Efficient production of wheat-barley hybrids and preferential elimination of barley chromosomes

Genome-Wide Association Study of Host Resistance to Hessian Fly in Barley

The Hessian fly (HF), Mayetiola destructor (Diptera: Cecidomyiidae), is one of the most devastating insect pests of cereals including wheat, barley, and rye. Although wheat is the preferred host for HF, this continuously evolving pest has been emerging as a threat to barley production. However, characterization and identification of genetic resistance to HF has not been conducted in barley. In the present study, we used a genome-wide association study (GWAS) to identify barley resistance loci to HF using a geographically diverse set of 234 barley accessions. The results showed that around 90% of barley lines were highly susceptible, indicating a significant vulnerability to HF in barley, and a total of 29 accessions were resistant, serving as potential resistance resources. GWAS with a mixed linear model revealed two marker-trait associations, both on chromosome 4H. The resistance loci and associated markers will facilitate barley improvement and development for breeders. In addition, our results are fundamental for genetic studies to understand the HF resistance mechanism in barley.

Rapid and cost-effective molecular karyotyping in wheat, barley, and their cross-progeny by chromosome-specific multiplex PCR

BACKGROUND

Interspecific hybridisation is a powerful tool for increasing genetic diversity in plant breeding programmes. Hexaploid wheat (Triticum aestivum, 2n = 42) × barley (Hordeum vulgare, 2n = 14) intergeneric hybrids can contribute to the transfer of agronomically useful traits by creating chromosome addition or translocation lines as well as full hybrids. Information on the karyotype of hybrid progenies possessing various combinations of wheat and barley chromosomes is thus essential for the subsequent breeding steps. Since the standard technique of chromosome in situ hybridisation is labour-intensive and requires specific skills. a routine, cost-efficient, and technically less demanding approach is beneficial both for research and breeding.

RESULTS

We developed a Multiplex Polymerase Chain Reaction (MPCR) method to identify individual wheat and barley chromosomes. Chromosome-specific primer pairs were designed based on the whole genome sequences of 'Chinese Spring' wheat and 'Golden Promise' barley as reference cultivars. A pool of potential primers was generated by applying a 20-nucleotide sliding window with consecutive one-nucleotide shifts on the reference genomes. After filtering for optimal primer properties and defined amplicon sizes to produce an ordered ladder-like pattern, the primer pool was manually curated and sorted into four MPCR primer sets for the wheat A, B, and D sub-genomes, and for the barley genome. The designed MPCR primer sets showed high chromosome specificity in silico for the genome sequences of all 18 wheat and barley cultivars tested. The MPCR primers proved experimentally also chromosome-specific for the reference cultivars as well as for 13 additional wheat and four barley genotypes. Analyses of 16 wheat × barley F1 hybrid plants demonstrated that the MPCR primer sets enable the fast and one-step detection of all wheat and barley chromosomes. Finally, the established genotyping system was fully corroborated with the standard genomic in situ hybridisation (GISH) technique.

CONCLUSIONS

Wheat and barley chromosome-specific MPCR offers a fast, labour-friendly, and versatile alternative to molecular cytogenetic detection of individual chromosomes. This method is also suitable for the high-throughput analysis of distinct (sub)genomes, and, in contrast to GISH, can be performed with any tissue type. The designed primer sets proved to be highly chromosome-specific over a wide range of wheat and barley genotypes as well as in wheat × barley hybrids. The described primer design strategy can be extended to many species with precise genome sequence information.

Composition and random elimination of paternal chromosomes in a large population of wheat × barley (Triticum aestivum L. × Hordeum vulgare L.) hybrids

Statistical analysis of the chromosomal composition in a population of 210 primary plants regenerated from two intergeneric wheat-barley cross combinations revealed the random nature of uniparental elimination for barley chromosomes. Uniparental chromosome elimination is a common process in interspecific and intergeneric cereal hybrids. To characterize the frequency of paternal chromosomes, a population of 218 independent green plants was generated from two wheat (♀) × barley (♂) cross combinations via embryo rescue. The chromosomal composition of 210 primary plants was analyzed with chromosome-specific DNA markers representing all seven barley chromosomes. The analysis revealed an equal proportion of haploid and full hybrids (20.5% and 19.5%, respectively), while the rest of the population contained hypoploids (partial hybrids) with no preference for any possible numbers (one to six) of barley chromosome additions. Contrary to the previous reports, there was no statistical bias or preferential elimination for any individual barley chromosome (1H-7H) in this population. The reasons for the apparent contradiction and the implications of the above findings for cereal breeding are discussed.

