Identification of Genes Controlling Earliness per se and Short Day Photoperiod Response in Bread Wheat

Major genes controlling photoperiod and vernalization sensitivity have been cloned. A knowledge gap exists in the identification of genes controlling Earliness per se (Eps) and short day specific (SDS) genes. We describe the positional cloning of an Eps locus on wheat 1DL named Eps-D1. Eps-D1 is due to a deletion including several genes in the sub-telomeric region. Using near isogenic lines (NILs), and key recombinants, we identified TaELF3-D1 within Eps-D1 a homologue of the Arabidopsis thaliana circadian clock gene ELF3 as the most likely candidate for Eps-D1. Gene expression, using NILs, showed altered TaGIGANTEA (TaGI) expression consistent with an ELF3 mutation. We also describe the identification of two short day specific QTLs on wheat 1BS and 1DL using doubled haploid populations grown under short and long days. Using genomics, bioinformatics and synteny with Brachypodium distachyon, we identified TaTOE1-B1 and TaFT3-B1 the homologues of ZmTOE1 and HvFT3 as the more likely candidates for the QTLs on 1BS and 1DL respectively. Gene expression analysis suggests that TaTOE1 homoeologues are repressors of FT1, expression of TaTOE1 was higher in the juvenile plant, and under short days a result which was consistent with the role of TOE1 in Arabidopsis thaliana suggesting a similar function in both species. TaFT3 homoeologues were also expressed at higher levels under short days in barley. These genes will give options for breeding by design using the KASP markers we designed and will also enable further academic research to unravel the complex flowering time regulation pathways in temperate cereals.