The version of microevolutionary relationships between biotypes close to Elymus caninus (Poaceae) according to the sequencing of the nuclear gene GBSS1 (waxy)

A comparative study of the sequences of the GBSS1 gene fragment in accessions of species close to Elymus caninus:E. prokudinii, E. viridiglumis, E. goloskokovii, as well as a number of morphologically deviating forms (MDF) from the territoryof Russia and Kazakhstan was carried out. The StH-genomic constitution was established or confirmed in all studied taxa andMDF, and the microevolutionary relationships between species were assessed by constructing separate NJ dendrograms based onexons and introns together and exons only. Differences in the location of Y subgenomes in reference StY-genomic species on twotypes of constructed dendrograms were noted. Possible evolutionary reasons for these differences are discussed. A characteristicfeature of all taxa close to E. caninus is the presence of only St2clones of the St subgenome, which are closer in composition tothe North American ancestral line Pseudoroegneria spicata than to the Asiatic line ascending to P. strigosa. The reference Polishaccession E. caninus can_5274 is farthest from the Asian accessions in the St2subgenome, but closer to the diploid carrier ofthe St genome P. spicata. According to the levels of differentiation of the H subgenome, all putative relatives of E. caninus havevariants of the H1subgenome around the Asian diploid host Hordeum jubatum, while being divided into two distinct subgroups.Only the accessions of four reference species gravitate towards the North American species Hordeum californicum – the carrierof the H2gene variant. It should be noted that the gene variants of the Ural endemic E. uralensis are close to the main group ofE. caninus accessions in both subgenomes. Together with the results of sexual hybridization, this fact gives grounds to considerE. uralensis as closely related to the main group of taxa deserving the intraspecific rank of E. caninus s. l.

Wheat, Rye, and Barley Genomes Can Associate during Meiosis in Newly Synthesized Trigeneric Hybrids

Polyploidization, or whole genome duplication (WGD), has an important role in evolution and speciation. One of the biggest challenges faced by a new polyploid is meiosis, in particular, discriminating between multiple related chromosomes so that only homologs recombine to ensure regular chromosome segregation and fertility. Here, we report the production of two new hybrids formed by the genomes of species from three different genera: a hybrid between Aegilops tauschii (DD), Hordeum chilense (HchHch), and Secale cereale (RR) with the haploid genomic constitution HchDR (n = 7× = 21); and a hybrid between Triticum turgidum spp. durum (AABB), H. chilense, and S. cereale with the constitution ABHchR (n = 7× = 28). We used genomic in situ hybridization and immunolocalization of key meiotic proteins to establish the chromosome composition of the new hybrids and to study their meiotic behavior. Interestingly, there were multiple chromosome associations at metaphase I in both hybrids. A high level of crossover (CO) formation was observed in HchDR, which shows the possibility of meiotic recombination between the different genomes. We succeeded in the duplication of the ABHchR genome, and several amphiploids, AABBHchHchRR, were obtained and characterized. These results indicate that recombination between the genera of three economically important crops is possible.

Intragenomic Polymorphism of the ITS 1 Region of 35S rRNA Gene in the Group of Grasses with Two-Chromosome Species: Different Genome Composition in Closely Related Zingeria Species

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.

Identification of genome compositions in allopolyploid species of the genus Elymus(Poaceae: Triticeae) in the Asian part of Russia by CAPS analysis

The genus ElymusL., together with wheat, rye, and barley, belongs to the tribe Triticeae. Apart from its economic value, this tribe is characterized by abundance of polyploid taxa formed in the course of remote hybridization. Single-copy nuclear genes are convenient markers for identification of source genomes incorporated into polyploids. In the present work, a CAPS-marker is developed to distinguish basic St, H, and Y genomes comprising polyploid genomes of Asiatic species of the genus Elymus. The test is based on electrophoretic analysis of restriction patterns of a PCR-amplified fragment of the gene coding for beta-amylase. There are about 50 Elymusspecies in Russia, and most of them are supposed to possess one of three haplome combinations, StH, StY and StHY. Boreal StH-genomic species endemic for Russia are the least studied. On the basis of nucleotide sequences from public databases, TaqI restrictase was selected, as it produced patterns of restriction fragments specific for St, H, and Y haplomes easily recognizable in agarose gel. A sample of 68 accessions belonging to 32 species was analyzed. In 15 species, the earlier known genomic constitutions were confirmed, but in E. kamojithis assay failed to reveal the presence of H genome. This unusual H genome was suggested to originate from a different Hordeum species. In 16 species, genomic constitutions were identified for the first time. Fifteen accessions from Asian Russia possessed the genomic constitution StStHH, and E. amurensis, phylogenetically close to the StY-genomic species E. ciliaris, had the genomic constitution StStYY. It is inferred that the center of species diversity of the StH-genomic group is shifted to the north as compared to the center of origin of StY-genomic species, confined to China.

