Pseudo-linkage or real-linkage of rust resistance genes in a wheat-Thinopyrum intermedium translocation line

KEY MESSAGE

We analysed the chromosomal structures of two wheat-Thinopyrum intermedium addition lines Z4 and Z5 and resolved the linkage relationship between the leaf rust and stripe rust resistance genes in Z4. Wheat addition lines Z4 and Z5 carrying rust resistance genes from Thinopyrum intermedium (JJJsJsStSt, 2n = 6x = 42) together with three wheat lines involved in the production of these addition lines were analysed by rust response, 90K SNP genotyping, and molecular cytogenetic analysis. Seedling leaf rust (LR) responses to five diverse pathotypes indicated that the LR resistance gene(s) was located in translocation chromosome T3DS-3AS.3AL-7StS common to Z4 and Z5. The stripe rust (YR) resistance gene(s) was located in translocation chromosome T3AL-7StS.7StL, which is unique to Z4, based on the seedling YR responses to four diverse pathotypes. Backcross and selfed populations involving the addition lines and various wheat cultivars were studied to understand the inheritance of the alien resistance genes. Although inheritance studies indicated genetic linkage, the alien genes for resistance to leaf rust (LR) and stripe rust (YR) in Z4 were present in different wheat-Th. intermedium translocation chromosomes. We found that LR and YR were in pseudo-linkage, rather than true linkage.

Precise Identification of Chromosome Constitution and Rearrangements in Wheat–Thinopyrum intermedium Derivatives by ND-FISH and Oligo-FISH Painting

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 J^S 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.

Applied phenomics and genomics for improving barley yellow dwarf resistance in winter wheat

Barley yellow dwarf is one of the major viral diseases of cereals. Phenotyping barley yellow dwarf in wheat is extremely challenging due to similarities to other biotic and abiotic stresses. Breeding for resistance is additionally challenging as the wheat primary germplasm pool lacks genetic resistance, with most of the few resistance genes named to date originating from a wild relative species. The objectives of this study were to (1) evaluate the use of high-throughput phenotyping to improve barley yellow dwarf assessment; (2) identify genomic regions associated with barley yellow dwarf resistance; and (3) evaluate the ability of genomic selection models to predict barley yellow dwarf resistance. Up to 107 wheat lines were phenotyped during each of 5 field seasons under both insecticide treated and untreated plots. Across all seasons, barley yellow dwarf severity was lower within the insecticide treatment along with increased plant height and grain yield compared with untreated entries. Only 9.2% of the lines were positive for the presence of the translocated segment carrying the resistance gene Bdv2. Despite the low frequency, this region was identified through association mapping. Furthermore, we mapped a potentially novel genomic region for barley yellow dwarf resistance on chromosome 5AS. Given the variable heritability of the trait (0.211–0.806), we obtained a predictive ability for barley yellow dwarf severity ranging between 0.06 and 0.26. Including the presence or absence of Bdv2 as a covariate in the genomic selection models had a large effect for predicting barley yellow dwarf but almost no effect for other observed traits. This study was the first attempt to characterize barley yellow dwarf using field-high-throughput phenotyping and apply genomic selection to predict disease severity. These methods have the potential to improve barley yellow dwarf characterization, additionally identifying new sources of resistance will be crucial for delivering barley yellow dwarf resistant germplasm.

Cytogenetic identification and molecular marker development for the novel stripe rust-resistant wheat-Thinopyrum intermedium translocation line WTT11

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.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-021-00060-3.

Virus Diseases of Cereal and Oilseed Crops in Australia: Current Position and Future Challenges

This review summarizes research on virus diseases of cereals and oilseeds in Australia since the 1950s. All viruses known to infect the diverse range of cereal and oilseed crops grown in the continent's temperate, Mediterranean, subtropical and tropical cropping regions are included. Viruses that occur commonly and have potential to cause the greatest seed yield and quality losses are described in detail, focusing on their biology, epidemiology and management. These are: barley yellow dwarf virus, cereal yellow dwarf virus and wheat streak mosaic virus in wheat, barley, oats, triticale and rye; Johnsongrass mosaic virus in sorghum, maize, sweet corn and pearl millet; turnip yellows virus and turnip mosaic virus in canola and Indian mustard; tobacco streak virus in sunflower; and cotton bunchy top virus in cotton. The currently less important viruses covered number nine infecting nine cereal crops and 14 infecting eight oilseed crops (none recorded for rice or linseed). Brief background information on the scope of the Australian cereal and oilseed industries, virus epidemiology and management and yield loss quantification is provided. Major future threats to managing virus diseases effectively include damaging viruses and virus vector species spreading from elsewhere, the increasing spectrum of insecticide resistance in insect and mite vectors, resistance-breaking virus strains, changes in epidemiology, virus and vectors impacts arising from climate instability and extreme weather events, and insufficient industry awareness of virus diseases. The pressing need for more resources to focus on addressing these threats is emphasized and recommendations over future research priorities provided.

Assessment of Resistance to Cereal Cyst Nematode, Stripe Rust, and Powdery Mildew in Wheat-Thinopyrum intermedium Derivatives and Their Chromosome Composition

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.

Management of yellow dwarf disease in Europe in a post-neonicotinoid agriculture

Barley/cereal yellow dwarf viruses (YDVs) cause yellow dwarf disease (YDD), which is a continuous risk to cereals production worldwide. These viruses cause leaf yellowing and stunting, resulting in yield reductions of up to 80%. YDVs have been a consistent but low-level problem in European cereal cultivation for the last three decades, mostly due to the availability of several effective insecticides (largely pyrethroids and more recently neonicotinoids) against aphid vectors. However, this has changed recently, with many insecticides being lost, culminating in a recent European Union (EU) regulation prohibiting outdoor use of the neonicotinoid-insecticide compounds. This change is coupled with the growing challenge of insecticide-resistant aphids, the lack of genetic resources against YDVs, and a knowledge deficit around the parameters responsible for the emergence and spread of YDD. This means that economic sustainability of cereal cultivation in several European countries including France and United Kingdom is now again threatened by this aphid-vectored viral disease. In this review, we summarize the current knowledge on the YDV pathosystem, describe management options against YDD, analyse the impacts of the neonicotinoid ban in Europe, and consider future strategies to control YDV. © 2020 Society of Chemical Industry.

Genome wide association study reveals novel QTL for barley yellow dwarf virus resistance in wheat

Background

Barley yellow dwarf (BYD) is an important virus disease that causes significant reductions in wheat yield. For effective control of Barley yellow dwarf virus through breeding, the identification of genetic sources of resistance is key to success. In this study, 335 geographically diverse wheat accessions genotyped using an Illumina iSelect 90 K single nucleotide polymorphisms (SNPs) bead chip array were used to identify new sources of resistance to BYD in different environments.

Results

A genome-wide association study (GWAS) performed using all the generalised and mixed linkage models (GLM and MLM, respectively) identified a total of 36 significant marker-trait associations, four of which were consistently detected in the K model. These four novel quantitative trait loci (QTL) were identified on chromosomes 2A, 2B, 6A and 7A and associated with markers IWA3520, IWB24938, WB69770 and IWB57703, respectively. These four QTL showed an additive effect with the average visual symptom score of the lines containing resistance alleles of all four QTL being much lower than those with less favorable alleles. Several Chinese landraces, such as H-205 (Baimazha) and H-014 (Dahongmai) which have all four favorable alleles, showed consistently higher resistance in different field trials. None of them contained the previously described Bdv2, Bdv3 or Bdv4 genes for BYD resistance.

