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Thinopyrum intermedium (2n = 6x = 42, JJJSJSStSt) has been hybridized extensively with common wheat and proven to be a valuable germplasm source for improving disease resistance and yield potential of wheat. A novel disease-resistant wheat-Th. intermedium double substitution line X479, carrying 1St(1B) and 4St-4JS (4B), was identified using multi-color non-denaturing fluorescence in situ hybridization (ND-FISH). With the aim of transferring Thinopyrum-specific chromatin to wheat, a total of 573 plants from F2 and F3 progenies of X479 crossed with wheat cultivar MY11 were developed and characterized using sequential ND-FISH with multiple probes. Fifteen types of wheat-Thinopyrum translocation chromosomes were preferentially transmitted in the progenies, and the homozygous wheat-1St, and wheat-4JSL translocation lines were identified using ND-FISH, Oligo-FISH painting and CENH3 immunostaining. The wheat-4JSL translocation lines exhibited high levels of resistance to stripe rust prevalent races in field screening. The gene for stripe rust resistance was found to be physically located on FL0–0.60 of the 4JSL, using deletion lines and specific DNA markers. The new wheat-Th. intermedium translocation lines can be exploited as useful germplasms for wheat improvement.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat (Triticum aestivum L.) worldwide. Xiaoyan 78829, a partial amphidiploid developed by crossing common wheat with Thinopyrum intermedium, is immune to wheat stripe rust. To transfer the resistance gene of this excellent germplasm resource to wheat, the translocation line WTT11 was produced by pollen irradiation and assessed for immunity to stripe rust races CYR32, CYR33 and CYR34. A novel stripe rust-resistance locus derived from Th. intermedium was confirmed by linkage and diagnostic marker analyses. Molecular cytogenetic analyses revealed that WTT11 carries a TTh·2DL translocation. The breakpoint of 1B was located at 95.5 MB, and the alien segments were found to be homoeologous to wheat-group chromosomes 6 and 7 according to a wheat660K single-nucleotide polymorphism (SNP) array analysis. Ten previously developed PCR-based markers were confirmed to rapidly trace the alien segments of WTT11, and 20 kompetitive allele-specific PCR (KASP) markers were developed to enable genotyping of Th. intermedium and common wheat. Evaluation of agronomic traits in two consecutive crop seasons uncovered some favorable agronomic traits in WTT11, such as lower plant height and longer main panicles, that may be applicable to wheat improvement. As a novel genetic resource, the new resistance locus may be useful for wheat disease-resistance breeding.

Wide hybridization between wheat and wild relatives such as Thinopyrum intermedium is important for broadening genetic diversity and improving disease resistance in wheat. We developed 30 wheat-Th. intermedium derivatives. Here, we report assessments of their resistance to different pathogens including cereal cyst nematode (CCN; Heterodera spp.), Puccinia striiformis f. tritici Erikss. causing stripe rust, and Blumeria graminis f. tritici (DC.) Speer inciting powdery mildew. Under natural field infection, all the wheat-Th. intermedium lines were resistant to at least one of the pathogens, and four lines were resistant to multiple pathogens. Twenty-nine of 30 tested lines exhibited resistance to H. avenae, a dominant CCN species in wheat fields. Twenty-four lines were resistant to H. filipjevi, an emerging threat to wheat production. Tests of phenotypic responses in the naturally infected field nurseries identified six stripe rust-resistant lines and 13 powdery mildew-resistant lines. Mitotic observation demonstrated that these newly developed wheat-Th. intermedium derivatives included not only octoploid but also chromosome addition, substitution, and translocation lines. Chromosome compositions of the four lines resistant to multiple pathogens were analyzed by genomic in situ hybridization and fluorescence in situ hybridization. The octoploid lines Zhong 10-68 and Zhong 10-117 carried both intact Th. intermedium chromosomes and translocated chromosomes. Line Zhong 10-149 had 42 wheat chromosomes and two wheat ditelosomes plus a pair of T3BS·J translocated chromosomes. Line Zhong 10-160 carried 41 wheat chromosomes plus one pair of the J genome chromosomes of Th. intermedium. The multiple disease-resistant wheat-Th. intermedium derivatives, especially lines with chromosome counts close to that of common wheat, provide valuable materials for wheat resistance breeding programs.

Thinopyrum intermedium has been used as a resource for improving resistance to biotic and abiotic stresses and yield potential in common wheat. Wheat line SN304 was derived from a cross between common wheat cultivar Yannong 15 and Th. intermedium. Genomic in situ hybridization (GISH) produced no hybridization signal in SN304 using Th. intermedium genomic DNA as a probe, but fluorescence in situ hybridization (FISH) using oligonucleotides AFA-3, AFA-4, pAs1-1, pAs1-3, pAs1-4, pAs1-6, pSc119.2-1, and (GAA)10 as probes detected hybridization signals on chromosomes 2A, 7A, 2B, 3B, 6B, and 7B in SN304 that differed from Yannong 15. Results of specific markers also indicated that there were Th. intermedium chromatin introgressions on different chromosomes in SN304. In a hydroponic culture experiment, SN304 not only produced more biomass and higher stem and leaf dry weight but also accumulated more phosphorus than Yannong 15 under phosphorus-deficiency stress. Moreover, SN304 produced a lower pH and released more organic acids, especially oxalic acid, than Yannong 15, which suggests that SN304 exudates enabled more absorbance of P than Yannong 15 under comparable conditions. The results indicate that SN304 is a wheat-Th. intermedium introgression line with tolerance to phosphorus-deficiency stress.

Thinopyrum intermedium possesses many desirable agronomic traits that make it a valuable genetic source for wheat improvement. The precise identification of individual chromosomes of allohexaploid Th. intermedium is a challenge due to its three sub-genomic constitutions with complex evolutionary ancestries. The non-denaturing fluorescent in situ hybridization (ND-FISH) using tandem-repeat oligos, including Oligo-B11 and Oligo-pDb12H, effectively distinguished the St, J and JS genomes, while Oligo-FISH painting, based on seven oligonucleotide pools derived from collinear regions between barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.), was able to identify each linkage group of the Th. intermedium chromosomes. We subsequently established the first karyotype of Th. intermedium with individual chromosome recognition using sequential ND-FISH and Oligo-FISH painting. The chromosome constitutions of 14 wheat–Th. intermedium partial amphiploids and addition lines were characterized. Distinct intergenomic chromosome rearrangements were revealed among Th. intermedium chromosomes in these amphiploids and addition lines. The precisely defined karyotypes of these wheat–Th. intermedium derived lines may be helpful for further study on chromosome evolution, chromatin introgression and wheat breeding programs.

Premise Nucleic acid integrity can be compromised under many abiotic stresses. To date, however, few studies have considered whether nucleic acid damage and damage repair play a role in cold-stress adaptation. A further insufficiently explored question concerns how age affects cold stress adaptation among mature perennials. As a plant ages, the optimal trade-off between growth and stress tolerance may shift. Methods Oxidative damage to RNA and expression of genes involved in DNA repair were compared in multiple mature cohorts of Thinopyrum intermedium (an emerging perennial cereal) and in wheat and barley under intermittent freezing stress and under nonfreezing conditions. Activity of glutathione peroxidase (GPX) and four other antioxidative enzymes was also measured under these conditions. DNA repair genes included photolyases involved in repairing ultraviolet-induced damage and two genes involved in repairing oxidatively induced damage (ERCC1, RAD23). Results Freezing stress was accompanied by large increases in photolyase expression and ERCC1 expression (in wheat and Thinopyrum) and in GPX and GR activity (particularly in Thinopyrum). This is the first report of DNA photolyases being overexpressed under freezing stress. Older Thinopyrum had lower photolyase expression and less freezing-induced overexpression of ERCC1. Younger Thinopyrum plants sustained more oxidative damage to RNA. Conclusions Overexpression of DNA repair genes is an important aspect of cold acclimation. When comparing adult cohorts, aging was associated with changes in the freezing stress response, but not with overall increases or decreases in stress tolerance.

