Vrn-A1 Loci Research Articles

Evaluation of the Allelic Variations in Vernalisation (VRN1) and Photoperiod (PPD1) Genes and Genetic Diversity in a Spanish Spelt Wheat Collection.

Allelic variation within genes controlling the vernalisation requirement (VRN1) and photoperiod response (PPD1) determines the adaptation of wheat to different environmental growing conditions as well as influences other traits related to grain yield. This study aimed to screen a Spanish spelt wheat collection using gene-specific molecular markers for VRN-A1, VRN-B1, VRN-D1, and PPD-D1 loci and to phenotype for heading date (HD) in both field and greenhouse experiments under a long photoperiod and without vernalisation. Fifty-five spelt genotypes (91.7%) exhibited a spring growth habit, and all of them carried at least one dominant VRN1 allele, whereas five (8.3%) genotypes had a winter growth habit, and they carried the triple recessive allele combination. The Vrn-D1s was the most frequent allele in the studied set of spelt accessions, and it was found in combination with both the dominant Vrn-A1b and/or Vrn-B1a alleles in 88.3% of the spelt accessions tested. All spelt accessions carried the photoperiod-sensitive Ppd-D1b allele, which may explain the late heading of spelt germplasm compared to the commercial spring bread wheat Setenil used as a control. The least significant difference test showed significant differences between allelic combinations, the earliest accessions being those carrying two or three dominant alleles, followed by the one-gene combinations. In addition, the genetic diversity was evaluated through capillary electrophoresis using 15 wheat simple sequence repeat (SSR) markers. Most markers had high levels of polymorphism, producing 95 different alleles which ranged between 53 and 279 bp in size. Based on the polymorphic information content values obtained (from 0.51 to 0.97), 12 out of the 15 SSRs were catalogued as informative markers (values > 0.5). According to the dendrogram generated, the spelt accessions clustered as a separate group from the commercial bread wheat Setenil. Knowledge of VRN1 and PPD1 alleles, heading time, and genetic variability using SSR markers is valuable for spelt wheat breeding programs.

Grain yield and adaptation of spring wheat to Norwegian growing conditions is driven by allele frequency changes at key adaptive loci discovered by genome-wide association mapping

Key messageAdaptation to the Norwegian environment is associated with polymorphisms in the Vrn-A1 locus. Historical selection for grain yield in Nordic wheat is associated with TaGS5-3A and TaCol-5 loci.Grain yields in Norwegian spring wheat increased by 18 kg ha−1 per year between 1972 and 2019 due to introduction of new varieties. These gains were associated with increments in the number of grains per spike and extended length of the vegetative period. However, little is known about the genetic background of this progress. To fill this gap, we conducted genome-wide association study on a panel consisting of both adapted (historical and current varieties and lines in the Nordics) and important not adapted accessions used as parents in the Norwegian wheat breeding program. The study concerned grain yield, plant height, and heading and maturity dates, and detected 12 associated loci, later validated using independent sets of recent breeding lines. Adaptation to the Norwegian cropping conditions was found to be associated with the Vrn-A1 locus, and a previously undescribed locus on chromosome 1B associated with heading date. Two loci associated with grain yield, corresponding to the TaGS5-3A and TaCol-5 loci, indicated historical selection pressure for high grain yield. A locus on chromosome 2A explained the tallness of the oldest accessions. We investigated the origins of the beneficial alleles associated with the wheat breeding progress in the Norwegian material, tracing them back to crosses with Swedish, German, or CIMMYT lines. This study contributes to the understanding of wheat adaptation to the Norwegian growing conditions, sheds light on the genetic basis of historical wheat improvement and aids future breeding efforts by discovering loci associated with important agronomic traits in wheat.