Conclusions

This study identified multiple novel QTL for BYD resistance and some resistant wheat genotypes. These will be useful for breeders to generate combinations with and/or without Bdv2 to achieve higher levels and more stable BYD resistance.

Identification of New QTL Contributing to Barley Yellow Dwarf Virus-PAV (BYDV-PAV) Resistance in Wheat

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.

Host-Induced Gene Silencing: A Powerful Strategy to Control Diseases of Wheat and Barley

Wheat and barley are the most highly produced and consumed grains in the world. Various pathogens-viruses, bacteria, fungi, insect pests, and nematode parasites-are major threats to yield and economic losses. Strategies for the management of disease control mainly depend on resistance or tolerance breeding, chemical control, and biological control. The discoveries of RNA silencing mechanisms provide a transgenic approach for disease management. Host-induced gene silencing (HIGS) employing RNA silencing mechanisms and, specifically, silencing the targets of invading pathogens, has been successfully applied in crop disease prevention. Here, we cover recent studies that indicate that HIGS is a valuable tool to protect wheat and barley from diseases in an environmentally friendly way.

Characterization of Chromosomal Rearrangement in New Wheat—Thinopyrum intermedium Addition Lines Carrying Thinopyrum—Specific Grain Hardness Genes

The wild species, Thinopyrum intermedium. (Genome StStJSJSJJ), serves as a valuable germplasm resource providing novel genes for wheat improvement. In the current study, non-denaturing fluorescence in situ hybridization (ND-FISH) with multiple probes and comparative molecular markers were applied to characterize two wheat-Th. intermedium chromosome additions. Sequential ND-FISH with new labeled Th. intermedium specific oligo-probes were used to precisely determine the chromosomal constitution of Th. intermedium, wheat—Th. intermedium partial amphiploids and addition lines Hy36 and Hy37. The ND-FISH results showed that the added JS-St translocated chromosomes in Hy36 had minor Oligo-5S ribosomal DNA (rDNA) signals at the short arm, while a pair of J-St chromosomes in Hy37 had major Oligo-pTa71 and minor Oligo-5S rDNA signals. The 90K SNP array and PCR-based molecular markers that mapped on wheat linkage group 5 and 3 facilitated the identification of Thinopyrum chromosome introgressions in the addition lines, and confirmed that added chromosomes in Hy36 and Hy37 were 5JSS.3StS and 5JS.3StS, respectively. Complete coding sequences at the paralogous puroindoline-a (Pina) loci from Th. intermedium were cloned and localized on the short arm of chromosome 5JS of Hy36. Line Hy36 showed a reduction in the hardness index, which suggested that Th. intermedium-specific Pina gene sequences may be associated with the softness trait in wheat background. The molecular cytogenetic identification of novel wheat—Th. intermedium derivatives indicated that the frequent chromosome rearrangement occurred in the progenies of wheat-Thinopyrum hybridization. The new wheat-Thinopyrum derived lines may increase the genetic diversity for wheat breeding.

Precise identification of wheat - Thinopyrum intermedium translocation chromosomes carrying resistance to wheat stripe rust in line Z4 and its derived progenies

The wheat - Thinopyrum intermedium derived line Z4 has displayed novel and effective stripe rust resistance for over 40 years. This study aimed to precisely identify the chromosome constitution of line Z4 and determine the stripe rust resistance contribution using multicolor fluorescent in situ hybridization (FISH) and molecular marker analysis. The results indicated that the Z4 line (2n = 44) contained two pairs of non-Robertsonian translocations without the 3A chromosomes of wheat. FISH karyotypes of F₃ progenies derived from crosses between Z4 and MY11 indicated that the transmission of the translocated chromosomes appeared normal and the number of wheat chromosomes 3A and 3D frequently varied. The FISH signal distribution of a new repetitive probe, named Oligo-3A1, confirmed the physical breakage points on chromosome 3AL incorporated into translocated chromosomes. PLUG markers revealed the breakage points on chromosomes 3A, 7J^S, and 3D invloved in the translocated chromosomes, and they were designated as T3DS-3AS.3AL-7J^SS and T3AL-7J^SS.7J^SL. Stripe rust resistances surveys indicated that the proximal region of 7J^SS or 7J^SL may confer the resistance at the adult plant stage. The precise characterization of the chromosome complements of wheat - Th. intermedium Z4 and derived progenies has demonstrated the importance of combining cytogenetic and molecular approaches in the genomics era for further wheat genetic manipulation and breeding purposes.

Introduction of Thinopyrum intermedium ssp. trichophorum chromosomes to wheat by trigeneric hybridization involving Triticum, Secale and Thinopyrum genera

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 2J^S addition line, two substitution lines of 4J^S(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 4J^S and 2J^S 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.

Chromosomal localization of genes conferring desirable agronomic traits from Agropyron cristatum chromosome 1P

Agropyron cristatum (L.) Gaertn. (2n = 4x = 28, PPPP), a wild relative of common wheat, possesses many potentially valuable genes for wheat breeding. To transfer these genes into wheat, a series of wheat-A. cristatum derivatives have been obtained in our laboratory. In this study, a wheat-A. cristatum derivative II-3-1 was obtained, which was proven to contain a 1P (1A) disomic substitution and 2P disomic addition line with 40 wheat chromosomes and two pairs of A. cristatum chromosomes by genomic in situ hybridization (GISH) and molecular markers analysis. By further backcrossing with the wheat parent Fukuhokomugi (Fukuho) and self-fertilization, three different lines were separated from II-3-1, including wheat-A. cristatum 1P disomic addition line II-3-1a, 2P disomic addition line II-3-1b and 1P (1A) disomic substitution line II-3-1c. Because 2P addition line had been reported before, we aimed to investigate 1P disomic addition line II-3-1a and wheat-A. cristatum 1P (1A) disomic substitution line II-3-1c. Analysis of different genetic populations demonstrated that 1P chromosome harbored multiple agronomic traits, such as elevated spike length, increased tillering ability, reduced plant height and spikelet density. Besides, bristles on the glume ridges as an important morphological marker was located on 1P chromosome. Therefore, the novel 1P addition and substitution lines will be used as important genetic materials to widen the genetic resources of wheat.

