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In wheat ( Triticum aestivum  L.), time from planting to spike emergence is influenced by genes controlling vernalization requirement and photoperiod response. Characterizing the available genetic diversity of known and novel alleles of  VERNALIZATION1  ( VRN1 ) and  PHOTOPERIOD1  ( PPD1 ) in winter wheat can inform approaches for breeding climate resilient cultivars. This study identified QTL for heading date (HD) associated with multiple  VRN1  and  PPD1  loci in a population developed from a cross between two early flowering winter wheat cultivars. When the population was grown in the greenhouse after partial vernalization treatment, major heading date QTLs co-located with the  VRN-A1  and  VRN-B1  loci. Copy number variation at the  VRN-A1  locus influenced HD such that RIL having three copies required longer cold exposure to transition to flowering than RIL having two  VRN-A1  copies. Sequencing  vrn-B1  winter alleles of the parents revealed multiple polymorphisms in the first intron that were the basis of mapping a major HD QTL coinciding with  VRN-B1 . A 36 bp deletion in the first intron of  VRN-B1  was associated with earlier HD after partial vernalization in lines having either two or three haploid copies of  VRN-A1 . The  VRN1  loci interacted significantly and influenced time to heading in field experiments in Louisiana, Georgia and North Carolina. The  PPD1  loci were significant determinants of heading date in the fully vernalized treatment in the greenhouse and in all field environments. Heading date QTL were associated with alleles having large deletions in the upstream regions of  PPD-A1  and  PPD-D1  and with copy number variants at the  PPD-B1  locus. The  PPD-D1  locus was determined to have the largest genetic effect, followed by  PPD-A1  and  PPD-B1 . Our results demonstrate that  VRN1  and  PPD1  alleles of varying strength allow fine tuning of flowering time in diverse winter wheat growing environments.

Heading Date QTL in Winter Wheat (Triticum aestivum L.) Coincide with Major Developmental Genes VERNALIZATION1 and PHOTOPERIOD1