Dissection and cytological mapping of barley chromosome 2H in the genetic background of common wheat

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.

Molecular identification of a laccase that catalyzes the oxidative coupling of a hydroxycinnamic acid amide for hordatine biosynthesis in barley

Plants produce dimerized phenolic compounds as secondary metabolites. Hordatine A (HA), a dehydrodimer of p-coumaroylagmatine (pCA), is an antifungal compound accumulated at high levels in young barley (Hordeum vulgare) seedlings. The enzyme responsible for the oxidative dimerization of pCA, which is the final step of the hordatine biosynthetic pathway, has not been identified. In this study, we first verified the presence of this enzyme activity in the crude extract of barley seedlings. Because the enzyme activity was not dependent on H2 O2 , the responsible enzyme was not peroxidase, which was previously implicated in HA biosynthesis. The analysis of the dissection lines of wheat (Triticum aestivum) carrying aberrant barley 2H chromosomes detected HA in the wheat lines carrying the distal part of the 2H short arm. This chromosomal region contains two laccase genes (HvLAC1 and HvLAC2) that are highly expressed at the seedling stage and may encode enzymes that oxidize pCA during the formation of HA. Changes in the HvLAC transcript levels coincided with the changes in the HA biosynthesis-related enzyme activities in the crude extract and the HA content in barley seedlings. Moreover, HvLAC genes were heterologously expressed in Nicotiana benthamiana leaves and in bamboo (Phyllostachys nigra) suspension cells and HA biosynthetic activities were detected in the crude extract of transformed N. benthamiana leaves and bamboo suspension cells. The HA formed by the enzymatic reaction had the same stereo-configuration as the naturally occurring HA. These results demonstrate that HvLAC enzymes mediate the oxidative coupling of pCA during HA biosynthesis.

Dissection and cytological mapping of chromosome arm 4VS by the development of wheat-Haynaldia villosa structural aberration library

A cytological map of Haynaldia villosa chromosome arm 4VS was constructed to facilitate the identification and utilization of beneficial genes on 4VS. Induction of wheat-alien chromosomal structure aberrations not only provides new germplasm for wheat improvement, but also allows assignment of favorable genes to define physical regions. Especially, the translocation or introgression lines carrying alien chromosomal fragments with different sizes are useful for breeding and alien gene mapping. Chromosome arm 4VS of Haynaldia villosa (L.) Schur (syn. Dasypyrum villosum (L.) P. Candargy) confers resistances to eyespot and wheat yellow mosaic virus (WYMV). In this research, we used both irradiation and the pairing homoeologous gene (Ph) mutant to induce chromosomal aberrations or translocations. By using the two approaches, a structural aberration library of chromosome arm 4VS was constructed. In this library, there are 57 homozygous structural aberrations, in which, 39 were induced by the Triticum aestivum cv. Chinese Spring (CS) ph1b mutant (CS ph1b) and 18 were induced by irradiation. The aberrations included four types, i.e., terminal translocation, interstitial translocation, deletion and complex structural aberration. The 4VS cytological map was constructed by amplification in the developed homozygous aberrations using 199 4VS-specific markers, which could be allocated into 39 bins on 4VS. These bins were further assigned to their corresponding physical regions of chromosome arm 4DS based on BLASTn search of the marker sequences against the reference sequence of Aegilops tauschii Cosson. The developed genetic stocks and cytological map provide genetic stocks for wheat breeding as well as alien gene tagging.

Physical mapping of Agropyron cristatum chromosome 6P using deletion lines in common wheat background

Genetically stable deletion lines of Agropyron cristatum chromosome 6P in common wheat background were generated, which allowed for physical mapping of 255 6P-specific STS markers and leaf rust resistance gene(s). Chromosomal deletion lines are valuable tools for gene discovery and localization. The chromosome 6P of Agropyron cristatum (2n = 4x = 28, PPPP) confers many desirable agronomic traits to common wheat, such as higher grain number per spike, multiple fertile tiller number, and enhanced resistance to certain diseases. Although many elite genes from A. cristatum have been identified, their chromosomal locations were largely undetermined due to the lack of A. cristatum 6P deletion lines. In this study, various A. cristatum 6P deletion lines were developed using a wheat-A. cristatum 6P disomic addition line 4844-12 subjected to (60)Co-γ irradiation as well as an Aegilops cylindrica gametocidal chromosome. Twenty-six genetically stable A. cristatum 6P deletion lines in the genetic background of common wheat were obtained, and their genetic constitutions were elucidated by genomic in situ hybridization (GISH) and sequence-tagged site (STS) markers specific to A. cristatum chromosome 6P. Moreover, 255 novel chromosome 6P-specific STS markers were physically mapped to 14 regions of chromosome 6P. Field evaluation of leaf rust resistance of various deletion lines and BC1F2 populations indicated that the A.cristatum chromosome 6P-originated leaf rust resistance gene(s) was located in the region 6PS-0.81-1.00. This study will provide not only useful tools for characterization and utilization of wheat materials with alien chromosomal segments, but also novel wheat germplasms potentially valuable in wheat breeding and improvement.