Cytogenetic study and stripe rust response of the derivatives from a wheat - Thinopyrum intermedium - Psathyrostachys huashanica trigeneric hybrid

To transfer multiple desirable alien genes into common wheat, we previously reported a new trigeneric hybrid synthesized by crossing a wheat - Thinopyrum intermedium partial amphiploid with wheat - Psathyrostachys huashanica amphiploid. Here, the meiotic behavior, chromosome constitution, and stripe rust resistance of F₅ derivatives from the wheat - Th. intermedium - P. huashanica trigeneric hybrid were studied. Cytological analysis indicated the F₅ progenies had chromosome numbers of 42-50 (average 44.96). The mean meiotic configuration was 1.28 univalents, 21.74 bivalents, 0.04 trivalents, and 0.02 tetravalents per pollen mother cell. In 2n = 42 lines, the average pairing configuration was 0.05 I + 19.91 II (ring) + 1.06 II (rod) + 0.003 IV, suggesting these lines were cytologically stable. Most lines with 2n = 43, 44, 46, 48, or 50, bearing a high frequency of univalents or multivalents, showed abnormal meiotic behavior. Genomic in situ hybridization karyotyping results revealed that 25 lines contained 1-7 Th. intermedium chromosomes, but no P. huashanica chromosomes were found among the 27 self-pollinated progenies. At meiosis, univalents (1-5) possessing Th. intermedium hybridization signals were detected in 19 lines. Bivalents (1-3) expressing fluorescence signals were observed in 12 lines. Importantly, 21 lines harbored wheat - Th. intermedium chromosomal translocations with various alien translocation types. Additionally, two homozygous lines, K13-668-10 and K13-682-12, possessed a pair of wheat - Th. intermedium small fragmental translocations. Compared with the recurrent parent Zhong 3, most lines showed high resistance to the stripe rust (Puccinia striiformis f. sp. tritici) pathogens prevalent in China, including race V26/Gui22. This paper reports a highly efficient technical method for inducing alien translocation between wheat and Th. intermedium by trigeneric hybridization. These lines might be potentially valuable germplasm resources for further wheat improvement.

The effects of chromosome 6P on fertile tiller number of wheat as revealed in wheat-Agropyron cristatum chromosome 5A/6P translocation lines

This study explored the genetic constitutions of several wheat- A. cristatum translocation lines and determined the effects of A. cristatum 6P chromosome segments on fertile tiller number in wheat. Progress in wheat breeding is hampered by a relatively narrow range of genetic variation. To overcome this hurdle, wild relatives of common wheat with superior agronomic traits are often used as donors of desirable genes in wheat-breeding programs. One of the successfully utilized wheat wild relatives is Agropyron cristatum (L.) Gaertn (2n = 4x = 28; genomes PPPP). We previously reported that WAT31-13 was a wheat-A. cristatum 5A-6P reciprocal translocation line with higher fertile tiller number and grain number per spike compared to common wheat. However, WAT31-13 was genetically unstable. In this study, we analyzed the 43 genetically stable progenies from WAT31-13 using genomic in situ hybridization, dual-color fluorescence in situ hybridization, and molecular markers. We classified them into three translocation types (TrS, TrL and TrA) and seven subtypes, and also pinpointed the translocation breakpoint. The genotypic data, combined with the phenotypes of each translocation type, enabled us to physically map agronomic traits to specific A. cristatum 6P chromosome arms or segments. Our results indicated that A. cristatum chromosome 6P played an important role in regulating fertile tiller number, and that positive and negative regulators of fertile tiller number existed on the A. cristatum chromosome arm 6PS and 6PL, respectively. By exploring the relationship between fertile tiller number and A. cristatum chromosome segment, this study presented a number of feasible approaches for creation, analysis, and utilization of wheat-alien chromosome translocation lines in genetic improvement of wheat.

Potential new sources of wheat curl mite resistance in wheat to prevent the spread of yield-reducing pathogens

The wheat curl mite (WCM), Aceria tosichella Keifer (Trombidiformes: Eriophyidae), is a major pest in cropping regions of the world and is recognised as the primary vector of several yield-reducing pathogens, primarily affecting wheat. Management of WCM is complicated due to several aspects of the mite's biology and ecology; however, commercially viable mite resistant wheat varieties may offer practical long-term management options. Unfortunately, mite populations have adapted to previously identified sources of resistance, highlighting the need for further sources of resistance and the value of stacking different resistances to give greater degrees and longevity of control. In this study we assessed the susceptibility of 42 wheat-derived genotypes to mite population growth using a new experimental method that overcomes methodological limitations of previous studies. Experimental wheat lines included a variety of wheat genotypes, related Triticeae species, wheat-alien chromosome amphiploids, and chromosome addition or substitution lines. From these we identify new promising sources of WCM resistance associated with Thinopyrum intermedium, Th. ponticum and Hordeum marinum chromosomes. More specifically we identify group 1J and 5J chromosomes of the L3 and L5 wheat-Th. intermedium addition lines as new sources of resistance that could be exploited to transfer resistance onto homoeologous wheat chromosomes. This study offers new methods for reliable in situ estimations of mite abundance on cereal plants, and new sources of WCM resistance that may assist management of WCM and associated viruses in wheat.

The Pontin series of recombinant alien translocations in bread wheat: single translocations integrating combinations of Bdv2, Lr19 and Sr25 disease-resistance genes from Thinopyrum intermedium and Th. ponticum

Two bread wheat lines each with a translocation on chromosome 7DL from either Thinopyrum intermedium (TC5 and TC14) or Thinopyrum ponticum (T4m), were hybridized in a ph1b mutant background to enhance recombination between the two translocated chromosomal segments. The frequency of recombinants was high in lines derived from the larger and similar-sized translocations (TC5/T4m), but much lower when derived from different-sized translocations (TC14/T4m). Recombinant translocations contained combinations of resistance genes Bdv2, Lr19 and Sr25 conferring resistance to Barley yellow dwarf virus (BYDV), leaf rust and stem rust, respectively. Their genetic composition was identified using bioassays and molecular markers specific for the two progenitor Thinopyrum species. This set of 7DL Th. ponticum/intermedium recombinant translocations was termed the Pontin series. In addition to Thinopyrum markers, the size of the translocation was estimated with the aid of wheat markers mapped on each of the 7DL deletion bins. Bioassays for BYDV, leaf rust and stem rust were performed under greenhouse and field conditions. Once separated from ph1b background, the Pontin recombinant translocations were stable and showed normal inheritance in successive backcrosses. The reported Pontin translocations integrate important resistance genes in a single linkage block which will allow simultaneous selection of disease resistance. Combinations of Bdv2 + Lr19 or Lr19 + Sr25 in both long and short translocations, are available to date. The smaller Pontins, comprising only 20 % of the distal portion of 7DL, will be most attractive to breeders.

Development and characterization of a Psathyrostachys huashanica Keng 7Ns chromosome addition line with leaf rust resistance

The aim of this study was to characterize a Triticum aestivum-Psathyrostachys huashanica Keng (2n = 2x = 14, NsNs) disomic addition line 2-1-6-3. Individual line 2-1-6-3 plants were analyzed using cytological, genomic in situ hybridization (GISH), EST-SSR, and EST-STS techniques. The alien addition line 2-1-6-3 was shown to have two P. huashanica chromosomes, with a meiotic configuration of 2n = 44 = 22 II. We tested 55 EST-SSR and 336 EST-STS primer pairs that mapped onto seven different wheat chromosomes using DNA from parents and the P. huashanica addition line. One EST-SSR and nine EST-STS primer pairs indicated that the additional chromosome of P. huashanica belonged to homoeologous group 7, the diagnostic fragments of five EST-STS markers (BE404955, BE591127, BE637663, BF482781 and CD452422) were cloned, sequenced and compared. The results showed that the amplified polymorphic bands of P. huashanica and disomic addition line 2-1-6-3 shared 100% sequence identity, which was designated as the 7Ns disomic addition line. Disomic addition line 2-1-6-3 was evaluated to test the leaf rust resistance of adult stages in the field. We found that one pair of the 7Ns genome chromosomes carried new leaf rust resistance gene(s). Moreover, wheat line 2-1-6-3 had a superior numbers of florets and grains per spike, which were associated with the introgression of the paired P. huashanica chromosomes. These high levels of disease resistance and stable, excellent agronomic traits suggest that this line could be utilized as a novel donor in wheat breeding programs.

