Winter wheats require several weeks at low temperature to flower. This process, vernalization, is controlled mainly by the VRN1 gene. Using 6,190 gametes, we found VRN1 to be completely linked to MADS-box genes AP1 and AGLG1 in a 0.03-centimorgan interval flanked by genes Cysteine and Cytochrome B5. No additional genes were found between the last two genes in the 324-kb Triticum monococcum sequence or in the colinear regions in rice and sorghum. Wheat AP1 and AGLG1 genes were similar to Arabidopsis meristem identity genes AP1 and AGL2, respectively. AP1 transcription was regulated by vernalization in both apices and leaves, and the progressive increase of AP1 transcription was consistent with the progressive effect of vernalization on flowering time. Vernalization was required for AP1 transcription in apices and leaves in winter wheat but not in spring wheat. AGLG1 transcripts were detected during spike differentiation but not in vernalized apices or leaves, suggesting that AP1 acts upstream of AGLG1. No differences were detected between genotypes with different VRN1 alleles in the AP1 and AGLG1 coding regions, but three independent deletions were found in the promoter region of AP1. These results suggest that AP1 is a better candidate for VRN1 than AGLG1. The epistatic interactions between vernalization genes VRN1 and VRN2 suggested a model in which VRN2 would repress directly or indirectly the expression of AP1. A mutation in the promoter region of AP1 would result in the lack of recognition of the repressor and in a dominant spring growth habit.

The broad adaptability of wheat and barley is in part attributable to their flexible growth habit, in that spring forms have recurrently evolved from the ancestral winter growth habit. In diploid wheat and barley growth habit is determined by allelic variation at the VRN-1 and/or VRN-2 loci, whereas in the polyploid wheat species it is determined primarily by allelic variation at VRN-1. Dominant Vrn-A1 alleles for spring growth habit are frequently associated with mutations in the promoter region in diploid wheat and in the A genome of common wheat. However, several dominant Vrn-A1, Vrn-B1, Vrn-D1 (common wheat) and Vrn-H1 (barley) alleles show no polymorphisms in the promoter region relative to their respective recessive alleles. In this study, we sequenced the complete VRN-1 gene from these accessions and found that all of them have large deletions within the first intron, which overlap in a 4-kb region. Furthermore, a 2.8-kb segment within the 4-kb region showed high sequence conservation among the different recessive alleles. PCR markers for these deletions showed that similar deletions were present in all the accessions with known Vrn-B1 and Vrn-D1 alleles, and in 51 hexaploid spring wheat accessions previously shown to have no polymorphisms in the VRN-A1 promoter region. Twenty-four tetraploid wheat accessions had a similar deletion in VRN-A1 intron 1. We hypothesize that the 2.8-kb conserved region includes regulatory elements important for the vernalization requirement. Epistatic interactions between VRN-H2 and the VRN-H1 allele with the intron 1 deletion suggest that the deleted region may include a recognition site for the flowering repression mediated by the product of the VRN-H2 gene of barley.

Vernalization, the requirement of a long exposure to low temperatures to induce flowering, is an essential adaptation of plants to cold winters. We have shown recently that the vernalization gene VRN-1 from diploid wheat Triticum monococcum is the meristem identity gene APETALA1, and that deletions in its promoter were associated with spring growth habit. In this study, we characterized the allelic variation at the VRN-1 promoter region in polyploid wheat. The VrnA1a allele has a duplication including the promoter region. Each copy has similar foldback elements inserted at the same location and is flanked by identical host direct duplications (HDD). This allele was found in more than half of the hexaploid varieties but not among the tetraploid lines analyzed here. The Vrn-A1b allele has two mutations in the HDD region and a 20-bp deletion in the 5¢ UTR compared with the winter allele. The Vrn-A1b allele was found in both tetraploid and hexaploid accessions but at a relatively low frequency. Among the tetraploid wheat accessions, we found two additional alleles with 32 bp and 54 bp deletions that included the HDD region. We found no size polymorphisms in the promoter region among the winter wheat varieties. The dominant Vrn-A1 allele from two spring varieties from Afghanistan and Egypt (Vrn-A1c allele) and all the dominant Vrn-B1 and Vrn-D1 alleles included in this study showed no differences from their respective recessive alleles in promoter sequences. Based on these results, we concluded that the VRN-1 genes should have additional regulatory sites outside the promoter region studied here.

