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.

Relaunching a Traditional Durum Wheat Product: New Cultivars and Introgression Lines Identified for Frike Making in Turkey

Frike is an ancient and traditional food product prepared from early harvested whole wheat grain, particularly durum wheat (DW). Due to its many health beneficial effects, frike is considered a functional food. It is also a lucrative commodity, produced in various West Asian and North African countries and typically in Southeastern Turkey. However, no systematic assessment of the most-suitable genotypes for frike production in the region is available. This study aimed to carry out such an evaluation, based on frike yield, quality traits, marketing price, and profitability, on a set of 20 DW cultivars and DW-Thinopyrum ponticum introgression lines (ILs). The results based on a field trial performed in Gölbaşı (Adıyaman, Turkey) in the 2021-2022 season revealed the Turkish varieties Tüten-2002, Edessa, Artuklu, and Perre, together with the R5 IL to have the highest frike yields measured on 3 kg of roasted fresh spikes. The highest marketing prices were obtained by Turkish varieties Sariçanak-98, Burgos, Sümerli, and Artuklu, along with the R112 IL, excelling in quality traits. Considering all parameters, the Turkish cultivars Artuklu, Firat-93, and Sariçanak-98, besides the R112 IL, resulted in being the most-convenient genotypes for frike making, thus representing good candidates for maintaining cultural and genetic diversity in food production from a staple crop such as DW.

The launch of satellite: DNA repeats as a cytogenetic tool in discovering the chromosomal universe of wild Triticeae

Fluorescence in situ hybridization is a powerful tool that enables plant researchers to perform systematic, evolutionary, and population studies of wheat wild relatives as well as to characterize alien introgression into the wheat genome. This retrospective review reflects on progress made in the development of methods for creating new chromosomal markers since the launch of this cytogenetic satellite instrument to the present day. DNA probes based on satellite repeats have been widely used for chromosome analysis, especially for "classical" wheat probes (pSc119.2 and Afa family) and "universal" repeats (45S rDNA, 5S rDNA, and microsatellites). The rapid development of new-generation sequencing and bioinformatical tools, and the application of oligo- and multioligonucleotides has resulted in an explosion in the discovery of new genome- and chromosome-specific chromosome markers. Owing to modern technologies, new chromosomal markers are appearing at an unprecedented velocity. The present review describes the specifics of localization when employing commonly used vs. newly developed probes for chromosomes in J, E, V, St, Y, and P genomes and their diploid and polyploid carriers Agropyron, Dasypyrum, Thinopyrum, Pseudoroegneria, Elymus, Roegneria, and Kengyilia. Particular attention is paid to the specificity of probes, which determines their applicability for the detection of alien introgression to enhance the genetic diversity of wheat through wide hybridization. The information from the reviewed articles is summarized into the TRepeT database, which may be useful for studying the cytogenetics of Triticeae. The review describes the trends in the development of technology used in establishing chromosomal markers that can be used for prediction and foresight in the field of molecular biology and in methods of cytogenetic analysis.

Wheat-Thinopyrum Substitution Lines Imprint Compensation Both From Recipients and Donors

Even frequently used in wheat breeding, we still have an insufficient understanding of the biology of the products via distant hybridization. In this study, a transcriptomic analysis was performed for six Triticum aestivum-Thinopyrum elongatum substitution lines in comparison with the host plants. All the six disomic substitution lines showed much stronger "transcriptomic-shock" occurred on alien genomes with 57.43-69.22% genes changed expression level but less on the recipient genome (2.19-8.97%). Genome-wide suppression of alien genes along chromosomes was observed with a high proportion of downregulated genes (39.69-48.21%). Oppositely, the wheat recipient showed genome-wide compensation with more upregulated genes, occurring on all chromosomes but not limited to the homeologous groups. Moreover, strong co-upregulation of the orthologs between wheat and Thinopyrum sub-genomes was enriched in photosynthesis with predicted chloroplastic localization, which indicates that the compensation happened not only on wheat host genomes but also on alien genomes.