Microdissection and chromosome painting of the alien chromosome in an addition line of wheat--Thinopyrum intermedium

In this study, chromosome painting was developed and used to identify alien chromosomes in TAi-27, a wheat - Thinopyrumintermedium addition line, and the chromosomes of the three different genomes of Th. Intermedium. The smallest alien chromosome of TAi-27 was microdissected and its DNA amplified by DOP-PCR was used as a probe to hybridize with metaphase chromosomes of TAi-27 and Th. intermedium. Results showed that hybridization signals were observed in all regions of a pair of the smallest alien chromosomes and the pericentromeric area of another pair of alien chromosomes in TAi-27, indicating that the probe from microdissected chromosome is species specific. In Th. intermedium, 14 chromosomes had wide and strong hybridization signals distributed mainly on the pericentromere area and 9 chromosomes with narrow and weak signals on the pericentromere area. The remaining chromosomes displayed a very weak or no signal. Sequential FISH/GISH on Th. intermedium chromosomes using the DNAs of microdissected chromosome, Pseudoroegneriaspicata (St genome) and pDbH12 (a J^s genome specific probe) as the probes indicated that the microdissected chromosome belonged to the St genome, three genomes (J^s, J and St) in Th. intermedium could be distinguished, in which there is no hybridization signal on J genome that is similar to the genome of Th. bessarabicum. Our results showed that the smallest alien chromosomes may represent a truncated chromosome and the repetitive sequence distribution might be similar in different chromosomes within the St genome. However, the repetitive sequence distributions are different within the J^s genome, within a single chromosome, and among different genomes in Th. intermedium. Our results suggested that chromosome painting could be feasible in some plants and useful in detecting chromosome variation and repetitive sequence distribution in different genomes of polyploidy plants, which is helpful for understanding the evolution of different genomes in polyploid plants.

Wheat resistome in response to barley yellow dwarf virus infection

Barley yellow dwarf virus (BYDV) caused one of the most serious virus diseases of wheat (Triticum aestivum) worldwide. The wheat-Thinopyrum intermedium translocation line YW642 carries BYDV resistance gene Bdv2. To explore resistant wheat resistome in response to BYDV infection, we used Affymetrix GeneChip® Wheat Genome Arrays to analyze transcriptomes of YW642 and its susceptible parent Zhong8601 at 12 and 72 h postinoculation with BYDV compared to mock-inoculated controls. Relative to mock-inoculated control, 335 defense-related transcripts were upregulated in BYDV-inoculated YW642, among which 70 were upregulated only in BYDV-inoculated YW642 but not in BYDV-inoculated Zhong8601 through clustering analysis. Additional analysis using BYDV-inoculated Zhong8601 as reference revealed that 59 defense-related transcripts were upregulated in BYDV-inoculated YW642. Comparison of these upregulated defense transcripts obtained via the two analysis ways indicated that 19 overlapped defense-related transcripts were highly expressed in BYDV-inoculated YW642 relative to BYDV-inoculated Zhong8601 and mock-inoculated YW642, which likely are significant factors in Bdv2-mediated defense response to BYDV. High expression of some resistance homologous genes, pathogen-associated molecular pattern-triggered immunity-related genes, ABC transporter genes, pathogenesis-related protein genes, and genes in reactive oxygen species, phospholipid signaling, and jasmonic acid-signaling may contribute to Bdv2-mediated defense response to BYDV.

Synthesis and characterization of advanced durum wheat hybrids and addition lines with thinopyrum chromosomes

Durum wheat (Triticum turgidum L., 2n = 4x = 28; AABB genomes) is a natural hybrid-an allotetraploid between 2 wild species, Triticum urartu Tumanian (AA genome) and Aegilops speltoides Tausch (BB genome). Even at the allotetraploid level, durum wheat can tolerate chromosomal imbalance, for example, addition of alien chromosome 1E of diploid wheatgrass, Lophopyrum elongatum. Therefore, one way to broaden its genetic base is to add a desirable chromosome(s) from diploid wild relatives. We attempted chromosomal engineering with chromosomes of a diploid wheatgrass, Thinopyrum bessarabicum-a source of resistance to some diseases including Fusarium head blight. Several advanced hybrids and alien addition lines were studied using traditional cytology, multicolor fluorescent genomic in situ hybridization, and molecular markers. Hybrid derivatives varied in chromosome number from F1 to F8 generations and in backcross generations. In advanced generations, we exercised selection against 28-chromosome plants and in favor of 30-chromosome plants that helped recover 14 addition lines in the F8 generation, as indicated by the absence of segregation for 29-chromosome plants. Disomic additions showed regular meiosis with 15 bivalents, 14 of durum wheat, and 1 of Th. bessarabicum. The addition lines will facilitate further chromosome engineering work on durum wheat for broadening its genetic base.

Molecular cytogenetic analysis of Agropyron chromatin specifying resistance to barley yellow dwarf virus in wheat

Nine families of bread wheat (TC5, TC6, TC7, TC8, TC9, TC10, TC14, 5395-(243AA), and 5395) with resistance to barley yellow dwarf virus and containing putative translocations between wheat and a group 7 chromosome of Agropyron intermedium (L1 disomic addition line, 7Ai#1 chromosome) induced by homoeologous pairing or tissue culture were analyzed. C-banding, genomic in situ hybridization (GISH), and restriction fragment length polymorphism (RFLP) in combination with repetitive Agropyron-specific sequences and deletion mapping in wheat were used to determine the relative locations of the translocation breakpoints and the size of the transferred alien chromatin segments in hexaploid wheat-Agropyron translocation lines. All homoeologous compensating lines had complete 7Ai#1 or translocated 7Ai#1-7D chromosomes that substitute for chromosome 7D. Two complete 7Ai#1 (7D) substitution lines (5395-(243AA) and 5395), one T1BS-7Ai#1S∙7Ai#1L addition line (TC7), and two different translocation types, T7DS-7Ai#1S∙7Ai#1L (TC5, TC6, TC8, TC9, and TC10) and T7DS∙7DL-7Ai#1L (TC14), substituting for chromosome 7D were identified. The substitution line 5395-(243AA) had a reciprocal T1BS∙1BL-4BS/T1BL-4BS∙4BL translocation. TC14 has a 6G (6B) substitution. The RFLP data from deletion mapping studies in wheat using 37 group 7 clones provided 10 molecular tagged chromosome regions for homoeologous and syntenic group 7 wheat or Agropyron chromosomes. Together with GISH we identified three different sizes of the transferred Agropyron chromosome segments with approximate breakpoints at fraction length (FL) 0.33 in the short arm of chromosome T7DS-7Ai#1S∙7Ai#1L (TC5, TC6, TC8, TC9, and TC10) and another at FL 0.37 of the nonhomoeologous translocated chromosome T1BS-7Ai#1S∙7Ai#1L (TC7). One breakpoint was identified in the long arm of chromosome T7DS∙7DL-7Ai#1L (TC14) at FL 0.56. We detected some nonreciprocal translocations for the most proximal region of the chromosome arm of 7DL, which resulted in small duplications. Key words : C-banding, genomic in situ hybridization (GISH), physical mapping, translocation mapping, RFLP analysis.

