Tetraploid Species Research Articles

An integrated morpho‐molecular study of Salicornia (Amaranthaceae‐Chenopodiaceae) in Iran proves Irano‐Turanian region the major center of diversity of annual glasswort species

AbstractSalicornia (Chenopodiaceae) with ca. 25–30 annual, hyperhalophytic succulent species is a taxonomically difficult sub‐cosmopolitan genus. The taxonomic complexity arose from succulent shoots causing a lack of taxonomically useful characters, scarcity and variability of characters, and poor genetic differentiation. The Irano‐Turanian region, a major center for several lineages of chenopod diversification, is also an important diversity center and more likely the center of origin of annual Salicornia. This paper presents long‐term comprehensive morpho‐molecular and cytological studies of the genus in Iran, as the most species‐rich country in the Irano‐Turanian region. We originally generated 250 sequences of one nuclear (ETS) and two plastid markers (atpB‐rbcL spacer, intron rpl16). We analyzed a global ETS dataset including 257 sequences of putative 28 taxa using Bayesian inference and maximum likelihood analysis. In order to evaluate the application of plastid data in species taxonomy in annual Salicornia, we performed numerical morphological analysis (principal component analysis and agglomerative hierarchical clustering) of 186 Iranian accessions using 18 characters. Our results (1) confirm the efficiency of plastid sequences comparing to ETS sequences for clarifying species‐level phylogeny of Salicornia; (2) identify the S. persica clade as a monophyletic Irano‐Turanian endemic lineage; (3) recognize nine origins of the Irano‐Turanian Salicornia based on nuclear ETS sequences; (4) approve the monophyly of tetraploid species using plastid sequences; (5) provide a synopsis and diagnostic key for 10 Iranian taxa of Salicornia; (6) describe S. turanica sp. nov.; (7) classify S. iranica at infraspecific level (S. iranica subsp. iranica, S. iranica subsp. rudshurensis comb. nov., S. iranica subsp. sinus‐persica comb. & stat. nov.); (8) suggest three informal taxa to be studied in the future; and (9) discuss the threatened status of Salicornia‐dominated ecosystems in Iran.

Characterization of Each St and Y Genome Chromosome of Roegneria grandis Based on Newly Developed FISH Markers

The genera of the tribe Triticeae (family Poaceae), constituting many economically important plants with abundant genetic resources, carry genomes such as St, H, P, and Y. The genome symbol of Roegneria C. Koch (Triticeae) is StY. The St and Y genomes are crucial in Triticeae, and tetraploid StY species participate extensively in polyploid speciation. Characterization of St and Y nonhomologous chromosomes in StY-genome species could help understand variation in the chromosome structure and differentiation of StY-containing species. However, the high genetic affinity between St and Y genome and the deficiency of a complete set of StY nonhomologous probes limit the identification of St and Y genomes and variation of chromosome structures among Roegneria species. We aimed to identify St- and Y-enhanced repeat clusters and to study whether homoeologous chromosomes between St and Y genomes could be accurately identified due to high affinity. We employed comparative genome analyses to identify St- and Y-enhanced repeat clusters and generated a FISH-based karyotype of R. grandis (Keng), one of the taxonomically controversial StY species, for the first time. We explored 4 novel repeat clusters (StY_34, StY_107, StY_90, and StY_93), which could specifically identify individual St and Y nonhomologous chromosomes. The clusters StY_107 and StY_90 could identify St and Y addition/substitution chromosomes against common wheat genetic backgrounds. The chromosomes V_St, VII_St, I_Y, V_Y, and VII_Y displayed similar probe distribution patterns in the proximal region, indicating that the high affinity between St and Y genome might result from chromosome rearrangements or transposable element insertion among V_St/Y, VII_St/Y, and I_Y chromosomes during allopolyploidization. Our results can be used to employ FISH further to uncover the precise karyotype based on colinearity of Triticeae species by using the wheat karyotype as reference, to analyze diverse populations of the same species to understand the intraspecific structural changes, and to generate the karyotype of different StY-containing species to understand the interspecific chromosome variation.