Thinopyrum intermedium (2n = 6x = 42, E1E1E2E2XX) serves as an important gene source of desirable traits for genetic improvement of wheat cultivars resistant to stresses. This study used the comparative proteomic approach to identify stress defense related proteins in the developing grains of common wheat (Zhongmai 8601)-Thinopyron intermedium 7XL/7DS translocation line YW642 and to explore their potential values for improving wheat stress resistance. Two-dimensional electrophoresis identified 124 differentially accumulated protein spots representing 100 unique proteins, which mainly participated in stress defense, energy metabolism, protein metabolism and folding and storage protein synthesis. Among these, 16 were unique and 35 were upregulated in YW642. The upregulated DAPs were mainly involved in biotic and abiotic stress defense. Further cis-elements analysis of these stress-related DAP genes revealed that phytohormone responsive elements such as ABREs, G-box, CGTCA-motif and TGACG-motif, and environment responsive element As-1 were particularly abundant, which could play important roles in response to various stressors. Transcription expression analysis by RNA-seq and qRT-PCR demonstrated a large part of the stress-related DAP genes showed an upregulated expression in the early-to-middle stages of grain development. Our results proved that Thinopyron intermedium contains abundant stress responsive proteins that have potential values for the genetic improvement of wheat stress resistance.

Stripe rust is an important disease in wheat, and development of genetic resistance in cultivars is an effective approach to control the disease. Wild species of wheat, such as Thinopyrum intermedium, are an excellent gene source for wheat improvement. In this study, two stripe rust-resistant wheat–Th. intermedium chromosome translocation lines, CH4131 and CH4132, were characterized by cytogenetic and pathological methods. The introgressed chromosome fragment was tagged using amplified fragment-length polymorphism-derived sequence-characterized amplified region (SCAR) markers and intron targeting markers, indicating that CH4131 and CH4132 both possess a homologous group 3 chromatin of Th. intermedium. Genomic in situ hybridization results suggested that a very small Th. intermedium chromosome segment was translocated to the terminal region of wheat 1BS for both lines, forming a configuration of T3Ai-1BS.1BL. The two translocation lines were resistant to stripe rust, and the resistance gene, temporarily designated YrCH-1BS, was likely derived from Th. intermedium. The translocated chromosome fragments have no genetic linkage drag to agronomic performance. The grain quality indexes of these two translocations were higher than local wheat varieties. Therefore, CH4131 and CH4132 could be used as potential gene sources in wheat improvement programs. The SCAR markers are useful to select stripe rust resistance from Th. intermedium.

Thinopyrum intermedium (2n = 6x = 42, JJJsJsStSt) has been hybridized extensively with common wheat and has proven to be a valuable germplasm source for improving disease resistance, quality attributes, and yield potential in wheat. We characterized new disease resistant wheat-Th. intermedium derivatives A1082 and A5-5 using sequential multi-color fluorescence in situ hybridization (mc-FISH), genomic in situ hybridization (GISH), PCR-based landmark unique gene (PLUG) and intron targeting (IT) markers. A1082 was identified as a wheat-Th. intermedium 3J disomic addition line, and A5-5 was a T4BS·5JsL homozygous Robertsonian translocation line. Seventy-one and 106 pairs of primers amplified Th. intermedium-specific bands allowing chromosomes 3J and 5Js to be tracked, respectively. A new oligonucleotide probe, Oligo-6H-2-100, was developed for FISH labeling of the subterminal region of the long arm of chromosome 5Js. Both lines were highly resistant to stripe rust pathogen races prevalent in Chinese field screening nurseries. A5-5 also displayed a significant increase in tiller number compared to its wheat parent. The new lines can be exploited as useful germplasms for wheat improvement. Keywords: Disease resistance, FISH, GISH, Stripe rust, Triticum aestivum

Barley yellow dwarf (BYD) is a major virus disease which dramatically reduces wheat yield. Introducing BYD resistance genes into commercial varieties has been proven to be effective in reducing damage caused by barley yellow dwarf virus (BYDV). However, only one major resistance gene is readily deployable for breeding; Bdv2 derived from Thinopyrum intermedium is deployed as a chromosomal translocation. In this study, a double haploid (DH) population was developed from a cross between XuBYDV (introduced from China showing very good resistance to BYD) and H-120 (a BYD-sensitive Chinese accession), and was used to identify QTL for BYD resistance. The population was genotyped using an Infinium iSelect bead chip array targeting 90K gene-based SNPs. The disease resistance of DH lines inoculated with BYDV was assessed at the heading stage. The infections were assessed by tissue blot immunoassay (TBIA). Three new QTL were identified on chromosomes 5A, 6A, and 7A for both symptom and TBIA, with all three resistance alleles being inherited from XuBYDV. Some DH lines with the resistance alleles from all three QTL showed high level resistance to BYD. These new QTL will be useful in breeding programs for pyramiding BYD resistance genes.

Background Interspecific hybridisation resulting in polyploidy is one of the major driving forces in plant evolution. Here, we present data from the molecular cytogenetic analysis of three cytotypes of Elytrigia ×mucronata using sequential fluorescence (5S rDNA, 18S rDNA and pSc119.2 probes) and genomic in situ hybridisation (four genomic probes of diploid taxa, i.e., Aegilops, Dasypyrum, Hordeum and Pseudoroegneria). Results The concurrent presence of Hordeum (descended from E. repens) and Dasypyrum + Aegilops (descended from E. intermedia) chromosome sets in all cytotypes of E. ×mucronata confirmed the assumed hybrid origin of the analysed plants. The following different genomic constitutions were observed for E. ×mucronata. Hexaploid plants exhibited three chromosome sets from Pseudoroegneria and one chromosome set each from Aegilops, Hordeum and Dasypyrum. Heptaploid plants harboured the six chromosome sets of the hexaploid plants and an additional Pseudoroegneria chromosome set. Nonaploid cytotypes differed in their genomic constitutions, reflecting different origins through the fusion of reduced and unreduced gametes. The hybridisation patterns of repetitive sequences (5S rDNA, 18S rDNA, and pSc119.2) in E. ×mucronata varied between and within cytotypes. Chromosome alterations that were not identified in the parental species were found in both heptaploid and some nonaploid plants. Conclusions The results confirmed that both homoploid hybridisation and heteroploid hybridisation that lead to the coexistence of four different haplomes within single hybrid genomes occur in Elytrigia allopolyploids. The chromosomal alterations observed in both heptaploid and some nonaploid plants indicated that genome restructuring occurs during and/or after the hybrids arose. Moreover, a specific chromosomal translocation detected in one of the nonaploids indicated that it was not a primary hybrid. Therefore, at least some of the hybrids are fertile. Hybridisation in Triticeae allopolyploids clearly and significantly contributes to genomic diversity. Different combinations of parental haplomes coupled with chromosomal alterations may result in the establishment of unique lineages, thus providing raw material for selection. Electronic supplementary material The online version of this article (10.1186/s12870-019-1806-y) contains supplementary material, which is available to authorized users.

Thinopyrum intermedium and barley are two close relatives of wheat and carry many genes that are potentially valuable for the improvement of various wheat traits. In this study we created wheat double substitution lines by hybridizing different wheat–Th. intermedium and wheat–barley disomic alien substitution lines, with the aim of using genes in Th. intermedium and barley for wheat breeding and investigating the genetic behavior of alien chromosomes and their wheat homoeologs. As expected, we obtained two types of wheat double substitution lines, 2D2Ai#2(2B)2H(2A) and 2A2Ai#2(2B)2H(2D), in which different group 2 wheat chromosomes were replaced by barley chromosome 2H and Th. intermedium chromosome 2Ai#2. The new materials were characterized using molecular markers, genomic in situ hybridization (GISH), and fluorescent in situ hybridization (FISH). GISH and FISH experiments revealed that the double substitution lines harbor 42 chromosomes including 38 wheat chromosomes, a pair of barley chromosomes, and a pair of Th. intermedium chromosomes. Analysis using specific DNA markers showed that two pairs of wheat homoeologous group 2 chromosomes in the new lines were substituted by a pair of 2H and a pair of 2Ai#2 chromosomes. Chromosome 2H showed a higher transmission rate than 2Ai#2, and both chromosomes were preferentially transmitted between generations via female gametes. Evaluation of botanic and agronomic traits demonstrated that, compared with their parents, the new lines showed similar growth habits and plant type but differences in plant height, flowering date, and self-fertility. Cytological observations using different probes suggested that the double substitution lines showed nearly normal genetic behavior before and during meiosis. The novel substitution lines can potentially be used in wheat meiosis research and breeding programs. Keywords: Wheat, Double substitution lines, Molecular markers, Transmission rate of alien chromosomes, Genomic in situ hybridization