Molecular cytogenetic and morphological characterization of two wheat-barley translocation lines

Barley chromosome 5H, carrying important QTLs for plant adaptation and tolerance to abiotic stresses, is extremely instable in the wheat genetic background and is eliminated in the early generations of wheat-barley crosses. A spontaneous wheat-barley 5HS-7DS.7DL translocation was previously obtained among the progenies of the Mv9kr1 x Igri hybrid. The present work reports on the transfer of the 5HS-7DS.7DL translocation into a modern wheat cultivar, Mv Bodri, in order to use it in the wheat breeding program. The comparison of the hybridization bands of DNA repeats HvT01, pTa71, (GAA)n and the barley centromere-specific (AGGGAG)n in Igri barley and the 5HS-7DS.7DL translocation, together with the visualization of the barley chromatin made it possible to determine the size of the introgressed barley segment, which was approximately 74% of the whole 5HS. Of the 29 newly developed PCR markers, whose source ESTs were selected from the Genome Zipper of barley chromosome 5H, 23 were mapped in the introgressed 1-0.26 FL 5HS bin, three were located in the missing C-0.26 FL region, while three markers were specific for 5HL. The translocation breakpoint was flanked by markers Hv7502 and Hv3949. A comparison of the parental wheat cultivars and the wheat-barley introgression lines indicated that the presence of the translocation improved tillering ability in the Mv9kr1 and Mv Bodri genetic background. The similar or better yield components under high- or low-input cultivation environments, respectively, indicated that the 5HS-7DS.7DL translocation had little or no negative effect on yield components, making it a promising genotype to improve wheat genetic diversity. These results promise to accelerate functional genomic studies on barley chromosome 5H and to support pre-breeding and breeding research on wheat.

High-frequency generation and characterization of intergeneric hybrids and haploids from new wheat-barley crosses

Hybrid plants and a high frequency of maternal haploids were obtained using an efficient wheat-barley hybridization system (with new genotype combinations) and confirmed by several cytological and molecular tools. An efficient hybridization system between wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) is presented on the basis of three new genotype combinations. A particularly high, 14% frequency of plant regeneration per florets was achieved in the wheat-barley genotype combination of 'Sichuan' × 'Morex'. The genome composition in 42 of the 95 plants regenerated by embryo rescue was determined using ploidy analysis, genomic in situ hybridization and the application of chromosome arm-specific molecular markers (SSR and STS). A high overall frequency (76%) of maternal (wheat) haploids was observed in all the tests for all three cross combinations. A major implication of this observation is that this new hybridization system represents a useful tool to study the mechanism of uniparental chromosome elimination in cereals.

Random chromosome elimination in synthetic Triticum-Aegilops amphiploids leads to development of a stable partial amphiploid with high grain micro- and macronutrient content and powdery mildew resistance

Synthetic amphiploids are the immortal sources for studies on crop evolution, genome dissection, and introgression of useful variability from related species. Cytological analysis of synthetic decaploid wheat (Triticum aestivum L.) - Aegilops kotschyi Boiss. amphiploids (AABBDDUkUkSkSk) showed some univalents from the C1 generation onward followed by chromosome elimination. Most of the univalents came to metaphase I plate after the reductional division of paired chromosomes and underwent equational division leading to their elimination through laggards and micronuclei. Substantial variation in the chromosome number of pollen mother cells from different tillers, spikelets, and anthers of some plants also indicated somatic chromosome elimination. Genomic in situ hybridization, fluorescence in situ hybridization, and simple sequence repeat markers analysis of two amphiploids with reduced chromosomes indicated random chromosome elimination of various genomes with higher sensitivity of D followed by the Sk and Uk genomes to elimination, whereas 1D chromosome was preferentially eliminated in both the amphiploids investigated. One of the partial amphiploids, C4 T. aestivum 'Chinese Spring' - Ae. kotschyi 396 (2n = 58), with 34 T. aestivum, 14 Uk, and 10 Sk had stable meiosis and high fertility. The partial amphiploids with white glumes, bold seeds, and tough rachis with high grain macro- and micronutrients and resistance to powdery mildew could be used for T. aestivum biofortification and transfer of powdery mildew resistance.