Якість зерна гібридних ліній пшениці м'якої ярої – потомків гібридів синтетиків з сортом Харківська 26

Якість зерна гібридних ліній пшениці м'якої ярої – потомків гібридів синтетиків з сортом Харківська 26

Spatial distribution of a single river endemic allotetraploid spined loach, Cobitis takenoi, in comparison with a co-inhabiting tetraploid congener species

Spatial distribution of a single river endemic allotetraploid spined loach, Cobitis takenoi, in comparison with a co-inhabiting tetraploid congener species

On the Origin of Tetraploid Vernal Grasses (Anthoxanthum) in Europe.

Polyploidy has played a crucial role in the evolution of many plant taxa, namely in higher latitudinal zones. Surprisingly, after several decades of an intensive research on polyploids, there are still common polyploid species whose evolutionary history is virtually unknown. Here, we addressed the origin of sweet vernal grass (Anthoxanthum odoratum) using flow cytometry, DNA sequencing, and in situ hybridization-based cytogenetic techniques. An allotetraploid and polytopic origin of the species has been verified. The chromosome study reveals an extensive variation between the European populations. In contrast, an autopolyploid origin of the rarer tetraploid vernal grass species, A. alpinum, has been corroborated. Diploid A. alpinum played an essential role in the polyploidization of both European tetraploids studied.

Genome wide analysis of IQD gene family in diploid and tetraploid species of cotton (Gossypium spp.)

Calmodulin (CaM) is considered as the most significant Ca2+ signaling messenger that mediate various biochemical and physiological reactions. IQ domain (IQD) proteins are plant specific CML/CaM calcium binding which are characterized by domains of 67 amino acids. 50, 50, 94, and 99 IQD genes were detected from G. arboreum (A2), G. raimondii (D5), G. barbadense (AD2) and G. hirsutum (AD1) respectively. Existence of more orthologous genes in cotton species than Arabidopsis, advocated that polyploidization produced new cotton specific orthologous gene clusters. Duplication of gene events depicts that IQD gene family of cotton evolution was under strong purifying selection. G. hirsutum exhibited high level synteny. GarIQD25 exhibited high expression in stem, root, flower, ovule and fiber in G. arboreum. In G. raimondii, GraIQD03 demonstrated upregulation across stem, ovule, fiber and seed. GbaIQD11 and GbaIQD62 exhibited upregulation in fiber development in G. barbadense. GhiIQD69 recognized as main candidate genes for plant parts, floral tissues, fiber and ovule development. Promotor analysis identified cis-regulatory elements were involved in plant growth and development. Overwhelmingly, present study paves the way to better understand the evolution of cotton IQD genes and lays a foundation for future investigation of IQD in cotton.

Gynogenetic diploids, tetraploids, or octoploids, and a path to polyploidy in anuran amphibians.

Unreduced gametes have been implicated in the evolution of polyploid species of plants and animals and are normally produced by female anuran amphibians. Such eggs may initiate the evolution of polyploid species that have arisen independently in several anuran families. Polyploid females could also produce unreduced eggs that might lead to species with higher ploidy levels, or their eggs may develop gynogenetically to reduce the ploidy level. Diploid Hyla chrysoscelis (2n = 24) and tetraploid H. versicolor (4n = 48) are sibling cryptic species of North American grey treefrogs. Artificial crosses using H. versicolor females and genetically distant diploid males were performed to produce haploid H. versicolor and to assess the production of unreduced eggs in this tetraploid species. Gynogenetic diploid (haploid H. versicolor), allotriploid, gynogenetic tetraploid, allopentaploid, autohexaploid, and gynogenetic octoploid tadpoles were confirmed using chromosome counts from tadpole tail tip squashes. The transformation and survival of different ploidies varied. Gynogenetic diploids transformed but expressed aspects of haploid syndrome and died before or shortly after transformation.