Introgression and characterization of barley yellow dwarf virus resistance from Thinopyrum intermedium into wheat

Wheatgrasses (species of Agropyron complex) have previously been reported to be resistant to barley yellow dwarf virus (BYDV). To introgress this resistance into wheat, Triticum aestivum x Thinopyrum (Agropyron) intermedium hybrids were advanced through a backcrossing program and reaction to BYDV, as determined by enzyme-linked immunosorbent assay (ELISA), is reported for the first time in backcross populations of wide hybrids between wheat and wheatgrasses. ELISA values revealed highly resistant to highly susceptible segregants in backcrosses. BYDV resistance was expressed in some backcross derivatives. Continued selection, based on cytology and ELISA in each generation, eliminated most of the unwanted wheatgrass chromosomes and produced self-fertile BYDV resistant wheat lines. The BYDV resistant lines with 2n = 42 had normal chromosome pairing similar to wheat, and their F1 hybrids with wheat had two univalents. DNA analyses showed that the source of alien chromatin in these BYDV resistant wheat lines is distinguishable from that in other Th. intermedium derived BYDV resistant wheat lines. Chromosome pairing and restriction fragment length polymorphism analyses indicated that the 42 chromosome resistant Purdue wheat lines are substitution lines in which chromosome 7D was replaced by a chromosome from Th. intermedium that was carrying gene(s) for BYDV resistance.

Structural organization of an alien Thinopyrum intermedium group 7 chromosome in U.S. soft red winter wheat (Triticum aestivum L.)

Barley yellow dwarf virus (BYDV) resistance in soft red winter wheat (SRWW) cultivars has been achieved by substituting a group 7 chromosome from Thinopyrum intermedium for chromosome 7D. To localize BYDV resistance, a detailed molecular genetic analysis was done on the alien group 7 Th. intermedium chromosome to determine its structural organization. Triticeae group 7 RFLP markers and rye specific repetitive sequences used in the analysis showed that the alien chromosome in the P29 substitution line has distinguishing features. The 350-480 bp rye telomeric sequence family was present on the long arm as determined by Southern and fluorescence in situ hybridization. However, further analysis using a rye dispersed repetitive sequence indicated that this alien chromosome does not contain introgressed segments from the rye genome. The alien chromosome is homoeologous to wheat chromosomes 7A and 7D as determined by RFLP analysis. Presence of the waxy gene on chromosomes 7A, 7B, and 7D but its absence on the alien chromosome in P29 suggests some internal structural differences on the short arm between Th. intermedium and wheat group 7 chromosomes. The identification of rye telomeric sequences on the alien Thinopyrum chromosome and the homoeology to wheat chromosomes 7A and 7D provide the necessary information and tools to analyze smaller segments of the Thinopyrum chromosome and to localize BYDV resistance in SRWW cultivars.

Molecular cytogenetic characterization of wheat--Thinopyrum elongatum addition, substitution and translocation lines with a novel source of resistance to wheat Fusarium Head Blight

Thinopyrum elongatum (2n=2x=14, EE), a wild relative of wheat, has been suggested as a potentially novel source of resistance to several major wheat diseases including Fusarium Head Blight (FHB). In this study, a series of wheat (cv. Chinese Spring, CS) substitution and ditelosomic lines, including Th. elongatum additions, were assessed for Type II resistance to FHB. Results indicated that the lines containing chromosome 7E of Th. elongatum gave a high level of resistance to FHB, wherein the infection did not spread beyond the inoculated floret. Furthermore, it was determined that the novel resistance gene(s) of 7E was located on the short-arm (7ES) based on sharp difference in FHB resistance between the two 7E ditelosomic lines for each arm. On the other hand, Th. elongatum chromosomes 5E and 6E likely contain gene(s) for susceptibility to FHB because the disease spreads rapidly within the inoculated spikes of these lines. Genomic in situ hybridization (GISH) analysis revealed that the alien chromosomes in the addition and substitution lines were intact, and the lines did not contain discernible genomic aberrations. GISH and multicolor-GISH analyses were further performed on three translocation lines that also showed high levels of resistance to FHB. Lines TA3499 and TA3695 were shown to contain one pair of wheat-Th. elongatum translocated chromosomes involving fragments of 7D plus a segment of the 7E, while line TA3493 was found to contain one pair of wheat-Th. elongatum translocated chromosomes involving the D- and A-genome chromosomes of wheat. Thus, this study has established that the short-arm of chromosome 7E of Th. elongatum harbors gene(s) highly resistant to the spreading of FHB, and chromatin of 7E introgressed into wheat chromosomes largely retained the resistance, implicating the feasibility of using these lines as novel material for breeding FHB-resistant wheat cultivars.

A new long terminal repeat (LTR) sequence allows to identify J genome from J S and St genomes of Thinopyrum intermedium

A repetitive sequence of 491 bp, named pMD232-500, was isolated from S. cereale cv. Kustro using wheat SSR marker Xgwm232. GenBank BLAST search revealed that the sequence of pMD232-500 was highly similar to a part of retrotransposon Nusif-1. Fluorescence in situ hybridization (FISH) analysis using pMD232-500 as probe indicated that only 14 Thinopyrum intermedium chromosomes and all the chromosomes of S. cereale cv. Kustro bear FISH signals, however, no FISH signals were observed on Dasypyrum villosum chromosomes. In addition, the FISH signals were distributed on whole arms except their terminal regions. Further genomic in situ hybridization (GISH) analysis using genomic DNA from Pseudoroegneria spicata indicated that the 14 Th. intermedium chromosomes bearing FISH signals should belong to J genome. Thereafter, the repetitive elements pMD232-500 showed the unambiguous features of genomic constitution of Th. intermedium. In addition, the results in the present study have indicated the similarity of genomes from Th. intermedium and S. cereale.

Development of EST-PCR markers for Thinopyrum intermedium chromosome 2Ai#2 and their application in characterization of novel wheat-grass recombinants

A series of expressed sequence tags-derived polymerase chain reaction (EST-PCR) markers specific to chromosome 2Ai#2 from Thinopyrum intermedium were developed in this study using a new integrative approach. The target alien chromosome confers high resistance to barley yellow dwarf virus (BYDV), which is a severe virus disease in wheat. To generate markers evenly distributed on 2Ai#2, a total of 105 primer pairs were designed based on mapped ESTs from 8 bins of wheat chromosome 2B with intron-prediction by aligning ESTs with genomic sequences of the new model plant Brachypodium distachyon. Eight and seven polymorphic markers on the short arm and the long arm of chromosome 2Ai#2, respectively, were obtained with a polymorphism rate of 14.3%. These chromosome 2Ai#2-specific EST-PCR markers were then used in tracing and exploring the structural variation of the alien chromosome in the population derived from the immature embryo culture of the cross between N452, a 2Ai#2(2D) substitution line, and common wheat CB037. Two centric fusion of translocations involving 2Ai#2 short or long arm with wheat chromosome 2D and some new genetic stocks including telosomes with the alien chromosome short or long arm were identified in the SC(3) generations, which provided basic materials to further study the mechanism of the BYDV resistance. BYDV tests in two field seasons suggest that the BYDV resistance was mainly conferred by the short arm, gene interaction on both arms of the alien chromosome was discussed.

