Origins and chromosome differentiation of Thinopyrum elongatum revealed by PepC and Pgk1 genes and ND-FISH

Phylogeny and taxonomy of the polyploid species that contain St genome (Triticeae; Poaceae) based on four nuclear DNA and three chloroplast genes

BACKGROUND

The genus Pseudoroegneria (Nevski) Á.Löve contributes the St genome for more than 60% of perennial Triticeae species. However, the strong dominant character of the St genome makes it challenging to distinguish each species and/or even genus based on single or combined morphological traits. Moreover, the phylogeny and taxonomy of the St-genome containing polyploid genera remain controversial.

RESULTS

In this study, we used nuclear and chloroplast DNA-based phylogenetic analyses to reveal the systematic relationships between the St-genome containing polyploid species. The maximum likelihood (ML) tree based on nuclear ribosomal internal transcribed spacer region (nrITS) and three single-copy nuclear genes data (Acc1 + Pgk1 + DMC1) showed that polyploid species with the St genome were separated into seven genera with StStHH, StStYY, StStYYHH, StStYYPP, StStYYWW, StStPP, and StStEE genome constitutions, moreover, the polyploid species in Caucasus, America, and Australia have independent polyploidization events. The ML tree for the chloroplast DNA fragments (matK + rbcL + trnL-trnF) displayed that the P genome served as a maternal donor of Kengyilia melanthera and K. dingqinensis from the Hengduan Mountains region, while the St or StY genome served as the maternal donor of other St-genome containing species. Herein, we reported the genomic constitution of Kengyilia tibetica, K. changduensis, and K. dingqinensis with the StStYYPP genome for the first time.

CONCLUSIONS

The St-genome-containing polyploid species should be treated as distinct genera according to different genome constitutions, and those species experienced independent allo-polyploidization events in different distribution regions and had two relatively independent maternal origins from the P or St/StY genomes. Besides, the Xp genome might have contributed to the unknown Y genome formation.

Using Transcriptomics to Determine the Mechanism for the Resistance to Fusarium Head Blight of a Wheat-Th. elongatum Translocation Line

Fusarium head blight (FHB), caused by the Fusarium graminearum species complex, is a destructive disease in wheat worldwide. The lack of FHB-resistant germplasm is a barrier in wheat breeding for resistance to FHB. Thinopyrum elongatum is an important relative that has been successfully used for the genetic improvement of wheat. In this study, a translocation line, YNM158, with the YM158 genetic background carrying a fragment of diploid Th. elongatum 7EL chromosome created using 60Co-γ radiation, showed high resistance to FHB under both field and greenhouse conditions. Transcriptome analysis confirmed that the horizontal transfer gene, encoding glutathione S-transferase (GST), is an important contributor to FHB resistance in the pathogen infection stage, whereas the 7EL chromosome fragment carries other genes regulated by F. graminearum during the colonization stage. Introgression of the 7EL fragment affected the expression of wheat genes that were enriched in resistance pathways, including the phosphatidylinositol signaling system, protein processing in the endoplasmic reticulum, plant-pathogen interaction, and the mitogen-activated protein kinase (MAPK) signaling pathway at different stages after F. graminearium infection. This study provides a novel germplasm for wheat resistance to FHB and new insights into the molecular mechanisms of wheat resistance to FHB.

Comparative Characterization of Pseudoroegneria libanotica and Pseudoroegneria tauri Based on Their Repeatome Peculiarities

Pseudoroegneria species play an important role among Triticeae grasses, as they are the putative donors of the St genome in many polyploid species. Satellite repeats are widely used as a reliable tool for tracking evolutionary changes because they are distributed throughout the genomes of plants. The aim of our work is to perform a comparative characterization of the repeatomes of the closely related species Ps. libanotica and Ps. tauri, and Ps. spicata was also included in the analysis. The overall repeatome structures of Ps. libanotica, Ps. tauri, and Ps. spicata were similar, with some individual peculiarities observed in the abundance of the SIRE (Ty1/Copia) retrotransposons, Mutator and Harbinger transposons, and satellites. Nine new satellite repeats that have been identified from the whole-genome sequences of Ps. spicata and Ps. tauri, as well as the CL244 repeat that was previously found in Aegilops crassa, were localized to the chromosomes of Ps. libanotica and Ps. tauri. Four satellite repeats (CL69, CL101, CL119, CL244) demonstrated terminal and/or distal localization, while six repeats (CL82, CL89, CL168, CL185, CL192, CL207) were pericentromeric. Based on the obtained results, it can be assumed that Ps. libanotica and Ps. tauri are closely related species, although they have individual peculiarities in their repeatome structures and patterns of satellite repeat localization on chromosomes. The evolutionary fate of the identified satellite repeats and their related sequences, as well as their distribution on the chromosomes of Triticeae species, are discussed. The newly developed St genome chromosome markers developed in the present research can be useful in population studies of Ps. libanotica and Ps. tauri; auto- and allopolyploids that contain the St genome, such as Thinopyrum, Elymus, Kengyilia, and Roegneria; and wide hybrids between wheat and related wild species.