Identification of new winter wheat – winter barley addition lines (6HS and 7H) using fluorescence in situ hybridization and the stability of the whole ‘Martonvásári 9 kr1’ – ‘Igri’ addition set

A previous paper reported the development of disomic addition lines (2H, 3H, 4H, and 1HS isochromosomic) from hybrids between the winter wheat ‘Martonvásári 9 kr1’ and the two-rowed winter barley cultivar ‘Igri’. The present paper describes the isolation of two new additions, the 7H disomic and 6HS ditelosomic additions, using fluorescence in situ hybridization with the repetitive DNA probes Afa-family and HvT01. The identification of the barley chromosomes in the wheat genome was confirmed with simple sequence repeat markers. The morphological characterization of the new addition lines is also discussed. Studies of the genetic stability of the whole set (2H, 3H, 4H, 7H, 1HS iso, 6HS) of ‘Martonvásári 9 kr1’ – ‘Igri’ additions revealed that the most stable disomic additions are 2H and 3H and the most unstable line is the 1HS isochromosomic addition.

Development and molecular cytogenetic identification of new winter wheat--winter barley ('Martonvásári 9 kr1' - 'Igri') disomic addition lines

This paper describes a series of winter wheat - winter barley disomic addition lines developed from hybrids between winter wheat line Triticum aestivum L. 'Martonvásári 9 kr1' and the German 2-rowed winter barley cultivar Hordeum vulgare L. 'Igri'. The barley chromosomes in a wheat background were identified from the fluorescent in situ hybridization (FISH) patterns obtained with various combinations of repetitive DNA probes: GAA-HvT01 and pTa71-HvT01. The disomic addition lines 2H, 3H, and 4H and the 1HS isochromosome were identified on the basis of a 2-colour FISH with the DNA probe pairs GAA-pAs1, GAA-HvT01, and pTa71-HvT01. Genomic in situ hybridization was used to confirm the presence of the barley chromosomes in the wheat genome. The identification of the barley chromosomes in the addition lines was further confirmed with simple-sequence repeat markers. The addition lines were also characterized morphologically.

Frequency and fidelity of alien chromosome transmission inGossypiumhexaploid bridging populations

The Australian diploid Gossypium species possess traits of potential agronomical value, such as gossypol-free seeds and Fusarium wilt resistance. However, they belong to the tertiary germplasm pool, which is the most difficult group of species from which to introgress genes into G. barbadense L. and G. hirsutum L. Interspecific triploid hybrids can be generated but they are sterile. The sterility barrier can be overcome using synthetic polyploids as introgression bridges, but whether there is sufficient homoeologous chromosome interaction at meiosis to allow recombination is still an open question. To ascertain, genetically, observable levels of homoeologous introgression, 2 synthetic hexaploid lines (2x G. hirsutum × G. australe and 2x G. hirsutum × G. sturtianum) were crossed to G. hirsutum to generate pentaploid F1plants that, in turn, were backcrossed to G. hirsutum to generate BC1and BC2multiple alien chromosome addition lines (MACALs). Gossypium australe F. Muell. and G. sturtianum Willis chromosome-specific markers were used to track the frequency and fidelity of chromosome transmission to the BC1and BC2MACALs. The chromosomal location of the AFLP markers was determined by their distribution among the MACALs and confirmed in parental F2families. Roughly half the available chromosomes were transmitted to the G. hirsutum × G. australe (54%) and G. hirsutum × G. sturtianum (52%) BC1MACALs. The BC2MACAL families again inherited about half of the available chromosomes. There were, however, notable exceptions for specific chromosomes. Some chromosomes were preferentially eliminated, while others were preferentially transmitted. Consistent with the genomic stability of Gossypium synthetic polyploids, the de novo loss or gain of AFLP fragments was rarely observed. While restructuring of the donor G. australe and G. sturtianum chromosomes was observed, this is more likely the result of chromatin loss, and no clear cases of introgression of donor chromatin into the recipient G. hirsutum genome were observed.