Vernalisation and photoperiod responses of diverse wheat genotypes

Context Wheat (Triticum aestivum L.) adaptation is highly dependent on crop lifecycle duration, particularly the time at which flowering occurs in a specific environment. Frost, low solar radiation, heat and drought can significantly reduce yield if a crop flowers too early or late. Wheat genotypes have different lifecycle durations determined by plant responses to temperature (thermal time accumulation and vernalisation) and photoperiod. These responses are largely controlled by five phenology genes (two PPD1 and three VRN1 genes). Advances in crop phenology modelling suggest that flowering time under field conditions could be accurately predicted with parameters derived from photoperiod and vernalisation responses obtained in controlled environments. Aims This study quantified photoperiod and vernalisation responses of 69 Australian wheat genotypes selected for diversity at the PPD1 and VRN1 loci. Methods Spring and winter genotypes were grown in four controlled environments at a constant temperature of 22°C with photoperiod (17 or 8 h) and vernalisation (0 or 8 weeks) treatments as factors. Key results Thermal time from coleoptile emergence to flowering in spring genotypes was typically decreased more by long photoperiod than by vernalisation; the opposite was true for winter genotypes. Spring genotypes that were sensitive to vernalisation contained a sensitive allele at the Vrn-A1 locus. Conclusions There is large diversity in phenological responses of wheat genotypes to photoperiod and vernalisation, including among those with matching multi-locus genotype. Implications Data from this study will be used to parameterise and test a wheat phenology model in a future study.

Allelic Variation Analysis at the Vernalization Response and Photoperiod Genes in Russian Wheat Varieties Identified Two Novel Alleles of Vrn-B3.

Heading time is an important agronomic trait affecting the adaptability and productivity of common wheat. In this study, 95 common wheat varieties from Russia and the late-maturing breeding line ‘Velut’ were tested for allelic diversity of genes having the strongest effect on heading. In this research, allelic variation at the Ppd-D1, Vrn-A1, Vrn-B1, Vrn-D1, and Vrn-B3 loci was tested. The Vrn-B1 and Vrn-B3 loci provided the largest contribution to genetic diversity. We found two novel allelic variants of the Vrn-B3 gene in the studied varieties. Ten varieties carried a 160 bp insertion in the promoter region, and the breeding line ‘Velut’ carried a 1617 bp insertion. These alleles were designated Vrn-B3e and Vrn-B3d, respectively. The analysis of the sequences showed the recent insertion of a retrotransposon homologous to the LTR retrotransposon (RLX_Hvul_Dacia_ RND-1) in the Vrn-B3d allele. Plants with the Vrn-B3e and the ‘Velut’ line with the Vrn-B3d allele headed later than the plants with the wild-type allele; among these plants, ‘Velut’ is the latest maturing wheat variety. Analysis of the gene expression of two groups of lines differing by the Vrn-B3 alleles (Vrn-B3d or vrn-B3) from the F2 population with ‘Velut’ as a parental line did not reveal a significant difference in the expression level between the groups. Additional research is required to study the reasons for the late maturation of the ‘Velut’ line. However, the studied wheat varieties could be used as a potential source of natural variation in genes controlling heading times.

Phenology and Dwarfing Gene Interaction Effects on the Adaptation of Selected Wheat (Triticum aestivum L.) Advanced Lines across Diverse Water-Limited Environments of Western Australia

Photoperiod, vernalization, and plant height controlling genes are major developmental genes in wheat that govern environmental adaptation and hence, knowledge on the interaction effects among different alleles of these genes is crucial in breeding cultivars for target environments. The interaction effects among these genes were studied in nineteen Australian advanced lines from diverse germplasm pools and four commercial checks. Diagnostic markers for the Vrn-A1 locus revealed the presence of the spring allele Vrn-A1a in 10 lines and Vrn-A1c in one line. The dominant alleles of Vrn-B1a and Vrn-D1a were identified in 19 and 8 lines, respectively. The most common photoperiod-insensitive allele of Ppd-D1a was identified in 19 lines and three and four copy photoperiod-insensitive alleles (Ppd-B1a and Ppd-B1c) were present in five and one lines, respectively. All the lines were photoperiod-sensitive for the Ppd-A1 locus. All lines were semi-dwarf, having either of the two dwarfing alleles; 14 lines had the Rht-B1b (Rht-1) and the remaining had the Rht-D1b (Rht-2) dwarfing allele. The presence of the photoperiod-insensitive allele Ppd-D1a along with one or two spring alleles at the Vrn1 loci resulted in an earlier heading and better yield. Dwarfing genes were found to modify the heading time—the Rht-D1b allele advanced heading by three days and also showed superior effects on yield-contributing traits, indicating its beneficial role in yield under rain-fed conditions along with an appropriate combination of photoperiod and vernalization alleles. This study also identified the adaptability value of these allelic combinations for higher grain yield and protein content across the different the water-limited environments.