Copy Number Variation of Transposable Elements in Thinopyrum intermedium and Its Diploid Relative Species

Diploid and polyploid wild species of Triticeae have complex relationships, and the understanding of their evolution and speciation could help to increase the usability of them in wheat breeding as a source of genetic diversity. The diploid species Pseudoroegneria spicata (St), Thinopyrum bessarabicum (J^b), Dasypyrum villosum (V) derived from a hypothetical common ancestor are considered to be possible subgenome donors in hexaploid species Th. intermedium (J^rJ^vsSt, where indices r, v, and s stand for the partial relation to the genomes of Secale, Dasypyrum, and Pseudoroegneria, respectively). We quantified 10 families of transposable elements (TEs) in P. spicata, Th. bessarabicum, D. villosum (per one genome), and Th. intermedium (per one average subgenome) using the quantitative real time PCR assay and compared their abundance within the studied genomes as well as between them. Sabrina was the most abundant among all studied elements in P. spicata, D. villosum, and Th. intermedium, and among Ty3/Gypsy elements in all studied species. Among Ty1/Copia elements, Angela-A and WIS-A showed the highest and close abundance with the exception of D. villosum, and comprised the majority of all studied elements in Th. bessarabicum. Sabrina, BAGY2, and Angela-A showed similar abundance among diploids and in Th. intermedium hexaploid; Latidu and Barbara demonstrated sharp differences between diploid genomes. The relationships between genomes of Triticeae species based on the studied TE abundance and the role of TEs in speciation and polyploidization in the light of the current phylogenetic models is discussed.

New ND-FISH-Positive Oligo Probes for Identifying Thinopyrum Chromosomes in Wheat Backgrounds

Thinopyrum has been widely used to improve wheat (Triticum aestivum L.) cultivars. Non-denaturing fluorescence in situ hybridization (ND-FISH) technology using oligonucleotides (oligo) as probes provides a convenient and efficient way to identify alien chromosomes in wheat backgrounds. However, suitable ND-FISH-positive oligo probes for distinguishing Thinopyrum chromosomes from wheat are lacking. Two oligo probes, Oligo-B11 and Oligo-pThp3.93, were designed according to the published Thinopyrum ponticum (Th. ponticum)-specific repetitive sequences. Both Oligo-B11 and Oligo-pThp3.93 can be used for ND-FISH analysis and can replace conventional GISH and FISH to discriminate some chromosomes of Th. elongatum, Th. intermedium, and Th. ponticum in wheat backgrounds. The two oligo probes provide a convenient way for the utilization of Thinopyrum germplasms in future wheat breeding programs.

Generation of amphidiploids from hybrids of wheat and related species from the genera Aegilops, Secale, Thinopyrum, and Triticum as a source of genetic variation for wheat improvement

We aim to improve diversity of domesticated wheat by transferring genetic variation for important target traits from related wild and cultivated grass species. The present study describes the development of F1 hybrids between wheat and related species from the genera Aegilops, Secale, Thinopyrum, and Triticum and production of new amphidiploids. Amphidiploid lines were produced from 20 different distant relatives. Both colchicine and caffeine were successfully used to double the chromosome numbers. The genomic constitution of the newly formed amphidiploids derived from seven distant relatives was determined using genomic in situ hybridization (GISH). Altogether, 42 different plants were analysed, 19 using multicolour GISH separating the chromosomes from the A, B, and D genomes of wheat, as well as the distant relative, and 23 using single colour GISH. Restructuring of the allopolyploid genome, both chromosome losses and aneuploidy, was detected in all the genomes contained by the amphidiploids. From the observed chromosome numbers there is an indication that in amphidiploids the B genome of wheat suffers chromosome losses less frequently than the other wheat genomes. Phenotyping to realize the full potential of the wheat-related grass germplasm is underway, linking the analyzed genotypes to agronomically important target traits.