Characterization of a partial wheat-Thinopyrum intermedium amphiploid and its reaction to fungal diseases of wheat

Partial amphiploids between wheat (Triticum aestivum L.) and Thinopyrum species play an important role in the transfer and use of traits from alien species. A wheat-Thinopyrum intermedium partial amphiploid, TAI8335, and its alien parent were characterized by a combination of genomic in situ hybridization (GISH) and cytological observations. Evidence from GISH indicated that the donor parent Th. intermedium possessed seven pairs of S, seven J(s) and 21 J chromosomes. Mitotic observation showed that the majority of TAI8335 plants had 56 chromosomes, but a few had 54 to 55, in some cases with two to three additional telochromosomes. The chromosomes in most pollen mother cells of plants with 2n = 56 formed 28 bivalents, averaging 27.12 in 223 cells, suggesting a basic cytological stability. Sequential GISH patterns using genomic Pseudoroegneria spicata and genomic Th. intermedium DNA as probes revealed that TAI8335 had fourteen chromosomes derived from Th. intermedium and its alien genome consisted of one pair of S-, three pairs of J(s) - and one pair of J-genome chromosomes as well as two translocated chromosome pairs, one being a Robertsonian translocation and another an intercalary translocation, both of which involved J and S genome. Two of the telochromosomes in the aneuploid plants originated from the J genome and one from wheat. Disease screening demonstrated this line was highly resistant to leaf rust, stem rust, stripe rust and powdery mildew. This study showed that the partial amphiploid TAI8335 appears to serve as a novel source for the transfer of resistance genes for multiple fungal pathogens to wheat.

Molecular markers show a complex mosaic pattern of wheat-Thinopyrum intermedium translocations carrying resistance to YDV

Thinopyrum intermedium translocations derived from the wheat (Triticum aestivum L.) substitution line P-29 were previously characterized by RFLP. We have further analyzed these lines and additional related germplasm with publicly available STS and SSRs. Primers which showed a polymorphism between wheat and P-29, were tested in all recombinant and nulli-tetrasomic lines confirming their position on chromosome 7D. The resulting 7D/7E chromosome maps appeared as a mosaic of wheat and Th. intermedium chromatin sections. To verify the composition of the translocation lines suggested by the RFLP-PCR map, F(2) progeny of two crosses (CS/216-1 and CS/260-1) were analyzed with molecular markers. Both populations gave an unexpectedly diverse number of recombinant individuals, suggesting that interstitial translocations occur more frequently than previously thought. This analysis also showed that there is a wide range in the number and position of the interstitial translocations within a given line such as the mosaic chromosome in recombinant line 260-1/CS-26, which has four Th. intermedium chromosome segments. Phenotypic data of the two populations suggested the presence of one gene which we have called Bdv3 to differentiate it from the previously reported orthologous gene Bdv2. Using the PCR-based molecular markers identified in this study, 5 out of 12 elite lines that showed good yields and no YDV symptoms contained Th. intermedium chromatin. Due to the multiple components involved in the YDV disease complex, combining selection for YDV resistance with the molecular markers and maps identified in this study will increase the efficiency of introgressing Th. intermedium chromatin containing YDV resistance or other beneficial traits into elite wheat germplasm.

Mapping of a BYDV resistance gene from Thinopyrum intermedium in wheat background by molecular markers

The wheat line H960642 is a homozygous wheat-Thinopyrum intermedium translocation line with resistance to BYDV by genomic in situ hybridization (GISH) and RFLP analysis. The genomic DNA of Th. intermedium was used as a probe, and common wheat genomic DNA as a blocking in GISH experiment. The results showed that the chromosome segments of Th. intermedium were transferred to the distal end of a pair of wheat chromosomes. RFLP analysis indicated that the translocation line H960642 is a T7DS-7DL-7XL translocation by using 8 probes mapped on the homoeologous group 7 in wheat. The translocation breakpoint is located between Xpsr680 and Xpsr965 about 90-99 cM from the centromere. The RFLP markers psr680 and psr687 were closely linked with the BYDV resistance gene. The gene is located on the distal end of 7XL around Xpsr680 and Xpsr687.

Cytogenetic and molecular characterization of a durum alien disomic addition line with enhanced tolerance to Fusarium head blight

Current durum wheat (Triticum turgidum L. subsp. durum (Desf.)) cultivars have little or no resistance to Fusarium head blight (FHB), a ravaging disease of cereal crops. A diploid wheatgrass, Lophopyrum elongatum (Host) A. Löve (2n = 2x = 14, EE genome), is an excellent source of FHB resistance. Through an extensive intergeneric hybridization using durum cultivar Langdon, we have developed a disomic alien addition line, named DGE-1 (2n = 28 + 2), with a wheatgrass chromosome pair. We used a unique method for isolating the addition line taking advantage of unreduced gametes functioning in Langdon x L. elongatum F1 hybrids in their first backcross to the Langdon parent, resulting in 35-chromosome plants from which we derived DGE-1. The addition line DGE-1 has a plant type similar to its Langdon parent, although it is shorter in height with narrower leaves and shorter spikes. It is meiotically and reproductively stable, generally forming 15 bivalents with two chiasmata each. The alien chromosome pair from the grass confers FHB resistance to the addition line, which has less than 21% infection on the visual scale, mean = 6.5%. Using various biochemical and molecular techniques (Giemsa C-banding, fluorescent genomic in situ hybridization (fl-GISH), chromosome-specific simple sequence repeat (SSR) markers, targeted region amplified polymorphism (TRAP) markers, and sodium dodecyl sulfate - polyacrylamide gel electrophoresis (SDS-PAGE)), we have shown that the extra chromosome involved is 1E of L. elongatum. This is the first time that FHB resistance has been discovered on chromosome 1E. We have established a chromosome-specific marker for 1E that may be used to screen fertile hybrid derivatives and durum addition lines for this chromosome that confers FHB resistance.

Comparison ofThinopyrum intermediumderivatives carrying barley yellow dwarf virus resistance in wheat

Resistance to both barley yellow dwarf virus (BYDV) and cereal yellow dwarf virus (CYDV) has been demonstrated in wheat genetic stocks with Thinopyrum intermedium chromatin. A number of resistance-bearing translocations have been reported on chromosome arm 7DL from two independent Th. intermedium sources; one source is the addition line L1 and the other is the spontaneous substitution line P29. Another source of resistance in wheat cytogenetic stocks is available as a 2Ai(2D) substitution line. We used a set of 38 molecular markers and the available deletion stocks to compare the size of the 7DL translocations more comprehensively than has been done previously. We also compared the efficacy of BYDV resistance of the various genetic stocks both before and after transfer to a common genetic background. TC14 was confirmed as carrying the smallest translocation, replacing about 20% of the distal end of 7DL. TC5 and TC10 had 90% of the chromosome arm replaced by Th. intermedium chromatin; the proximal 10% corresponded to wheat chromatin. YW642 appeared to have the whole 7DL replaced by Th. intermedium chromatin, as confirmed by the co-dominant marker cfd68 mapping on the bin nearest the centromere. Translocation line P961341 had bins 3, 7, and 8 replaced by Th. intermedium chromatin, making this the second smallest translocation with BYDV and CYDV resistance. The translocation sizes reported here differ from some of the previous estimates. The translocated Th. intermedium segments appeared to be bigger than the replaced wheat 7DL fragments. All the resistances derived from the L1 and P29 group 7 chromosomes and the 2Ai#2 chromosome were effective in reducing the number of infected plants and the mean virus titre, regardless of the background. Some evidence is discussed suggesting the long arm of the Th. intermedium group 7 chromosome 7Ai#1 carries two resistances, the distal Bdv2 and a proximal second gene.

