Search Results (8)

The GLABROUS1 Enhancer Binding Protein (GeBP) family, plant-specific transcription factors with a non-classical Leu-zipper motif, plays crucial roles in plant development and stress responses. Although GeBP genes have been characterized in several Gramineae crops, including a preliminary genome-wide identification of 11 GeBP genes in common wheat (Triticum aestivum L.), a comprehensive and systematic analysis of the TaGeBP family remains lacking. In this study, 37 TaGeBP genes were identified in the wheat genome (cv. Chinese Spring), representing a substantially higher number than the 11 reported in the prior study. This discrepancy is likely attributable to the integration of updated genome assemblies, refined gene identification criteria, and comprehensive domain validation. Phylogenetic analysis classified these 37 TaGeBPs into four distinct groups, with members within the same subgroup sharing conserved exon–intron architectures and protein motif compositions. Promoter cis-acting element analysis revealed significant enrichment of motifs associated with abiotic stress responses and phytohormone signaling, implying potential involvement of TaGeBPs in mediating plant adaptive processes. Evolutionary analysis indicated that TaGeBP family expansion was primarily driven by allopolyploidization and segmental duplication, with purifying selection constraining their sequence divergence. Members within the same subgroup shared similar exon–intron structures and conserved protein motifs. Promoter analysis revealed that TaGeBP genes are enriched with cis-elements related to stress and phytohormone responses, suggesting their potential involvement in adaptive processes. Gene expansion in the TaGeBP family was mainly driven by allopolyploidization and segmental duplication, with evolution dominated by purifying selection. Tissue-specific expression profiling demonstrated that most TaGeBPs are preferentially expressed in roots and spikes, with varying expression patterns across different tissues. Under salt and drought stresses, qRT-PCR results indicated diverse response profiles among TaGeBPs. Furthermore, subcellular localization confirmed the nuclear presence of selected TaGeBPs, supporting their predicted role as transcription factors. These findings offer important insights for further functional characterization of TaGeBP genes, particularly regarding their roles in abiotic stress tolerance. Full article

Artificial hybrids between cultivated Avena species and wild Avena macrostachya that possess genes for resistance to biotic and abiotic stresses can be important for oat breeding. For the first time, a comprehensive study of genomes of artificial fertile hybrids Avena sativa × Avena macrostachya and their parental species was carried out based on the chromosome FISH mapping of satellite DNA sequences (satDNAs) and also analysis of intragenomic polymorphism in the 18S–ITS1–5.8S rDNA region, using NGS data. Chromosome distribution patterns of marker satDNAs allowed us to identify all chromosomes in the studied karyotypes, determine their subgenomic affiliation, and detect several chromosome rearrangements. Based on the obtained cytogenomic data, we revealed differences between two A. macrostachya subgenomes and demonstrated that only one of them was inherited in the studied octoploid hybrids. Ribotype analyses showed that the second major ribotype of A. macrostachya was species-specific and was not represented in rDNA pools of the octoploids, which could be related to the allopolyploid origin of this species. Our results indicate that the use of marker satDNAs in cytogenomic studies can provide important data on genomic relationships within Avena allopolyploid species and hybrids, and also expand the potential for interspecific crosses for breeding. Full article

Plant species complexes represent a particularly interesting example of taxonomically complex groups (TCGs), linking hybridization, apomixis, and polyploidy with complex morphological patterns. In such TCGs, mosaic-like character combinations and conflicts of morphological data with molecular phylogenies present a major problem for species classification. Here, we used the large polyploid apomictic European Ranunculus auricomus complex to study relationships among five diploid sexual progenitor species and 75 polyploid apomictic derivate taxa, based on geometric morphometrics using 11,690 landmarked objects (basal and stem leaves, receptacles), genomic data (97,312 RAD-Seq loci, 48 phased target enrichment genes, 71 plastid regions) from 220 populations. We showed that (1) observed genomic clusters correspond to morphological groupings based on basal leaves and concatenated traits, and morphological groups were best resolved with RAD-Seq data; (2) described apomictic taxa usually overlap within trait morphospace except for those taxa at the space edges; (3) apomictic phenotypes are highly influenced by parental subgenome composition and to a lesser extent by climatic factors; and (4) allopolyploid apomictic taxa, compared to their sexual progenitor, resemble a mosaic of ecological and morphological intermediate to transgressive biotypes. The joint evaluation of phylogenomic, phenotypic, reproductive, and ecological data supports a revision of purely descriptive, subjective traditional morphological classifications. Full article

The complex genomic composition of allopolyploid plants leads to morphologically diverse species. The traditional taxonomical treatment of the medium-sized, hexaploid shrub willows distributed in the Alps is difficult based on their variable morphological characters. In this study, RAD sequencing data, infrared-spectroscopy, and morphometric data are used to analyze the phylogenetic relationships of the hexaploid species of the sections Nigricantes and Phylicifoliae in a phylogenetic framework of 45 Eurasian Salix species. Both sections comprise local endemics as well as widespread species. Based on the molecular data, the described morphological species appeared as monophyletic lineages (except for S. phylicifolia s.str. and S. bicolor, which are intermingled). Both sections Phylicifoliae and Nigricantes are polyphyletic. Infrared-spectroscopy mostly confirmed the differentiation of hexaploid alpine species. The morphometric data confirmed the molecular results and supported the inclusion of S. bicolor into S. phylicifolia s.l., whereas the alpine endemic S. hegetschweileri is distinct and closely related to species of the section Nigricantes. The genomic structure and co-ancestry analyses of the hexaploid species revealed a geographical pattern for widespread S. myrsinifolia, separating the Scandinavian from the alpine populations. The newly described S. kaptarae is tetraploid and is grouped within S. cinerea. Our data reveal that both sections Phylicifoliae and Nigricantes need to be redefined. Full article

