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

Improving genomic selection in hexaploid wheat with sub-genome additive and epistatic models

The goal of wheat breeding is the development of superior cultivars tailored to specific environments, and the identification of promising crosses is crucial for the success of breeding programs. Although genomic estimated breeding values were developed to estimate additive effects of genotypes before testing as parents, application has focused on predicting performance of candidate lines, ignoring nonadditive genetic effects. However, nonadditive genetic effects are hypothesized to be especially important in allopolyploid species due to the interaction between homeologous genes. The objectives of this study were to model additive and additive-by-additive epistatic effects to better delineate the genetic architecture of grain yield in wheat and to improve the accuracy of genome-wide predictions. The data set utilized consisted of 3,740 F5:6 experimental lines tested in the K-State wheat breeding program across the years 2016 and 2018. Covariance matrices were calculated based on whole- and sub-genome marker data, and the natural and orthogonal interaction approach was used to estimate variance components for additive and additive-by-additive epistatic effects. Incorporating epistatic effects in additive models resulted in nonorthogonal partitioning of genetic effects but increased total genetic variance and reduced deviance information criteria. Estimation of sub-genome effects indicated that genotypes with the greatest whole-genome effects often combine sub-genomes with intermediate to high effects, suggesting potential for crossing parental lines that have complementary sub-genome effects. Modeling epistasis in either whole-genome or sub-genome models led to a marginal (3%) improvement in genomic prediction accuracy, which could result in significant genetic gains across multiple cycles of breeding.

Exploitation of the genetic potential of Thinopyrum and Agropyron genera to protect wheat from diseases and environmental stresses

Common wheat is one of the most important food crops in the world. Grain harvests can be increased by reducing losses from diseases and environmental stresses. The tertiary gene pool, including Thinopyrum spp., is a valuable resource for increasing genetic diversity and wheat resistance to fungal diseases and abiotic stresses. Distant hybridization between wheat and Thinopyrum spp. began in the 1920s in Russia, and later continued in different countries. The main results were obtained using the species Th. ponticum and Th. intermedium. Additionally, introgression material was created based on Th. elongatum, Th. bessarabicum, Th. junceiforme, Agropyron cristatum. The results of introgression for resistance to diseases (leaf, stem, and stripe rusts; powdery mildew; Fusarium head blight; and Septoria blotch) and abiotic stresses (drought, extreme temperatures, and salinity) to wheat was reviewed. Approaches to improving the agronomic properties of introgression breeding material (the use of irradiation, ph-mutants and compensating Robertsonian translocations) were described. The experience of long-term use in the world of a number of genes from the tertiary gene pool in protecting wheat from leaf and stem rust was observed. Th. ponticum is a nonhost for Puccinia triticina (Ptr) and P. graminis f. sp. tritici (Pgt) and suppresses the development of rust fungi on the plant surface. Wheat samples with the tall wheatgrass genes Lr19, Lr38, Sr24, Sr25 and Sr26 showed defence mechanisms similar to nonhosts resistance. Their influence led to disruption of the development of surface infection structures and fungal death when trying to penetrate the stomata (prehaustorial resistance or stomatal immunity). Obviously, a change in the chemical properties of fungal surface structures of races virulent to Lr19, Lr24, Sr24, Sr25, and Sr26 leads to a decrease in their adaptability to the environment. This possibly determined the durable resistance of cultivars to leaf and stem rusts in different regions. Alien genes with a similar effect are of interest for breeding cultivars with durable resistance to rust diseases and engineering crops with the help of molecular technologies.

QTL mapping for the flag leaf-related traits using RILs derived from Trititrigia germplasm line SN304 and wheat cultivar Yannong15 in multiple environments

BACKGROUND

Developing and enriching genetic resources plays important role in the crop improvement. The flag leaf affects plant architecture and contributes to the grain yield of wheat (Triticum aestivum L.). The genetic improvement of flag leaf traits faces problems such as a limited genetic basis. Among the various genetic resources of wheat, Thinopyrum intermedium has been utilized as a valuable resource in genetic improvement due to its disease resistance, large spikes, large leaves, and multiple flowers. In this study, a recombinant inbred line (RIL) population was derived from common wheat Yannong15 and wheat-Th. intermedium introgression line SN304 was used to identify the quantitative trait loci (QTL) for flag leaf-related traits.