VARIABILITY OF THE INDIVIDUAL-GROUP COMPOSITION OF POLYPHENOLS OF THE FRUITS AND LEAVES OF BLUE HONEYSUCKLE SAMPLES OF DIFFERENT ECOLOGICAL AND GEOGRAPHICAL ORIGIN IN THE OB FOREST-STEPPE

The aim of the study was to compare the variability of the composition, chemical identity and content of biologically active phenolic compounds in the fruits and leaves of the blue honeysuckle (Lonicera subsection Caeruleae) plants of different environmental and geographic provenances, sampled from the introduction plantation station in the forest steppe zone near the Ob River (Novosibirsk, Russia). In extracts from the leaves 25 individual compounds representing various polyphenolic classes were identified using HPLC-MS technique; seven of the compounds were identified as hydroxycinnamic acids, five compounds were flavonols, and eight compounds represented flavones. The maximal number of individual compounds was present in samples of the Altai subspecies of the tetraploid species L. caerulea subsp. altaica, whereas the minimal number was detected in samples of L. boczkarnikowae, a diploid species from the Russian Far East (Primorsky region). The lowest total polyphenolics content (6,260 mg/100 g of air-dry phytomass) was found in samples of L. caeruleae subsp. pallasii, whereas the content in samples from other blue honeysuckle subspecies ranged within 11.620-14.030 mg/100 g of air-dry phytomass. High content of flavones in extracts from leaves, always exceeding the flavonol content, was found to be a characteristic feature of L. caerulea subsp. altaica. Among L. сaerulea subspecies, L. сaerulea subsp. pallasii was shown to have the largest ratio of flavonols to flavones. L. boczkarnikowae also had high content of flavonols, significantly exceeding the flavones content in the plants organs. The main component of anthocyanins was cyanidin-3-glucoside, accounting for up to 91%. The fruits of L. caerulea subsp. altaica, L. сaerulea subsp. venulosa and L. boczkarnikowae had the highest anthocyanin content, ranging 2.950–3.200 mg/100 g air-dry phytomass, whereas the fruits of L. сaerulea subsp. pallasii had the lowest one (1,573 mg/100g). Extracts from the leaves were found to have significantly higher polyphenolics content as compared to the ones from the fruits; thus the leaves can be recommended as a prospective medicinal source.

Geographical distribution and adaptive variation of VRN-A3 alleles in worldwide polyploid wheat (Triticum spp.) species collection.

The distribution of early flowering alleles of VRN-A3 was found to be biased to low latitudes, and these alleles may contribute to environmental adaptability to low latitudes in cultivated emmer wheat. In wheat (Triticum spp.), the flowering time is an important trait for successful seed production and yield by adapting to the regional environment. An early flowering allele of VRN-A3 with 7- and 25-bp insertions in the promoter region (Vrn-A3a-h1) has recently been reported from the analysis of an emmer wheat (Triticum turgidum L. ssp. dicoccum) accession, TN26. This early flowering allele of VRN-A3 might be associated with the regional adaptation of wheat. In this study, we elucidated its geographic distribution to assess the importance of the early flowering allele of VRN-A3 in worldwide wheat collection. From sequence analysis, we identified six VRN-A3 alleles with the 7- and 25-bp insertions, namely, Vrn-A3a-h2, Vrn-A3a-h3, Vrn-A3a-h4, Vrn-A3a-h5, Vrn-A3a-h6, and Vrn-A3c-h2 from wild emmer wheat, while we identified two VRN-A3 alleles with these insertions, Vrn-A3a-h2 and Vrn-A3c-h1 from cultivated tetraploid and hexaploid wheat species in addition to Vrn-A3a-h1. Among VRN-A3 alleles distributed in cultivated wheat, we found that Vrn-A3a-h2 promoted early heading, whereas Vrn-A3c-h1 did not affect heading time. Our analysis showed that the distribution of early flowering alleles of VRN-A3 dominated in cultivated emmer wheat in Ethiopia and India, which actually showed an early flowering phenotype. This implied that the early flowering alleles of VRN-A3 contribute to adaptability to a low-latitude environment in cultivated emmer wheat. We could not find durum (T. turgidum L. ssp. durum) and bread wheat (T. aestivum L. ssp. aestivum) accessions with these early flowering alleles. Our findings indicated that Vrn-A3a-h1 and Vrn-A3a-h2 were useful for breeding of early flowering cultivars in durum and bread wheat varieties.

Identification of the tetrad-sterility-causing Solanum stoloniferum Schltdl. & Bouché cytoplasm in interspecific hybrids with S. tuberosum L.

