The New Wheat Vernalization Response Allele Vrn-D1s is Caused by DNA Transposon Insertion in the First Intron

Abstract

Vernalization requirement in hexaploid wheat is largely controlled by a series of homoeologous VERNALIZATION (Vrn) genes, Vrn-A1, Vrn-B1, and Vrn-D1. The sequence of the promoter area and first intron of Vrn-D1 were analysed in 77 hexaploid accessions, representing five wheat species (Triticum compactum, Triticum sphaerococcum, Triticum spelta, Triticum vavilovii, and Triticum macha) sampled from different ecogeographic areas within 35 countries. Polymorphism was detected in the Vrn-D1 promoter, resulting in a new Vrn-D1 haplotype (named here, Hap-8T). Analysis of Vrn-D1 intron-1 sequences revealed a novel insertional mutation in a subset of T. spelta and T. compactum accessions. This mutant allele was designated Vrn-D1s. Analysis of the 844 bp insertion revealed it to be a nov el tra nspo sab le DNA e l emen t (nam ed DTA_Chimera_KF800714) not previously described in Triticum, belonging to the hAT superfamily. Finally, we describe a PCR-based assay that discriminates the wild-type vrn-D1 allele from the Vrn-D1s allele. Collectively, the work described here highlights the potential of utilizing minor hexaploid wheat species for the identification of novel alleles of agronomic importance.

INDEL variation in the regulatory region of the major flowering time gene LanFTc1 is associated with vernalization response and flowering time in narrow‐leafed lupin (Lupinus angustifolius L.)

“…The largest and most widely published allelic series identified to date involves VRN‐1 , a MADS‐box transcription factor that is orthologous to APETALA1 in Arabidopsis (Yan et al, ) and that is involved in maintaining down‐regulation of floral repressors following vernalization within members of the Poaceae family (A. Chen & Dubcovsky, ). Within the promoter and intronic regions, a staggering number of INDELs ranging in size from 20 to 6,850 bp, in addition to a single SNP, have been identified in the A, B, D, and G genomes of various diploid, tetraploid, and hexaploid wild and domestic wheats and their progenitors (Fu et al, ; Golovnina, Kondratenko, Blinov, & Goncharov, ; Konopatskaia, Vavilova, Kondratenko, Blinov, & Goncharov, ; Milec, Tomková, Sumíková, & Pánková, ; Muterko, Balashova, Cockram, Kalendar, & Sivolap, ; Santra, Santra, Allan, Campbell, & Kidwell, ; Shcherban, Efremova, & Salina, ; Takumi, Koyamam, Fujiwara, & Kobayashi, ; Yan et al, ; Zhang, Gao, Wang, Chen, & Cui, ), plus the H genome of barley ( Hordeum vulgare L.; Fu et al, ). Our study also adds to others in Arabidopsis (Liu et al, ; Schwartz et al, ), perennial ryegrass ( Lolium perenne ; Skøt et al, ), and wheats and barley (F. Chen et al, ; Yan et al, ) showing that FT orthologues have similarly been a common target for the evolution of natural flowering time variation in a range of plant families.…”

“…. Within the promoter and intronic regions, a staggering number of INDELs ranging in size from 20 to 6,850 bp, in addition to a single SNP, have been identified in the A, B, D, and G genomes of various diploid, tetraploid, and hexaploid wild and domestic wheats and their progenitors(Fu et al, 2005;Golovnina, Kondratenko, Blinov, & Goncharov, 2010;Konopatskaia, Vavilova, Kondratenko, Blinov, & Goncharov, 2016;Milec, Tomková, Sumíková, & Pánková, 2012;Muterko, Balashova, Cockram, Kalendar, & Sivolap, 2015;Santra, Santra, Allan, Campbell, & Kidwell, 2009;Shcherban, Efremova, & Salina, 2012;Takumi, Koyamam, Fujiwara, & Kobayashi, 2011;Yan et al, 2004;Zhang, Gao, Wang, Chen, & Cui, 2015), plus the H genome of barley (Hordeum vulgare L.;Fu et al, 2005). Our study also adds to others in Arabidopsis(Liu et al, 2014;Schwartz et al, 2009), perennial ryegrass (Lolium perenne;Skøt et al, 2011), and wheats and barley (F Chen et al, 2013;Yan et al, 2006).…”

Genetic Architecture of Flowering Phenology in Cereals and Opportunities for Crop Improvement

“…Autumn-sown winter cultivars that contain the ancestral VRN1 allele require vernalization during winter. By contrast, spring wheat varieties carrying mutations in regulatory regions including in the TaVRN1 promoter, first intron of TaVRN1 , or in the TaVRN4 region (Fu et al, 2005; Kippes et al, 2015; Muterko et al, 2015), do not require vernalization and are sown in spring. Very recently, Kippes et al (2016) developed a triple TaVRN2 mutant that contained three non-functional TaVRN2 alleles.…”

VRN1 genes variability in tetraploid wheat species with a spring growth habit

“…Most of the dominant alleles of VRN-B1 and VRN-D1 genes possess deletions in the first intron ( Vrn-B1a , Vrn-B1b , Vrn-B1c and Vrn-D1a ) [16, 19, 22, 24–27]. Several recently identified alleles ( Vrn-B1ins, Vrn-D1c, Vrn-D1s ) are characterized by different insertions within the promoter region [19, 28, 29]. The Vrn - D1b is characterized by the deletion in intron 1 identical to Vrn - D1a allele and a single nucleotide mutation at promoter and is associated with facultative growth habit [30].…”