RESULTS

QTL mapping was performed for flag leaf length (FLL), flag leaf width (FLW) and flag leaf area (FLA). A total of 77 QTLs were detected, and among these, 51 QTLs with positive alleles were contributed by SN304. Fourteen major QTLs for flag leaf traits were detected on chromosomes 2B, 3B, 4B, and 2D. Additionally, 28 QTLs and 8 QTLs for flag leaf-related traits were detected in low-phosphorus and drought environments, respectively. Based on major QTLs of positive alleles from SN304, we identified a pair of double-ended anchor primers mapped on chromosome 2B and amplified a specific band of Th. intermedium in SN304. Moreover, there was a major colocated QTL on chromosome 2B, called QFll/Flw/Fla-2B, which was delimited to a physical interval of approximately 2.9 Mb and contained 20 candidate genes. Through gene sequence and expression analysis, four candidate genes associated with flag leaf formation and growth in the QTL interval were identified.

CONCLUSION

These results promote the fine mapping of QFll/Flw/Fla-2B, which have pleiotropic effects, and will facilitate the identification of candidate genes for flag leaf-related traits. Additionally, this work provides a theoretical basis for the application of Th. intermedium in wheat breeding.

Important wheat diseases in the US and their management in the 21st century

Wheat is a crop of historical significance, as it marks the turning point of human civilization 10,000 years ago with its domestication. Due to the rapid increase in population, wheat production needs to be increased by 50% by 2050 and this growth will be mainly based on yield increases, as there is strong competition for scarce productive arable land from other sectors. This increasing demand can be further achieved using sustainable approaches including integrated disease pest management, adaption to warmer climates, less use of water resources and increased frequency of abiotic stress tolerances. Out of 200 diseases of wheat, 50 cause economic losses and are widely distributed. Each year, about 20% of wheat is lost due to diseases. Some major wheat diseases are rusts, smut, tan spot, spot blotch, fusarium head blight, common root rot, septoria blotch, powdery mildew, blast, and several viral, nematode, and bacterial diseases. These diseases badly impact the yield and cause mortality of the plants. This review focuses on important diseases of the wheat present in the United States, with comprehensive information of causal organism, economic damage, symptoms and host range, favorable conditions, and disease management strategies. Furthermore, major genetic and breeding efforts to control and manage these diseases are discussed. A detailed description of all the QTLs, genes reported and cloned for these diseases are provided in this review. This study will be of utmost importance to wheat breeding programs throughout the world to breed for resistance under changing environmental conditions.

The Aegilops ventricosa 2NvS segment in bread wheat: cytology, genomics and breeding

KEY MESSAGE

The first cytological characterization of the 2NvS segment in hexaploid wheat; complete de novo assembly and annotation of 2NvS segment; 2NvS frequency is increasing 2NvS and is associated with higher yield. The Aegilops ventricosa 2NvS translocation segment has been utilized in breeding disease-resistant wheat crops since the early 1990s. This segment is known to possess several important resistance genes against multiple wheat diseases including root knot nematode, stripe rust, leaf rust and stem rust. More recently, this segment has been associated with resistance to wheat blast, an emerging and devastating wheat disease in South America and Asia. To date, full characterization of the segment including its size, gene content and its association with grain yield is lacking. Here, we present a complete cytological and physical characterization of this agronomically important translocation in bread wheat. We de novo assembled the 2NvS segment in two wheat varieties, 'Jagger' and 'CDC Stanley,' and delineated the segment to be approximately 33 Mb. A total of 535 high-confidence genes were annotated within the 2NvS region, with > 10% belonging to the nucleotide-binding leucine-rich repeat (NLR) gene families. Identification of groups of NLR genes that are potentially N genome-specific and expressed in specific tissues can fast-track testing of candidate genes playing roles in various disease resistances. We also show the increasing frequency of 2NvS among spring and winter wheat breeding programs over two and a half decades, and the positive impact of 2NvS on wheat grain yield based on historical datasets. The significance of the 2NvS segment in wheat breeding due to resistance to multiple diseases and a positive impact on yield highlights the importance of understanding and characterizing the wheat pan-genome for better insights into molecular breeding for wheat improvement.