Tetrad sterility, in which only clumps of four premature pollen grains are released from anthers, has been observed in some modern potato cultivars. It is a form of cytoplasmic male sterility caused by the cytoplasm derived from the Mexican tetraploid species Solanum stoloniferum Schltdl. & Bouché., an important source of resistance to Potato virus Y in potato breeding. However, since S. stoloniferum is highly polymorphic, the source of tetrad-sterility-causing cytoplasm is unknown among diverse S. stoloniferum accessions. In this study, we directly crossed 24 S. stoloniferum accessions with pollen from 4x S. tuberosum and obtained 39 hybrids from 12 accessions. Nineteen hybrids from six accessions showed tetrad sterility, with either D/γ- or W/γ-type cytoplasm, and were triploid, tetraploid, or hexaploid. The W/γ-type cytoplasm was not necessarily associated with tetrad sterility. Sequence comparisons of 17 mitochondrial genes and their intergenic regions revealed a length polymorphism in the intergenic region between rpl5 and rps10, in which an amplified band of 859 bp was associated with tetrad sterility. This specific cytoplasm causing tetrad sterility is named TSCsto. The 859-bp band will be a useful diagnostic marker for identifying TSCsto in potato breeding.

Characterization of 1Sty13, a novel high-molecular-weight glutenin subunit from Elymus sibiricus L.

AbstractHigh-molecular-weight glutenin subunit (HMW-GS) is a key factor affecting dough-processing quality. 1Sty13 is a novel HMW-GS found in the tetraploid species, Elymus sibiricus L. 1Sty13 has faster electrophoretic mobility than the 1Dy12 subunit on sodium dodecyl sulphate (SDS)-polyacrylamide gel electrophoresis. The gene encoding the 1Sty13 subunit was composed of 1803 nucleotide base pairs with an open reading frame that was 599 amino acids in length. Analysis of the predicted amino acid sequence of 1Sty13 indicated that the N-terminal domain was similar to the y-type subunit, whereas the C-terminal domains were similar to the x-type subunit. Five cysteine residues were found in 1Sty13, which is one less than the published HMW-GS in the St genome. The 1Sty13 protein was purified at a scale sufficient for incorporation into flour for the SDS sedimentation test, which indicated that incorporating 1Sty13 improved dough quality.

Ectopic expression of VRT-A2 underlies the origin of Triticum polonicum and Triticum petropavlovskyi with long outer glumes and grains

Polish wheat (Triticum polonicum) is a unique tetraploid wheat species characterized by an elongated outer glume. The genetic control of the long-glume trait by a single semi-dominant locus, P1 (from Polish wheat), was established more than 100 years ago, but the underlying causal gene and molecular nature remain elusive. Here, we report the isolation of VRT-A2, encoding an SVP-clade MADS-box transcription factor, as the P1 candidate gene. Genetic evidence suggests that in T. polonicum, a naturally occurring sequence rearrangement in the intron-1 region of VRT-A2 leads to ectopic expression of VRT-A2 in floral organs where the long-glume phenotype appears. Interestingly, we found that the intron-1 region is a key ON/OFF molecular switch for VRT-A2 expression, not only because it recruits transcriptional repressors, but also because it confers intron-mediated transcriptional enhancement. Genotypic analyses using wheat accessions indicated that the P1 locus is likely derived from a single natural mutation in tetraploid wheat, which was subsequently inherited by hexaploid T. petropavlovskyi. Taken together, our findings highlight the promoter-proximal intron variation as a molecular basis for phenotypic differentiation, and thus species formation in Triticum plants.

Re-evaluation of common carp (Cyprinus carpio L.) housekeeping genes for gene expression studies – considering duplicated genes