cultivars by the use of the ph1 gene (Riley and Chapman, 1958) that promotes homeologous chromosome Rust resistance genes Lr37, Sr38, and Yr17 are located within a recombination. The ph1 mutation has been extensively segment of Triticum ventricosum (Tausch) Cess. chromosome 2NS translocated to the short arm of bread wheat chromosome 2AS. Char-used to incorporate new disease resistance genes in acterization of this chromosome segment by 13 restriction fragment wheat from wild Triticeae species such as T. monococlength polymorphism (RFLP) markers indicated that the 2NS translocum L., T. speltoides (Tausch) Gren., and T. ventricosum cation replaced approximately half of the short arm of chromosome (McIntosh et al., 1995; Friebe et al., 1996; Dubcovsky 2A (distal 25-38 centimorgans, cM). The objective of this study was et al., 1998). to develop polymerase chain reaction (PCR) assays based on RFLP The Yr17, Lr37, and Sr38 rust resistance genes, which marker cMWG682 to facilitate the transfer of this cluster of rust confer resistance in wheat against stripe rust (caused by resistance genes into commercial wheat (Triticum aestivum L.) culti-Puccinia striiformis West. f. sp. tritici), leaf rust (caused vars. DNA sequence was obtained from the A-, B-, D-, and N-alleles by Puccinia triticina Eriks), and stem rust (caused by of cMWG682 and was used to design N-allele specific primers. The Puccinia graminis Pers. f. sp. tritici Eriks. & E. Henn.), 2NS fragment amplified by PCR primers cosegregated with the presence of the RFLP-2NS band in all backcross populations. A cleaved respectively, have been used by breeders in different amplified polymorphic sequence (CAPS) was used to develop a parts of the world (Dyck and Lukow, 1988; McIntosh marker for the 2A-allele. This marker can be used to differentiate et al., 1995; Robert et al., 1999; Seah et al., 2000). These homozygous and heterozygous plants carrying the 2NS translocation linked resistance genes were initially introgressed in the in the final cycle of backcross introgression or in screenings for homowinter bread wheat 'VPM1' from Triticum ventricosum zygous plants in segregating populations. Finally, a third PCR assay (Maia, 1967) and are located in a 2NS/2AS translocation was developed by means of TaqMan technology as a high-throughput (Bariana and McIntosh, 1993;McIntosh et al., 1995). alternative for selection of the 2NS/2AS translocation in large segre-Rust races with virulence to Yr17 and Lr37 have been gating populations in breeding programs that have access to real time identified in different countries (Robert et al., 1999; PCR equipment. These molecular markers were used to develop four J. Kolmer unpublished data) but this gene cluster still hard red spring isogenic lines homozygous for the 2NS chromosome segment. One of the isogenic lines, derived from 'Anza,' did not show provides resistance to a wide range of races and is useful the expected resistance in spite of the presence of all the RFLP in combination with other rust resistance genes. markers for the ...

The concentration of yellow carotenoid pigments in durum wheat grain is an important quality criterion and is determined both by their accumulation and by their degradation by lipoxygenase enzymes (Lpx loci). The existence of a duplication at the Lpx-B1 locus and the allelic variation for a deletion of the Lpx-B1.1 copy is reported. This deletion was associated with a 4.5-fold reduction in lipoxygenase activity and improved pasta color (Po0.0001) but not semolina color, suggesting reduced pigment degradation during pasta processing. A molecular marker for the deletion was mapped on chromosome 4B in a population obtained from the cross between durum line UC1113 and variety Kofa. A second lipoxygenase locus, designated Lpx-A3, was mapped on the homoeologous region on chromosome 4A and was associated with semolina and pasta color (Po0.01) but not with lipoxygenase activity in the mature grain. Selection for both the UC1113 allele for Lpx-A3 and the Kofa Lpx-B1.1 deletion resulted in a 10% increase in yellow scores for dry pasta relative to the opposite allele combination. This result indicates that the markers and the new allelic variants reported here will be useful tools to manipulate the wheat Lpx loci and to improve pasta color. r