Wheat, Rye, and Barley Genomes Can Associate during Meiosis in Newly Synthesized Trigeneric Hybrids

Polyploidization, or whole genome duplication (WGD), has an important role in evolution and speciation. One of the biggest challenges faced by a new polyploid is meiosis, in particular, discriminating between multiple related chromosomes so that only homologs recombine to ensure regular chromosome segregation and fertility. Here, we report the production of two new hybrids formed by the genomes of species from three different genera: a hybrid between Aegilops tauschii (DD), Hordeum chilense (H^chH^ch), and Secale cereale (RR) with the haploid genomic constitution H^chDR (n = 7× = 21); and a hybrid between Triticum turgidum spp. durum (AABB), H. chilense, and S. cereale with the constitution ABH^chR (n = 7× = 28). We used genomic in situ hybridization and immunolocalization of key meiotic proteins to establish the chromosome composition of the new hybrids and to study their meiotic behavior. Interestingly, there were multiple chromosome associations at metaphase I in both hybrids. A high level of crossover (CO) formation was observed in H^chDR, which shows the possibility of meiotic recombination between the different genomes. We succeeded in the duplication of the ABH^chR genome, and several amphiploids, AABBH^chH^chRR, were obtained and characterized. These results indicate that recombination between the genera of three economically important crops is possible.

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.

Fertile introgression products generated via somatic hybridization between wheat and Thinopyrum intermedium

Fertile hybrids were produced with genetic material transferred from Th. intermedium into a wheat background and supply a source of genetic variation to wheat improvement. Both symmetric and asymmetric somatic hybrids have been obtained from the combination of wheatgrass (Thinopyrum intermedium) and bread wheat (Triticum aestivum). Two wheat protoplast populations, one derived from embryogenic calli and the other from a non-regenerable, rapidly dividing cell line, were fused with Th. intermedium protoplasts which had been (or not been) pre-irradiated with UV. Among the 124 regenerated calli, 64 could be categorized as being of hybrid origin on the basis of plant morphology, peroxidase isozyme, RAPD DNA profiling and karyological analysis. Numerous green plantlets were regenerated from 13 calli recovered from either the symmetric hybrid (no UV pre-treatment) or the asymmetric one (30 s UV irradiation). One of these hybrid plants proved to be vigorous and self-fertile. The regenerants were all closer in phenotype to wheat than to Th. intermedium. Genomic in situ hybridization analysis showed that the chromosomes in the hybrids were largely intact wheat ones, although a few Th. intermedium chromosome fragments had been incorporated within them.

Strategies for transferring resistance into wheat: from wide crosses to GM cassettes

The domestication of wheat in the Fertile Crescent 10,000 years ago led to a genetic bottleneck. Modern agriculture has further narrowed the genetic base by introducing extreme levels of uniformity on a vast spatial and temporal scale. This reduction in genetic complexity renders the crop vulnerable to new and emerging pests and pathogens. The wild relatives of wheat represent an important source of genetic variation for disease resistance. For nearly a century farmers, breeders, and cytogeneticists have sought to access this variation for crop improvement. Several barriers restricting interspecies hybridization and introgression have been overcome, providing the opportunity to tap an extensive reservoir of genetic diversity. Resistance has been introgressed into wheat from at least 52 species from 13 genera, demonstrating the remarkable plasticity of the wheat genome and the importance of such natural variation in wheat breeding. Two main problems hinder the effective deployment of introgressed resistance genes for crop improvement: (1) the simultaneous introduction of genetically linked deleterious traits and (2) the rapid breakdown of resistance when deployed individually. In this review, we discuss how recent advances in molecular genomics are providing new opportunities to overcome these problems.