Quantitative real-time PCR is one of the most widely used techniques for measuring changes in the expression of target transcripts due to its sensitivity, specificity, and cost-effectiveness. However, the essential step that determines appropriate and correct data interpretation is the selection of proper endogenous control genes. Identifying useful reference genes with stable expression is critical for accurate normalization and precise results. Functional divergence of duplicated genes in tetraploid species, like common carp, can complicate the choice for a proper reference gene. In the present study, we determined the expression stability of duplicated genes of 40s, b2m, ef1α, gapdh, g6pd, and odc1 in different tissues of common carp (Cyprinus carpio L.). Gene expression analysis comprised healthy control fish, fish under bacterial and parasitic infections, and across the early stage of common carp development. Obtained data were compared with the actb gene, which is used widely as a reference in RT-qPCR analysis. The application of the three different algorithms - geNorm, NormFinder, BestKeeper, allowed comparative evaluation of the expression stability of the tested genes. Subsequently, the RefFinder, a web-based tool, was used to rank the examined housekeeping genes comprehensively. We demonstrate variable transcription stability levels in the examined mRNAs as well as differences in expression between paralog gene copies. The 40s, b2m, ef1α and actb genes showed the most stable expression across all physiological conditions and tissues. The gapdh, odc1, and g6pd gene variants demonstrated lower stability. Differences in expression patterns between duplicated genes underline the possibility of functional divergence between them. This aspect should be considered in polyploid species before selecting the reference gene(s). Our study also points on the importance of choice for a reference gene (paralog) when expressing newly identified genes and the spatial expression profile is performed. SubjectsAquaculture, Molecular Biology, Fish Science.

THE NATURE OF INHERITANCE OF THE COLORED COTTON FIBER TRAIT

The article provides information on the biology of diploid and tetraploid cotton species, character and patterns of inheritance of fiber color. The fabric obtained from naturally colored cotton fibers has the properties of greater hygiene and hypoallergenic. Clothing made from such a fabric does not cause irritation on the skin, as the fabric perfectly passes air.

Adaptation and Agronomic Performance of Domesticated Moroccan Oat (Avena magna ssp. domestica) Lines under Subsistence Farming Conditions at Multiple Locations in Morocco

Common hexaploid oat (Avena sativa L.) is an important global cereal crop. A Moroccan tetraploid sister species, A. magna Murphy et Terrel, was exclusively a wild species until recently. The goal of domestication was to exploit its superior groat-protein content and climatic tolerances. We set up replicated trials of 41 domesticated A. magna lines on eight Moroccan farms during the 2017–2018 and 2018–2019 growing seasons. Twenty traits were measured and analyses of variance detected significant differences among lines. The highest grain yield was at Berrechid in 2017–2018 (63.56 q/ha), with an average annual yield across sites of 43.50 q/ha, the site factor explaining 82% and the genotype-environment interaction explaining 15% of the variability. In the second year, El Kebab recorded the highest yield at 20.03 q/ha over the annual average of 14.78 q/ha. In this second year, the site factor was highly significant, explaining 42.25% of the variation, with the genotype-environment interaction explaining 26.61% of the variability. An additional main effect and multiplicative interaction analysis of the eight two-year trials identified several accessions with good yield stability. Twelve lines exhibited a ASVs ≤ 1.50, with five accessions (A34, A40, A23, A05, A04) exceeding the overall average yield of 29.53 and A34 having the greatest mean grain yield and stability. The versatility and stability of A. magna can provide a sustainable protein source and an economic resource for farmers seeking products that are resilient to climatic instability.

Panicum virgatum (Poaceae)

Switchgrass (Panicum virgatum L.) is a promising biofuel crop and one of the dominant species in North American tallgrass prairies. It grows rapidly, reaching up to 2.7 m, and planted fields remain productive for 15 years. The large, highly repetitive, and highly heterozygous genome of the generally tetraploid species have always been challenging for sequencing and assembly. Using PacBio long-read sequencing and bacterial artificial chromosome clone technology, researchers recently published a highly continuous genome assembly (v5) of a lowland switchgrass genotype AP13, which consisted of 626 contigs with a contig N50 of 5.5 Mb and a total of 97.2% bases that were assembled in the chromosomes.

Chromosome and Molecular Analyses Reveal Significant Karyotype Diversity and Provide New Evidence on the Origin of Aegilops columnaris.