Association Mapping of Seedling Resistance to Tan Spot (Pyrenophora tritici-repentis Race 1) in CIMMYT and South Asian Wheat Germplasm

Tan spot caused by Pyrenophora tritici-repentis (Ptr) is an important disease of wheat in many wheat producing areas of the world. A genome wide association study (GWAS) was conducted using 11,401 SNP markers of the Illumina Infinium 15K Bead Chip with whole genome coverage to identify genomic regions associated with resistance to tan spot in a diverse panel of 184 wheat genotypes originating from South Asia and CIMMYT. The GWAS panel was phenotyped for seedling resistance to tan spot with Ptr race 1 in two greenhouse experiments. Besides CIMMYT germplasm, several lines from South Asia (India, Bangladesh and Nepal) showed good degree of resistance to tan spot. Association mapping was conducted separately for individual experiments and for pooled data using mixed linear model (MLM) and Fixed and random model Circulating Probability Unification (FarmCPU) model; no significant MTAs were recorded through the MLM model, whereas FarmCPU model reported nine significant MTAs located on chromosomes 1B, 2A, 2B, 3B, 4A, 5A, 5B, 6A, and 7D. The long arms of chromosomes 5A and 5B were consistent across both environments, in which the Vrn-A1 locus was found in identified region of chromosome 5A, and MTA at IACX9261 on 5BL appears to represent the resistance gene tsn 1. MTAs observed on chromosomes 1B, 2A, 2B, 3B, 4A, 6A, and 7D have not been reported previously and are likely novel.

Genetic analyses of native Fusarium head blight resistance in two spring wheat populations identifies QTL near the B1, Ppd-D1, Rht-1, Vrn-1, Fhb1, Fhb2, and Fhb5 loci.

QTL analyses of two bi-parental mapping populations with AC Barrie as a parent revealed numerous FHB-resistance QTL unique to each population and uncovered novel variation near Fhb1. Fusarium head blight (FHB) is a destructive disease of wheat worldwide, leading to severe yield and quality losses. The genetic basis of native FHB resistance was examined in two populations: a recombinant inbred line population from the cross Cutler/AC Barrie and a doubled haploid (DH) population from the cross AC Barrie/Reeder. Numerous QTL were detected among the two mapping populations with many being cross-specific. Photoperiod insensitivity at Ppd-D1 and dwarfing at Rht-B1 and Rht-D1 was associated with increased FHB susceptibility. Anthesis date QTL at or near the Vrn-A1 and Vrn-B1 loci co-located with major FHB-resistance QTL in the AC Barrie/Reeder population. The loci were epistatic for both traits, such that DH lines with both late alleles were considerably later to anthesis and had reduced FHB symptoms (i.e., responsible for the epistatic interaction). Interestingly, AC Barrie contributed FHB resistance near the Fhb1 locus in the Cutler population and susceptibility in the Reeder population. Analyses of the Fhb1 candidate genes PFT and TaHRC confirmed that AC Barrie, Cutler, and Reeder do not carry the Sumai-3 Fhb1 gene. Resistance QTL were also detected at the expected locations of Fhb2 and Fhb5. The native FHB-resistance QTL detected near Fhb1, Fhb2, and Fhb5 do not appear to be as effective as Fhb1, Fhb2, and Fhb5 from Sumai-3. The presence of awns segregated at the B1 awn inhibitor locus in both populations, but was only associated with FHB resistance in the Cutler/AC Barrie population suggesting linkage caused the association rather than pleiotropy.