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 compensating wheat-Thinopyrum intermedium Robertsonian translocation with Sr44 resistance to stem rust (Ug99)

The emergence of the highly virulent Ug99 race complex of the stem rust fungus (Puccinia graminis Pers. f. sp. tritici Eriks. and Henn.) threatens wheat (Triticum aestivum L.) production worldwide. One of the effective genes against the Ug99 race complex is Sr44, which was derived from Thinopyrum intermedium (Host) Barkworth and D.R. Dewey and mapped to the short arm of 7J (designated 7J#1S) present in the noncompensating T7DS-7J#1L∙7J#1S translocation. Noncompensating wheat-alien translocations are known to cause genomic duplications and deficiencies leading to poor agronomic performance, precluding their direct use in wheat improvement. The present study was initiated to produce compensating wheat-Th. intermedium Robertsonian translocations with Sr44 resistance. One compensating RobT was identified consisting of the wheat 7DL arm translocated to the Th. intermedium 7J#1S arm resulting in T7DL∙7J#1S. The T7DL∙7J#1S stock was designated as TA5657. The 7DL∙7J#1S stock carries Sr44 and has resistance to the Ug99 race complex. This compensating RobT with Sr44 resistance may be useful in wheat improvement. In addition, we identified an unnamed stem rust resistance gene located on the 7J#1L arm that confers resistance not only to Ug99, but also to race TRTTF, which is virulent to Sr44. However, the action of the second gene can be modified by the presence of suppressors in the recipient wheat cultivars.

Detection of quantitative trait loci associated with leaf rust resistance in bread wheat

Leaf rust, caused by Puccinia recondita Rob. ex Desm., is a common disease in wheat. The objective of this study was to develop molecular markers associated with the quantitative trait loci (QTLs) putatively conferring durable leaf rust resistance in Triticum aestivum L. em. Thell. A population of 77 recombinant inbred lines (RILs) developed from 'Parula' (resistant) and 'Siete Cerros' (moderately susceptible) was used. Bulked segregant analysis was done using random amplified polymorphic DNAs (RAPDs) with DNA enriched for low-copy sequences using hydroxyapatite chromatography. Out of 400 decamer primers screened, 3 RAPD markers were identified between the bulk of the most resistant and the bulk of the most susceptible lines. These were cloned and used as probes on the RILs in Southern hybridizations. Two probes revealed two tightly linked loci. One-way analysis of variance showed that these two loci, and another revealed by the third probe, were linked to QTLs controlling leaf rust resistance based on data taken from 2 years of replicated field trials. Cytogenetic analysis placed the two tightly linked loci on the long arm of chromosome 7B. The third probe detected loci located on the short arms of chromosomes 1B and 1D. It is suggested that the QTL detected on 7BL may well be homoeoallelic to Lr34.

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.

Alien introgression in the grasses Lolium perenne (perennial ryegrass) and Festuca pratensis (meadow fescue): the development of seven monosomic substitution lines and their molecular and cytological characterization

BACKGROUND AND AIMS

To address the issues associated with food security, environmental change and bioenergy in the context of crop plants, the production, identification and evaluation of novel plant phenotypes is fundamental. One of the major routes to this end will be wide hybridization and introgression breeding. The transfer of chromosomes and chromosome segments between related species (chromosome engineering or alien introgression) also provides an important resource for determining the genetic control of target traits. However, the realization of the full potential of chromosome engineering has previously been hampered by the inability to identify and characterize interspecific introgressions accurately.

METHODS

Seven monosomic substitution lines have been generated comprising Festuca pratensis as the donor species and Lolium perenne as the recipient. Each of the seven lines has a different L. perenne chromosome replaced by the homoeologous F. pratensis chromosome (13 L. perenne + 1 F. pratensis chromosome). Molecular markers and genomic in situ hybridization (GISH) were used to assign the F. pratensis chromosomes introgressed in each of the monosomic substitutions to a specific linkage group. Cytological observations were also carried out on metaphase I of meiosis in each of the substitution lines.

RESULTS

A significant level of synteny was found at the macro-level between L. perenne and F. pratensis. The observations at metaphase I revealed the presence of a low level of interspecific chromosomal translocations between these species.

DISCUSSION

The isolation of the seven monosomic substitution lines provides a resource for dissecting the genetic control of important traits and for gene isolation. Parallels between the L. perenne/F. pratensis system and the Pooideae cereals such as wheat, barley, rye, oats and the model grass Brachypodium distachyon present opportunities for a comparison across the species in terms of genotype and phenotype.

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.

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.

