic approaches showed that in both cases alleles conferring altered flowering time had an increased copy number of the gene and altered gene expression. Alleles with an increased copy number of Ppd-B1 confer an early flowering day neutral phenotype and have arisen independently at least twice. Plants with an increased copy number of Vrn-A1 have an increased requirement for vernalization so that longer periods of cold are required to potentiate flowering. The results suggest that copy number variation (CNV) plays a significant role in wheat adaptation.

Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia

“…We characterized two common wheat varieties with reduced vernalization requirement linked to the VRN-A1 locus (6,44). Jagger (KS-82-W-418/STE-PHENS), a hard red winter wheat, was the most widely planted variety in Kansas and Oklahoma for 12 y.…”

“…The second haplotype, found in VRN-D4 and the related VRN-A1 sequences in CS, Jagger, and Claire (henceforth RIP-3 VRN-D4 ), included the previous T2783C SNP and two additional SNPs at positions 2,780 (G2780C) and 2,784 (C2784T). Interestingly, the VRN-A1 alleles from Jagger and Claire have been previously linked to a weak vernalization requirement (6,44).…”

“…The VRN-A1 allele from CS has not been characterized in detail, but the winter wheat varieties Jagger and Claire have a reduced vernalization requirement (6,44) that maps to the VRN-A1 locus. The cause of the reduced vernalization requirement is still controversial and has been attributed to copy number variation in Claire (6) and to a polymorphism (A180V) in the VRN-A1 protein in Jagger (44). The discovery that both Claire and Jagger carry the RIP-3 VRN-D4 allele provides an alternative explanation for their reduced vernalization requirement.…”

“…This last interpretation is consistent with the expression reported for these two varieties. VRN-A1 transcript levels increased more rapidly in Jagger than in the winter line 2174 (RIP-3 VRN-A1 ) (44) and also more rapidly in Claire than in the winter varieties Malacca and Hereward (6).…”

“…Wheat adaptation to different latitudes and planting dates is mainly associated with natural variation in the photoperiod gene PPD1 that promotes flowering under long days (4)(5)(6) and in the vernalization gene VRN1 that modulates the requirement of long exposures to cold temperatures (vernalization) to induce flowering (7)(8)(9). The photoperiod and vernalization pathways converge at the regulation of FT1 (= VRN3 in wheat) (10), which encodes a mobile protein that travels from leaves to the shoot apical meristem (SAM) (11,12).…”