A wheat chromosome 5AL region confers seedling resistance to both tan spot and Septoria nodorum blotch in two mapping populations

Tan spot (TS) and Septoria nodorum blotch (SNB), caused by Pyrenophora tritici-repentis and Parastagonospora nodorum, respectively, are important fungal leaf-spotting diseases of wheat that cause significant losses in grain yield. In this study, two recombinant inbred line populations, ‘Bartai’ × ‘Ciano T79’ (referred to as B × C) and ‘Cascabel’ × ‘Ciano T79’ (C × C) were tested for TS and SNB response in order to determine the genetic basis of seedling resistance. Genotyping was performed with the DArTseq genotyping-by-sequencing (GBS) platform. A chromosome region on 5AL conferred resistance to TS and SNB in both populations, but the effects were larger in B × C (R2 = 11.2%–16.8%) than in C × C (R2 = 2.5%–9.7%). Additionally, the chromosome region on 5BL (presumably Tsn1) was significant for both TS and SNB in B × C but not in C × C. Quantitative trait loci (QTL) with minor effects were identified on chromosomes 1B, 2A, 2B, 3A, 3B, 4D, 5A, 5B, 5D, 6B, and 6D. The two CIMMYT breeding lines ‘Bartai’ and ‘Cascabel’ contributed resistance alleles at both 5AL and 5BL QTL mentioned above. The QTL on 5AL showed linkage with the Vrn-A1 locus, whereas the vrn-A1 allele conferring lateness was associated with resistance to TS and SNB.

Genomic selection for winter survival ability among a diverse collection of facultative and winter wheat genotypes

Winter survival ability is important for autumn sown winter wheat (Triticum aestivum L.) in regions with cold winters. Wheat vernalization and photoperiod genes influence adaptation by regulating the timing of the transition from vegetative to reproductive growth to protect the floral meristem from cold temperatures. We evaluated winter injury of 287 genotypes from the Facultative and Winter Wheat Observation Nursery (FAWWON) in six field environments over 3 years (2014 to 2016) in Colorado. Entries were genotyped using single-nucleotide polymorphisms (SNPs) obtained by genotyping by sequencing (GBS) and at known vernalization (Vrn-A1, Vrn-B1, and Vrn-D1) and photoperiod (Ppd-B1 and Ppd-D1) loci using Kompetitive Allele Specific PCR (KASP) assays. Winter injury was observed and visually scored in five of the six environments. Mean GS prediction accuracies across the five environments, obtained through ridge regression best linear unbiased prediction (RR-BLUP) using 23,269 SNPs alone as random effects, ranged from 0.26 ± 0.01 to 0.74 ± 0.00. Incorporation of alleles at Vrn-A1, Vrn-B1, and Vrn-D1 loci as fixed effects in the GS models together with GBS markers as random effects provided the highest prediction accuracy with mean GS accuracies ranging from 0.34 ± 0.01 to 0.78 ± 0.00 across the five environments. Genomic selection models incorporating photoperiod alleles as fixed effects rarely improved GS prediction accuracy of winter injury. Genomic selection models that incorporate both major and minor genetic factors that influence low-temperature tolerance improved the model predictions for identifying genotypes that are best adapted to regions where cold winter temperatures are an important production constraint.

Resistance to Spot Blotch in Two Mapping Populations of Common Wheat Is Controlled by Multiple QTL of Minor Effects.

