Fine physical mapping of Ph1, a chromosome pairing regulator gene in polyploid wheat

Development of wheat-Dasypyrum villosum T6V#4S·6AL translocation lines with enhanced inheritance for powdery mildew resistance

New translocation lines with T6V#4S·6AL in the Ph1 and ph1b backgrounds were developed with improved inheritance of powdery mildew resistance. The wheat-Dasypyrum villosum T6V#4S·6DL translocation line Pm97033, which exhibits strong powdery mildew (PM) resistance, was developed many years ago, but has limited application in wheat breeding. One of the major reasons for this is that the translocation chromosome has low transmission rate, which makes it difficult to obtain ideal genotype through recombination with other elite agronomic traits in a limited segregating population. Further modifications are thus needed to make better use of this genetic resource. In this study, Pm97033 and the T6V#2S·6AL translocation line NY-W were hybridized with the CS ph1b mutant, and two F₁ hybrids were hybridized with each other. Then, plants homozygous for the ph1b deletion carrying the alien chromosome arm(s) 6V#2S and 6V#4S were identified from the segregating populations using molecular markers. New T6V#4S·6AL and T6V#2-6V#4S·6AL translocations were identified by molecular markers and confirmed by genomic in situ hybridization (GISH). Individuals that were heterozygous or homozygous for the translocation chromosome in Ph1 and ph1b backgrounds were obtained. The ratio of PM resistance vs. susceptibility in the self-pollinated heterozygous plants was 3:1, and the phenotype was completely consistent with the KASP genotyping. Thus, the new translocation chromosomes had higher transmission rate than the original T6V#4S·6DL, and so can be effectively applied in breeding programs.

Consequences of whole genome duplication for 2n pollen performance

The vegetative cell of the angiosperm male gametophyte (pollen) functions as a free-living, single-celled organism that both produces and transports sperm to egg. Whole-genome duplication (WGD) should have strong effects on pollen because of the haploid to diploid transition and because of both genetic and epigenetic effects on cell-level phenotypes. To disentangle historical effects of WGD on pollen performance, studies can compare 1n pollen from diploids to neo-2n pollen from diploids and synthetic autotetraploids to older 2n pollen from established neo-autotetraploids. WGD doubles both gene number and bulk nuclear DNA mass, and a substantial proportion of diploid and autotetraploid heterozygosity can be transmitted to 2n pollen. Relative to 1n pollen, 2n pollen can exhibit heterosis due to higher gene dosage, higher heterozygosity and new allelic interactions. Doubled genome size also has consequences for gene regulation and expression as well as epigenetic effects on cell architecture. Pollen volume doubling is a universal effect of WGD, whereas an increase in aperture number is common among taxa with simultaneous microsporogenesis and pored apertures, mostly eudicots. WGD instantly affects numerous evolved compromises among mature pollen functional traits and these are rapidly shaped by highly diverse tissue interactions and pollen competitive environments in the early post-WGD generations. 2n pollen phenotypes generally incur higher performance costs, and the degree to which these are met or evolve by scaling up provisioning and metabolic vigor needs further study.

Some characteristics of crossing over in induced recombination between chromosomes of wheat and rye

Allopolyploid wheat (Triticum aestivum L.) carries three pairs of homoeologous genomes but its meiotic pairing is diploid-like. This is the effect of the Ph (pairing homoeologous) system which restricts chromosome pairing to strictly homologous. Ph1 is the locus with the strongest effect. Disabling Ph1 permits pairing between homoeologues and is routinely used in chromosome engineering to introgress alien variation into breeding stocks. Whereas the efficiency of Ph1 and the general pattern of homoeologous crossovers in its absence are quite well known from numerous studies, other characteristics of such crossovers remain unknown. This study analyzed the crossover points in four sets of the ph1b-induced recombinants between wheat homologues as well as between three wheat and rye (Secale cereale) homoeologous chromosome arms, and compared them to crossovers between homologues in a reference wheat population. The results show the Ph1 locus also controls crossing over of homologues, and the general patterns of homologous (with Ph1) and homoeologous (with ph1b) crossing over are the same. In all intervals analyzed, homoeologous crossovers fell within the range of frequency distribution of homologous crossovers among individual families of the reference population. No specific DNA sequence characteristics were identified that could be recognized by the Ph1 locus; the only difference between homologous and homoeologous crossing over appears to be in frequency. It is concluded that the Ph1 locus likely recognizes DNA sequence similarity; crossing over is permitted between very similar sequences. In the absence of Ph1 dissimilarities are ignored, in proportion to the level of the sequence divergence.

Ph2 encodes the mismatch repair protein MSH7-3D that inhibits wheat homoeologous recombination

Meiotic recombination is a critical process for plant breeding, as it creates novel allele combinations that can be exploited for crop improvement. In wheat, a complex allohexaploid that has a diploid-like behaviour, meiotic recombination between homoeologous or alien chromosomes is suppressed through the action of several loci. Here, we report positional cloning of Pairing homoeologous 2 (Ph2) and functional validation of the wheat DNA mismatch repair protein MSH7-3D as a key inhibitor of homoeologous recombination, thus solving a half-century-old question. Similar to ph2 mutant phenotype, we show that mutating MSH7-3D induces a substantial increase in homoeologous recombination (up to 5.5 fold) in wheat-wild relative hybrids, which is also associated with a reduction in homologous recombination. These data reveal a role for MSH7-3D in meiotic stabilisation of allopolyploidy and provides an opportunity to improve wheat's genetic diversity through alien gene introgression, a major bottleneck facing crop improvement.

Chromosome Pairing in Polyploid Grasses

Polyploids are species in which three or more sets of chromosomes coexist. Polyploidy frequently occurs in plants and plays a major role in their evolution. Based on their origin, polyploid species can be divided into two groups: autopolyploids and allopolyploids. The autopolyploids arise by multiplication of the chromosome sets from a single species, whereas allopolyploids emerge from the hybridization between distinct species followed or preceded by whole genome duplication, leading to the combination of divergent genomes. Having a polyploid constitution offers some fitness advantages, which could become evolutionarily successful. Nevertheless, polyploid species must develop mechanism(s) that control proper segregation of genetic material during meiosis, and hence, genome stability. Otherwise, the coexistence of more than two copies of the same or similar chromosome sets may lead to multivalent formation during the first meiotic division and subsequent production of aneuploid gametes. In this review, we aim to discuss the pathways leading to the formation of polyploids, the occurrence of polyploidy in the grass family (Poaceae), and mechanisms controlling chromosome associations during meiosis, with special emphasis on wheat.

Analytical Methodology of Meiosis in Autopolyploid and Allopolyploid Plants

Meiosis is the cellular process responsible for producing gametes with half the genetic content of the parent cells. Integral parts of the process in most diploid organisms include the recognition, pairing, synapsis, and recombination of homologous chromosomes, which are prerequisites for balanced segregation of half-bivalents during meiosis I. In polyploids, the presence of more than two sets of chromosomes adds to the basic meiotic program of their diploid progenitors the possibility of interactions between more than two chromosomes and the formation of multivalents, which has implications on chromosome segregations and fertility. The mode of how chromosomes behave in meiosis in competitive situations has been the aim of many studies in polyploid species, some of which are considered here. But polyploids are also of interest in the study of meiosis because some of them tolerate the loss of chromosome segments or complete chromosomes as well as the addition of chromosomes from related species. Deletions allow to assess the effect of specific chromosome segments on meiotic behavior. Introgression lines are excellent materials to monitor the behavior of a given chromosome in the genetic background of the recipient species. We focus on this approach here as based on studies carried out in bread wheat, which is commonly used as a model species for meiosis studies. In addition to highlighting the relevance of the use of materials derived from polyploids in the study of meiosis, cytogenetics tools such as fluorescence in situ hybridization and the immunolabeling of proteins interacting with DNA are also emphasized.

