Genetic mapping of the Lr20-Pm1 resistance locus reveals suppressed recombination on chromosome arm 7AL in hexaploid wheat.

The Lr20-Sr15-Pm1 resistance locus in hexaploid wheat confers resistance to three different fungal wheat pathogens (leaf rust, stem rust, and powdery mildew). It was previously localized in the distal region of chromosome arm 7AL. As a first step towards the isolation of this complex locus, we performed molecular mapping of the Lr20 and Pm1 genes in three F2 populations. In two populations, a cluster of 8 and 12 markers, respectively, cosegregated with the resistance genes. In a third population based on a cross between a susceptible lr20 mutant and a resistant cultivar, all clustered markers were monomorphic. However, in this population the recombination frequency proximal to the Lr20 gene was up to 60 times higher, indicating that the complete genetic linkage of the clustered markers is not due to a close physical linkage of the probes but is caused by suppressed recombination. This was supported by the analysis of Triticum monococcum BAC clones where no physical linkage between cosegregating probes was observed. Suppressed recombination at the Lr20-Pm1 locus is likely the result of an alien introgression of chromatin from an unidentified wild relative species or is due to chromosomal rearrangements.     

Identification of a 4A/7R and a 7B/4R wheat-rye chromosome translocation

Summary By producing chromosome substitutions with Imperial rye chromosomes 4R (C) and 7R (D) in the wheat cultivar Chinese Spring two spontaneous translocation lines were obtained. One involves segments of wheat chromosome 4A and rye chromosome 7R, the other involves portions of wheat chromosome 7B and rye chromosome 4R     

Comparative physical mapping between wheat chromosome arm 2BL and rice chromosome 4

Physical maps of chromosomes provide a framework for organizing and integrating diverse genetic information. DNA microarrays are a valuable technique for physical mapping and can also be used to facilitate the discovery of single feature polymorphisms (SFPs). Wheat chromosome arm 2BL was physically mapped using a Wheat Genome Array onto near-isogenic lines (NILs) with the aid of wheat-rice synteny and mapped wheat EST information. Using high variance probe set (HVP) analysis, 314 HVPs constituting genes present on 2BL were identified. The 314 HVPs were grouped into 3 categories: HVPs that match only rice chromosome 4 (298 HVPs), those that match only wheat ESTs mapped on 2BL (1), and those that match both rice chromosome 4 and wheat ESTs mapped on 2BL (15). All HVPs were converted into gene sets, which represented either unique rice gene models or mapped wheat ESTs that matched identified HVPs. Comparative physical maps were constructed for 16 wheat gene sets and 271 rice gene sets. Of the 271 rice gene sets, 257 were mapped to the 18-35?Mb regions on rice chromosome 4. Based on HVP analysis and sequence similarity between the gene models in the rice chromosomes and mapped wheat ESTs, the outermost rice gene model that limits the translocation breakpoint to orthologous regions was identified.     

Reciprocal translocation between Y chromosome long arm euchromatin and the short arm of chromosome 1

A case with an apparently balanced reciprocal translocation between the long arm of the Y chromosome and the short arm of chromosome 1 t(Y;1)(q11.2;p34.3) is described. The translocation was found in a phenotypically normal male ascertained by infertility and presenting for intra-cytoplasmatic sperm injection treatment. Histological examination of testicular biopsies revealed spermatogenic failure. Chromosome painting with probes for chromosome 1 and for the euchromatic part of the Y chromsome confirmed the translocation of euchromatic Y chromosomal material onto the short arm of chromosome 1 and of a substantial part of the short arm of chromosome 1 onto the Y chromosome. Among the Y/autosome translocations, the rearrangements involving long arm euchromatin of the Y chromosome are relatively rare and mostly associated with infertility. Microdeletion screening at the azoospermia locus revealed no deletions, suggesting another mechanism causing infertility in this translocation carrier.     