Spot blotch (SB) is an important fungal disease of wheat in South Asia and South America. Host resistance is regarded as an economical and environmentally friendly approach of controlling SB, and the inheritance of resistance is mostly quantitative. In order to gain a better understanding on the SB resistance mechanism in CIMMYT germplasm, two bi-parental mapping populations were generated, both comprising 232 F2:7 progenies. Elite CIMMYT breeding lines, BARTAI and WUYA, were used as resistant parents, whereas CIANO T79 was used as susceptible parent in both populations. The two populations were evaluated for field SB resistance at CIMMYT’s Agua Fria station for three consecutive years, from the 2012–2013 to 2014–2015 cropping seasons. Phenological traits like plant height (PH) and days to heading (DH) were also determined. Genotyping was performed using the DArTSeq genotyping-by-sequencing (GBS) platform, and a few D-genome specific SNPs and those for phenological traits were integrated for analysis. The most prominent quantitative trait locus (QTL) in both populations was found on chromosome 5AL at the Vrn-A1 locus, explaining phenotypic variations of 7–27%. Minor QTL were found on chromosomes 1B, 3A, 3B, 4B, 4D, 5B and 6D in BARTAI and on chromosomes 1B, 2A, 2D and 4B in WUYA, whereas minor QTL contributed by CIANO T79 were identified on chromosome 1B, 1D, 3A, 4B and 7A. In summary, resistance to SB in the two mapping populations was controlled by multiple minor QTL, with strong influence from Vrn-A1.

Transcriptomic Insights into Phenological Development and Cold Tolerance of Wheat Grown in the Field.

Cold acclimation and winter survival in cereal species is determined by complicated environmentally regulated gene expression. However, studies investigating these complex cold responses are mostly conducted in controlled environments that only consider the responses to single environmental variables. In this study, we have comprehensively profiled global transcriptional responses in crowns of field-grown spring and winter wheat (Triticum aestivum) genotypes and their near-isogenic lines with the VRN-A1 alleles swapped. This in-depth analysis revealed multiple signaling, interactive pathways that influence cold tolerance and phenological development to optimize plant growth and development in preparation for a wide range of over-winter stresses. Investigation of genetic differences at the VRN-A1 locus revealed that a vernalization requirement maintained a higher level of cold response pathways while VRN-A1 genetically promoted floral development. Our results also demonstrated the influence of genetic background on the expression of cold and flowering pathways. The link between delayed shoot apex development and the induction of cold tolerance was reflected by the gradual up-regulation of abscisic acid-dependent and C-REPEAT-BINDING FACTOR pathways. This was accompanied by the down-regulation of key genes involved in meristem development as the autumn progressed. The chromosome location of differentially expressed genes between the winter and spring wheat genetic backgrounds showed a striking pattern of biased gene expression on chromosomes 6A and 6D, indicating a transcriptional regulation at the genome level. This finding adds to the complexity of the genetic cascades and gene interactions that determine the evolutionary patterns of both phenological development and cold tolerance traits in wheat.

The occurrence of spring forms in tetraploid Timopheevi wheat is associated with variation in the first intron of the VRN-A1 gene.