Chromosomal rearrangements in wheat: their types and distribution

Four hundred and sixty polyploid wheat accessions and 39 triticale forms from 37 countries of Europe, Asia, and USA were scored by C-banding for the presence of translocations. Chromosomal rearrangements were detected in 70 of 208 accessions of tetraploid wheat, 69 of 252 accessions of hexaploid wheat, and 3 of 39 triticale forms. Altogether, 58 types of major chromosomal rearrangements were identified in the studied material; they are discussed relative to 11 additional translocation types described by other authors. Six chromosome modifications of unknown origin were also observed. Among all chromosomal aberrations identified in wheat, single translocations were the most frequent type (39), followed by multiple rearrangements (9 types), pericentric inversions (9 types), and paracentric inversions (3 types). According to C-banding analyses, the breakpoints were located at or near the centromere in 60 rearranged chromosomes, while in 52 cases they were in interstitial chromosome regions. In the latter case, translocation breakpoints were often located at the border of C-bands and the euchromatin region or between two adjacent C-bands; some of these regions seem to be translocation "hotspots". Our results and data published by other authors indicate that the B-genome chromosomes are involved in translocations most frequently, followed by the A- and D-genome chromosomes; individual chromosomes also differ in the frequencies of translocations. Most translocations were detected in 1 or 2 accessions, and only 11 variants showed relatively high frequencies or were detected in wheat varieties of different origins or from different species. High frequencies of some translocations with a very restricted distribution could be due to a "bottleneck effect". Other types seem to occur independently and their broad distribution can result from selective advantages of rearranged genotypes in diverse environmental conditions. We found significant geographic variation in the spectra and frequencies of translocation in wheat: the highest proportions of rearranged genotypes were found in Central Asia, the Middle East, Northern Africa, and France. A low proportion of aberrant genotypes was characteristic of tetraploid wheat from Transcaucasia and hexaploid wheat from Middle Asia and Eastern Europe.

CAPS markers specific to Eb, Ee, and R genomes in the tribe Triticeae

Wild Triticeae grasses serve as important gene pools for forage and cereal crops. Understanding their genome compositions is pivotal for efficient use of this vast gene pool in germplasm-enhancement programs. Several cleaved amplified polymorphic sequence (CAPS) markers were developed to distinguish the Eb, Ee, and R genomes. With the aid of disomic addition lines of wheat, it was confirmed that all 7 chromosomes of Eb, Ee, and R genomes carry these genome-specific CAPS markers. Thus, the identified CAPS markers are useful in detecting and monitoring the chromosomes of these 3 genomes. This study also provides evidence suggesting that some Purdue and Chinese germplasm lines developed for barley yellow dwarf virus (BYDV) resistance are different from those developed in Australia. Furthermore, Thinopyrum intermedium and Thinopyrum ponticum were shown to have different genome constitutions. Sequence analyses of the 1272 bp sequences, containing Ty3/gypsy retrotransposons, from the Eb, Ee, and R genomes also shed light on the evolution of these 3 genomes.

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.

Transfer of resistance to potato virus Y (PVY) from Nicotiana africana to Nicotiana tabacum: possible influence of tissue culture on the rate of introgression

A disomic chromosome addition line of tobacco, Nicotiana tabacum L., was established previously that possesses a single chromosome pair from N. africana [Merxm. and Buttler]. This addition chromosome carries a gene that confers increased resistance to severe strains of potato virus Y (PVY). Methods to increase the probability of gene transfer from alien chromosomes to tobacco (2n=48) are desired. In the research described here, the PVY resistance gene was transferred to a tobacco chromosome from the N. africana addition chromosome in seven independent cases. One introgression event was obtained using conventional backcrossing of the disomic addition line to N. tabacum cv. Petite Havana, while the remaining six events were obtained using a scheme that involved exposure of explants of the addition line to tissue culture. Twenty-six derived 2n=48 individuals heterozygous for PVY resistance were found to exhibit 24 bivalents or 23 bivalents + 2 univalents at metaphase I. Ovular transmission rates for the PVY resistance factor ranged from 25% to 52%, while pollen transmission rates were much lower, ranging from 0 to 39%. Fifty-one random amplified polymorphic DNA (RAPD) markers specific for the intact addition chromosome were identified and used to characterize derived 2n=48/PVY-resistant genotypes. Variability was observed among these plants with respect to the total number of N. africana RAPD markers that were present, which is an indication that crossing over was occurring within each of the seven introgressed chromosome segments. A limited molecular marker-assisted backcrossing experiment allowed for selection of a 2n=48/PVY-resistant individual that possessed only 6 of the 51 original N. africana RAPD markers. In vitro culture is potentially a valuable system for increasing the rate of alien gene transfer in tobacco, and the successful transfer of PVY resistance from N. africana may allow for an increased level and range of resistance to this virus in tobacco.