Recombination between homoeologous chromosomes induced in durum wheat by the Aegilops speltoides Su1-Ph1 suppressor

Su1-Ph1, which we previously introgressed into wheat from Aegilops speltoides, is a potent suppressor of Ph1 and a valuable tool for gene introgression in tetraploid wheat. We previously introgressed Su1-Ph1, a suppressor of the wheat Ph1 gene, from Aegilops speltoides into durum wheat cv Langdon (LDN). Here, we evaluated the utility of the introgressed suppressor for inducing introgression of alien germplasm into durum wheat. We built LDN plants heterozygous for Su1-Ph1 that simultaneously contained a single LDN chromosome 5B and a single Ae. searsii chromosome 5S^se, which targeted them for recombination. We genotyped 28 BC₁F₁ and 84 F₂ progeny with the wheat 90-K Illumina single-nucleotide polymorphism assay and detected extensive recombination between the two chromosomes, which we confirmed by non-denaturing fluorescence in situ hybridization (ND-FISH). We constructed BC₁F₁ and F₂ genetic maps that were 65.31 and 63.71 cM long, respectively. Recombination rates between the 5B and 5S^se chromosomes were double the expected rate computed from their meiotic pairing, which we attributed to selection against aneuploid gametes. Recombination rate between 5B and 5S^se was depressed compared to that between 5B chromosomes in the proximal region of the long arm. We integrated ND-FISH signals into the genetic map and constructed a physical map, which we used to map a 172,188,453-bp Ph1 region. Despite the location of the region in a low-recombination region of the 5B chromosome, we detected three crossovers in it. Our data show that Su1-Ph1 is a valuable tool for gene introgression and gene mapping based on recombination between homoeologous chromosomes in wheat.

The novel function of the Ph1 gene to differentiate homologs from homoeologs evolved in Triticum turgidum ssp. dicoccoides via a dramatic meiosis-specific increase in the expression of the 5B copy of the C-Ph1 gene

The Ph1 gene is the principal regulator of homoeologous chromosome pairing control (HECP) that ensures the diploid-like meiotic chromosome pairing behavior of polyploid wheat. The HECP control was speculated to have evolved after the first event of polyploidization. With the objective to accurately understand the evolution of the HECP control, wild emmer wheat accessions previously known to differ for HECP control were characterized for the structure and expression of the candidate Ph1 gene, C-Ph1. The C-TdPh1-5A and 5B gene copies of emmer wheat showed 98 and 99% DNA sequence similarity respectively with the corresponding hexaploid wheat copies. Further, the C-TdPh1-5B carried the C-Ph1-5B specific structural changes and transcribed three splice variants as observed in the hexaploid wheat. Further, single nucleotide changes differentiating accessions varying for HECP control were identified. Analyzed by quantitative expression analysis, the wild emmer accessions with HECP control showed ~ 10,000-fold higher transcript abundance of the C-TdPh1-5B copy during prophase-I compared to accessions lacking the control. Differential transcriptional regulation of C-TdPh1-5B splice variants further revealed that C-Ph1-5B^alt1 variant is mainly responsible for differential accumulation of C-Ph1-5B copy in accessions with HECP control. Taken together, these results showed that the HECP control evolved via transcriptional regulation of splice variants during meiosis.

Delimitation of wheat ph1b deletion and development of ph1b-specific DNA markers

We detected the deletion breakpoints of wheat ph1b mutant and the actual size of the deletion. Also, we developed ph1b deletion-specific markers useful for ph1b-mediated gene introgression and genome studies. The Ph1 (pairing homoeologous) locus has been considered a major genetic system for the diploidized meiotic behavior of the allopolyploid genome in wheat. It functions as a defense system against meiotic homoeologous pairing and recombination in polyploid wheat. A large deletion of the genomic region harboring Ph1 on the long arm of chromosome 5B (5BL) led to the ph1b mutant in hexaploid wheat 'Chinese Spring,' which has been widely used to induce meiotic homoeologous recombination for gene introgression from wild grasses into wheat. However, the breakpoints and physical size of the deletion remain undetermined. In the present study, we first anchored the ph1b deletion on 5BL by the high-throughput wheat 90K SNP assay and then delimited the deletion to a genomic region of 60,014,523 bp by chromosome walking. DNA marker and sequence analyses detected the nucleotide positions of the distal and proximal breakpoints (DB and PB) of the ph1b deletion and the deletion junction as well. This will facilitate understanding of the genomic region harboring the Ph1 locus in wheat. In addition, we developed user-friendly DNA markers specific for the ph1b deletion. These new ph1b deletion-specific markers will dramatically improve the efficacy of the ph1b mutant in the meiotic homoeologous recombination-based gene introgression and genome studies in wheat and its relatives.

Transgressive segregations for agronomic improvement using interspecific crosses between C. arietinum L. x C. reticulatum Ladiz. and C. arietinum L. x C. echinospermum Davis species

The wild species of chickpea have tremendous potential for enhancing genetic gains of cultigen and have resistant accessions against major biotic and abiotic stresses. In the present study, two wild annual accessions, one each of C. reticulatum Ladiz. (ILWC 229) and C. echinospermum Davis (ILWC 246) were assessed for their agro-morphological features and hybridized with different cultivated varieties (BGD 72, PBG 5, ICKG 96029, Pusa 372 and JG 11) of chickpea. Fertile F1 plants were developed as revealed by their normal meiotic chromosomal configuration including high pollen stainability percentage and seed set. The effect of genetic and non-genetic factors on crossability performance with respect to pod and seed set was also evident under two growing conditions of North-Western Indian Himalayas. The segregation analysis using F2 phenotypic ratio of some distinct morphological (plant growth habit, stem pigmentation at seedling stage and testa texture) characters indicated their monogenic inheritance pattern. The study would also be useful to chickpea breeders to identify true to type interspecific plants. Further, the F1, F2 and F3 generations of all seven crosses along with parents were evaluated under natural field condition to determine the extent of variability created into the cultivated background of chickpea. There was a wide range of variation in F3 population against cold stress, suggesting selection of tolerant recombinant lines at an early stage. We also studied fruitful heterosis (%) as a useful approach, instead of residual heterosis to identify better performing transgressive segregants. The values of most of the interspecific crosses for important traits assessed in F2 and F3 generations were higher than that of better parent, suggesting isolation of inbred vigour for pod numbers and earliness. The results indicated that wild Cicer annual accessions of C. reticulatum and C. echinospermum species can be exploited after proper screening for traits of interest for diversification of cultivated gene pool and subsequent use in chickpea improvement.