Agronomic Evaluation and Molecular Cytogenetic Characterization of Triticum aestivum × Thinopyrum spp. Derivative Breeding Lines Presenting Perennial Growth Habits

The transition from annual to perennial growth habits can contribute to increased sustainability and diversification of staple cropping systems like those based on annual wheat. Amphiploids between Triticum aestivum and Thinopyrum spp. can present a wheat-like morphology and post sexual cycle regrowth. The complex and unpredictable nature of the chromosomal rearrangements typical of inter-generic hybrids can hamper progress in the development of this new crop. By using fluorescence in situ hybridization, we described the genomic constitution of three perennial wheat breeding lines that regrew and completed a second year of production in field conditions in Washington state (USA). Two breeding lines presented stable, 56-chromosome partial amphiploids; however, their chromosome composition differed significantly. The third breeding line presented an unstable karyotype with a chromosome number ranging from 53 to 58 across eight individuals. The agronomic performance of the perennial breeding lines was evaluated for two growing seasons from 2020 to 2022. The grain yields of the perennial lines were lower than the grain production of the annual wheat control line in the first season. The perennial lines displayed vigorous regrowth after the initial harvest; however, worsening environmental conditions in the second season of growth hampered subsequent growth and grain yield. This information facilitates the breeding work necessary to improve key traits by grouping agronomically valuable individuals according to their genomic constitution.

Chromosome-specific painting in Thinopyrum species using bulked oligonucleotides

Chromosome-specific painting probes were developed to identify the individual chromosomes from 1 to 7E in Thinopyrum species and detect alien genetic material of the E genome in a wheat background. The E genome of Thinopyrum is closely related to the ABD genome of wheat (Triticum aestivum L.) and harbors genes conferring beneficial traits to wheat, including high yield, disease resistance, and unique end-use quality. Species of Thinopyrum vary from diploid (2n = 2x = 14) to decaploid (2n = 10x = 70), and chromosome structural variation and differentiation have arisen during polyploidization. To investigate the variation and evolution of the E genome, we developed a complete set of E genome-specific painting probes for identification of the individual chromosomes 1E to 7E based on the genome sequences of Th. elongatum (Host) D. R. Dewey and wheat. By using these new probes in oligonucleotide-based chromosome painting, we showed that Th. bessarabicum (PI 531711, EbEb) has a close genetic relationship with diploid Th. elongatum (EeEe), with five chromosomes (1E, 2E, 3E, 6E, and 7E) maintaining complete synteny in the two species except for a reciprocal translocation between 4 and 5Eb. All 14 pairs of chromosomes of tetraploid Th. elongatum have maintained complete synteny with those of diploid Th. elongatum (Thy14), but the two sets of E genomes have diverged. This study also demonstrated that the E genome-specific painting probes are useful for rapid and effective detection of the alien genetic material of E genome in wheat-Thinopyrum derived lines.

Autoploid origin and rapid diploidization of the tetraploid Thinopyrum elongatum revealed by genome differentiation and chromosome pairing in meiosis

Polyploidy is a common mode of evolution in flowering plants. Both the natural tetraploid Thinopyrum elongatum and the diploid one from the same population show a diploid-like pairing in meiosis. However, debate on the chromosome composition and origin of the tetraploid Th. elongatum is ongoing. In the present study, we obtained the induced tetraploid Th. elongatum and found that the induced and natural tetraploids are morphologically close, except for slower development and lower seed setting. Using probes developed from single chromosome microdissection and a Fosmid library, obvious differentiations were discovered between two chromosome sets (E₁ and E₂ ) of the natural tetraploid Th. elongatum but not the induced one. Interestingly, hybrid F₁ derived from the two different wheat-tetraploid Th. elongatum amphiploids 8802 and 8803 produced seeds well. More importantly, analysis of meiosis in F₂ individuals revealed that chromosomes from E₁ and E₂ could pair well on the durum wheat background with the presence of Ph1. No chromosome set differentiation on the FISH level was discovered from the S1 to S4 generations in the induced one. In metaphase of the meiosis first division in the natural tetraploid, more pairings were bivalents and fewer quadrivalents with ratio of 13.94 II + 0.03 IV (n = 31). Chromosome pairing configuration in the induced tetraploid is 13.05 II + 0.47 IV (n = 19), with the quadrivalent ratio being only slightly higher than the ratio in the natural tetraploid. Therefore, the natural tetraploid Th. elongatum is of autoploid origin and the induced tetraploid Th. elongatum evolutionarily underwent rapid diploidization in the low generation.