Dissection of barley chromosomes 1H and 6H by the gametocidal system

We dissected barley chromosomes 1H and 6H added to common wheat by the gametocidal system and identified structural changes of the chromosomes by fluorescence in situ hybridization and genomic in situ hybridization. We found five aberrations of chromosome 1H, all of which lacked the long arm: one small fragment with the subtelomeric HvT01 sequence, one terminal deletion, and three telocentric chromosomes of the short arm. We established 33 dissection lines carrying single aberrant 6H chromosomes, of which 15 were deletions, 16 were translocations and two were isochromosomes. We conducted PCR analysis of the aberrant barley chromosomes using 75 and 81 EST markers specific to chromosomes 1H and 6H, respectively. This enabled us to construct a cytological map of chromosome 6H and to compare it to the previously reported genetic map and also to the physical map, which were released by the International Barley Genome Sequencing Consortium. The marker orders on the three maps were largely in agreement. The cytological map had better resolution in the proximal region of chromosome 6H than the corresponding genetic map. We discuss some of the discrepancies in marker order between the three maps that might be due to intraspecific polymorphism and gene duplication, as well as to technical problems inherent in the physical mapping process.

Cytogenetic mapping with centromeric bacterial artificial chromosomes contigs shows that this recombination-poor region comprises more than half of barley chromosome 3H

Genetic maps are based on the frequency of recombination and often show different positions of molecular markers in comparison to physical maps, particularly in the centromere that is generally poor in meiotic recombinations. To decipher the position and order of DNA sequences genetically mapped to the centromere of barley (Hordeum vulgare) chromosome 3H, fluorescence in situ hybridization with mitotic metaphase and meiotic pachytene chromosomes was performed with 70 genomic single-copy probes derived from 65 fingerprinted bacterial artificial chromosomes (BAC) contigs genetically assigned to this recombination cold spot. The total physical distribution of the centromeric 5.5 cM bin of 3H comprises 58% of the mitotic metaphase chromosome length. Mitotic and meiotic chromatin of this recombination-poor region is preferentially marked by a heterochromatin-typical histone mark (H3K9me2), while recombination enriched subterminal chromosome regions are enriched in euchromatin-typical histone marks (H3K4me2, H3K4me3, H3K27me3) suggesting that the meiotic recombination rate could be influenced by the chromatin landscape.

Radiation Hybrid Map of Barley Chromosome 3H

Assembly of the barley (Hordeum vulgare L.) genome is complicated by its large size (5.1 Gb) and proportion of repetitive elements (84%). This process is facilitated by high resolution maps for aligning bacterial artificial chromosome (BAC) contigs along chromosomes. Available genetic maps, however, do not provide accurate information on the physical position of a large portion of the genome located in recombination-poor regions. Radiation hybrid (RH) mapping is an alternative approach, which is based on radiation-induced deletions along the length of chromosomes. In this study, the first RH map for barley chromosome 3H was developed. In total, 373 in vivo RH lines were generated by irradiating wheat (Triticum aestivum L.)-barley chromosome 3H addition lines and crossing them to a normal wheat cultivar. Each RH informative line (containing deletions) had, on average, three deletions. The induced deletion size varied from 36.58 Kb to 576.00 Mb, with an average length of 52.42 Mb. This initial chromosome 3H radiation hybrid (3H-RH) map had a 9.53× higher resolution than an analogous genetic map, reaching a maximum of >262.40× resolution in regions around the centromere. The final RH map was 3066.1 cR in length, with a 0.76 Mb resolution. It was estimated that the map resolution can be improved to an average of 30.34 Kb by saturating the 3H-RH map with molecular markers. The generated RH panel enabled alignment of BAC and sequenced contigs as small as 1.50 Kb in size. The high resolution and the coverage of poor-recombination regions make RH maps an ideal resource for barley genome assembly, as well as other genetic studies.

PCR and sequence analysis of barley chromosome 2H subjected to the gametocidal action of chromosome 2C

Gametocidal (Gc) chromosomes induce various types of chromosomal mutations during gametogenesis in the chromosomes of common wheat and alien chromosomes added to common wheat. However, it is not yet known whether the Gc chromosome causes aberrations at the nucleotide level because mutations caused by Gc chromosomes have been studied only by cytological screening. In order to know whether the Gc chromosome induces point mutations, we conducted PCR analysis and sequencing with the progeny of a common wheat line that is disomic for barley chromosome 2H and monosomic for Gc chromosome 2C. We analyzed 18 2H-specific EST sequences using 81 progeny plants carrying a cytologically normal-appearing 2H chromosome and found no nucleotide changes in the analyzed 1,419 sequences (in total 647,075 bp). During this analysis, we found six plants for which some ESTs could not be PCR amplified, suggesting the presence of chromosomal mutations in these plants. The cytological and PCR analyses of the progeny of the six plants confirmed the occurrence of chromosomal mutations in the parental plants. These results suggested that the Gc chromosome mostly induced chromosomal aberrations, not nucleotide changes, and that the Gc-induced chromosomal mutations in the six plants occurred after fertilization.