Inducement and identification of chromosome introgression and translocation of Gossypium australe on Gossypium hirsutum

Background

We previously reported the development of a set of Gossypium hirsutum-G. australe alien chromosome addition lines. Naturally, however, G. hirsutum-G. australe chromosome exchanges were very limited, impeding the stable transference of useful genes from G. australe (G₂G₂ genome) into the most cultivated cotton, G. hirsutum (AADD).

Results

In the present report, the pollen from a pentaploid (2n = AADDG₂) of G. hirsutum-G. australe was irradiated with seven different doses ranging from 10 to 40 Grays and used to pollinate emasculated flowers of G. hirsutum over three consecutive years. Irradiation greatly increased the genetic recombination rates of the G. hirsutum and G. australe chromosomes and a total of 107 chromosome introgression individuals in 192 GISH-negative (with no GISH signal on chromosome) survived individuals, 11 chromosome translocation individuals (containing 12 chromosome translocation events) and 67 chromosome addition individuals were obtained in 70 GISH-positive (with GISH signal(s) on chromosome(s)) survived individuals, which are invaluable for mining desirable genes from G. australe. Multicolor genomic in situ hybridization results showed that there were three types of translocation, whole arm translocation, large alien segment translocation and small alien segment translocation, and that all translocations occurred between the G₂-genome and the A-subgenome chromosomes in G. hirsutum. We also found that higher doses induced much higher rates of chromosome variation but also greatly lowered the seed viability and seedling survivability.

Conclusions

Irradiation has been successfully employed to induce chromosome introgressions and chromosome translocations and promote chromosome exchanges between cultivated and wild species. In addition, by balancing the rates of chromosome introgression and translocation to those of seed set, seed germination, and seedling rates in the M1 generation, we conclude that the dosage of 20 Grays is the most suitable. The established methodology may guide the utilization of the tertiary gene pool of Gossypium species such as G. australe in cotton breeding in the future.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4398-7) contains supplementary material, which is available to authorized users.

Chromosomal constitutions of five wheat - Elytrigia elongata partial amphiploids as revealed by GISH, multicolor GISH and FISH

A combination of meiotic pairing analysis and in situ hybridization (genomic in situ hybridization [GISH], multicolor GISH [mcGISH] and fluorescence in situ hybridization [FISH]) of five Triticum aestivum (Linnaeus, 1753) - Elytrigia elongata (Podpěra, 1902) (2n = 10x = 70) amphiploids was employed to investigate the genomic constitution and relationships between wheat and alien chromosomes. GISH, multicolor GISH and FISH patterns of mitotic chromosomes indicate that the genomic constitution of the five partial amphiploids (XY693, XY7430, SN19, SN20 and SN122) are 14A + 12B + 14D + 8Js + 8J, 12A + 16B + 14D + 2St + 8Js + 2J + 2 W-E, 14A + 14B + 14D + 4St + 8Js, 14A + 14B + 14D + 2St + 10Js + 2J, and 14A + 14B + 14D + 2St + 8Js + 4J, respectively. Analysis of meiotic chromosome pairing in the F₁ hybrids between these five partial amphiploids suggests that SN20 and SN122 are the most closely related amphiploids and are somewhat related with XY693 and XY7430. However, the alien chromosome constitutions of SN19 differed from the other four amphiploids. In addition, a new pairing between wheat and E. elongata chromosomes was distinguished in some cells of the hybrids SN19 × XY7430, SN20 × XY7430 and SN122 × XY7430.

Manipulation of Homologous and Homoeologous Chromosome Recombination in Wheat

Given the sizes of the three genomes in wheat (A, B, and D) and a limited number of chiasmata formed in meiosis, recombination by crossing-over is a very rare event. It is also restricted to very similar homologues; the pairing homoeologous (Ph) system of wheat prevents differentiated chromosomes from pairing and crossing-over. This chapter presents an overview and describes several systems by which the frequency or density of crossing-over can be increased, both in homologues and homoeologues. It also presents the standard system of E.R. Sears for engineering alien chromosome transfers into wheat.

Forcing the shift of the crossover site to proximal regions in wheat chromosomes

Terminal deletions obligate the first crossover to be formed in more proximal positions. This increases the recombination rate in intercalary intervals but not in the proximity of the centromere. Crossovers are not uniformly distributed along chromosomes in wheat. They take place preferentially in distal positions. The effect of the chromosomal architecture on crossover positioning has been analyzed from the chiasmate bonds at metaphase I formed by the truncated arms of 51 terminal deletion lines of eight wheat chromosomes. Chromosome 4A and the B genome chromosomes, in their standard or truncated conformation, and their arms, were identified by C-banding. Chromosomes studied show a similar chiasma distribution. Reduction of the size of the truncated arms is accompanied by a gradual decrease of the chiasma frequency in chromosome arms 1BL, 3BS, 3BL, 4BL, 5BS, 5BL, 6BL, 7BS, 7BL and 4AL. In chromosome arm 1BS, most chiasmata are concentrated in the distal half of the satellite and, in 4AS, in the distal 24 %. The arms 2BS, 2BL and 6BS do not show a simple decreasing gradient of the recombination rate, the chiasma frequency increases in subdistal intervals compared to more distal regions. Although terminal deletions usually induce an increase of chiasma frequency in intercalary regions, the level of intact chromosome arms is maintained in only a few deletion lines. Truncated arms containing only the 20 % proximal of the intact arm do not form chiasmata. The relationships of chiasma positioning with chromatin structure and genome organization is discussed.

Silencing of a metaphase I-specific gene results in a phenotype similar to that of the Pairing homeologous 1 (Ph1) gene mutations

Although studied extensively since 1958, the molecular mode of action of the Pairing homeologous 1 (Ph1) gene is still unknown. In polyploid wheat, the diploid-like chromosome pairing is principally controlled by the Ph1 gene via preventing homeologous chromosome pairing (HECP). Here, we report a candidate Ph1 gene (C-Ph1) present in the Ph1 locus, transient as well as stable silencing of which resulted in a phenotype characteristic of the Ph1 gene mutants, including HECP, multivalent formation, and disrupted chromosome alignment on the metaphase I (MI) plate. Despite a highly conserved DNA sequence, the C-Ph1 gene homeologues showed a dramatically different structure and expression pattern, with only the 5B copy showing MI-specific expression, further supporting our claim for the Ph1 gene. In agreement with the previous reports about the Ph1 gene, the predicted protein of the 5A copy of the C-Ph1 gene is truncated, and thus perhaps less effective. The 5D copy is expressed around the onset of meiosis; thus, it may function during the earlier stages of chromosome pairing. Along with alternate splicing, the predicted protein of the 5B copy is different from the protein of the other two copies because of an insertion. These structural and expression differences among the homeologues concurred with the previous observations about Ph1 gene function. Stable RNAi silencing of the wheat gene in Arabidopsis showed multivalents and centromere clustering during meiosis I.