BackgroundMiniature inverted-repeat transposable elements (MITEs) are short, non-autonomous class II transposable elements present in a high number of conserved copies in eukaryote genomes. An accurate identification of these elements can help to shed light on the mechanisms controlling genome evolution and gene regulation. The structure and distribution of these elements are well-defined and therefore computational approaches can be used to identify MITEs sequences.ResultsHere we describe MITE Tracker, a novel, open source software program that finds and classifies MITEs using an efficient alignment strategy to retrieve nearby inverted-repeat sequences from large genomes. This program groups them into high sequence homology families using a fast clustering algorithm and finally filters only those elements that were likely transposed from different genomic locations because of their low scoring flanking sequence alignment.ConclusionsMany programs have been proposed to find MITEs hidden in genomes. However, none of them are able to process large-scale genomes such as that of bread wheat. Furthermore, in many cases the existing methods perform high false-positive rates (or miss rates). The rice genome was used as reference to compare MITE Tracker against known tools. Our method turned out to be the most reliable in our tests. Indeed, it revealed more known elements, presented the lowest false-positive number and was the only program able to run with the bread wheat genome as input. In wheat, MITE Tracker discovered 6013 MITE families and allowed the first structural exploration of MITEs in the complete bread wheat genome.Electronic supplementary materialThe online version of this article (10.1186/s12859-018-2376-y) contains supplementary material, which is available to authorized users.

This study identified Rht25, a new plant height locus on wheat chromosome arm 6AS, and characterized its pleiotropic effects on important agronomic traits. Understanding genes regulating wheat plant height is important to optimize harvest index and maximize grain yield. In modern wheat varieties grown under high-input conditions, the gibberellin-insensitive semi-dwarfing alleles Rht-B1b and Rht-D1b have been used extensively to confer lodging tolerance and improve harvest index. However, negative pleiotropic effects of these alleles (e.g., poor seedling emergence and reduced biomass) can cause yield losses in hot and dry environments. As part of current efforts to diversify the dwarfing alleles used in wheat breeding, we identified a quantitative trait locus (QHt.ucw-6AS) affecting plant height in the proximal region of chromosome arm 6AS (< 0.4 cM from the centromere). Using a large segregating population (~ 2800 gametes) and extensive progeny tests (70-93 plants per recombinant family), we mapped QHt.ucw-6AS as a Mendelian locus to a 0.2 cM interval (144.0-148.3 Mb, IWGSC Ref Seq v1.0) and show that it is different from Rht18. QHt.ucw-6AS is officially designated as Rht25, with Rht25a representing the height-increasing allele and Rht25b the dwarfing allele. The average dwarfing effect of Rht25b was found to be approximately half of the effect observed for Rht-B1b and Rht-D1b, and the effect is greater in the presence of the height-increasing Rht-B1a and Rht-D1a alleles than in the presence of the dwarfing alleles. Rht25b is gibberellin-sensitive and shows significant pleiotropic effects on coleoptile length, heading date, spike length, spikelet number, spikelet density, and grain weight. Rht25 represents a new alternative dwarfing locus that should be evaluated for its potential to improve wheat yield in different environments.

The aim of this work was to map quantitative trait loci (QTLs) associated with flour yellow color (Fb*) and yellow pigment content (YPC) in durum wheat (Triticum turgidum L. var. durum). Additionally, QTLs affecting flour redness (Fa*) and brightness (FL*) color parameters were investigated. A population of 93 RILs (UC1113 9 Kofa) was evaluated in three locations of Argentina over 2 years. High heritability values ([94%) were obtained for Fb* and YPC, whereas FL* and Fa* showed intermediate to high values. The main QTLs affecting Fb* and YPC overlapped on chromosome arms 4AL (4AL.2), 6AL (6AL.2), 7AS, 7AL, 7BS (7BS.2) and 7BL (7BL.2).The 7BL.1 QTL included the Psy-B1 locus, but one additional linked QTL was detected. A novel minor QTL located on 7AS affected Fb*, with an epistatic effect on YPC. An epistatic interaction occurred between the 7AL and 7BL.2 QTLs. The 4AL.2 QTL showed a strong effect on Fb* and was involved in two digenic epistatic interactions. The 6AL.2 QTL explained most of the variation for Fb* and YPC. The main QTLs affecting FL* and Fa* were located on 2BS and 7BL, respectively. These results confirm the complex inheritance of flour color traits and open the possibility of developing perfect markers to improve pasta quality in Argentinean breeding programs.Electronic supplementary material The online version of this article (