Isolation of expressed sequences from a specific chromosome of Thinopyrum intermedium infected by BYDV

To map important ESTs to specific chromosomes and (or) chromosomal regions is difficult in hexaploid wheat because of its large genome size and serious interference of homoeologous sequences. Large-scale EST sequencing and subsequent chromosome localization are both laborious and time-consuming. The wheat alien addition line TAi-27 contains a pair of chromosomes of Thinopyrum intermedium (Host) Barkworth & D.R. Dewey that carry the resistance gene against barley yellow dwarf virus. In this research, we developed a modified technique based on chromosome microdissection and hybridization-specific amplification to isolate expressed sequences from the alien chromosome of TAi-27 by hybridization between the DNA of the microdissected alien chromosome and cDNA of Th. intermedium infected by barley yellow dwarf virus. Twelve clones were selected, sequenced, and analyzed. Three of them were unknown genes without any hit in the GenBank database and the other nine were highly homologous with ESTs of wheat, barley, and (or) other plants in Gramineae induced by abiotic or biotic stress. The method used in this research to isolate expressed sequences from a specific chromosome has the following advantages: (i) the obtained expressed sequences are larger in size and have 3' end information and (ii) the operation is less complicated. It would be an efficient improved method for genomics and functional genomics research of polyploid plants, especially for EST development and mapping. The obtained expressed sequence data are also informative in understanding the resistance genes on the alien chromosome of TAi-27.

Inheritance and mapping of powdery mildew resistance gene Pm43 introgressed from Thinopyrum intermedium into wheat

Powdery mildew resistance from Thinopyrum intermedium was introgressed into common wheat (Triticum aestivum L.). Genetic analysis of the F(1), F(2), F(3) and BC(1) populations from powdery mildew resistant line CH5025 revealed that resistance was controlled by a single dominant allele. The gene responsible for powdery mildew resistance was mapped by the linkage analysis of a segregating F(2) population. The resistance gene was linked to five co-dominant genomic SSR markers (Xcfd233, Xwmc41, Xbarc11, Xgwm539 and Xwmc175) and their most likely order was Xcfd233-Xwmc41-Pm43-Xbarc11-Xgwm539-Xwmc175 at 2.6, 2.3, 4.2, 3.5 and 7.0 cM, respectively. Using the Chinese Spring nullisomic-tetrasomic and ditelosomic lines, the polymorphic markers and the resistance gene were assigned to chromosome 2DL. As no powdery mildew resistance gene was previously assigned to chromosome 2DL, this new resistance gene was designated Pm43. Pm43, together with the identified closely linked markers, could be useful in marker-assisted selection for pyramiding powdery mildew resistance genes.

Trigenomic chromosomes by recombination of Thinopyrum intermedium and Th. ponticum translocations in wheat

Rusts and barley yellow dwarf virus (BYDV) are among the main diseases affecting wheat production world wide for which wild relatives have been the source of a number of translocations carrying resistance genes. Nevertheless, along with desirable traits, alien translocations often carry deleterious genes. We have generated recombinants in a bread wheat background between two alien translocations: TC5, ex-Thinopyrum (Th) intermedium, carrying BYDV resistance gene Bdv2; and T4m, ex-Th. ponticum, carrying rust resistance genes Lr19 and Sr25. Because both these translocations are on the wheat chromosome arm 7DL, homoeologous recombination was attempted in the double hemizygote (TC5/T4m) in a background homozygous for the ph1b mutation. The identification of recombinants was facilitated by the use of newly developed molecular markers for each of the alien genomes represented in the two translocations and by studying derived F(2), F(3) and doubled haploid populations. The occurrence of recombination was confirmed with molecular markers and bioassays on families of testcrosses between putative recombinants and bread wheat, and in F(2) populations derived from the testcrosses. As a consequence it has been possible to derive a genetic map of markers and resistance genes on these previously fixed alien linkage blocks. We have obtained fertile progeny carrying new tri-genomic recombinant chromosomes. Furthermore we have demonstrated that some of the recombinants carried resistance genes Lr19 and Bdv2 yet lacked the self-elimination trait associated with shortened T4 segments. We have also shown that the recombinant translocations are fixed and stable once removed from the influence of the ph1b. The molecular markers developed in this study will facilitate selection of individuals carrying recombinant Th. intermedium-Th. ponticum translocations (Pontin series) in breeding programs.

Characterization of derivatives from wheat-Thinopyrum wide crosses

Partial amphiploids are lines that contain 42 (38-42) wheat and 14 (14-18) alien chromosomes. They are derived by backcrossing wheat onto hybrids between wheat and either Thinopyrum intermedium (6x) or Th. ponticum (10x). GISH analysis has shown that, with possibly one exception, the alien genomes (chromosome sets) in partial amphiploids are found to be hybrids i.e. composed of chromosomes from more than one alien genome. The individual partial amphiploids are meiotically stable and nearly perfectly fertile, but hybrids between different lines were characterized by varying numbers of unpaired chromosomes and consequently variable degrees of sterility. Translocated chromosomes involving different Thinopyrum genomes or Thinopyrum and wheat genomes were found in partial amphiploids and consequently in the addition lines derived from them. Partial amphiploids have proven to be an excellent tertiary gene pool for wheat improvement, containing resistance to biotic stresses not present in wheat itself. Resistance to Barley Yellow Dwarf Virus (BYDV) and Wheat Streak Mosaic Virus (WSMV) have been found in partial amphiploids and addition lines derived from both Th. intermedium and Th. ponticum. Excellent resistance to Fusarium head blight has been found on a Th. intermedium chromosome that had substituted for chromosome 2D in wheat. Genes for resistance to leaf rust and stem rust have already been incorporated into wheat and tagged with molecular markers.

Cloning of resistance gene analogs located on the alien chromosome in an addition line of wheat-Thinopyrum intermedium

Homology-based gene/gene-analog cloning method has been extensively applied in isolation of RGAs (resistance gene analogs) in various plant species. However, serious interference of sequences on homoeologous chromosomes in polyploidy species usually occurred when cloning RGAs in a specific chromosome. In this research, the techniques of chromosome microdissection combined with homology-based cloning were used to clone RGAs from a specific chromosome of Wheat-Thinopyrum alien addition line TAi-27, which was derived from common wheat and Thinopyrum intermedium with a pair of chromosomes from Th. intermedium. The alien chromosomes carry genes for resistance to BYDV. The alien chromosome in TAi-27 was isolated by a glass needle and digested with proteinase K. The DNA of the alien chromosome was amplified by two rounds of Sau3A linker adaptor-mediated PCR. RGAs were amplified by PCR with the degenerated primers designed based on conserved domains of published resistance genes (R genes) by using the alien chromosome DNA, genomic DNA and cDNA of Th. intermedium, TAi-27 and 3B-2 (a parent of TAi-27) as templates. A total of seven RGAs were obtained and sequenced. Of which, a constitutively expressed single-copy NBS-LRR type RGA ACR 3 was amplified from the dissected alien chromosome of TAi-27, TcDR 2 and TcDR 3 were from cDNA of Th. intermedium, AcDR 3 was from cDNA of TAi-27, FcDR 2 was from cDNA of 3B-2, AR 2 was from genomic DNA of TAi-27 and TR 2 was from genomic DNA of Th. intermedium. Sequence homology analyses showed that the above RGAs were highly homologous with known resistance genes or resistance gene analogs and belonged to NBS-LRR type of R genes. ACR 3 was recovered by PCR from genomic DNA and cDNA of Th. intermedium and TAi-27, but not from 3B-2. Southern hybridization using the digested genomic DNA of Th. intermedium, TAi-27 and 3B-2 as the template and ACR 3 as the probe showed that there is only one copy of ACR 3 in the genome of Th. intermedium and TAi-27, but it is absent in 3B-2. The ACR 3 could be used as a specific probe of the R gene on the alien chromosome of TAi-27. Results of Northern hybridization suggested that ACR 3 was constitutively expressed in Th. intermedium and TAi-27, but not 3B-2, and expressed higher in leaves than in roots. This research demonstrated a new way to clone RGAs located on a specific chromosome. The information reported here should be useful to understand the resistance mechanism of, and to clone resistant genes from, the alien chromosome in TAi-27.