Emerging perennial grain crops yield less grain than annual crops, but the economic viability of these perennial systems could be improved if both forage and grain are harvested. However, the belowground consequences of forage removal in perennial grain systems are unknown. This study aimed to determine the effect of the additional harvest of forage biomass on overall plant biomass allocation and labile soil C and N dynamics within a perennial grain dual-use system. Plant biomass and associated soil samples of a perennial grain [Kernza (Thinopyrum intermedium)] were taken monthly over the first three growing seasons under three harvest regiments: No Cut (0x), Summer Cut (1x), and Summer and Fall Cut (2x). The harvesting of forage biomass significantly increased both above- and belowground biomass. The once and twice forage-harvested treatments averaged 39% and 73% greater root biomass in 2016 and 39% and 49% greater root biomass in 2017 relative to the treatment not harvested for forage. Soil indicators of carbon and nitrogen storage were not affected by forage harvest but mineralizable carbon, an indicator of nutrient cycling, was greater under the forage harvested treatments. The harvest of forage and grain promoted nutrient availability and overall productivity (forage, root and grain biomass) relative to harvesting for grain only. Our findings suggest dual-use management of Kernza can provide a productive and profitable pathway for perennial grain adoption.

In an era of constrained and depleted natural resources, perennial grains could provide sustainable food production along with beneficial ecosystem services like reduced erosion and increased atmospheric carbon capture. Intermediate wheatgrass (IWG) [Thinopyrum intermedium (Host) Barkworth & D. R. Dewey subsp. intermedium] has been undergoing continuous breeding for domestication to develop a perennial grain crop since the 1980s. As a perennial, IWG has required 2–5 yr per selection generation, but starting in 2017, genomic selection (GS) was initiated in the breeding program at The Land Institute, Salina, KS (TLI), enabling one complete cycle per year. For each cycle, ∼4,000 seedlings were profiled using genotyping‐by‐sequencing (GBS) and genomic estimated breeding values (GEBVs) were calculated. Selection based on GEBVs identified ∼100 individuals to advance as parents each generation, while validation populations of 1,000–1,200 genets for GS model training were also selected using the genomic relationship matrix to represent genetic diversity in each cycle. The selected parents were randomly intermated in a greenhouse crossing block to form the subsequent cycle, while the validation populations were transplanted to irrigated and nonirrigated field sites for phenotypic evaluations in the following years. For priority breeding traits of seed mass, free threshing, and nonshattering, correlations between predicted values and observed data were >.5. The realized selection differential ranged from 11–23% for selected traits, and the expected genetic gains for these traits, including spike yield, ranged from 6 to 14% per year. Genomic selection is a powerful tool to speed the domestication and development of IWG and other perennial crops with extended breeding timelines.

Thinopyrum intermedium (2n = 6x = 42, JJJSJSStSt) is one of the important resources for the wheat improvement. So far, a few Th. intermedium (Thi)-specific molecular markers have been reported, but the number is far from enough to meet the need of identifying alien fragments in wheat-Th. intermedium hybrids. In this study, 5,877,409 contigs were assembled using the Th. intermedium genotyping-by-sequencing (GBS) data. We obtained 5,452 non-redundant contigs containing mapped Thi-GBS markers with less than 20% similarity to the wheat genome and developed 2,019 sequence-tagged site (STS) molecular markers. Among the markers designed, 745 Thi-specific markers with amplification products in Th. intermedium but not in eight wheat landraces were further selected. The distribution of these markers in different homologous groups of Th. intermedium varied from 47 (7/12/28 on 6J/6St/6JS) to 183 (54/62/67 on 7J/7St/7JS). Furthermore, the effectiveness of these Thi-specific markers was verified using wheat-Th. intermedium partial amphidiploids, addition lines, substitution lines, and translocation lines. Markers developed in this study provide a convenient, rapid, reliable, and economical method for identifying Th. intermedium chromosomes in wheat. In addition, this set of Thi-specific markers can also be used to estimate genetic and physical locations of Th. intermedium chromatin in the introgression lines, thus providing valuable information for follow-up studies such as alien gene mining.

Previous work indicated that bran removal promotes network formation in breads prepared from intermediate wheatgrass (IWG) flour. However, refinement reduces yields as well as contents of nutritionally beneficial compounds such as fiber. This study evaluated xylanase pretreatment of IWG bran as a processing option to enhance the properties of bread made with half of the original bran content. Xylanase pretreatment did not affect stickiness but significantly reduced hardness and increased specific loaf volumes compared to negative (without xylanase) and positive controls (with xylanase but without pretreatment). However, the surface of breads with pretreated bran was uneven due to structural collapse during baking. Fewer but larger gas cells were present due to pretreatment. Addition of ascorbic acid modulated these effects, but did not prevent uneven surfaces. Accessible thiol concentrations were slightly but significantly increased by xylanase pretreatment, possibly due to a less compact crumb structure. Endogenous xylanases (apparent activity 0.46 and 5.81 XU/g in flour and bran, respectively) may have been activated during the pretreatment. Moreover, Triticum aestivum xylanase inhibitor activity was also detected (193 and 410 InU/g in flour and bran). Overall, xylanase pretreatment facilitates incorporation of IWG bran into breads, but more research is needed to improve bread appearance.

Perennial grain crops have the potential to improve agricultural sustainability but few existing species produce sufficient grain yield to be economically viable. The outcrossing, allohexaploid, and perennial forage species intermediate wheatgrass (IWG) [Thinopyrum intermedium (Host) Barkworth & D. R. Dewey] has shown promise in undergoing direct domestication as a perennial grain crop using phenotypic and genomic selection. However, decades of selection will be required to achieve yields on par with annual small‐grain crops. Marker‐aided selection could accelerate progress if important genomic regions associated with domestication were identified. Here we use the IWG nested association mapping (NAM) population, with 1,168 F1 progeny across 10 families to dissect the genetic control of brittle rachis, floret shattering, and threshability. We used a genome‐wide association study (GWAS) with 8,003 single nucleotide polymorphism (SNP) markers and linkage mapping—both within‐family and combined across families—with a robust phenotypic dataset collected from four unique year‐by‐location combinations. A total of 29 quantitative trait loci (QTL) using GWAS and 20 using the combined linkage analysis were detected, and most large‐effect QTL were in common across the two analysis methods. We reveal that the genetic control of these traits in IWG is complex, with significant QTL across multiple chromosomes, sometimes within and across homoeologous groups and effects that vary depending on the family. In some cases, these QTL align within 216 bp to 31 Mbp of BLAST hits for known domestication genes in related species and may serve as precise targets of selection and directions for further study to advance the domestication of IWG.

Thinopyrum intermedium (2n = 6x = 42, JJJSJSStSt) is one of the important resources for the wheat improvement. So far, a few Th. intermedium (Thi)-specific molecular markers have been reported, but the number is far from enough to meet the need of identifying alien fragments in wheat-Th. intermedium hybrids. In this study, 5,877,409 contigs were assembled using the Th. intermedium genotyping-by-sequencing (GBS) data. We obtained 5,452 non-redundant contigs containing mapped Thi-GBS markers with less than 20% similarity to the wheat genome and developed 2,019 sequence-tagged site (STS) molecular markers. Among the markers designed, 745 Thi-specific markers with amplification products in Th. intermedium but not in eight wheat landraces were further selected. The distribution of these markers in different homologous groups of Th. intermedium varied from 47 (7/12/28 on 6J/6St/6JS) to 183 (54/62/67 on 7J/7St/7JS). Furthermore, the effectiveness of these Thi-specific markers was verified using wheat-Th. intermedium partial amphidiploids, addition lines, substitution lines, and translocation lines. Markers developed in this study provide a convenient, rapid, reliable, and economical method for identifying Th. intermedium chromosomes in wheat. In addition, this set of Thi-specific markers can also be used to estimate genetic and physical locations of Th. intermedium chromatin in the introgression lines, thus providing valuable information for follow-up studies such as alien gene mining.