Aegilops columnaris Zhuk. is tetraploid grass species (2n = 4x = 28, UcUcXcXc) closely related to Ae. neglecta and growing in Western Asia and a western part of the Fertile Crescent. Genetic diversity of Ae. columnaris was assessed using C-banding, FISH, nuclear and chloroplast (cp) DNA analyses, and gliadin electrophoresis. Cytogenetically Ae. columnaris was subdivided into two groups, C-I and C-II, showing different karyotype structure, C-banding, and FISH patterns. C-I group was more similar to Ae. neglecta. All types of markers revealed significant heterogeneity in C-II group, although group C-I was also polymorphic. Two chromosomal groups were consistent with plastogroups identified in a current study based on sequencing of three chloroplast intergenic spacer regions. The similarity of group C-I of Ae. columnaris with Ae. neglecta and their distinctness from C-II indicate that divergence of the C-I group was associated with minor genome modifications. Group C-II could emerge from C-I relatively recently, probably due to introgression from another Aegilops species followed by a reorganization of the parental genomes. Most C-II accessions were collected from a very narrow geographic region, and they might originate from a common ancestor. We suggest that the C-II group is at the initial stage of species divergence and undergoing an extensive speciation process.

Imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species (Achillea, Asteraceae)

BackgroundPolyploid species often originate recurrently. While this is well known, there is little information on the extent to which distinct allotetraploid species formed from the same parent species differ in gene expression. The tetraploid yarrow species Achillea alpina and A. wilsoniana arose independently from allopolyploidization between diploid A. acuminata and A. asiatica. The genetics and geography of these origins are clear from previous studies, providing a solid basis for comparing gene expression patterns of sibling allopolyploid species that arose independently.ResultsWe conducted comparative RNA-sequencing analyses on the two Achillea tetraploid species and their diploid progenitors to evaluate: 1) species-specific gene expression and coexpression across the four species; 2) patterns of inheritance of parental gene expression; 3) parental contributions to gene expression in the allotetraploid species, and homeolog expression bias. Diploid A. asiatica showed a higher contribution than diploid A. acuminata to the transcriptomes of both tetraploids and also greater homeolog bias in these transcriptomes, possibly reflecting a maternal effect. Comparing expressed genes in the two allotetraploids, we found expression of ca. 30% genes were species-specific in each, which were most enriched for GO terms pertaining to “defense response”. Despite species-specific and differentially expressed genes between the two allotetraploids, they display similar transcriptome changes in comparison to their diploid progenitors.ConclusionTwo independently originated Achillea allotetraploid species exhibited difference in gene expression, some of which must be related to differential adaptation during their post-speciation evolution. On the other hand, they showed similar expression profiles when compared to their progenitors. This similarity might be expected when pairs of merged diploid genomes in tetraploids are similar, as is the case in these two particular allotetraploids.

Genome-wide investigation of the AP2/ERF superfamily and their expression under salt stress in Chinese willow (Salix matsudana).

AP2/ERF transcription factors (TFs) play indispensable roles in plant growth, development, and especially in various abiotic stresses responses. The AP2/ERF TF family has been discovered and classified in more than 50 species. However, little is known about the AP2/ERF gene family of Chinese willow (Salix matsudana), which is a tetraploid ornamental tree species that is widely planted and is also considered as a species that can improve the soil salinity of coastal beaches. In this study, 364 AP2/ERF genes of Salix matsudana (SmAP2/ERF) were identified depending on the recently produced whole genome sequencing data of Salix matsudana. These genes were renamed according to the chromosomal location of the SmAP2/ERF genes. The SmAP2/ERF genes included three major subfamilies: AP2 (55 members), ERF (301 members), and RAV (six members) and two Soloist genes. Genes’ structure and conserved motifs were analyzed in SmAP2/ERF family members, and introns were not found in most genes of the ERF subfamily, some unique motifs were found to be important for the function of SmAP2/ERF genes. Syntenic relationships between the SmAP2/ERF genes and AP2/ERF genes from Populus trichocarpa and Salix purpurea showed that Salix matsudana is genetically more closely related to Populus trichocarpa than to Salix purpurea. Evolution analysis on paralog gene pairs suggested that progenitor of S. matsudana originated from hybridization between two different diploid salix germplasms and underwent genome duplication not more than 10 Mya. RNA sequencing results demonstrated the differential expression patterns of some SmAP2/ERF genes under salt stress and this information can help reveal the mechanism of salt tolerance regulation in Salix matsudana.

Investigation and classification of the five tetraploid Fragaria species native to China

Investigation and classification of the five tetraploid <i>Fragaria</i> species native to China