Meiotic chromosome pairing behaviour of natural tetraploids and induced autotetraploids of Actinidia chinensis

Non-preferential chromosome pairing was identified in tetraploid Actinidia chinensis and a higher mean multivalent frequency in pollen mother cells was found in colchine-induced tetraploids of A. chinensis compared with naturally occurring tetraploids. Diploid and tetraploid Actinidia chinensis are used for the development of kiwifruit cultivars. Diploid germplasm can be exploited in a tetraploid breeding programme via unreduced (2n) gametes and chemical-induced chromosome doubling of diploid cultivars and selections. Meiotic chromosome behaviour in diploid A. chinensis 'Hort16A' and colchicine-induced tetraploids from 'Hort16A' was analysed and compared with that in a diploid male and tetraploid males of A. chinensis raised from seeds sourced from the wild in China. Both naturally occurring and induced tetraploids formed multivalents, but colchicine-induced tetraploids showed a higher mean multivalent frequency in the pollen mother cells. Lagging chromosomes at anaphase I and II were observed at low frequencies in the colchicine-induced tetraploids. To investigate whether preferential or non-preferential chromosome pairing occurs in tetraploid A. chinensis, the inheritance of microsatellite alleles was analysed in the tetraploid progeny of crosses between A. chinensis (4x) and A. arguta (4x). The frequencies of inherited microsatellite allelic combinations in the hybrids suggested that non-preferential chromosome pairing had occurred in the tetraploid A. chinensis parent.

Gametocidal genes in wheat and its relatives. IV. Functional relationships between six gametocidal genes

Gametocidal (Gc) genes in Aegilops species are known to cause gamete abortion and chromosome breakage when they are introduced into the wheat genetic background. Interactions of five Gc genes so far identified were investigated by analysis of wheat hybrids among lines carrying different gametocidal genes. As a result, the genes were classified into three functional groups. The first group includes two Gc genes of Ae. speltoides (Gc1a and Gc1b) and one gene (Gc-Sl3) on chromosome 2S1 of Ae. sharonensis. These genes were hypostatic to the genes (Gc-Sl1, Gc-Sl2) on chromosome 4S1 of Ae. longissima and Ae. sharonensis, which constitute the second group. In addition, plants carrying Gc genes of both the first and the second group produced progeny with higher frequencies of chromosome breakage than those found in the progeny of single gene carriers. It was concluded that there were specific interactions between these genes to enhance chromosome breakage. On the other hand, there was no interaction between the Gc gene (Gc-C) of Ae. triuncialis, the third group, and Gc genes belonging to the former two groups. These functional groups might be a reflection of the mechanisms by which Gc genes induce gamete abortion and chromosome breakage. Based on functional and local relationships, the symbols of the Gc genes were systematically redesignated.

Development of a deletion and genetic linkage map for the 5A and 5B chromosomes of wheat (Triticum aestivum)

The aims of the present study were to provide deletion maps for wheat ( Triticum aestivum L.) chromosomes 5A and 5B and a detailed genetic map of chromosome 5A enriched with popular microsatellite markers, which could be compared with other existing maps and useful for mapping major genes and quantitative traits loci (QTL). Physical mapping of 165 gSSR and EST-SSR markers was conducted by amplifying each primer pair on Chinese Spring, aneuploid lines, and deletion lines for the homoeologous group 5 chromosomes. A recombinant inbred line (RIL) mapping population that is recombinant for only chromosome 5A was obtained by crossing the wheat cultivar Chinese Spring and the disomic substitution line Chinese Spring-5A dicoccoides and was used to develop a genetic linkage map of chromosome 5A. A total of 67 markers were found polymorphic between the parental lines and were mapped in the RIL population. Sixty-three loci and the Q gene were clustered in three linkage groups ordered at a minimum LOD score of 5, while four loci remained unlinked. The whole genetic 5A chromosome map covered 420.2 cM, distributed among three linkage groups of 189.3, 35.4, and 195.5 cM. The EST sequences located on chromosomes 5A and 5B were used for comparative analysis against Brachypodium distachyon (L.) P. Beauv. and rice ( Oryza sativa L.) genomes to resolve orthologous relationships among the genomes of wheat and the two model species.

Preliminary characterisation of two early meiotic wheat proteins after identification through 2D gel electrophoresis proteomics

Various genetic-based approaches including mutant population screens, microarray analyses, cloning and transgenesis have broadened our knowledge of gene function during meiosis in plants. Nonetheless, these genetic tools are not without inherent limitations. One alternative approach to studying plant meiosis, especially in polyploids such as Triticum aestivum L. (bread wheat), is proteomics. However, protein-based approaches using proteomics have seldom been described, with only two attempts at studying early plant meiosis reported. Here, we report the investigation of early bread wheat meiosis using proteomics. Five differentially expressed protein spots were identified using 2D gel electrophoresis (2DGE) on protein extracts from four pooled stages of meiosis and three genotypes (Chinese Spring wild-type, ph1b and ph2a wheat mutant lines). Tandem mass spectrometry (MS/MS) identification of peptides from these protein spots led to the isolation and characterisation of the full-length clones of a wheat Speckle-type POZ protein, an SF21-like protein and HSP70, and a partial coding sequence of a hexose transporter. Significantly, the putative functions of the Speckle-type POZ protein and HSP70 were confirmed using in vitro DNA binding assays. Through the use of a 2DGE proteomics approach, we show that proteomics is a viable alternative to genetic-based approaches when studying meiosis in wheat. More significantly, we report a potential role for a Speckle-type POZ protein and a HSP70 in chromosome pairing during the early stages of meiosis in bread wheat.

Targeted introgression of a wheat stem rust resistance gene by DNA marker-assisted chromosome engineering

Chromosome engineering is a useful strategy for transfer of alien genes from wild relatives into modern crops. However, this strategy has not been extensively used for alien gene introgression in most crops due to low efficiency of conventional cytogenetic techniques. Here, we report an improved scheme of chromosome engineering for efficient elimination of a large amount of goatgrass (Aegilops speltoides) chromatin surrounding Sr39, a gene that provides resistance to multiple stem rust races, including Ug99 (TTKSK) in wheat. The wheat ph1b mutation, which promotes meiotic pairing between homoeologous chromosomes, was employed to induce recombination between wheat chromosome 2B and goatgrass 2S chromatin using a backcross scheme favorable for inducing and detecting the homoeologous recombinants with small goatgrass chromosome segments. Forty recombinants with Sr39 with reduced surrounding goatgrass chromatin were quickly identified from 1048 backcross progenies through disease screening and molecular marker analysis. Four of the recombinants carrying Sr39 with a minimal amount of goatgrass chromatin (2.87-9.15% of the translocated chromosomes) were verified using genomic in situ hybridization. Approximately 97% of the goatgrass chromatin was eliminated in one of the recombinants, in which a tiny goatgrass chromosome segment containing Sr39 was retained in the wheat genome. Localization of the goatgrass chromatin in the recombinants led to rapid development of three molecular markers tightly linked to Sr39. The new wheat lines and markers provide useful resources for the ongoing global effort to combat Ug99. This study has demonstrated great potential of chromosome engineering in genome manipulation for plant improvement.

Understanding meiosis and the implications for crop improvement

Over the past 50 years, the understanding of meiosis has aged like a fine bottle of wine: the complexity is developing but the wine itself is still young. While emphasis in the plant kingdom has been placed on the model diploids Arabidopsis (Arabidopsis thaliana L.) and rice (Orzya sativa L.), our research has mainly focussed on the polyploid, bread wheat (Triticum aestivum L.). Bread wheat is an important food source for nearly two-thirds of the world's population. While creating new varieties can be achieved using existing or advanced breeding lines, we would also like to introduce beneficial traits from wild related species. However, expanding the use of non-adapted and wild germplasm in cereal breeding programs will depend on the ability to manipulate the cellular process of meiosis. Three important and tightly-regulated events that occur during early meiosis are chromosome pairing, synapsis and recombination. Which key genes control these events in meiosis (and how they do so) remains to be completely answered, particularly in crops such as wheat. Although the majority of published findings are from model organisms including yeast (Saccharomyces cerevisiae) and the nematode Caenorhabditis elegans, information from the plant kingdom has continued to grow in the past decade at a steady rate. It is with this new knowledge that we ask how meiosis will contribute to the future of cereal breeding. Indeed, how has it already shaped cereal breeding as we know it today?