Background Thinopyrum intermedium (2n = 6x = 42) is an important wild perennial Triticeae species exhibiting many potentially favorable traits for wheat improvement. Wheat-Th. intermedium partial amphiploids serve as a bridge to transfer desirable genes from Th. intermedium into common wheat. Results Three octoploid Trititrigia accessions (TE261–1, TE266–1, and TE346–1) with good resistances to stripe rust, powdery mildew and aphids were selected from hybrid progenies between Th. intermedium and the common wheat variety ‘Yannong 15’ (YN15). Genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH) and multicolor GISH (McGISH) analyses demonstrated that the three octoploid Trititrigia possess 42 wheat chromosomes and 14 Th. intermedium chromosomes. The 14 alien (Th. intermedium) chromosomes belong to a mixed genome consisting of J-, JS- and St-genome chromosomes rather than a single J, JS or St genome. Different types of chromosomal structural variation were also detected in the 1A, 6A, 6B, 2D and 7D chromosomes via FISH, McGISH and molecular marker analysis. The identity of the alien chromosomes and the variationes in the wheat chromosomes in the three Trititrigia octoploids were also different. Conclusions The wheat-Th. intermedium partial amphiploids possess 14 alien chromosomes which belong to a mixed genome consisting of J-, JS- and St- chromosomes, and 42 wheat chromosomes with different structural variations. These accessions could be used as genetic resources in wheat breeding for the transfer of disease and pest resistance genes from Th. intermedium to common wheat.

SummaryThe biotrophic fungal pathogen Blumeria graminis f. sp. tritici (Bgt) is a crucial factor causing reduction of global wheat production. Wild wheat relatives, e.g. Thinopyrum intermedium, is one of the wild-used parents in wheat disease-resistant breeding. From T. intermedium line, we identified the aspartic acid protein gene, TiAP1, which involved in resistance against Bgt. TiAP1 is a secreted protein that accumulates in large amounts at the infection sites of powdery mildew and extends to the intercellular space. Yeast two-hybrid showed that it interacted with the chitin deacetylase (BgtCDA1) of Bgt. The yeast expression, purification, and invitro test confirmed the chitin deacetylase activity of BgtCDA1. The bombardment and VIGS mediated host-induced gene silencing showed BgtCDA1 promotes the invasion of Bgt. Transcriptome analysis showed the cell wall xylan metabolism, lignin biosynthesis-related, and defence genes involved in the signal transduction were upregulated in the transgenic TiAP1 wheat induced by Bgt. The TiAP1 in wheat may inactivate the deacetylation function of BgtCDA1, cause chitin oligomers expose to wheat chitin receptor, then trigger the wheat immune response to inhibit the growth and penetration of Bgt, and thereby enhance the tolerance of wheat to pathogens.

A physical map of Thinopyrum intermedium chromosome 7J was constructed using translocation mapping, and a new seedling purple coleoptile gene was mapped to the bin of FL 0.35–0.63 of 7JS. Thinopyrum intermedium (2n = 6x = 42, JJJsJsStSt), a wild relative of common wheat, harbors numerous beneficial genes for wheat improvement. Previous studies showed that wheat–Th. intermedium partial amphiploid TAF46 and its derived addition line L1 had a purple coleoptile, which was derived from Th. intermedium chromosome 7J. To identify and physically map the purple coleoptile gene, 12 wheat–Th. intermedium 7J translocation lines were analyzed by sequential multicolor fluorescence in situ hybridization (mc-FISH), PCR-based landmark unique gene (PLUG) and intron targeting (IT) markers. A physical map of the 7J chromosome was constructed, consisting of eight chromosomal bins with 89 markers. Seedling evaluation of the coleoptile colors of all tested materials indicated that the purple coleoptile gene was located to the bin with a fraction length (FL) of 0.35–0.63 on chromosome 7JS. Furthermore, based on the syntenic relationships between Th. intermedium and wheat chromosomes, we developed a new chromosome 7J-specific EST-PCR marker from the chromosomal region corresponding to the purple coleoptile gene through the Triticeae multi-omics database. The approach of designing chromosome-specific markers has facilitated fine mapping of the Thinopyrum-specific purple coleoptile gene, and these translocation lines will be valuable for studying the function of the purple coleoptile gene in anthocyanin biosynthesis.

Perennial wheat is considered to be a practical way to increase the flexibility and profitability of sustainable agricultural system, as it can be either a forage grass or a grain crop. Four perennial wheat lines SX12-480, SX12-787, SX12-1150, and SX12-1269 were developed from a series of interspecific crosses between common wheat (Triticum aestivum, 2n = 42) or durum wheat (T. turgidum var. durum, 2n = 28) and the intermediate wheatgrass (Thinopyrum intermedium, 2n = 42). These lines were characterized by the vigorous regrowth for at least three years. The one- and two-year-old plants had higher grain yield potential than the three-year-old perennial plants. The decline of grain yield was associated with plant age-related effects on yield components. The perennial wheat lines were all resistant to both Heterodera avenae and H. filipjevi, the two distinct cereal cyst nematode species that occur in China, except that line SX12-787 exhibited moderate resistance only to H. avenae. The dual-purpose perennial wheat lines were evaluated for quality values of both defoliated grass and harvested grains in the form of amino acid profile, mineral concentration, and contents of protein and fiber. Difference in the quality profile was observed between the perennial lines. These perennial lines had an overall improved quality levels over those of the perennial wheat control Montana-2 (T. turgidum × Th. intermedium) and the annual wheat cultivar Jinchun 9. The amplification profiles of the molecular markers provided molecular evidence for the introgression of alien chromatin. Genomic in situ hybridization detected 16, 14, 14, and 12 Th. intermedium chromosomes in lines SX12-480 (2n = 48), SX12-787 (2n = 56), SX12-1150 (2n = 56), and SX12-1269 (2n = 54), respectively, in addition to either 32 or the complete set of wheat chromosomes. The four perennial wheat-Th. intermedium lines described here provide valuable sources of perennial wheat for the dual-purpose application of both grain and forage.

Perennial wheat is considered to be a practical way to increase the flexibility and profitability of sustainable agricultural system, as it can be either a forage grass or a grain crop. Four perennial wheat lines SX12-480, SX12-787, SX12-1150, and SX12-1269 were developed from a series of interspecific crosses between common wheat (Triticum aestivum, 2n = 42) or durum wheat (T. turgidum var. durum, 2n = 28) and the intermediate wheatgrass (Thinopyrum intermedium, 2n = 42). These lines were characterized by the vigorous regrowth for at least 3 years. The one- and 2-year-old plants had higher grain yield potential than the 3-year-old perennial plants. The decline of grain yield was associated with plant age-related effects on yield components. The perennial wheat lines were all resistant to both Heterodera avenae and H. filipjevi, the two distinct cereal cyst nematode species that occur in China, except that line SX12-787 exhibited moderate resistance only to H. avenae. The dual-purpose perennial wheat lines were evaluated for quality values of both defoliated grass and harvested grains in the form of amino acid profile, mineral concentration, and contents of protein and fiber. Difference in the quality profile was observed between the perennial lines. These perennial lines had an overall improved quality levels over those of the perennial wheat control Montana-2 (T. turgidum × Th. intermedium) and the annual wheat cultivar Jinchun 9. The amplification profiles of the molecular markers provided molecular evidence for the introgression of alien chromatin. Genomic in situ hybridization detected 16, 14, 14, and 12 Th. intermedium chromosomes in lines SX12-480 (2n = 48), SX12-787 (2n = 56), SX12-1150 (2n = 56), and SX12-1269 (2n = 54), respectively, in addition to either 32 or the complete set of wheat chromosomes. The four perennial wheat-Th. intermedium lines described here provide valuable sources of perennial wheat for the dual-purpose application of both grain and forage.