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.

Isolation of a chromosomally engineered durum wheat line carrying the Aegilops ventricosa Pch1 gene for resistance to eyespot

The chromosome 7Dv of Aegilops ventricosa (syn. Triticum ventricosum, 2n = 4x = 28, genome DvDvMvMv) carries the gene Pch1 for resistance to eyespot. This gene has previously been transferred to chromosome 7D of bread wheat, T. aestivum (2n = 6x = 42, genome AABBDD). To (1) enhance the level of resistance of bread wheat by increasing the copy number of Pch1, and (2) create eyespot-resistant triticales, meiotically stable Pch1-carrying durum lines were selected from the backcross progenies of a cross between Ae. ventricosa and T. durum cv. Creso ph1c (2n = 4x = 28, genome AABB). The Pch1 transfer, likely resulting from homoeologous recombination, was located at the distal position on the long arm of chromosome 7A. The 7A microsatellite marker Xgwm 698 was found closely linked in repulsion to the introgression in the resistant recombination lines, and the endopeptidase allele located on chromosome 7A of cv. Creso ph1c was lost.Key words: eyespot, introgression, homoeologous recombination, mapping, wheat.

Characterization of euploid backcross progenies derived from interspecific hybrids between Oryza sativa and O. eichingeri by restriction fragment length polymorphism (RFLP) analysis and genomic in situ hybridization (GISH)

Restriction fragment length polymorphism (RFLP) analysis and GISH (genomic in situ hybridization) were performed on euploid plants derived from crosses between Oryza sativa (2n = 24, AA) and two brown planthopper-resistant accessions of O. eichingeri (2n = 24, CC). After screening with 164 RFLP markers, 60 of the 67 euploid plants were identified as introgression lines, each carrying 1–6 small O. eichingeri segments integrated on chromosomes 1, 2, 6, or 10. In the somatic chromosome preparations of F1 hybrid, O. eichingeri chromosomes, fluorescing greenish-yellow in the sequential GISH, appeared to be longer and to contain more heterochromatin than O. sativa ones, and this karyotypic polymorphism can be used to detect some introgressed O. eichingeri segments in euploid plants. In addition, GISH identification presented direct evidence for the transfer of small segments from O. eichingeri to O. sativa chromosome(s) which were subsequently recognized according to their condensation pattern, arm ratio, and chromosome length. The present results would contribute to the molecular mapping and selection of O. eichingeri - derived brown planthopper-resistant gene and positive yield QTLs.Key words: Oryza sativa, Oryza eichingeri, introgression lines, RFLP, genomic in situ hybridization (GISH).

Expression of Thinopyrum intermedium-Derived Barley yellow dwarf virus Resistance in Elite Bread Wheat Backgrounds

ABSTRACT Resistance to Barley yellow dwarf virus (BYDV) is not found in wheat but is available in a Thinopyrum intermedium translocation (Ti) carried on chromosome 7DL of bread wheat recombinant lines. We used one of those lines (TC14/2*Spear) to introgress the Ti into bread wheat cultivars and to determine the influence of wheat backgrounds, with and without known tolerance to BYDV, on the expression of resistance. Two single and three backcross populations, segregating for the presence of the alien fragment, were tested under field conditions and artificial inoculation with BYDV isolates MAV-Mex and PAV-Mex. Lines containing the fragment were identified using the microsatellite marker gwm37. Tillering, biomass, grain yield, thousand-kernel weight, and seed quality were evaluated in inoculated and noninoculated plots. Resistance was assessed by enzyme-linked immunosorbent assay. In early generations, the alien fragment followed expected Mendelian segregation, whereas in the advanced ones a slight bias against its transmission was observed. No positive nor negative effects of Ti on agronomic performance and quality were found. A significant optical density reduction in individuals carrying the fragment was observed after PAV infection in crosses with lines Anza and Baviacora but not with Milan. In addition, the fragment was associated with a lower frequency of infected plants for both PAV and MAV isolates. The reduced yield loss associated with the presence of the translocation was due largely to the lower infection rate.