Meiotic genes and proteins in cereals

We review the current status of our understanding and knowledge of the genes and proteins controlling meiosis in five major cereals, rye, wheat, barley, rice and maize. For each crop, we describe the genetic and genomic infrastructure available to investigators, before considering the inventory of genes and proteins that have roles to play in this process. Emphasis is given throughout as to how translational genomic and proteomic approaches have enabled us to circumvent some of the intractable features of this important group of plants.

Fine structure mapping of a gene-rich region of wheat carrying Ph1, a suppressor of crossing over between homoeologous chromosomes

The wheat gene-rich region (GRR) 5L0.5 contains many important genes, including Ph1, the principal regulator of chromosome pairing. Comparative marker analysis identified 32 genes for the GRR controlling important agronomic traits. Detailed characterization of this region was accomplished by first physically localizing 213 wheat group 5L-specific markers, using group 5 nulli-tetrasomics, three Ph1 gene deletion/insertion mutants, and nine terminal deletion lines with their breakpoints around the 5L0.5 region. The Ph1 gene was localized to a much smaller region within the GRR (Ph1 gene region). Of the 61 markers that mapped in the four subregions of the GRR, 9 mapped in the Ph1 gene region. High stringency sequence comparison (e < 1 x10(-25)) of 157 group 5L-specific wheat ESTs identified orthologs for 80% sequences in rice and 71% in Arabidopsis. Rice orthologs were present on all rice chromosomes, although most (34%) were on rice chromosome 9 (R9). No single collinear region was identified in Arabidopsis even for a smaller region, such as the Ph1 gene region. Seven of the nine Ph1 gene region markers mapped within a 450-kb region on R9 with the same gene order. Detailed domain/motif analysis of the 91 putative genes present in the 450-kb region identified 26 candidates for the Ph1 gene, including genes involved in chromatin reorganization, microtubule attachment, acetyltransferases, methyltransferases, DNA binding, and meiosis/anther specific proteins. Five of these genes shared common domains/motifs with the meiosis specific genes Zip1, Scp1, Cor1, RAD50, RAD51, and RAD57. Wheat and Arabidopsis homologs for these rice genes were identified.

The gametocidal chromosome as a tool for chromosome manipulation in wheat

Many alien chromosomes have been introduced into common wheat (the genus Triticum) from related wild species (the genus Aegilops). Some alien chromosomes have unique genes that secure their existence in the host by causing chromosome breakage in the gametes lacking them. Such chromosomes or genes, called gametocidal (Gc) chromosomes or Gc genes, are derived from different genomes (C, S, S(l) and M(g)) and belong to three different homoeologous groups 2, 3 and 4. The Gc genes of the C and M(g) genomes induce mild, or semi-lethal, chromosome mutations in euploid and alien addition lines of common wheat. Thus, induced chromosomal rearrangements have been identified and established in wheat stocks carrying deletions of wheat and alien (rye and barley) chromosomes or wheat-alien translocations. The gametocidal chromosomes isolated in wheat to date are reviewed here, focusing on their feature as a tool for chromosome manipulation.

The gametocidal chromosome as a tool for chromosome manipulation in wheat

Many alien chromosomes have been introduced into common wheat (the genus Triticum) from related wild species (the genus Aegilops). Some alien chromosomes have unique genes that secure their existence in the host by causing chromosome breakage in the gametes lacking them. Such chromosomes or genes, called gametocidal (Gc) chromosomes or Gc genes, are derived from different genomes (C, S, S(l) and M(g)) and belong to three different homoeologous groups 2, 3 and 4. The Gc genes of the C and M(g) genomes induce mild, or semi-lethal, chromosome mutations in euploid and alien addition lines of common wheat. Thus, induced chromosomal rearrangements have been identified and established in wheat stocks carrying deletions of wheat and alien (rye and barley) chromosomes or wheat-alien translocations. The gametocidal chromosomes isolated in wheat to date are reviewed here, focusing on their feature as a tool for chromosome manipulation.

Capturing diversity in the cereals: many options but little promiscuity

It is generally recognized by geneticists and plant breeders alike that there is a need to further improve the ability to capture and manipulate genetic diversity. The effective harnessing of diversity in traditional breeding programmes is limited and, therefore, it is vital that meiotic recombination can be manipulated given that it plays a pivotal role in generating diversity. With the advent of a wider range of genomics technologies, our understanding of meiotic processes should increase rapidly. Although comparative genetics has been useful, particularly in the broader grass family, the development of physical maps, long-range sequencing and transcript profiles promises to unravel the complexities of genomes as large or larger than wheat. Highlighting the most significant findings to date, this review pools the knowledge on these tools and reproductive processes.

Physical and genetic mapping of amplified fragment length polymorphisms and the leaf rust resistance Lr3 gene on chromosome 6BL of wheat

The Argentinian wheat cultivar Sinvalocho MA carries the Lr3 gene for leaf rust resistance on distal chromosome 6BL. In this cultivar, 33 spontaneous susceptible lines were isolated and cytogenetically characterized by C-banding. The analysis revealed deletions on chromosome 6BL in most lines. One line was nulli-6B, two lines were ditelo 6BS, two, three, and ten lines had long terminal deletions of 40, 30, and 20%, respectively, three lines showed very small terminal deletions, and one line had an intercalary deletion of 11%. Physical mapping of 55 amplified fragment length polymorphism (AFLP) markers detected differences between deletions and led to the division of 6BL into seven bins delimited by deletion breakpoints. The most distal bin, with a length smaller than 5% of 6BL, contained 22 AFLP markers and the Lr3 gene. Polymorphism for nine AFLPs between Sinvalocho MA and the rust leaf susceptible cultivar Gamma 6 was used to construct a linkage map of Lr3. This gene is at a genetic distance of 0.9 cM from a group of seven closely linked AFLPs. The location of the gene in a high recombinogenic region indicated a physical distance of approximately 1 Mb to the markers.

Analysis of recombination and gene distribution in the 2L1.0 region of wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.)

Both wheat and barley belong to tribe Triticeae and are closely related. High-density detailed comparison of physical and genetic linkage maps revealed that wheat genes are present in physically small gene-rich regions (GRRs). One of the largest GRRs is located around fraction length 1.0 of the long arm of wheat homoeologous group 2 chromosomes termed the "2L1.0 region." The main objective of this study was to analyze the structural and functional organization of the 2L1.0 region in barley in comparison to wheat. Using the 29 physically mapped RFLP markers for the region, wheat and barley consensus genetic linkage maps of the 2L1.0 region were generated by combining information from 18 wheat and 7 barley genetic linkage maps. Comparative analysis using these consensus maps and other available wheat and barley mapping resources identified 227 DNA markers and ESTs for the region. The region accounted for 58% of the genes and 68% of the arm's recombination in wheat. However, the corresponding region in barley accounted for about 42% of the genes and 81% of the recombination. The kb/cM ratio for the region was 122 in barley compared to 244 in wheat. Distribution of genes and recombination varied between the two species even though the gene order and density were similar.