The development of perennial grain crops is driven by the vision of simultaneous food production and enhanced ecosystem services. Typically, perennial crops like intermediate wheatgrass (IWG)[Thinopyrum intermedium (Host) Barkworth & D.R Dewey] have low seed yield and other detrimental traits. Next‐generation sequencing has made genomic selection (GS) a tractable and viable breeding method. To investigate how an IWG breeding program may use GS, we evaluated 3,658 genets over 2 yr for 46 traits to build a training population. Six statistical models were used to evaluate the non‐replicated data, and a model using autoregressive order 1 (AR1) spatial correction for rows and columns combined with the genomic relationship matrix provided the highest estimates of heritability. Genomic selection models were built from 18,357 single nucleotide polymorphism markers via genotyping‐by‐sequencing, and a 20‐fold cross‐validation showed high predictive ability for all traits (r > .80). Predictive abilities improved with increased training population size and marker numbers, even with larger amounts of missing data per marker. On the basis of these results, we propose a GS breeding method that is capable of completing one cycle per year compared with a minimum of 2 yr per cycle with phenotypic selection. We estimate that this breeding approach can increase the rate of genetic gain up to 2.6× above phenotypic selection for spike yield in IWG, allowing GS to enable rapid domestication and improvement of this crop. These breeding methods should be transferable to other species with similar long breeding cycles or limited capacity for replicated observations.

Cold-hardy perennial wheatgrass plays an important role in the use of barren land for farming, soil and water conservation, variety improvement, and also for increasing grass yield. By crossing octoploid tritelytrigia (2n = 8x = 56, AABBDDEE) with Thinopyrum intermedium (2n = 6x = 42, StStJJJ S J S ), we developed 34 lines of perennial wheatgrass from F1 to F6 generations, which had vigorous regrowth and cold hardiness. The cold-hardy, perennial wheatgrass lines were well-adapted to the cold environment and developed root and rhizomes, with a longevity between 5 and 11 years and a better seed set. Some of them maintained wheat chromosomes beneficial for breeding perennial wheat. Molecular cytogenetic analysis demonstrated that the Th. intermedium chromosomes contributed the most to the synthetic genome of the wheatgrass hybrids and were associated with the perennial growth habit and winter hardiness. They were also preferentially maintained and transmitted to the progenies. Some wheat chromosomes were also transmitted from the F1 to F6 generations, although they were eliminated in each life cycle of the wheatgrass hybrids. The numbers of wheat and Th. intermedium chromosomes affected seed set and perennial growth habit. Seed set increased with the establishment of a more balanced genomic constitution in later generations. The cold-hardy and perennial wheatgrass lines were produced, which can be the starting point of domestication effort aimed at producing well-adapted ground cover plants under extreme environments.

Genomic selection (GS) based recurrent selection methods were developed to accelerate the domestication of intermediate wheatgrass [IWG, Thinopyrum intermedium (Host) Barkworth & D.R. Dewey]. A subset of the breeding population phenotyped at multiple environments is used to train GS models and then predict trait values of the breeding population. In this study, we implemented several GS models that investigated the use of additive and dominance effects and G×E interaction effects to understand how they affected trait predictions in intermediate wheatgrass. We evaluated 451 genotypes from the University of Minnesota IWG breeding program for nine agronomic and domestication traits at two Minnesota locations during 2017-2018. Genet-mean based heritabilities for these traits ranged from 0.34 to 0.77. Using four-fold cross validation, we observed the highest predictive abilities (correlation of 0.67) in models that considered G×E effects. When G×E effects were fitted in GS models, trait predictions improved by 18%, 15%, 20%, and 23% for yield, spike weight, spike length, and free threshing, respectively. Genomic selection models with dominance effects showed only modest increases of up to 3% and were trait-dependent. Cross-environment predictions were better for high heritability traits such as spike length, shatter resistance, free threshing, grain weight, and seed length than traits with low heritability and large environmental variance such as spike weight, grain yield, and seed width. Our results confirm that GS can accelerate IWG domestication by increasing genetic gain per breeding cycle and assist in selection of genotypes with promise of better performance in diverse environments.

Intermediate wheatgrass yielded 519 and 446 kg seed ha−1in years one and two after establishment. Autumn grazing increased seed yield compared with post-harvest residue removal or chopping. Inter-seeding legumes (alfalfa (Medicago sativa), sweet clover (Melilotus officinalis), and white clover (Trifolium repens) did not affect intermediate wheatgrass seed production.

Barley yellow dwarf virus (BYDV) can infect wheat (Triticum aestivum L.), leading to yield loss. Among four BYDV strains (GAV, GPV, PAV, and RMV) identified in China, BYDV-GAV is the prevailing isolate. YW642, a wheat–Thinopyrum intermedium translocation line, is resistant to BYDV isolates at both seedling and adult stages. Zhong 8601 is the wheat recurrent parent of YW642 and is susceptible to BYDV. In this study, we investigated the adult-stage resistance mechanism of YW642, measured BYDV titer and hydrogen peroxide (H2O2) in adult-stage leaves of YW642 and Zhong 8601 inoculated with BYDV-GAV, and identified transcriptional differences between YW642 and Zhong 8601 using microarray-based comparative transcriptomics. Enzyme-linked immunosorbent assay and H2O2 assay showed that both BYDV titer and H2O2 content were markedly lower in YW642 than in Zhong 8601 at 21, 28, 35, and 40 days post-inoculation (dpi). The transcriptomic comparison revealed that many types of genes were significantly up-regulated at 35 dpi in adult-stage leaves of YW642 compared to Zhong 8601. The important up-regulated genes associated with the adult-stage resistance encoded 15 resistance-like proteins, pathogenesis-related proteins (such as defensin and lipid transfer proteins), protein kinase homologs, transcription factors, reactive oxygen species scavenging-related proteins, and jasmonic acid and gibberellic acid biosynthesis enzymes. These results suggest that precise expression regulation of these proteins plays a crucial role in adult-stage resistance of YW642 against BYDV infection. Keywords: Barley yellow dwarf virus, Reactive oxygen species, Resistance at adult stage, Defense-associated genes, Phytohormone

Shifting the life cycle of grain crops from annual to perennial would usher in a new era of agriculture that is more environmentally friendly, resilient to climate change, and capable of soil carbon sequestration. Despite decades of work, transforming the annual grain crop wheat (Triticum aestivum) into a perennial has yet to be realized. Direct domestication of wild perennial grass relatives of wheat, such as Thinopyrum intermedium, is an alternative approach. Here we highlight protein coding sequences in the recently released T. intermedium genome sequence that may be orthologous to domestication genes identified in annual grain crops. Their presence suggests a roadmap for the accelerated domestication of this plant using new breeding technologies.

Progress in breeding of intermediate wheatgrass (Thinopyrum intermedium), a perennial grain with environmental benefits, has enabled bran removal. Thus, determination of optimum milling conditions for production of refined flours is warranted. This study explored the effect of tempering conditions on intermediate wheatgrass flour properties, namely composition, color, solvent retention capacity, starch damage, and polyphenol oxidase activity. Changes in flour attributes were evaluated via a 3 &times, 3 &times, 2 factorial design, with factors targeting moisture (comparing un-tempered controls to samples of 12% and 14% target moisture), time (4, 8, and 24 h), and temperature (30 and 45 &deg, C). All investigated parameters were significantly affected by target moisture, however, samples tempered to 12% moisture showed few differences to those tempered to 14%. Similarly, neither tempering time nor temperature exerted pronounced effects on most flour properties, indicating water uptake was fast and not dependent on temperature within the investigated range. Lactic acid retention capacity significantly correlated with ash (r = &minus, 0.739, p &lt, 0.01), insoluble dietary fiber (r = &minus, 0.746, p &lt, 0.01), polyphenol oxidase activity (r = &minus, 0.710, p &lt, 0.01), starch content (r = 0.841, p &lt, 0.01), and starch damage (r = 0.842, p &lt, 0.01), but not with protein (r = 0.357, p &gt, 0.05). In general, tempering resulted in flour with less bran contamination but only minor losses in protein.

Perennial crops have been proposed as a more sustainable alternative to annual crops, because they have extended growing seasons, continuous ground cover, reduced nutrient leakage, and sequester more carbon in the soils than annual crops. One example is intermediate wheatgrass (Thinopyrum intermedium), a perennial crop that has been used as a cool-season forage throughout the USA and Canada and also across its native range in Eurasia. Since the 1980's, intermediate wheatgrass has been under domestication to improve seed fertility and grain yield. Commercial products are being sold under the trade name Kernza, owned by The Land Institute, located in Salina, Kansas, USA. This review provides a comprehensive framework about the physical and biological aspects involving the water and carbon cycles in Kernza plants. The main aspects we highlight here are based on previous findings regarding Kernza: i) the ability of maintaining a relatively high water-use efficiency throughout the whole growing season, which is beneficial to mitigate water stress, representing an important physiological mean to acclimate under severe, unfavorable weather conditions, and ii) its higher evapotranspiration (ET) and net carbon uptake rates, particularly when compared to annual counterparts. Only a thorough multifaceted assessment of the repercussion for carbon and water fluxes of a shift from annual crops to Kernza will allow assessing the perspectives of such novel perennial crop to support food security and a number of ecosystem services, particularly under future climates.