Molecular cytogenetic analysis of intergeneric chromosomal translocations between wheat (Triticum aestivum L.) and Dasypyrum villosum arising from tissue culture

Fluorescence in situ hybridization (FISH) was applied with total genomic DNA extracted from Dasypyrum villosum (L.) Candargy as a probe to characterize chromosome translocations arising from tissue culture in hybrids of Triticum aestivum x (T. durum - D. villosum, amphiploid). Chromosome translocations between wheat and D. villosum occurred in callus cells at an average frequency of 1.9%. Translocations existed not only in callus cells but also in regenerants. Three plants with translocation chromosomes were characterized among 66 regenerants of T. aestivum 'Chinese Spring' x 'TH1W' and 'NPFP' x 'TH1'. One of them proved to be a reciprocal translocation with an exchange of about one third of a wheat chromosome arm with about one half of a chromosome arm of D. villosum. The breakpoints of the other two translocations were located at, or near centromeres. The results are similar for both callus cells and regenerants and provide further evidence that translocations take place in tissue culture. Other structural chromosomal changes, for example, fragments, telocentrics, dicentromeres, and deletions, as well as numerical alterations including aneuploidy and polyploidy were recorded both in callus cells and regenerants.

Identification and characterization of wheat-wheatgrass translocation lines and localization of barley yellow dwarf virus resistance

Stable introgression of agronomically important traits into crop plants through wide crossing often requires the generation and identification of translocation lines. However, the low efficiency of identifying lines containing translocations is a significant limitation in utilizing valuable alien chromatin-derived traits. Selection of putative wheatgrass-wheat translocation lines based on segregation ratios of progeny from γ-irradiated seed using a standard phenotypic analysis resulted in a low 4% success rate of identifying barley yellow dwarf virus (BYDV) resistant and susceptible translocation lines. However, 58% of the susceptible progeny of this irradiated seed contained a Thinopyrum intermedium chromosome-specific repetitive sequence, which indicated that γ-irradiation-induced translocations occurred at high rate. Restriction fragment length polymorphism (RFLP) analysis of susceptible lines containing alien chromatin, their resistant sister lines and other resistant lines showed that more than one third of the progeny of γ-irradiated double monosomic seeds contained wheatgrass-wheat translocations. Genomic in situ hybridization (GISH) analysis of selected lines confirmed that these were wheatgrass-wheat translocation lines. This approach of initially identifying BYDV susceptible deletion lines using an alien chromosome-specific repetitive sequence followed by RFLP analysis of their resistant sister lines efficiently identified resistant translocation lines and localized the BYDV resistance to the distal end of the introgressed Th. intermedium chromosome.Key words: gene introgression, wide crosses, chromosome, repetitive elements, RFLP, Thinopyrum intermedium.

Chromosome-mediated and direct gene transfers in wheat

Wild grasses, including relatives of wheat, have several desirable characters that can be introduced into both bread wheat and durum wheat. Since current wheat cultivars lack certain traits, for example, resistance to fusarium head blight (scab), related wild grasses may be the only option for useful variability. Wide hybridization of wheat with grasses, coupled with cytogenetic manipulation of the hybrid material, has been instrumental in the genetic improvement of wheat. Chromosome engineering methodologies, based on the manipulation of pairing control mechanisms and induced translocations, have been employed to transfer into wheat specific disease and pest resistance genes from annual (e.g., rye) or perennial (e.g., Thinopyrum spp., Lophopyrum spp., and Agropyron spp.) members of the wheat tribe, Triticeae. The advent of in situ hybridization techniques, for example, fluorescent GISH combined with Giemsa C-banding, has proved immensely useful in characterizing alien chromatin specifying resistance to various pathogens and pests. The use of DNA markers (RAPDs and RFLPs) helps to identify desirable genotypes more precisely and, thereby, facilitates gene transfer into wheat. Such markers may be particularly helpful in monitoring the introgression of alien genes in the wheat genome. In fact, several cultivars, particularly of bread wheat, contain superior traits of alien origin. The development of novel gene-transfer techniques in the past decade that allow direct delivery of DNA into regenerable embryogenic callus of wheat has opened up new avenues of alien-gene transfer into wheat cultivars. Thus, transgenic bread and durum wheats have been produced and methods of gene delivery standardized. The application of transgenic technology has not only yielded herbicide-resistant wheats, but has also helped to improve grain quality by modifying the protein and starch profiles of the grain. These in vitro approaches to gene transfer are developing rapidly, and promise to become an integral part of plant breeding efforts. However, the new biotechnological tools will complement, not replace, conventional plant breeding.Key words: alien-gene transfer, fluorescent GISH, Giemsa banding, homoeologous chromosome pairing, molecular markers, transgenic bread wheat, transgenic durum wheat.