Background Triticum araraticum and Triticum timopheevii are tetraploid species of the Timopheevi group. The former includes both winter and spring forms with a predominance of winter forms, whereas T. timopheevii is considered a spring species. In order to clarify the origin of the spring growth habit in T. timopheevii, allelic variability of the VRN-1 gene was investigated in a set of accessions of both tetraploid species, together with the diploid species Ae. speltoides, presumed donor of the G genome to these tetraploids.ResultsThe promoter region of the VRN-A1 locus in all studied tetraploid accessions of both T. araraticum and T. timopheevii represents the previously described allele VRN-A1f with a 50 bp deletion near the start codon. Three additional alleles were identified namely, VRN-A1f-del, VRN-A1f-ins and VRN-A1f-del/ins, which contained large mutations in the first (1st) intron of VRN-A1. The first allele, carrying a deletion of 2.7 kb in a central part of intron 1, occurred in a few accessions of T. araraticum and no accessions of T. timopheevii. The VRN-A1f-ins allele, containing the insertion of a 0.4 kb MITE element about 0.4 kb upstream from the start of intron 1, and allele VRN-A1f-del/ins having this insertion coupled with a deletion of 2.7 kb are characteristic only for T. timopheevii. Allelic variation at the VRN-G1 locus includes the previously described allele VRN-G1a (with the insertion of a 0.2 kb MITE in the promoter) found in a few accessions of both tetraploid species. We showed that alleles VRN-A1f-del and VRN-G1a have no association with the spring growth habit, while in all accessions of T. timopheevii this habit was associated with the dominant VRN-A1f-ins and VRN-A1f-del/ins alleles. None of the Ae. speltoides accessions included in this study had changes in the promoter or 1st intron regions of VRN-1 which might confer a spring growth habit. The VRN-1 promoter sequences analyzed herein and downloaded from databases have been used to construct a phylogram to assess the time of divergence of Ae. speltoides in relation to other wheat species.ConclusionsAmong accessions of T. araraticum, the preferentially winter predecessor of T. timopheevii, two large mutations were found in both VRN-A1 and VRN-G1 loci (VRN-A1f-del and VRN-G1a) that were found to have no effect on vernalization requirements. Spring tetraploid T. timopheevii had one VRN-1 allele in common for two species (VRN-G1a), and two that were specific (VRN-A1f-ins, VRN-A1f-del/ins). The latter alleles include mutations in the 1st intron of VRN-A1 and also share a 0.4 kb MITE insertion near the start of intron 1. We suggested that this insertion resulted in a spring growth habit in a progenitor of T. timopheevii which has probably been selected during subsequent domestication. The phylogram constructed on the basis of the VRN-1 promoter sequences confirmed the early divergence (~3.5 MYA) of the ancestor(s) of the B/G genomes from Ae. speltoides.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0925-y) contains supplementary material, which is available to authorized users.

QTL Characterization of Fusarium Head Blight Resistance in CIMMYT Bread Wheat Line Soru#1.

Fusarium head blight (FHB) resistant line Soru#1 was hybridized with the German cultivar Naxos to generate 131 recombinant inbred lines for QTL mapping. The population was phenotyped for FHB and associated traits in spray inoculated experiments in El Batán (Mexico), spawn inoculated experiments in Ås (Norway) and point inoculated experiments in Nanjing (China), with two field trials at each location. Genotyping was performed with the Illumina iSelect 90K SNP wheat chip, along with a few SSR and STS markers. A major QTL for FHB after spray and spawn inoculation was detected on 2DLc, explaining 15–22% of the phenotypic variation in different experiments. This QTL remained significant after correction for days to heading (DH) and plant height (PH), while another QTL for FHB detected at the Vrn-A1 locus on 5AL almost disappeared after correction for DH and PH. Minor QTL were detected on chromosomes 2AS, 2DL, 4AL, 4DS and 5DL. In point inoculated experiments, QTL on 2DS, 3AS, 4AL and 5AL were identified in single environments. The mechanism of resistance of Soru#1 to FHB was mainly of Type I for resistance to initial infection, conditioned by the major QTL on 2DLc and minor ones that often coincided with QTL for DH, PH and anther extrusion (AE). This indicates that phenological and morphological traits and flowering biology play important roles in resistance/escape of FHB. SNPs tightly linked to resistance QTL, particularly 2DLc, could be utilized in breeding programs to facilitate the transfer and selection of those QTL.

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

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.

Characterization of new allele influencing flowering time in bread wheat introgressed from Triticum militinae

Flowering time variation was identified within a mapping population of doubled haploid lines developed from a cross between the introgressive line 8.1 and spring bread wheat cv. Tähti. The line 8.1 carried introgressions from tetraploid Triticum militinae in the cv. Tähti genetic background on chromosomes 1A, 2A, 4A, 5A, 7A, 1B and 5B. The most significant QTL for the flowering time variation was identified within the introgressed region on chromosome 5A and its largest effect was associated with the VRN-A1 locus, accounting for up to 70% of phenotypic variance. The allele of T. militinae origin was designated as VRN-A1f-like. The effect of the VRN-A1f-like allele was verified in two other mapping populations. QTL analysis identified that in cv. Tähti and cv. Mooni genetic background, VRN-A1f-like allele incurred a delay of 1.9-18.6 days in flowering time, depending on growing conditions. Sequence comparison of the VRN-A1f-like and VRN-A1a alleles from the parental lines of the mapping populations revealed major mutations in the promoter region as well as in the first intron, including insertion of a MITE element and a large deletion. The sequence variation allowed construction of specific diagnostic PCR markers for VRN-A1f-like allele determination. Identification and quantification of the effect of the VRN-A1f-like allele offers a useful tool for wheat breeding and for studying fine-scale regulation of flowering pathways in wheat.