Intermediate wheatgrass (Thinopyrum intermedium [Host] Barkworth & D.R. Dewey) (syn. Agropyron intermedium [Host] Beauv.) is becoming an important forage grass species in Alberta, Canada. Severe losses in seed yield due to stem smut (Ustilago hypodytes [Schlecht.] Fr.) were noted in a 70-acre field near Warner, AB, in 1999. The crop had been established in 1993 and harvested for seed each year. Smut symptoms (5% incidence) were noted initially in 1997. Incidence, determined by counting the number of symptomatic stems, increased to 10% in 1998 and 50% in 1999. The symptoms usually appeared in the first week of June. Brown sori developed on infected stems, especially between the uppermost node and the leaf below the flag leaf, and gradually became black during the period of seed filling, which is characteristic of stem smut (1). Teliospores were smooth, spherical to oval, light to dark brown, and 4.5 to 5.0 × 5.0 to 6.8 μm in dimension, which is also consistent with previous descriptions of U. hypodytes. Infected stems occasionally flowered, but did not set seed, so seed yield losses were proportional to disease incidence. Plants infected with stem smut were often stunted. Tissues in the smutty stem often became sunken and stems became twisted and thinner than normal due to the propagation of sori in the stem over time. Stem smut has been reported on crested wheatgrass and slender wheatgrass in other parts of Canada (2) and on T. intermedium in the United States (3). This is the first report of stem smut affecting commercial grass seed production in Alberta, Canada. This disease could also have a significant impact on the seed production of intermediate wheatgrass elsewhere. References: (1) G. W. Fischer. 1953. Manual of the North American Smut Fungi. Ronald Press, New York. (2) B. D. Gossen and D. Regnier. Can. Plant Dis. Surv. 71:88–89, 1991. (3) J. F. Karn and J. M. Krupinsky. Phytopathology 73:1152–1155, 1983.

Intermediate wheatgrass (Thinopyrum intermedium [Host] Barkworth & D.R. Dewey) (synonyms: Agropyron intermedium [Host] Beauv.; Elytrigia intermedia [Host] Nevski) is widely grown as a forage crop and is also used to control soil erosion. In a seed production field of cv. Rush in Washington County, ID, more than 80% of the plants were found affected by a disease with leaf stripe symptoms. The lesions were initially elongated, water-soaked, and translucent, later developing into brown, necrotic, interveinal stripes that often coalesced. Frequently, yellowish, dried, granular, or flaky exudate was present on the lesion surfaces. Microscopic examination of cut pieces of symptomatic tissue showed profuse bacterial streaming. Isolations on nutrient agar and King's medium B agar consistently yielded smooth, circular, butyrous, yellow, raised bacterial colonies. The bacterium was rod-shaped, Gram-negative, oxidase-negative, aerobic, and did not reduce nitrate. Substrate utilization profiles (Biolog Inc.), and cellular fatty acid analysis (Analytical Services Inc.) identified the bacterium as a pathovar of Xanthomonas translucens (syn: X. campestris pv. translucens). For pathogenicity tests, 3- to 5-week-old greenhouse-grown seedlings were injected in the whorl with a water suspension of 24-h-old culture (approximately 107 cfu/ml) of the bacterium. Control plants were injected with sterile distilled water. The plants were incubated at 25 to 28°C and observations were recorded after 6 to 10 days. The bacterium was pathogenic (causing water-soaked lesions, often with bacterial exudate) to T. intermedium cvs. Rush, Tegmar, PI 547316, and PI 380636; wheat cvs. Stephens, Vandal, FF 301, and FFR 525; barley cvs. Galena, Lud, and Steptoe; oat cvs. Boone, Clinton, Erban, Marion, Mohawk, Nemaha, Olena, and Tama; rye cvs. Florida 401, Hazel, Musketeer, Oklon, Rymin, Wintermore, and Wrens 96; Agropyron cristatum cv. Ephraim; A. cristatum × desertorum cv. Hycrest; Bromus arvensis; B. briziformis; B. catharticus; B. inermisssp. inermis; B. inermis ssp. pumpellianus; B. japonicus; B. marginatus; B. popovii; B. rigidus; B. tomentellus; Dactylis glomerata cvs. Paiute and Potomac; Elymus repens; Leymus mollis; L. angustus cv. Prairieland; Lolium arundinaceum cv. Fawn; L. perenne cv. Zero Nui; and Psathyrostachys juncea cv. Bozoisky. It was only weakly pathogenic (with small, chlorotic or water-soaked lesions and no exudation) to Phleum pratense cv. Climax and Pseudoroegneria spicata ssp. spicata cv. Goldar. It was not pathogenic to Andropogon gerardii cv. Pawnee; Festuca ovina; Oryza sativa cvs. Cypress, Newbonnet, and M201; or Schizachyrium scoparium cv. Camper. Based on the pathogen's natural host and its wide host range among cereals and grasses as verified by inoculation, the bacterium was identified as X. translucens pv. cerealis. This is the first report of natural occurrence of this pathogen on T. intermedium. A sample (105 g) of seed used for planting the affected field was found contaminated with 7.5 × 104 cfu/g of the pathogen, and seed to seedling transmission was observed in greenhouse tests. Contaminated seed, thus, may serve as a source of primary inoculum to intermediate wheatgrass, which in turn may serve as an inoculum source to other susceptible cereals and grasses growing in the vicinity.

Cox, C. M., Garrett, K. A., Cox, T. S., Bockus, W. W., and Peters, T. 2005. Reactions of perennial grain accessions to four major cereal pathogens of the Great Plains. Plant Dis. 89:12351240. Methods of disease management used in annual grain crops, especially cultural practices designed to disrupt the disease cycle of a particular pathogen, will not necessarily be applicable to perennial grain crops. Resistance to multiple pathogens, therefore, will clearly be important in disease management. The objective of this research was to evaluate disease resistance in 10 perennial grain accessions (one to two accessions of each: perennial wheat (Thinopyrum sp. × Triticum aestivum), intermediate wheatgrass (Thinopyrum intermedium), perennial rye (Secale montanum), hexaploid triticale (Triticum turgidum × S. montanum), octoploid triticale (Triticum aestivum × S. montanum), tetraploid perennial rye (Secale cereale × S. montanum), and tall wheatgrass (Thinopyrum ponticum)) to tan spot (caused by Pyrenophora tritici-repentis), take-all (caused by Gaeumannomyces graminis var. tritici), wheat streak mosaic, and barley yellow dwarf, four important diseases of the Great Plains. Several of the grasses were resistant to tan spot, barley yellow dwarf, and wheat streak mosaic. Indeed, the wild grasses and perennial donors T. intermedium (including BFPMC1), T. ponticum, and S. montanum, in addition to Permontra, a tetraploid perennial rye, were highly resistant to all three diseases. Additionally, the remaining grasses tested were also more resistant to tan spot than the susceptible wheat control. However, none of the 10 grass accessions appeared highly resistant to take-all, and substantial losses in biomass were observed, although such effects may be moderated under field conditions due to the potential for take-all decline in perennial plantings.

A wheat line 14-569 developed from a hybrid of common wheat cv. Chuannong 10 with the wheat–Thinopyrum intermedium partial amphiploid TAI7045 exhibits stable double spikelets per node character in the lower middle portion of a spike, is highly resistant to stripe rust, and produces kernels with a higher 1000-kernel weight than those of its wheat parent. Chromosome counting and an analysis of meiosis demonstrated that line 14-569 is a disomic addition line with 2n = 44, 22II. Sequential genomic in situ hybridization and non-denaturing fluorescence in situ hybridization analyses indicated that one pair of St-genomic chromosomes from Th. intermedium was added to the wheat complement and that the wheat complement included one pair of 1RS/1BL wheat–rye translocation chromosomes. PCR-based landmark unique gene molecular marker analysis revealed that the added pair of chromosomes comprised 3St chromosomes, which suggested that the added 3St chromosomes from Th. intermedium might carry the genes to control the high yield-related characters and stripe rust resistance. This addition line will potentially be useful resource for improvements in wheat yields and stripe rust resistance.