Recent developments in durum wheat chromosome engineering

Transfer of alien chromosome segments from various Triticeae species into cultivated wheats, commonly referred to as "chromosome engineering", is currently benefiting from the recent, impressive advancements in molecular genetics, cytogenetics and genomics, which are providing new insights into the genetic and physical organization of even complex plant genomes, such as those of the Triticeae. The powerful analytical tools presently available are making the assessment of desired genotypes in the course of chromosome engineering far more precise and effective than in the past, thus giving this transfer strategy renewed and increased potential for meaningful practical achievements. Examples are given here of the application of such tools to the engineering of the durum wheat genome with small alien segments containing genes with beneficial impact on disease resistance and quality traits.

Synthesis and cytological characterization of trigeneric hybrids of durum wheat with and withoutPh1

Wild grasses in the tribe Triticeae, some in the primary or secondary gene pool of wheat, are excellent reservoirs of genes for superior agronomic traits, including resistance to various diseases. Thus, the diploid wheatgrasses Thinopyrum bessarabicum (Savul. and Rayss) Á. Löve (2n = 2x = 14; JJ genome) and Lophopyrum elongatum (Host) Á. Löve (2n = 2x = 14; EE genome) are important sources of genes for disease resistance, e.g., Fusarium head blight resistance that may be transferred to wheat. By crossing fertile amphidiploids (2n = 4x = 28; JJEE) developed from F1hybrids of the 2 diploid species with appropriate genetic stocks of durum wheat, we synthesized trigeneric hybrids (2n = 4x = 28; ABJE) incorporating both the J and E genomes of the grass species with the durum genomes A and B. Trigeneric hybrids with and without the homoeologous-pairing suppressor gene, Ph1, were produced. In the absence of Ph1, the chances of genetic recombination between chromosomes of the 2 useful grass genomes (JE) and those of the durum genomes (AB) would be enhanced. Meiotic chromosome pairing was studied using both conventional staining and fluorescent genomic in situ hybridization (fl-GISH). As expected, the Ph1-intergeneric hybrids showed low chromosome pairing (23.86% of the complement), whereas the trigenerics with ph1b (49.49%) and those with their chromosome 5B replaced by 5D (49.09%) showed much higher pairing. The absence of Ph1 allowed pairing and, hence, genetic recombination between homoeologous chromosomes. Fl-GISH analysis afforded an excellent tool for studying the specificity of chromosome pairing: wheat with grass, wheat with wheat, or grass with grass. In the trigeneric hybrids that lacked chromosome 5B, and hence lacked the Ph1 gene, the wheat–grass pairing was elevated, i.e., 2.6 chiasmata per cell, a welcome feature from the breeding standpoint. Using Langdon 5D(5B) disomic substitution for making trigeneric hybrids should promote homoeologous pairing between durum and grass chromosomes and hence accelerate alien gene transfer into the durum genomes.Key words: alien gene transfer, chiasma (xma) frequency, chromosome pairing, fluorescent genomic in situ hybridization (fl-GISH), homoeologous-pairing regulator, specificity of chromosome pairing, wheatgrass.

Molecular mapping of Stb1, a potentially durable gene for resistance to septoria tritici blotch in wheat

Septoria tritici blotch (STB), caused by the ascomycete Mycosphaerella graminicola (anamorph Septoria tritici), was the most destructive disease of wheat in Indiana and adjacent states before deployment of the resistance gene Stb1 during the early 1970s. Since then, Stb1 has provided durable protection against STB in widely grown wheat cultivars. However, its chromosomal location and allelic relationships to most other STB genes are not known, so the molecular mapping of Stb1 is of great interest. Genetic analyses and molecular mapping were performed for two mapping populations. A total of 148 F1 plants (mapping population I) were derived from a three-way cross between the resistant line P881072-75-1 and the susceptible lines P881072-75-2 and Monon, and 106 F6 recombinant-inbred lines (mapping population II) were developed from a cross between the resistant line 72626E2-12-9-1 and the susceptible cultivar Arthur. Bulked-segregant analysis with random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and microsatellite or simple-sequence repeat (SSR) markers was conducted to identify those that were putatively linked to the Stb1 gene. Segregation analyses confirmed that a single dominant gene controls the resistance to M. graminicola in each mapping population. Two RAPD markers, G7(1200) and H19(520), were tightly linked to Stb1 in wheat line P881072-75-1 at distances of less than 0.68 cM and 1.4 cM, respectively. In mapping population II, the most closely linked marker was SSR Xbarc74, which was 2.8 cM proximal to Stb1 on chromosome 5BL. Microsatellite loci Xgwm335 and Xgwm213 also were proximal to Stb1 at distances of 7.4 cM and 8.3 cM, respectively. The flanking AFLP marker, EcoRI-AGC/ MseI-CTA-1, was 8.4 cM distal to Stb1. The two RAPD markers, G7(1200) and H19(520), and AFLP EcoRI-AGC/ MseI-CTA-1, were cloned and sequenced for conversion into sequence-characterized amplified region (SCAR) markers. Only RAPD allele H19(520) could be converted successfully, and none of the SCAR markers was diagnostic for the Stb1 locus. Analysis of SSR and the original RAPD primers on several 5BL deletion stocks positioned the Stb1 locus in the region delineated by chromosome breakpoints at fraction lengths 0.59 and 0.75. The molecular markers tightly linked to Stb1 could be useful for marker-assisted selection and for pyramiding of Stb1 with other genes for resistance to M. graminicola in wheat.

Microsatellite-based deletion bin system for the establishment of genetic-physical map relationships in wheat (Triticum aestivum L.)

Because of polyploidy and large genome size, deletion stocks of bread wheat are an ideal material for physically allocating ESTs and genes to small chromosomal regions for targeted mapping. To enhance the utility of deletion stocks for chromosome bin mapping, we characterized a set of 84 deletion lines covering the 21 chromosomes of wheat using 725 microsatellites. We localized these microsatellite loci to 94 breakpoints in a homozygous state (88 distal deletions, 6 interstitial), and 5 in a heterozygous state representing 159 deletion bins. Chromosomes from homoeologous groups 2 and 5 were the best covered (126 and 125 microsatellites, respectively) while the coverage for group 4 was lower (80 microsatellites). We assigned at least one microsatellite in up to 92% of the bins (mean 4.97 SSR/bin). Only a few discrepancies concerning marker order were observed. The cytogenetic maps revealed small genetic distances over large physical regions around the centromeres and large genetic to physical map ratios close to the telomeres. As SSRs are the markers of choice for many genetic and breeding studies, the mapped microsatellite loci will be useful not only for deletion stock verifications but also for allocating associated QTLs to deletion bins where numerous ESTs that could be potential candidate genes are currently assigned.