The version of microevolutionary relationships between the Siberian species Elymus margaritae, E. komarovii, and E. transbaicalensis (Poaceae) according to sequencing of the nuclear gene GBSS1 (waxy)

A comparative study was made of the sequence of the GBSS1 gene fragment in accessions of closely related species Elymus margaritae, E. komarovii, and E. transbaicalensis from Siberia. Nucleotide sequences of the gene were determined for St subgenomes in accessions of E. margaritae and E. komarovii from classical habitats. The StH-genomic constitution was confirmed, and microevolutionary relationships between species were evaluated by constructing the NJ dendrogram. It was shown that variants of the St subgenomes in accessions E. margaritae GUK-1009 and E. komarovii AUK-9803 belong to the North American ancestral line St2 of the genus Pseudoroegneria, in contrast to accessions E. margaritae AUK-0650 and E. komarovii GAR-0501. The latter belong to the Asian branch of St1, together with variants of subgenomes in the species E. gmelinii and E. pendulinus. That is, according to the differentiation levels of the St subgenome, accession E. margaritae GUK-1009 (holotype) is significantly distanted from the accession AUK-0650 (paratype), which in turn is close to accessions of E. komarovii and E. transbaicalensis from East Sayan. According to levels of differentiation of the H subgenome, the studied species did not show noticeable differences.

Genome constitution and differentiation of subgenomes in Siberian and Far Eastern endemic species of the genus Elymus (Poaceae) according to the sequencing of the nuclear gene waxy

Fifty-three species of perennial grasses in the genus Elymus L. (Poaceae), which are widespread in Russia, are generally assumed to have three haplome combinations: StH, StY and StHY. The StH-genome species, endemic to Russia, remain the least studied. R. Mason-Gamer and co-authors have previously shown in a series of studies that a molecular phylogenetic analysis of the low-copy gene waxy (GBSS1) sequences significantly complements cytogenetic data on the genomic constitution and evolutionary relationships among both North American and Asian species of the genus Elymus. To determine the species’ genomic constitution and to evaluate the level of phylogenetic differentiation, we examined the GBSS1 gene in 18 species of Elymus from Siberia and the Russian Far East, including the fol- lowing 14 endemics: E. charkeviczii, E. jacutensis, E. kamczadalorum, E. komarovii, E. kronokensis, E. lenensis, E. macrourus, E. margaritae, E. subfibrosus, E. sajanensis, E. transbaicalensis, E. peschkovae, E. uralensis, and E. viridiglumis.PCR amplification products of GBSS1 gene fragments (including exons 9–14) were cloned and 6–8 clones per accession were sequenced. It appears that all the species studied have St and H subgenomic gene variations. The most significant differences between the subgenomic variants St and H were found in intron 13. The H subgenome contains a 21-bp-long deletion in intron 13 in all Elymus genotypes, probably derived from a common ancestor of the H and P genomes. Instead of this deletion, all St subgenomes have a relatively conservative sequence similar to that of the genus Pseudoroegneria, whose ancestor is considered to be the donor of the modern St subgenome for all Elymus species. Cluster phylogenetic analysis revealed differentiation in St and H subgenome sequences into two evolutionary variants: St1 vs. St2 and H1 vs. H2, respectively. Variants of the St and H subgenomes were found homologous to various modern species of the ancestral genera Pseudoroegneria and Hordeum: St1 to P. strigosa, St2 to P. spicata, H1 to H. jubatum, and H2 to H. californicum. The details of the relationships between Russian and North American species of the genus, as well as a number of microevolutionary interconnections in the group of boreal endemic species of Siberia and the Russian Far East were revealed. The new results obtained here are essential for the development of a phylogenetically oriented taxonomic system for the genus Elymus.