Frequency of vernalization requirement associated dominant VRN-A1 gene and earliness related Esp-A1 candidate genes in advanced wheat mutant lines and effect of allele on flowering time

Seeds of the spring bread wheat variety Zhenis, registered in Kazakhstan, were irradiated with 100 and 200 Gray doses from a [60Co] γ-ray radiation source. Promising advanced M5 mutant lines were obtained and evaluated for mapping density of vernalization requirement associated dominant VRN-A1 gene and earliness related Esp-A1 candidate genes in 30 spring wheat mutant lines along with parent. Differences among generated mutant lines and parent were observed on frequency of distribution of VRN-A1 gene and Eps-A1 candidate gene alleles. Allelic variation at the VRN-A1 loci was observed in the 8 mutant lines (26.6%), mostly in 100 Gy mutant lines. A dominant (VRN) allele at its loci, which was present and indicated in these lines is sufficient to confer a spring growth habit. As for the candidate gene Esp-A1, eleven 100 Gy M5 mutant and six 200 Gy M5 lines, had Esp-A1 candidate gene allele. The two lines24(2) and 43(4) carrying dominant allele of VRN-A1 had higher thousand kernel weight. Mutant lines carrying allele of Eps-A1 candidate gene found significantly differed from the parent especially in 100 Gy lines (73.3%) in flowering time.

Genetic variation for flowering time and height reducing genes and important traits in western Canadian spring wheat

Genetic variation is prerequisite for wheat improvement. High grain yield and protein content and early maturity are some of the major objectives in global as well as Canadian wheat breeding programs. We investigated genetic diversity for earliness related and plant height reducing (Rht) genes in 82 spring wheat cultivars, registered in western Canada, through eight diagnostic DNA markers. Allelic variation was observed at the Vrn-A1, Vrn-B1, Vrn-D1 and Ppd-D1 loci but not at Ppd-A1 and Ppd-B1 loci in the 82 cultivars. Spring type allele of Vrn-A1 was present in 94 % cultivars, whereas only two cultivars carried spring allele of Vrn-D1. Among the four earliness related genes, the most frequent combination was Vrn-A1a, Vrn-B1, vrn-D1 and Ppd-D1b, which was found in 32 cultivars. As for the Rht genes, eight cultivars had Rht-B1b and 13 cultivars had Rht-D1b. All cultivars carrying dominant allele of Vrn-B1, photoperiod-insensitive allele of Ppd-D1 and height reducing allele of Rht-1 had shorter plants and higher grain yield but lower grain protein content. Days to heading and maturity showed positive genetic (rg = 0.65) and phenotypic (rp = 0.44) correlation, and were also positively correlated with grain yield and kernel weight but negatively correlated with test weight and protein content. Plant height was positively correlated with grain protein content (rg = 0.53; rp = 0.42), but negatively correlated with grain yield (rg = −0.47; rp = −0.14). Grain yield and protein content showed negative genetic correlation (rg = −0.57). Among the sixty cultivars from Canada Western Red Spring Class released over 100 years, the newest cultivar yielded 23 % more grain and had 15 % higher grain protein than the oldest cultivar ‘Red Fife’. Breeders in western Canada have incorporated vernalization and photoperiod insensitive and Rht genes in modern cultivars to promote early maturity, to make use of off-season nurseries abroad, and to improve lodging tolerance.

Multiply to conquer: Copy number variations at Ppd-B1 and Vrn-A1 facilitate global adaptation in wheat.