Chromosome arrangement and behaviour of two rye homologous telosomes at the onset of meiosis in disomic wheat-5RL addition lines with and without the Ph1 locus

Fluorescence in-situ hybridization (FISH) of total genomic and repetitive DNA on microsporocytes of ditelocentric addition lines of rye 5RL in hexaploid wheat was performed to study the behaviour of the rye homologous chromosome arms in relation to centromere and telomere dynamics at premeiotic interphase and meiotic prophase I. By comparing isogenic lines with and without the Ph1 locus, we established the effect of the Ph1 gene on appearance and behaviour of the rye chromosomes. Ph1 and ph1b lines demonstrated similar premeiotic chromosome arrangement with the two rye homologues occupying separated domains despite the occurrence of centromere association. Our study confirmed that bouquet arrangement of telomeres follows the Rabl configuration. In cells displaying bouquet clustering of telomeres, centromeres of the 5RL telosomes are still at the opposite pole, suggesting anchoring of centromeres at the cytoskeleton. Once the telomeres complete clustering, the rye centromeres migrate to the telomere pole, and the rye chromosomes begin to loosen their structure. While the rye homologues in the wild-type keep separate territories in the nucleus, they become intermingled in the ph1b mutant, possibly because of their lower condensation. In a subsequent stage, the 5RL homologues appear intimately associated mainly at the distal region. Our study suggests that the lower rate of chromosome synapsis in the ph1b mutant results from abnormal chromatin decondensation and organization.

Meiosis in allopolyploids -- the importance of 'Teflon' chromosomes

Polyploids possess two or more sets of related chromosomes as a result of either the doubling of chromosomes following sexual hybridization within the same species (autopolyploidy), or between closely related species containing related but not completely homologous (homoeologous) genomes (allopolyploidy). For allopolyploids to produce viable gametes and be fertile, they must behave as diploids during meiosis, so that only identical chromosomes (homologues) pair. A solution to this problem is an enhanced ability to resolve incorrect pairing, which in turn promotes correct pairing. This gives nonhomologous chromosomes an almost 'Teflon'-like status, so that only the correct pairs 'stick'.

Genotypic variation in tetraploid wheat affecting homoeologous pairing in hybrids with Aegilops peregrina

The Ph1 gene has long been considered the main factor responsible for the diploid-like meiotic behavior of polyploid wheat. This dominant gene, located on the long arm of chromosome 5B (5BL), suppresses pairing of homoeologous chromosomes in polyploid wheat and in their hybrids with related species. Here we report on the discovery of genotypic variation among tetraploid wheats in the control of homoeologous pairing. Compared with the level of homoeologous pairing in hybrids between Aegilops peregrina and the bread wheat cultivar Chinese Spring (CS), significantly higher levels of homoeologous pairing were obtained in hybrids between Ae. peregrina and CS substitution lines in which chromosome 5B of CS was replaced by either 5B of Triticum turgidum ssp. dicoccoides line 09 (TTD09) or 5G of Triticum timopheevii ssp. timopheevii line 01 (TIM01). Similarly, a higher level of homoeologous pairing was found in the hybrid between Ae. peregrina and a substitution line of CS in which chromosome arm 5BL of line TTD140 substituted for 5BL of CS. It appears that the observed effect on the level of pairing is exerted by chromosome arm 5BL of T. turgidum ssp. dicoccoides, most probably by an allele of Ph1. Searching for variation in the control of homoeologous pairing among lines of wild tetraploid wheat, either T. turgidum ssp. dicoccoides or T. timopheevii ssp. armeniacum, showed that hybrids between Ae. peregrina and lines of these two wild wheats exhibited three different levels of homoeologous pairing: low, low intermediate, and high intermediate. The low-intermediate and high-intermediate genotypes may possess weak alleles of Ph1. The three different T. turgidum ssp. dicoccoides pairing genotypes were collected from different geographical regions in Israel, indicating that this trait may have an adaptive value. The availability of allelic variation at the Ph1 locus may facilitate the mapping, tagging, and eventually the isolation of this important gene.Key words: diploid-like meiotic behavior, genetic control of pairing, Ph1 gene, Triticum turgidum ssp. dicoccoides, wild emmer.

Candidate-gene cloning and targeted marker enrichment of wheat chromosomal regions using RNA fingerprinting - differential display

The usefulness of the RNA fingerprinting – differential display technique in gene cloning and targeted marker enrichment in wheat is demonstrated. A small region of chromosome 5BL was targeted that contains Ph1, a chromosome-pairing regulator gene. The cultivar Chinese Spring (CS) and mutant ph1b are almost identical except for chromosome 5BL, which, in the mutant line, carries an interstitial deletion encompassing the Ph1 gene. Poly(A)+RNA of the two lines from anthers at developmental stages ranging from pre-meiotic mitosis to anaphase II was PCR-amplified using 38 pairwise combinations of 19 primers. The35S-labeled amplified products were size-separated on denaturing polyacrylamide-urea gels. A total of 3154 fragment bands were observed, of which 43 were present in CS but absent in the ph1b mutant. These 43 fragment bands were eluted, re-amplified, and used as probes in gel-blot DNA analyses of wheat group 5 nullisomic-tetrasomic lines and the ph1b mutant. Twenty-four of these 43 probes were single- or few-copy sequences. Eight of the 24 probes mapped to wheat group 5 and five mapped to the deletion of the ph1b mutant. Three of these five probes were further localized to the submicroscopic region containing the Ph1 gene, by using two deletion lines flanking the region. Northern-blot analysis revealed that the gene corresponding to one of these three probes expresses mainly during meiosis and is from the B genome.Key words: RNA fingerprinting – differential display, wheat, gene cloning, marker enrichment, Ph1 gene.

Meiotic metaphase I pairing behavior of a 5BL recombinant isochromosome in wheat

A recombinant isochromosome i5BLrec of wheat was developed with one arm and the proximal 36% of the other arm of Chinese Spring (CS) origin and the distal 64% of the recombined arm of Triticum turgiduM subsp. dicoccoides origin. The i5BLrec provides an unusual opportunity to analyze the role of the centromere or arm heterozygosity in chromosome prealignment and synapsis during meiosis. In monosomic condition, the i5BLrec formed a ring univalent in 86.8% of the pollen mother cells (PMCs) at meiotic metaphase I. In the disomic condition, the two i5BLrec preferentially paired as a normal bivalent in 74.8% of the PMCs, which differed significantly (p <0.01) from the normal bivalent pairing of 51% observed in diisosomic 5BL chromosomes of the CS (Di5BL(CS)) control plants. In plants with one i5BLrec and a normal 5B(CS), the long arm of 5B(CS) paired with the homologous arm of i5BLrec in 54.4% of the PMCs, and 40.4% of the PMCs had a 5B(CS) univalent and a i5BLrec ring univalent. The implications of the i5BLrec pairing data on the mechanism of Ph1 gene action are discussed.

Different chromosomal distribution patterns of radiation-induced interchange breakpoints in barley: First post-treatment mitosis versus viable offspring

Translocation breakpoints (TBs) induced by ionizing radiation are nonrandomly distributed along barley chromosomes. When first post-treatment mitoses were evaluated, centromeres and the heterochromatin-containing proximal segments tended to be more than randomly involved, and terminal segments to be less than randomly involved in translocations. Contrary to this, small chromosomal regions in median and distal arm positions, characterized by high recombination rates and high gene density, were identified as preferred sites for the origination of viable translocations, probably due to deviations in chromatin organization. Apparently, the position of a TB has an influence on the rate of viability versus elimination of the carrier cells. Surprisingly, TBs within centromeres and heterochromatin-containing segments seem to be more harmful for survival than those induced in gene-rich regions.Key words: Hordeum vulgare, radiation-induced chromosome breaks, translocation lines, breakpoint distribution.

