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

Abstract Background Vernalization genes VRN1 play a major role in the transition from vegetative to reproductive growth in wheat. In di-, tetra- and hexaploid wheats the presence of a dominant allele of at least one VRN1 gene homologue (Vrn-A1, Vrn-B1, Vrn-G1 or Vrn-D1) determines the spring growth habit. Allelic variation between the Vrn-1 and vrn-1 alleles relies on mutations in the promoter region or the first intron. The origin and variability of the dominant VRN1 alleles, determining the spring growth habit in tetraploid wheat species have been poorly studied. Results Here we analyzed the growth habit of 228 tetraploid wheat species accessions and 25 % of them were spring type. We analyzed the promoter and first intron regions of VRN1 genes in 57 spring accessions of tetraploid wheats. The spring growth habit of most studied spring accessions was determined by previously identified dominant alleles of VRN1 genes. Genetic experiments proof the dominant inheritance of Vrn-A1d allele which was widely distributed across the accessions of Triticum dicoccoides. Two novel alleles were discovered and designated as Vrn-A1b.7 and Vrn-B1dic. Vrn-A1b.7 had deletions of 20 bp located 137 bp upstream of the start codon and mutations within the VRN-box when compared to the recessive allele of vrn-A1. So far the Vrn-A1d allele was identified only in spring accessions of the T. dicoccoides and T. turgidum species. Vrn-B1dic was identified in T. dicoccoides IG46225 and had 11 % sequence dissimilarity in comparison to the promoter of vrn-B1. The presence of Vrn-A1b.7 and Vrn-B1dic alleles is a predicted cause of the spring growth habit of studied accessions of tetraploid species. Three spring accessions T. aethiopicum K-19059, T. turanicum K-31693 and T. turgidum cv. Blancal possess recessive alleles of both VRN-A1 and VRN-B1 genes. Further investigations are required to determine the source of spring growth habit of these accessions. Conclusions New allelic variants of the VRN-A1 and VRN-B1 genes were identified in spring accessions of tetraploid wheats. The origin and evolution of VRN-A1 alleles in di- and tetraploid wheat species was discussed

DEP1 gene in wheat species with normal, compactoid and compact spikes

Abstract Background In rice, a variant of DEP1 gene results in erect panicle architecture, well-developed vascular bundles, an increase in the number of grains per panicle and a consequent increase in the grain yield. Interestingly, DEP1 homologs are present in the other cereals including species of wheat and barley (Hordeum vulgare), even though they do not produce panicles but spikes. In barley, HvDEP1 alleles do not differ between strains of various ear types and geographic origins, while in at least three OsDEP1 variants have been described. Results In this work, we have studied the DEP1 gene from eight accessions which belong to four wheat species, T. monococcum, T. durum, T. compactum, and T. spelta, with either compact, compactoid or normal spike phenotypes. The nucleotide sequences of the 5th exon of DEP1 were determined for all eight accessions. Obtained sequences were species specific. Despite the interspecies diversity, all wheat sequences encoded polypeptides of the same size, similarly to the 5th exons of the DEP1 homologs in T. aestivum, T. urartu, and H. vulgare. For further study, the full-length sequences of the DEP1 gene for all four species were studied. The full-length DEP1 genomic copies were isolated from the genomic sequences of T. aestivum, T. urartu, and Aegilops tauschii. The genome of tetraploid wheat T. durum contains two variants of the DEP1 originating from A and B genomes. In the hexaploid wheats T. aestivum, T. compactum, and T. spelta, three variants of this gene originating from A, B, and D genomes were detected. DEP1 genes of the diploid wheats T. monococcum and T. urartu differ. It seems that a precursor of the DEP1 gene in T. monococcum originates from the wild progenitor T. boeoticum. Conclusion No DEP1-related differences of nucleotide sequences between the compact (or compactoid) and normal spike phenotypes in the tested wheat species were detected. Therefore, DEP1 gene does not directly participate in the control of the spike architecture in wheats

Additional file 1: Table S1. of VRN1 genes variability in tetraploid wheat species with a spring growth habit