BackgroundCopy number variation was found to be a frequent type of DNA polymorphism in the human genome often associated with diseases but its importance in crops and the effects on agronomic traits are still largely unknown.ResultsHere, we employed a large worldwide panel of 1110 winter wheat varieties to assess the frequency and the geographic distribution of copy number variants at the Photoperiod-B1 (Ppd-B1) and the Vernalization-A1 (Vrn-A1) loci as well as their effects on flowering time under field conditions. We identified a novel four copy variant of Vrn-A1 and based on the phylogenetic relationships among the lines show that the higher copy variants at both loci are likely to have arisen independently multiple times. In addition, we found that the frequency of the different copy number variants at both loci reflects the environmental conditions in the varieties’ region of origin and based on multi-location field trials show that Ppd-B1 copy number has a substantial effect on the fine-tuning of flowering time.ConclusionsIn conclusion, our results show the importance of copy number variation at Ppd-B1 and Vrn-A1 for the global adaptation of wheat making it a key factor for wheat success in a broad range of environments and in a wider context substantiate the significant role of copy number variation in crops.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0258-0) contains supplementary material, which is available to authorized users.

Characterization of wild emmer wheat Triticum dicoccoides germplasm for vernalization alleles

The flowering in winter and wild wheats is induced by extended exposure to cold temperatures, a process called vernalization while spring wheats do not have any such requirement. In the present study, we analyzed 45 accessions of wild emmer wheat T. dicoccoides for the allelic composition of the vernalization genes at VRN-A1 and VRN-B1 loci. Three gene based markers for VRN-A1 and two for VRN-B1 locus were used. Thirty five T. dicoccoides accessions had only winter type allele vrn-A1 at VRN-A1 locus. One accession each had VRN-A1a and Vrn-A1d allele, and two accessions each showed the presence of VRN-A1b and Vrn-A1c, potent spring type alleles. Three accessions, however, had multiple alleles at VRN-A1 locus. At the VRN-B1 locus 35 accessions had winter type allele vrn-B1 and 10 accession had dominant Vrn-B1 allele. These T. dicoccoides accessions constitute a very useful resource for incorporation of alternative vernalization alleles in the cultivated wheat gene pool for developing better adaptive wheat varieties.

Copy number and haplotype variation at the VRN-A1 and central FR-A2 loci are associated with frost tolerance in hexaploid wheat.

The interaction between VRN - A1 and FR - A2 largely affect the frost tolerance of hexaploid wheat. Frost tolerance is critical for wheat survival during cold winters. Natural variation for this trait is mainly associated with allelic differences at the VERNALIZATION 1 (VRN1) and FROST RESISTANCE 2 (FR2) loci. VRN1 regulates the transition between vegetative and reproductive stages and FR2, a locus including several tandemly duplicated C-REPEAT BINDING FACTOR (CBF) transcription factors, regulates the expression of Cold-regulated genes. We identified sequence and copy number variation at these two loci among winter and spring wheat varieties and characterized their association with frost tolerance. We identified two FR-A2 haplotypes-'FR-A2-S' and 'FR-A2-T'-distinguished by two insertion/deletions and ten single nucleotide polymorphisms within the CBF-A12 and CBF-A15 genes. Increased copy number of CBF-A14 was frequently associated with the FR-A2-T haplotype and with higher CBF14 transcript levels in response to cold. Factorial ANOVAs revealed significant interactions between VRN1 and FR-A2 for frost tolerance in both winter and spring panels suggesting a crosstalk between vernalization and cold acclimation pathways. The model including these two loci and their interaction explained 32.0 and 20.7 % of the variation in frost tolerance in the winter and spring panels, respectively. The interaction was validated in a winter wheat F 4:5 population segregating for both genes. Increased VRN-A1 copy number was associated with improved frost tolerance among varieties carrying the FR-A2-T allele but not among those carrying the FR-A2-S allele. These results suggest that selection of varieties carrying the FR-A2-T allele and three copies of the recessive vrn-A1 allele would be a good strategy to improve frost tolerance in wheat.