Intermediate wheatgrass [Thinopyrum intermedium (Host) Barkworth & D. R. Dewey] plant introductions (PI) have played a critical role in the development of improved intermediate wheatgrass cultivars. The objective of this study was to characterize a large number of intermediate wheatgrass populations over its native range for dry matter yield (DMY), crude protein (CP), in vitro true digestibility (IVTD), neutral detergent fibre (NDF), and rhizome development and genetic diversity and structure to identify superior populations and possible geographical regions in which to collect. Analysis of molecular variance using 643 AFLP bands partitioned 31% of the total genetic variation among these populations with 69% variance detected within populations. Bayesian cluster analysis identified two large groups designated as Asian and European under K = 2. In general, European accessions had greater DMY than did Asian accessions. Observed trends were towards greater CP values in populations with Asian ancestry. Selection index values above zero were observed in populations with European ancestry, and the exception was the late-maturing (208 days to bloom) populations with Asian ancestry. Plant populations 383 551, 383 561, 401 161, 401 173, 440 021, 578 692 (cv. Tegmar) and 598 740 had rhizome scores greater than 7.0. Despite significant differences detected between populations (ΦST = 0.3136; P

Highlight We explore interactive effects of plant age and cold stress on photosynthetic rates and key photosynthetic enzymes in a herbaceous perennial in the field., Effects of plant age on resource acquisition and stress tolerance processes is a largely unstudied subject in herbaceous perennials. In a field experiment, we compared rates of photosynthesis (A), ribulose-1,5-bisphosphate (RuBP) carboxylation capacity (V Cmax), maximum electron transport rate (J max), and triose phosphate utilization (TPU), as well as concentrations of Rubisco and sucrose-phosphate synthase (SPS) in 5-year-old and 2-year-old intermediate wheatgrass (Thinopyrum intermedium) under both optimal growing conditions and cold stress in early spring and autumn. This species is a relative of wheat undergoing domestication. An additional experiment compared photosynthetic rates in different cohorts at mid-season and under colder conditions. We hypothesized that photosynthetic capacity in older plants would be lower under favorable conditions but higher under cold stress. Our hypothesis was generally supported. Under cold stress, 5-year-old plants exhibited higher A, TPU, and temperature-adjusted V Cmax than younger plants, as well as 50% more SPS and 37% more Rubisco. In contrast, at mid-season, photosynthetic capacities in older plants were lower than in younger plants in one experiment, and similar in the other, independent of differences in water status. Both cohorts increased A, temperature-adjusted TPU and J max, [Rubisco], and [SPS] under cold stress, but changes were greater in older plants. Photosynthetic differences were largest at 1.2 ºC in very early spring, where older plants had 200% higher A and maintained up to 17% of their peak photosynthetic capacity. We find evidence of increased cold tolerance in older cohorts of wheatgrass, consistent with a growing body of research in woody perennials.

New molecular markers were developed for targeting Thinopyrum intermedium 1St#2 chromosome, and novel FISH probe representing the terminal repeats was produced for identification of Thinopyrum chromosomes. Thinopyrum intermedium has been used as a valuable resource for improving the disease resistance and yield potential of wheat. A wheat-Th. intermedium ssp. trichophorum chromosome 1St#2 substitution and translocation has displayed superior grain protein and wet gluten content. With the aim to develop a number of chromosome 1St#2 specific molecular and cytogenetic markers, a high throughput, low-cost specific-locus amplified fragment sequencing (SLAF-seq) technology was used to compare the sequences between a wheat-Thinopyrum 1St#2 (1D) substitution and the related species Pseudoroegneria spicata (St genome, 2n = 14). A total of 5142 polymorphic fragments were analyzed and 359 different SLAF markers for 1St#2 were predicted. Thirty-seven specific molecular markers were validated by PCR from 50 randomly selected SLAFs. Meanwhile, the distribution of transposable elements (TEs) at the family level between wheat and St genomes was compared using the SLAFs. A new oligo-nucleotide probe named Oligo-pSt122 from high SLAF reads was produced for fluorescence in situ hybridization (FISH), and was observed to hybridize to the terminal region of 1St#L and also onto the terminal heterochromatic region of Th. intermedium genomes. The genome-wide markers and repetitive based probe Oligo-pSt122 will be valuable for identifying Thinopyrum chromosome segments in wheat backgrounds.

Exploitation of host resistance is important for controlling powdery mildew of wheat (Triticum aestivum L.). In this study, a wheat-Thinopyrum intermedium introgression line, designated WE99, conferred seedling resistance to 47 of 49 Blumeria graminis f. sp. tritici isolates. Genetic analysis demonstrated that the resistance segregation deviated significantly from a single gene Mendelian ratio. However, marker analysis indicated that only a single recessive resistance gene, temporarily designated PmWE99, conferred powdery mildew resistance (Pm). PmWE99 was mapped to chromosome arm 2BS and linked to the three simple-sequence repeat markers Gwm148, Gwm271, and Barc55. Using race spectrum analysis, PmWE99 was shown to be significantly different from the documented genes Pm42 and MlIW170 located on chromosome arm 2BS and, thus, appeared to be a new Pm gene. Examination of the genotype frequencies in the F2:3 families showed that a genetic variation in the PmWE99 interval that favored the transmission of the WE99 allele could be the cause of the deviated segregation. Further investigation revealed that the abnormal segregation only occurred at the PmWE99 interval and was not common at other loci in this population. Identification of PmWE99 will increase the diversity of the Pm genes for wheat improvement.

Elymus s. l. is a critical topic on which only a little light has begun to be made regarding phylogenetic reticulation, genome evolution and consistency of genera. In Italy, Elymus s. l. officially includes ten species (nine native, one alien) and some well-established and widespread hybrids generally not treated as little or nothing is known of them. In this paper fourteen species (with two subspecies) and six hybrids are taken into account and the following seven new combinations are proposed: Thinopyrum acutum (DC.) Banfi, Thinopyrum corsicum (Hack.) Banfi, Thinopyrum intermedium (Host) Barkworth and Dewey subsp. pouzolzii (Godr.) Banfi, Thinopyrum obtusiflorum (DC.) Banfi, Thinopyrum ×duvalii (Loret) Banfi, ×Thinoelymus drucei (Stace) Banfi, ×Thinoelymus mucronatus (Opiz) Banfi. Some observations are provided for each subject and a key to species, subspecies and hybrids is made available.

Wheatgrass Thinopyrum intermedium (Host), or Agropyron intermedium (Host) (2n = 42; genome formula, EEEstEstStSt) is one of the most valuable sources of highly effective resistance genes in wheat breeding. Bread wheat cultivars Tulaikovskaya 5, Tulaikovskaya 10, and Tulaikovskaya 100 derived from wheat—Thinopyrum crosses are highly resistant to leaf rust and powdery mildew, and moderately resistant to stem and yellow rust. C-banding, in situ hybridization, and assays with PLUG and SSR markers have demonstrated that wheat chromosome 6D in all three cultivars is substituted by the Th. intermedium homoeologous chromosome, 6Ai. This chromosome was designated 6Ai#2, because it differs from the earlier described homoeologous chromosome 6Ai#1. In situ hybridization with Pseudoroegneria spicata and Dasypyrum villosum genomic DNAs has allowed chromosome 6Ai#2 to be assigned to the E (=J) subgenome. Chromosome 6Ai#2 remained intact over long-term breeding efforts. Tests of leaf rust resistance of in F2 and F3 populations from a cross of a leaf rust–susceptible cultivar with Tulaikovskaya 10 has demonstrated that chromosome 6Ai#2 carries at least one gene locus for leaf rust resistance. This locus was designated Lr6Ai#2. It must be different from the known gene locus Lr38, located on the long arm of chromosome 7Ai#2 and now present in many translocation variants in bread wheat. The effect of a chromosome from the Th. intermedium subgenome E on resistance to powdery mildew, stem and yellow rust in Tulaikovskaya 5, Tulaikovskaya 10, and Tulaikovskaya 100 is discussed.