Molecular aids for integration of alien chromatin through wide crosses

Wide crosses in wheat have now been performed for over 100 years. In that time, approximately 100 genes have been transferred for numerous traits, including biotic and abiotic stresses and value-added traits. Resistance genes from alien sources do become defeated with time, so the search for additional variability must continue. Recent screening of alien species has identified accessions with multiple pest resistance plus combinations of pest resistance and value-added traits. The majority of existing induced recombinants are of a noncompensating type with considerable linkage drag, so sequential useage of Ph mutants is recommended to produce smaller interstitial recombinants. Molecular methods, including GISH, RAPD, RFLP, AFLP, and microsatellites, are being widely used to identify integrated alien chromosomes, chromosome segments, and genes.Key words: Triticum aestivium, molecular markers, disease resistance, gene introgression, interspecific hybrids.

Characterization of wheatgrass-derived barley yellow dwarf virus resistance in a wheat alien chromosome substitution line

ABSTRACT Wheatgrass (Thinopyrum intermedium) possesses a high level of resistance to barley yellow dwarf virus (BYDV) subgroup I and subgroup II strains. A wheat line (P29), in which the 7D chromosome has been substituted with a group 7 chromosome from T. intermedium, was examined for the level of resistance to two subgroup I and two subgroup II BYDV strains. In P29 plants inoculated with the subgroup I PAV strains, the titer of virus in leaf and stem tissue was typically reduced 42 to 52% when compared with the BYDV-susceptible cv. Abe. P29 and 'Abe' had the same content of PAV in roots. These results and the absence of detectable virus in inoculated T. intermedium plants indicate that the complete resistance to subgroup I possessed by the wheatgrass has not been introgressed into P29. In contrast, P29 was completely resistant throughout the plant to the subgroup II strains, NY-RPV and NY-RMV, demonstrating that the complete resistance to subgroup II in T. intermedium was incorporated into P29. Further analysis of this resistance to NY-RPV showed that NY-RPV can replicate in mesophyll protoplasts of P29 and 'Abe', suggesting that this resistance is not operating at the single-cell level. Molecular marker analysis confirmed that the T. intermedium chromosome present in P29 is a different group 7 wheatgrass chromosome than that present in L1, a wheat line with BYDV resistance properties similar to those of P29.

Characterization of the translocated chromosome using fluorescence in situ hybridization and random amplified polymorphic DNA on two Triticum aestivum-Thinopyrum intermedium translocation lines resistant to wheat streak mosaic or barley yellow dwarf virus

Fluorescence in situ hybridization (FISH) was used to determine the breakpoint of the translocation chromosome in two bread wheat (Triticum aestivum) germplasm lines with Thinopyrum intermedium chromatin carrying resistance to either wheat streak mosaic virus (WSMV) or barley yellow dwarf virus (BYDV). In addition, genome-specific random amplified polymorphic DNA (RAPD) markers were used to ascertain the genomic sources of the Th. intermedium chromosome carrying the WSMV or BYDV resistance. CI17766, a WSMV-resistant wheat germplasm line derived from induced homoeologous pairing by using the ph1b mutant, had a translocation chromosome composed of the complete 4AL and about 45% of proximal 4AS from wheat, and the entire 4ES of Th. intermedium. The BYDV-resistant translocation line, TC14, derived from tissue culture, had a very short distal segment of 7StL from Th. intermedium terminally attached to 56% of the proximal 7DL. These observations indicate that translocations in these wheat germplasm lines did not involve centromeric breaks and fusion but were a result of homoeologous chromosomes recombination.