List of tetraploid wheat species used in the study and their growth habit. Species names are given according to Dorofeev et al. [1] and Goncharov [2]. Table S2. Set of primers used in the present study. (PDF 444 kb

Additional file 1: Table S1. of DEP1 gene in wheat species with normal, compactoid and compact spikes

Morphological characteristics of the wheat species used in the present study. Table S2. List of DEP1 gene sequences of Triticum and Aegilops species obtained from WGS database. Table S3. Set of primers and PCR conditions used in the present study. Table S4. p-distances between wheat DEP1 genes sequences from A, B and D genomes. Table S5. p-distances between wheat VRN1 genes sequences from A, B and D genomes. Figure S1. Schematic representation of the primer pairs positions. Figure S2. Nucleotide alignment of 5th exon of DEP1 gene from different wheat species, Ae. tauschii and barley. Sequence of T. aestivum (FAOM01374184) was used as a reference. Sequences obtained by experimental methods in the present study are marked in bold. Nucleotides, that match with reference sequence, are designated by dots. Nonsynonymous and synonymous amino acid substitutions are indicated by red and green arrows, respectively. (PDF 8916 kb

Evidence for Karyotype Polymorphism in the Free-Living Flatworm, Macrostomum lignano, a Model Organism for Evolutionary and Developmental Biology

Over the past decade, the free-living flatworm Macrostomum lignano has been successfully used in many areas of biology, including embryology, stem cells, sexual selection, bioadhesion and aging. The increased use of this powerful laboratory model, including the establishment of genomic resources and tools, makes it essential to have a detailed description of the chromosome organization of this species, previously suggested to have a karyotype with 2n = 8 and one pair of large and three pairs of small metacentric chromosomes. We performed cytogenetic analyses for chromosomes of one commonly used inbred line of M. lignano (called DV1) and uncovered unexpected chromosome number variation in the form of aneuploidies of the largest chromosomes. These results prompted us to perform karyotypic studies in individual specimens of this and other lines of M. lignano reared under laboratory conditions, as well as in freshly field-collected specimens from different natural populations. Our analyses revealed a high frequency of aneuploids and in some cases other numerical and structural chromosome abnormalities in laboratory-reared lines of M. lignano, and some cases of aneuploidy were also found in freshly field-collected specimens. Moreover, karyological analyses were performed in specimens of three further species: Macrostomum sp. 8 (a close relative of M. lignano), M. spirale and M. hystrix. Macrostomum sp. 8 showed a karyotype that was similar to that of M. lignano, with tetrasomy for its largest chromosome being the most common karyotype, while the other two species showed a simpler karyotype that is more typical of the genus Macrostomum. These findings suggest that M. lignano and Macrostomum sp. 8 can be used as new models for studying processes of partial genome duplication in genome evolution

Morphometric analysis of <i>Macrostomum</i> karyotypes.

<p>Morphometric analysis of <i>Macrostomum</i> karyotypes.</p

Chromosomes of <i>Macrostomum lignano</i> at different condensation levels, stained with DAPI (inverted image).

<p>(a-c) mitotic metaphase chromosomes; (d) pachytene chromosomes. AT-positive bands are marked with arrows. Scale bar 10 μm.</p

Inheritance patterns of additional large chromosomes from one aneuploid 2n = 9 parent crossed in all combinations with another parent with one of the three main karyotypes.

<p>Inheritance patterns of additional large chromosomes from one aneuploid 2n = 9 parent crossed in all combinations with another parent with one of the three main karyotypes.</p

Karyotype variation among <i>Macrostomum</i> species.

<p>(a) the 'normal' chromosome set of <i>Macrostomum lignano</i>, 2n = 8, (b) the 'normal' chromosome set of <i>Macrostomum</i> sp. 8, 2n = 10, and the invariant chromosome sets of (c) <i>M</i>. <i>spirale</i>, 2n = 6, and (d) <i>M</i>. <i>hystrix</i>, 2n = 6. DAPI-staining (inverted image). Scale bar 10 μm.</p