Mitotic instability in wheat x Thinopyrum ponticum derivatives revealed by chromosome counting, nuclear DNA content and histone H3 phosphorylation pattern

To evaluate the mitotic stability of Triticum aestivum x Thinopyrum ponticum derivatives (BC(2)F(7) and BC(2)F(5) doubled haploids), chromosome counting by both conventional and immunostaining techniques, and measurement of DNA content were performed. The wheat progenitor line, PF 839197, the wheat recurrent parent CEP 19 and the control Chinese Spring were also investigated. In the hybrid derivatives, chromosome number ranged from 2n=36 to 60, with a predominance of chromosome numbers higher than 2n=42, that was confirmed by determination of nuclear DNA content. Chinese Spring' and PF 839197 were stable, but CEP 19 showed chromosome number variation (20%). Analyses of non-pretreated cells revealed the presence of anaphase bridges, lagging chromatids, chromosome fragments and micronuclei. Immunostaining with an antibody recognizing histone H3 phosphorylated showed dicentric chromatids forming anaphase bridges and pericentromeric phosphorylation at centric chromosome fragments but not at lagging chromatids. The possible causes of the observed mitotic instability are discussed.

Molecular cytogenetic analysis of wheat-barley hybrids using genomic in situ hybridization and barley microsatellite markers

In the present investigation, genomic in situ hybridization (GISH) and barley microsatellite markers were used to analyse the genome constitution of wheat-barley hybrids from two backcross generations (BC1 and BC2). Two BC1 plants carried 3 and 6 barley chromosomes, respectively, according to GISH data. Additional chromosomal fragments were detected using microsatellites. Five BC2 plants possessed complete barley chromosomes or chromosome segments and six BC2 plants did not preserve barley genetic material. Molecular markers revealed segments of the barley genome with the size of one marker only, which probably resulted from recombination between wheat and barley chromosomes. The screening of backcrossed populations from intergeneric hybrids could be effectively conducted using both genomic in situ hybridization and molecular microsatellite markers. GISH images presented a general overview of the genome constitution of the hybrid plants, while microsatellite analysis revealed the genetic identity of the alien chromosomes and chromosomal segments introgressed. These methods were complementary and provided comprehensive information about the genomic constitution of the plants produced.

Molecular and physical mapping of a barley gene on chromosome arm 1 HL that causes sterility in hybrids with wheat

Addition of the long arm of barley chromosome 1H (1HL) to wheat causes severe meiotic abnormalities and complete sterility of the plants. To map the barley gene responsible for the 1H-induced sterility of wheat, a series of addition lines of translocated 1H chromosomes were developed from the crosses between the wheat 'Shinchunaga' and five reciprocal translocation lines derived from the barley line St.13559. Examination of the seed fertility of the addition lines revealed that the sterility gene is located in the interstitial 25% region of the 1HL arm. The genetic location of the sterility gene was also estimated by physically mapping sequence-tagged site (STS) markers and simple-sequence repeat (SSR) markers with known map locations. The sterility gene is designated Shw (sterility in hybrids with wheat). Comparison of the present physical map of 1HL with two previously published genetic maps revealed a paucity of markers in the proximal 30% region and non-random distribution of SSR markers. Two inconsistencies in marker order were found between the present physical map and the consensus genetic map of group 1 chromosomes of Triticeae. On the basis of the effects on meiosis and chromosomal location, the relationship of the present sterility gene with other fertility-related genes of Triticeae is discussed.

Compensating ability in pollen fertilization between group-6 and -7 homoeologous chromosomes of barley and wheat

By using alpha-amylase isozymes as markers for chromosomes of homoeologous groups 6 and 7, we analyzed the segregation of chromosome constitution in the progenies from crosses between double-ditelosomic or ditelosomic lines of hexaploid wheat cultivar 'Chinese Spring' (CS) as the female parent and double-monosomic F1 hybrids of CS x wheat-barley substitution lines for barley chromosomes 6H or 7H. From this analysis we estimated the transmission rate via pollen of barley chromosomes 6H and 7H in the double-monosomics and evaluated the compensating ability between barley and wheat chromosomes in homoeologous groups 6 and 7. The results indicated that both 6H and 7H showed their highest compensating ability for their respective homoeologous wheat chromosomes 6A (37.5% transmission rate) and 7A (39.4%), intermediate for 6D (34.1%) and 7D (29.6%), and lowest for 6B (26.6%) and 7B (22.6%) chromosomes.