Understanding the classification and biosystematics of species in Triticeae Dumort., an economically important tribe in the grass family (Poaceae), is not an easy task, particularly for some perennial species. Does genomic analysis facilitate the understanding of evolutionary relationships of these Triticeae species? We reviewed literature published after 1984 to address questions concerning: (1) genome relationships among the monogenomic diploid species; (2) progenitors of the unknown Y genome in Elymus polyploids, X genome in Thinopyrum intermedium, and Xm genome in Leymus; and (3) genome constitutions of some perennial Triticeae species that were unknown or misidentified. A majority of publications have substantiated the close affinity of the Eb and Ee genomes in Th. bessarabicum and Th. elongatum, supporting the use of a common basic genome symbol. The E genome is close to the St genome of Pseudoroegneria and ABD genomes of Triticum/Aegilops complex, providing an explanation for transferring genes from the E to ABD genomes with relative ease. Although the solid proof is still lacking, the W, P, and especially Xp genomes are possible origins for the Y genome of polyploid Elymus. The absence of the E genome and the allopolyploidy nature of tetraploid Leymus species have been unequivocally confirmed by both cytogenetic and molecular studies. However, the donor of the Xm genomes of Leymus was only speculated to be related to the P genome of Agropyron and F genome of Eremopyrum. Intermediate wheatgrass (Th. intermedium) has been extensively studied. The presence of the St (as the previously designated X) genome in Th. intermedium is now unequivocal. Its two more closely related E1 and E2 genomes are shown to be older versions of the E genome rather than the current Eb and Ee genomes. Speciation of Th. intermedium was similar to that of Triticum aestivum, in which the Js/Es (like B) genomes had the greatest differentiation from the current J (Eb) genome owning to repetitive sequences of the V genome, whereas its St (like D) had the least differentiation from the current St genome. Species with unknown or misidentified genomes have been correctly designated, including those with the ESt, StP, StPY, StWY, EStP, HW, StYHW, and NsXm genomes. Some of those species have been transferred to and renamed in appropriate genera.

To study the influence of genes from Thinopyrum intermedium on traits affecting the bread-making quality of wheat, two derivatives from a putative disomic addition line in cultivar ‘Vilmorin 27’ were used in cytological, biochemical and molecular characterization. Cytological analysis suggested that one of the derivatives (Line-1) had a terminal deletion involving the long arm of chromosome 1D (2n = 42, Del-1DL”), and the other (Line-2) was a conventional addition line, but also carried the same deletion on chromosome 1D (2n = 44, Thi”+Del-1DL”). Amplification and sequencing of high-molecular-weight glutenin subunit (HMW-GS) genes coded by the Th. intermedium chromosome in Line-2 indicated the presence of one x-type with an extra cysteine and four (rather than one) unique y-type genes. Rheological studies of Line-1 showed significantly lower dough strength compared to ‘Vilmorin 27’, confirming the recognized role of Glu-1D coded HMW-GSs. Line-2 showed significantly higher dough strength compared to the background cultivar, indicating a significant potential of Th. intermedium for improvement of bread-making quality in wheat.

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 (Jb), Dasypyrum villosum (V) derived from a hypothetical common ancestor are considered to be possible subgenome donors in hexaploid species Th. intermedium (JrJvsSt, 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.

In the published version, the article title was presented incorrectly. The word “cycling” was inadvertently deleted. The correct title is shown here.

Thinopyrum intermedium has been hybridized extensively with wheat (Triticum aestivum L.) and several genes for disease resistance have been introgressed to cultivated wheat. However, there are very few reports about the Th. intermedium-derived seed storage protein genes which have been transferred into a wheat background by chromosome manipulation. Our aim is to identify several wheat–Th. intermedium ssp. trichophorum derivatives, and document these lines by genomic in situ hybridization (GISH), molecular markers and seed storage protein analysis. We found that a novel Th. intermedium 1St#2 chromosome-specific high-molecular-weight glutenin subunit (HMW-GS) was transferred to the wheat–Thinopyrum derivative lines. The genomic sequence of the Thinopyrum-derived HMW-GS was characterized and designated Glu-1St#2x, since it resembled x-type glutenins in both the N-terminal domain and C-terminal domain. It is much shorter than that of reported HMW-GS genes. The Glu-1St#2x sequence was successfully expressed in Escherichia coli and resulted in the identical weight to the native protein. The GISH and newly developed chromosome Thinopyrum-specific DNA markers enabled physically location of Glu-1St#2x to the region FL0.60–1.00 on Th. intermedium 1St#2L chromosome arm. Phylogenetic analysis revealed that the Glu-1St#2x evolved earlier than other x-type HMW-GS homoeologues in modern wheat genomes. The effect of Glu-1St#2x on protein content, sodium dodecyl sulphate sedimentation value and improvement of solvent retention capacity in wheat background suggested that Th. intermedium chromosome 1St#2 may have potential for improvement of wheat end-product quality.

Development of perennial grains is being promoted to aid in moving agriculture towards sustainable production. How long does it take to identify perennial yielding ability? Intermediate wheatgrass [Thinopyrum intermedium (Host) Bark. & Dewey] nurseries were transplanted in 2011 (4500 plants) and 2012 (1000 plants) at Carman, MB. Productive, healthy plants were harvested on a yearly basis. Intolerance to late frosts after spring regrowth initiation in 2012 (approximately 55% of the plants) and in 2014 (the entire 2012 nursery) led to these plants not being harvested. Mean yield plant−1 was 37.25, 66.70, and 57.81 g for the 2012, 2013, and 2014 overall harvests, respectively. Individual plants showed divergent seed yielding patterns across years, especially with respect to the third harvest year. A number of plants were identified that had consistent relative seed yields over the 3 yr of harvest for the 2011 nursery. Linear regression indicated that the first year of seed production was a poor indicator of ...

Fluorescence in situ hybridization and molecular markers have confirmed that several chromosomes from Thinopyrum intermedium ssp. trichophorum have been added to a wheat background, which originated from a cross between a wheat– Thinopyrum partial amphiploid and triticale. The lines displayed blue grains and resistance to wheat stripe rust. Thinopyrum intermedium has been used as a valuable resource for improving the disease resistance and yield potential of wheat. With the aim to transfer novel genetic variation from Th. intermedium species for sustainable wheat breeding, a new trigeneric hybrid was produced by crossing an octoploid wheat–Th. intermedium ssp. trichophorum partial amphiploid with hexaploid triticale. Fluorescence in situ hybridization (FISH) revealed that Thinopyrum chromosomes were transmitted preferably and the number of rye chromosomes tended to decrease gradually in the selfed derivatives of the trigeneric hybrids. Four stable wheat–Th. intermedium chromosome substitution, addition and translocation lines were selected, and a 2JS addition line, two substitution lines of 4JS(4B) and 4J(4B), and a small 4J.4B translocation line were identified by FISH and molecular markers. It was revealed that the gene(s) responsible for blue grains may located on the FL0.60–1.00 of long arm of Th. intermedium-derived 4J chromosome. Disease resistance screenings indicated that chromosomes 4JS and 2JS appear to enhance the resistance to stripe rust in the adult plant stage. The new germplasm with Th. intermedium introgression shows promise for utilization of Thinopyrum chromosome segments in future wheat improvement.

This paper reports detailed FISH-based karyotypes for three diploid wheatgrass species Agropyron cristatum (L.) Beauv., Thinopyrum bessarabicum (Savul.&Rayss) A. Love, Pseudoroegneria spicata (Pursh) A. Love, the supposed ancestors of hexaploid Thinopyrum intermedium (Host) Barkworth & D.R.Dewey, compiled using DNA repeats and comparative genome analysis based on COS markers. Fluorescence in situ hybridization (FISH) with repetitive DNA probes proved suitable for the identification of individual chromosomes in the diploid JJ, StSt and PP genomes. Of the seven microsatellite markers tested only the (GAA)n trinucleotide sequence was appropriate for use as a single chromosome marker for the P. spicata AS chromosome. Based on COS marker analysis, the phylogenetic relationship between diploid wheatgrasses and the hexaploid bread wheat genomes was established. These findings confirmed that the J and E genomes are in neighbouring clusters.