The production and characterization of recombination between chromosome 3N of Aegilops uniaristata and chromosome 3A of wheat

Six wheat lines with recombination between Aegilops uniaristata chromosome 3N and wheat chromosome 3A were produced. These were characterized in terms of exchange points by RFLP analysis. Chromosome 3N carries an undesirable brittle rachis gene and three of the recombinant lines had lost this character. The results also support previously published evidence of a pericentric inversion in chromosome 3N relative to the wheat homoeologous group 3 chromosomes.

Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints

We have developed a new technique for the physical mapping of barley chromosomes using microdissected translocation chromosomes for PCR with sequence-tagged site primers derived from >300 genetically mapped RFLP probes. The positions of 240 translocation breakpoints were integrated as physical landmarks into linkage maps of the seven barley chromosomes. This strategy proved to be highly efficient in relating physical to genetic distances. A very heterogeneous distribution of recombination rates was found along individual chromosomes. Recombination is mainly confined to a few relatively small areas spaced by large segments in which recombination is severely suppressed. The regions of highest recombination frequency (</=1 Mb/cM) correspond to only 4.9% of the total barley genome and harbor 47.3% of the 429 markers of the studied RFLP map. The results for barley correspond well with those obtained by deletion mapping in wheat. This indicates that chromosomal regions characterized by similar recombination frequencies and marker densities are highly conserved between the genomes of barley and wheat. The findings for barley support the conclusions drawn from deletion mapping in wheat that for all plant genomes, notwithstanding their size, the marker-rich regions are all of similar gene density and recombination activity and, therefore, should be equally accessible to map-based cloning.

Induction and characterization of Ph1 wheat mutants

The cloning of genes for complex traits in polyploid plants that possess large genomes, such as hexaploid wheat, requires an efficient strategy. We present here one such strategy focusing on the homologous pairing suppressor (Ph1) locus of wheat. This locus has been shown to affect both premeiotic and meiotic processes, possibly suggesting a complex control. The strategy combined the identification of lines carrying specific deletions using multiplex PCR screening of fast-neutron irradiated wheat populations with the approach of physically mapping the region in the rice genome equivalent to the deletion to reveal its gene content. As a result, we have located the Ph1 factor controlling the euploid-like level of homologous chromosome pairing to the region between two loci (Xrgc846 and Xpsr150A). These loci are located within 400 kb of each other in the rice genome. By sequencing this region of the rice genome, it should now be possible to define the nature of this factor.

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.

Effect of the pairing gene Ph1 and premeiotic colchicine treatment on intra- and interchromosome pairing of isochromosomes in common wheat

The analysis of the pattern of isochromosome pairing allows one to distinguish factors affecting presynaptic alignment of homologous chromosomes from those affecting synapsis and crossing-over. Because the two homologous arms in an isochromosome are invariably associated by a common centromere, the suppression of pairing between these arms (intrachromosome pairing) would indicate that synaptic or postsynaptic events were impaired. In contrast, the suppression of pairing between an isochromosome and its homologous chromosome (interchromosome pairing), without affecting intrachromosome pairing, would suggest that homologous presynaptic alignment was impaired. We used such an isochromosome system to determine which of the processes associated with chromosome pairing was affected by the Ph1 gene of common wheat-the main gene that restricts pairing to homologues. Ph1 reduced the frequency of interchromosome pairing without affecting intrachromosome pairing. In contrast, intrachromosome pairing was strongly reduced in the absence of the synaptic gene Syn-B1. Premeiotic colchicine treatment, which drastically decreased pairing of conventional chromosomes, reduced interchromosome but not intrachromosome pairing. The results support the hypothesis that premeiotic alignment is a necessary stage for the regularity of meiotic pairing and that Ph1 relaxes this alignment. We suggest that Ph1 acts on premeiotic alignment of homologues and homeologues as a means of ensuring diploid-like meiotic behavior in polyploid wheat.

Effect of the pairing gene Ph1 on centromere misdivision in common wheat

The cytologically diploid-like meiotic behavior of hexaploid wheat (i.e., exclusive bivalent pairing of homologues) is largely controlled by the pairing homoeologous gene Ph1. This gene suppresses pairing between homoeologous (partially homologous) chromosomes of the three closely related genomes that compose the hexaploid wheat complement. It has been previously proposed that Ph1 regulates meiotic pairing by determining the pattern of premeiotic arrangement of homologous and homoeologous chromosomes. We therefore assume that Ph1 action may be targeted at the interaction of centromeres with spindle microtubules--an interaction that is critical for movement of chromosomes to their specific interphase positions. Using monosomic lines of common wheat, we studied the effect of this gene on types and rates of centromere division of univalents at meiosis. In the presence of the normal two doses of Ph1, the frequency of transverse breakage (misdivision) of the centromere of univalent chromosomes was high in both first and second meiotic divisions; whereas with zero dose of the gene, this frequency was drastically reduced. The results suggest that Ph1 is a trans-acting gene affecting centromere-microtubules interaction. The findings are discussed in the context of the effect of Ph1 on interphase chromosome arrangement.

Detailed comparative mapping of cereal chromosome regions corresponding to the Ph1 locus in wheat

Detailed physical mapping of markers from rice chromosome 9, and from syntenous (at the genetic level) regions of other cereal genomes, has resulted in rice yeast artificial chromosome (YAC) contigs spanning parts of rice 9. This physical mapping, together with comparative genetic mapping, has demonstrated that synteny has been largely maintained between the genomes of several cereals at the level of contiged YACs. Markers located in one region of rice chromosome 9 encompassed by the YAC contigs have exhibited restriction fragment length polymorphism (RFLP) using deletion lines for the Ph1 locus. This has allowed demarcation of the region of rice chromosome 9 syntenous with the ph1b and ph1c deletions in wheat chromosome 5B. A group of probes located in wheat homoeologous group 5 and barley chromosome 5H, however, have synteny with rice chromosomes other than 9. This suggests that the usefulness of comparative trait analysis and of the rice genome as a tool to facilitate gene isolation will differ from one region to the next, and implies that the rice genome is more ancestral in structure than those of the Triticeae.

Engineering of interstitial foreign chromosome segments containing the K(+)/Na (+) selectivity gene Kna1 by sequential homoeologous recombination in durum wheat

Targeted homoeologous recombination mediated by the absence of the Ph1 locus is currently the most efficient technique by which foreign genes can be introgressed into polyploid wheat species. Because intra-arm homoeologous double cross-overs are rare, introgressed foreign genes are usually on terminal foreign chromosome segments. Since the minimum length of such a segment is determined by the position of a gene in the chromosome, large chromosome segments with undesirable genetic effects are often introgressed. Introgression of foreign genes on short interstitial segments based on two cycles of homoeologous recombination is described here. The utility of the technique is demonstrated by the introgression of the Kna1 locus, which controls K(+)/Na(+) selectivity in T. aesivum L., on short interstitial segments of chromosome 4D into chromosome 4B of Triticum turgidum L. The level of recombination in a homoeologous segment is not significantly affected by a juxtaposed proximal homologous segment in the absence of the Ph1 locus.