Screening and analysis of differentially expressed genes from an alien addition line of wheat Thinopyrum intermedium induced by barley yellow dwarf virus infection

The alien addition line TAI-27 contains a pair of chromosomes of Thinopyrum intermedium that carry resistance against barley yellow dwarf virus (BYDV). A subtractive library was constructed using the leaves of TAI-27, which were infected by Schizaphis graminum carrying the GAV strain of BYDV, and the control at the three-leaf stage. Nine differentially expressed genes were identified from 100 randomly picked clones and sequenced. Two of the nine clones were highly homologous with known genes. Of the remaining seven cDNA clones, five clones matched with known expressed sequence tag (EST) sequences from wheat and (or) barley whereas the other two clones were unknown. Five of the nine differentially expressed sequences (WTJ9, WTJ11, WTJ15, WTJ19, and WTJ32) were highly homologous (identities >94%) with ESTs from wheat or barley challenged with pathogens. These five sequences and another one (WTJ18) were also highly homologous (identities >86%) with abiotic stress induced ESTs in wheat or barley. Reverse Northern hybridization showed that seven of the nine differentially expressed cDNA sequences hybridized with cDNA of T. intermedium infected by BYDV. Three of these also hybridized with cDNA of line 3B-2 (a parent of TAI-27) infected by BYDV. The alien chromosome in TAI-27 was microdissected. The second round linker adaptor mediated PCR products of the alien chromosomal DNA were labeled with digoxygenin and used as the probe to hybridize with the nine differentially expressed genes. The analysis showed that seven differentially expressed genes were homologous with the alien chromosome of TAI-27. These seven differentially expressed sequences could be used as ESTs of the alien chromosome of TAI-27. This research laid the foundation for screening and cloning of new specific functional genes conferring resistance to BYDV and probably other pathogens.

Detection of alien chromatin introgression from Thinopyrum into wheat using S genomic DNA as a probe – A landmark approach for Thinopyrum genome research

The introduction of alien genetic variation from the genus Thinopyrum through chromosome engineering into wheat is a valuable and proven technique for wheat improvement. A number of economically important traits have been transferred into wheat as single genes, chromosome arms or entire chromosomes. Successful transfers can be greatly assisted by the precise identification of alien chromatin in the recipient progenies. Chromosome identification and characterization are useful for genetic manipulation and transfer in wheat breeding following chromosome engineering. Genomic in situ hybridization (GISH) using an S genomic DNA probe from the diploid species Pseudoroegneria has proven to be a powerful diagnostic cytogenetic tool for monitoring the transfer of many promising agronomic traits from Thinopyrum. This specific S genomic probe not only allows the direct determination of the chromosome composition in wheat-Thinopyrum hybrids, but also can separate the Th. intermedium chromosomes into the J, J(S) and S genomes. The J(S) genome, which consists of a modified J genome chromosome distinguished by S genomic sequences of Pseudoroegneria near the centromere and telomere, carries many disease and mite resistance genes. Utilization of this S genomic probe leads to a better understanding of genomic affinities between Thinopyrum and wheat, and provides a molecular cytogenetic marker for monitoring the transfer of alien Thinopyrum agronomic traits into wheat recipient lines.

Genomic constitution and variation in five partial amphiploids of wheat--Thinopyrum intermedium as revealed by GISH, multicolor GISH and seed storage protein analysis

Genomic in situ hybridization (GISH) and multicolor GISH (mcGISH) methodology were used to establish the cytogenetic constitution of five partial amphiploid lines obtained from wheat x Thinopyrum intermedium hybridizations. Line Zhong 1, 2 n=52, contained 14 chromosomes from each of the wheat genomes plus ten Th. intermedium chromosomes, with one pair of A-genome chromosomes having a Th. intermedium chromosomal segment translocated to the short arm. Line Zhong 2, 2 n=54, had intact ABD wheat genome chromosomes plus 12 Th. intermedium chromosomes. The multicolor GISH results, using different fluorochrome labeled Th. intermedium and the various diploid wheat genomic DNAs as probes, indicated that both Zhong 1 and Zhong 2 contained one pair of Th. intermedium chromosomes with a significant homology to the wheat D genome. High-molecular-weight (HMW) glutenin and gliadin analysis revealed that Zhong 1 and Zhong 2 had identical banding patterns that contained all of the wheat bands and a specific HMW band from Th. intermedium. Zhong 1 and Zhong 2 had good HMW subunits for wheat breeding. Zhong 3 and Zhong 5, both 2 n=56, possessed no gross chromosomal aberrations or translocations that were detectable at the GISH level. Zhong 4 also had a chromosome number of 2 n=56 and contained the complete wheat ABD-genome chromosomes plus 14 Th. intermedium chromosomes, with one pair of Th. intermedium chromosomes being markedly smaller. Multicolor GISH results indicated that Zhong 4 also contained two pairs of reciprocally translocated chromosomes involving the A and D genomes. Zhong 3, Zhong 4 and Zhong 5 contained a specific gliadin band from Th. intermedium. Based on the above data, it was concluded that inter-genomic transfer of chromosomal segments and/or sequence introgression had occurred in these newly synthesized partial amphiploids despite their diploid-like meiotic behavior and disomic inheritance.

Development of novel PCR markers linked to the BYDV resistance gene Bdv2 useful in wheat for marker-assisted selection

The distal segment of the long arm of the Thinopyrum intermedium chromosome 7Ai1 carries the barley yellow dwarf virus (BYDV) resistance gene Bdv2. This segment was transferred to the distal region of the long arm of wheat chromosome 7D in the Yw series of translocation lines by using the ph1b mutant to induce homoeologous pairing. To transfer Bdv2 to commercial varieties, we developed two resistance gene-analog polymorphism (RGAP) markers, Tgp-1(350) and Tgp-2(210), and one randomly amplified polymorphic DNA (RAPD) marker, OPD04(1300). The diagnostic fragments of the RGAP marker Tgp-1(350) and the RAPD marker OPD04(1300) were cloned, sequenced and converted into sequence-characterized amplified region (SCAR) markers, named SC-gp1 and SC-D04, respectively. SC-gp1 and SC-D04 were validated based on available translocation lines and segregating F(2) individuals. Our results indicated that the SCAR markers co-segregated with the BYDV resistance associated with Bdv2. Therefore, they can be used as a low-cost, high-throughput alternative to conventional phenotypic screening in wheat-breeding programs exploiting Bdv2. The marker-assisted selection for BYDV resistance was successfully performed in a wheat-breeding program.