Use of meiotic FISH for identification of a new monosome in Gossypium hirsutum L

The extensive use of molecular cytogenetics in human genetics and clinical diagnostics indicates that analogous applications in plants are highly feasible. One sort of application would be the identification of new aneuploids, which traditionally involves either direct karyotypic identification, which is feasible in only a few plant species, or tests with markers (cytogenetic, genetic, or molecular), which require sexual hybridization and at least one subsequent seed or plant generation. We have used meiotic fluorescence in situ hybridization (FISH) to analyze a new monosome of cotton (Gossypium hirsutum L., 2n = 4x = 52, 2(AD)1) that had a phenotype which seemed to be distinct from monosomes in the Cotton Cytogenetic Collection. Painting with A2-genome DNA revealed the monosome's D-subgenome origin. DAPI-PI staining showed that the monosome carries a major NOR, delimiting it to the major NOR-bearing chromosomes of the D-subgenome, i.e., 16 or 23. Dual-color FISH with 5S and 18S-28S rDNAs indicated that the monosome contains separate major clusters of each of these two tandemly repeated rDNA elements, thus delimiting the monosome to chromosome 23, for which the Cotton Cytogenetic Collection has previously been devoid of any sort of deficiency. Of the 26 chromosomes in the cotton genome, the Collection now provides coverage for 16 (70%) in the form of monosomy, and 20 (77%) in the form of monosomy and (or) telosomy. Use of molecular cytogenetic methods to identify a new plant aneuploid in cotton exemplifies the fact that a physicochemical karyotypic chromosome identification system is not required a priori for application of new molecular cytogenetic methods, thus indicating their potential applicability to nearly all plant species.

High crossability of wild barley (Hordeum spontaneum C. Koch) with bread wheat and the differential elimination of barley chromosomes in the hybrids

Four bread wheat (Triticum aestivum L.) cultivars, 'Aobakomugi', 'Chinese Spring', 'Norin 61' and 'Shinchunaga', were pollinated with five barley lines/cultivars consisting of three cultivated barley (Hordeum vulgare L.) lines, 'Betzes', 'Kinai 5' and OHL089, and two wild barley (Hordeum spontaneum C. Koch) lines, OUH602 and OUH324. Crossability, expressed as the percentage of embryo formation, varied from 0 to 55.4% among the cross combinations. The two wild barley lines generally had a higher crossability than the previously reported best pollinator, 'Betzes', and some Japanese wheat cultivars were better as the female parent than 'Chinese Spring'. Ninety four hybrid plants were obtained from 250 embryos cultured, and their somatic chromosome numbers ranged from 21 to 36. Eighteen plants were mosaic in chromosome number. Twenty one-chromosome plants appeared most frequently (45.7%) followed by 28-chromosome plants (14.9%). C-banding analysis revealed that elimination of barley chromosomes was mainly responsible for the occurrence of aneuploid plants. In hypoploids derived from 'Betzes'-crosses, chromosome 5 was preferentially eliminated as previously reported, while in hypoploids derived from OUH602-crosses, chromosome 4 was preferentially eliminated. The wild barley line OUH602 may be a useful parent for producing a new wheat-barley addition set because of its high crossability with wheat and a different pattern of chromosome elimination.

Morphological and cytological characteristics of some wheat x barley hybrids

As initial step in the transfer of dwarf bunt resistance from barley into wheat, the two cereal crops were hybridized. Using the wheat cultivars 'Fukuhokomugi' and 'Chinese Spring' (AABBDD genomes) as female parents and barley cultivar 'Luther' (II genome) as male, we synthesized 9 euploid hybrids (2n = 4x = 28; ABDI genomes). The hybrids were vigorous, but highly sterile. Meiotic analyses of seven hybrids showed considerable variation in chromosome pairing. Of the hybrids involving 'Fukuhokomugi' 3 had high pairing with a mean of 5.08-6.72 chiasmata per cell, while others had 2.16-3.52 chiasmata per cell. As many as 12 bivalents in some pollen mother cells would suggest at least some pairing between wheat and barley chromosomes. This level of homoeologous pairing, coupled with some, albeit low, female fertility of the F1 hybrids, could offer an opportunity for intergeneric gene transfers from barley into wheat and vice versa.