Life history and resource acquisition: Photosynthetic traits in selected accessions of three perennial cereal species compared with annual wheat and rye

PREMISE OF THE STUDY

Few previous studies have considered how plant age affects photosynthetic physiology in herbaceous perennials or how photosynthetic capacity in annual cereals compares to perennial relatives. Newly developed perennial cereals offer novel systems for addressing these questions. Our study makes a novel contribution by considering how life history differences affect photosynthetic physiology.

METHODS

In two linked field studies, we evaluated effects of life history and plant age on photosynthetic rates (A), and related biochemical, morphological, and water-relations traits, comparing 1- and 2-yr-old cohorts of perennial wheat, intermediate wheatgrass, and perennial rye to close annual relatives (wheat and rye).

KEY RESULTS

Photosynthetic rates (A) were 10-50% higher in perennial cereals compared to annuals. In wheatgrass, elevated A was associated with higher carboxylation (VC), triose phosphate utilization (TPU) and electron transport rates (J), and higher leaf soluble protein and chlorophyll. Younger wheatgrass plants maintained higher A, TPU, J, and VC than older plants did. Perennial wheat and rye differed from annual relatives in some but not all of these parameters. Differences in stomatal limitation were not involved, while differences in stomatal conductance (gs) became evident under drier conditions.

CONCLUSIONS

This study demonstrates that some perennial cereal species can maintain higher midseason A than their annual crop relatives. These changes are not fully explainable by increased access to soil water and may reflect trade-offs between allocation to reproduction and to resource acquisition. We also found evidence for age-related changes in photosynthetic physiology in a herbaceous perennial plant.

Resistance of Auto- and Allotetraploid Triticeae Species and Accessions to Meloidogyne chitwoodi based on Genome Composition

The Columbia root-knot nematode Meloidogyne chitwoodi parasitizes several plant species, including grasses that have been developed for semiarid environments, and substantially reduces the productivity of cereals and the longevity of perennial grasses growing under semiarid conditions throughout the intermountain region. Thirty-two auto- and allotetraploid (2n = 28) taxa in the perennial Triticeae were evaluated as possible sources of resistance to M. chitwoodi. Low levels of root galling were observed on roots of all accessions; root-gall indices ranged from 0 (no galls) to 1.95 in the grasses compared to 4.67 for the susceptible 'Ranger' alfalfa check on a scale of 1 to 6. Even though the gall ratings were low, significant (P < 0.01) differences among accessions of the same species, among species, and among genera with different genomes were observed. Within the reproductive indices, which ranged from 0.01 to 1.20 in the grasses compared to 65.38 for the alfalfa check, there was no difference among genera with different genomes and accessions within the same species and genome; however, there was a significant (P < 0.05) difference among species with the same genomes. This variation can be traced to Thinopyrum nodosum (Jaaska-19), which was the only accession with a reproductive factor greater than 1.00. Based on the data, all auto- and allotetraploids are considered resistant to M. chitwoodi.

Resistance of Diploid Triticeae Species and Accessions to the Columbia Root-knot Nematode, Meloidogyne chitwoodi

The Columbia root-knot nematode, Meloidogyne chitwoodi race 2, is associated with several plant species, including members of the tribe Triticeae. We evaluated 15 diploid species for M. chitwoodi gall and reproductive indices from the following genera: Agropyron, Pseudoroegneria, Hordeum, Psathyrostachys, and Thinopyrum. Species from the genus Thinopyrum (Thinopyrum bessarabicum; J genome) and Psathyrostachys (Psathyrostachys fragilis, P. juncea, P. stoloniformis; N genome) expressed more resistance to M. chitwoodi than species within the genera Agropyron (Agropyron cristatum and A. mongolicum; P genome), Pseudoroegneria (Pseudoroegneria spicata, P. stipifolia, A. aegilopoicles, P. libanotica; S genome), and Hordeum (Hordeum bogdanii, H. brevisubulatum, H. californicum, and H. chilensis; H genome), although there was variation among individuals within P. spicata, P. juncea, and P. fragilis. The variation among genera and within species indicates that it would be possible to select Triticeae grasses for resistance to M. chitwoodi in order to identify and introgress genes for resistance into cultivated cereals.