Zingeria (Poaceae) is a small genus that includes Z. biebersteiniana, a diploid species with the lowest chromosome number known in plants (2n = 4) as well as hexaploid Z. kochii and tetraploid Z. pisidica, and/or Z. trichopoda species. The relationship between these species and the other low-chromosomes species Colpodium versicolor are unclear. To explore the intragenomic polymorphism and genome composition of these species we examined the sequences of the internal transcribed spacer 1 of the 35S rRNA gene via NGS approach. Our study revealed six groups of ribotypes in Zingeria species. Their distribution confirmed the allopolyploid nature of Z. kochii, whose probable ancestors were Colpodium versicolor and Z. pisidica. Z. pisidica has 98% of rDNA characteristic only for this species, and about 0.3% of rDNA related to that of Z. biebersteiniana. We assume that hexaploid Z. kochii is either an old allopolyploid or a homodiploid that has lost most of the rRNA genes obtained from Z. biebersteiniana. In Z. trichopoda about 81% of rDNA is related to rDNA of Z. biebersteiniana and 19% of rDNA is derived from Poa diaphora sensu lato. The composition of the ribotypes of the two plants determined by a taxonomy specialist as Z. pisidica and Z. trichopoda is very different. Two singleton species are proposed on this base with ribotypes as discriminative characters. So, in all four studied Zingeria species, even if the morphological difference among the studied species was modest, the genomic constitution was significantly different, which suggests that these are allopolyploids that obtained genomes from different ancestors. Full article

Allopolyploids are known to have superior advantages such as high growth speed. Triploids have even greater heterozygosity, explaining more phenotypic variance than 2n hybrid F1 and have therefore become new resources in breeding. To date, the metabolomic basis underlying polyploidization vigor remains unclear. Here, we identified and compared 235 metabolites in the shoot apical buds between multiple allo-triploid populations and parental 2n hybrid F1 in Populus via metabolome profiling using liquid chromatography–mass spectrometry (LC–MS) assays. Associations with growth vigor in three types of allo-triploid populations, namely first division restitution (FDR), second division restitution (SDR) and postmeiotic restitution (PMR) generated from doubled 2n female gametes and male gametes of 2n hybrid, were also investigated. Each allo-triploid population has different sub-genome duplicated. Major metabolomes were amino acids, secondary metabolism associated, and carbohydrates. We mapped 181 metabolites into known metabolism pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG). Ten compounds, i.e., fructose 1,6-diphosphate and xylulose, were more abundant in all allo-triploids than the 2n hybrid. Principal component analysis revealed the abundance of metabolites fell into distinct clusters corresponding to ploidy composition. Heterozygosity in triploids mainly effected the contents of carbohydrates and secondary metabolites rather than lipids. Comparisons between subgroups with different growth rates revealed some carbohydrates and secondary metabolites of flavonoids were positively associated with gene expression and the high growth vigor. The results provided an informative metabolomic basis for factors conferring growth vigor in polyploid Populus. Full article

The GH3 gene family plays a vital role in the phytohormone-related growth and developmental processes. The effects of allopolyploidization on GH3 gene structures and expression levels have not been reported. In this study, a total of 38, 25, and 66 GH3 genes were identified in Brassica rapa (A_rA_r), Brassica oleracea (C_oC_o), and Brassica napus (A_nAC_nC_n), respectively. BnaGH3 genes were unevenly distributed on chromosomes with 39 on A_n and 27 on C_n, in which six BnaGH3 genes may appear as new genes. The whole genome triplication allowed the GH3 gene family to expand in diploid ancestors, and allopolyploidization made the GH3 gene family re-expand in B. napus. For most BnaGH3 genes, the exon-intron compositions were similar to diploid ancestors, while the cis-element distributions were obviously different from its ancestors. After allopolyploidization, the expression patterns of GH3 genes from ancestor species changed greatly in B. napus, and the orthologous gene pairs between A_n/A_r and C_n/C_o had diverged expression patterns across four tissues. Our study provides a comprehensive analysis of the GH3 gene family in B. napus, and these results could contribute to identifying genes with vital roles in phytohormone-related growth and developmental processes. Full article

Supernumerary chromosomal segments (SCSs) represent additional chromosomal material that, unlike B chromosomes, is attached to the standard chromosome complement. The Prospero autumnale complex (Hyacinthaceae) is polymorphic for euchromatic large terminal SCSs located on the short arm of chromosome 1 in diploid cytotypes AA and B⁷B⁷, and tetraploid AAB⁷B⁷ and B⁶B⁶B⁷B⁷, in addition to on the short arm of chromosome 4 in polyploid B⁷B⁷B⁷B⁷ and B⁷B⁷B⁷B⁷B⁷B⁷ cytotypes. The genomic composition and evolutionary relationships among these SCSs have been assessed using fluorescence in situ hybridisation (FISH) with 5S and 35S ribosomal DNAs (rDNAs), satellite DNA PaB6, and a vertebrate-type telomeric repeat TTAGGG. Neither of the rDNA repeats were detected in SCSs, but most contained PaB6 and telomeric repeats, although these never spanned whole SCSs. Genomic in situ hybridisation (GISH) using A, B⁶, and B⁷ diploid genomic parental DNAs as probes revealed the consistently higher genomic affinity of SCSs in diploid hybrid B⁶B⁷ and allopolyploids AAB⁷B⁷ and B⁶B⁶B⁷B⁷ to genomic DNA of the B⁷ diploid cytotype. GISH results suggest a possible early origin of SCSs, especially that on chromosome 1, as by-products of the extensive genome restructuring within a putative ancestral P. autumnale B⁷ genome, predating the complex diversification at the diploid level and perhaps linked to B-chromosome evolution. Full article