The isolation,characterization and application in the Triticeae of a set of wheat RFLP probes identifying each homoeologous chromosome arm

Summary To investigate the use of RFLP analysis in the Triticeae, a set of low copy number probes has been isolated from a wheat cDNA library. The probes identify each of the 14 homoeologous chromosome arms of wheat as determined by analysis of DNA fragments hybridizing to the probes in aneuploid lines of Chinese Spring. These probes can be used in RFLP analyses both for the assignment of homoeology of alien chromosomes or arms added to wheat, and for the determination of chromosome dosage in wheat aneuploids. Different chromosomes from various Triticeae species can therefore be followed in a wheat genetic background using a single technique. The potential uses of the set in facilitating the transfer of alien segments into wheat are outlined.     

Identification of the gene Pm47 on chromosome 7BS conferring resistance to powdery mildew in the Chinese wheat landrace Hongyanglazi

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is an important disease that causes substantial yield losses in wheat (Triticum aestivum) in China and other parts of the world. This foliar disease can be effectively managed by host resistance. The Chinese landrace Hongyanglazi from Shaanxi province is highly resistant to many Bgt isolates at the seedling stage. Genetic analysis using an F_2:3 population derived from a cross between Hongyanglazi and susceptible cultivar Zhongzuo 9504 indicated that Hongyanglazi carried a single recessive gene (tentatively designated PmHYLZ) conferring its resistance to Bgt isolate E09. PmHYLZ was flanked by EST marker BE606897 and microsatellite marker Xgwm46 on chromosome 7BS at genetic distances of 1.7 and 3.6 cM, respectively. This gene differed from Pm40, also located on 7BS, by origin, linked markers, and reactions to 13 Bgt isolates. Based on these findings, PmHYLZ was permanently designated as Pm47.     

A 2600-locus chromosome bin map of wheat homoeologous group 2 reveals interstitial gene-rich islands and colinearity with rice

The complex hexaploid wheat genome offers many challenges for genomics research. Expressed sequence tags facilitate the analysis of gene-coding regions and provide a rich source of molecular markers for mapping and comparison with model organisms. The objectives of this study were to construct a high-density EST chromosome bin map of wheat homoeologous group 2 chromosomes to determine the distribution of ESTs, construct a consensus map of group 2 ESTs, investigate synteny, examine patterns of duplication, and assess the colinearity with rice of ESTs assigned to the group 2 consensus bin map. A total of 2600 loci generated from 1110 ESTs were mapped to group 2 chromosomes by Southern hybridization onto wheat aneuploid chromosome and deletion stocks. A consensus map was constructed of 552 ESTs mapping to more than one group 2 chromosome. Regions of high gene density in distal bins and low gene density in proximal bins were found. Two interstitial gene-rich islands flanked by relatively gene-poor regions on both the short and long arms and having good synteny with rice were discovered. The map locations of two ESTs indicated the possible presence of a small pericentric inversion on chromosome 2B. Wheat chromosome group 2 was shown to share syntenous blocks with rice chromosomes 4 and 7.     

Functional features of a single chromosome arm in wheat (1AL) determined from its structure

Bread wheat (Triticum aestivum L.) is one of the most important crops globally and a high priority for genetic improvement, but its large and complex genome has been seen as intractable to whole genome sequencing. Isolation of individual wheat chromosome arms has facilitated large-scale sequence analyses. However, so far there is no such survey of sequences from the A genome of wheat. Greater understanding of an A chromosome could facilitate wheat improvement and future sequencing of the entire genome. We have constructed BAC library from the long arm of T. aestivum chromosome 1A (1AL) and obtained BAC end sequences from 7,470 clones encompassing the arm. We obtained 13,445 (89.99%) useful sequences with a cumulative length of 7.57 Mb, representing 1.43% of 1AL and about 0.14% of the entire A genome. The GC content of the sequences was 44.7%, and 90% of the chromosome was estimated to comprise repeat sequences, while just over 1% encoded expressed genes. From the sequence data, we identified a large number of sites suitable for development of molecular markers (362 SSR and 6,948 ISBP) which will have utility for mapping this chromosome and for marker assisted breeding. From 44 putative ISBP markers tested 23 (52.3%) were found to be useful. The BAC end sequence data also enabled the identification of genes and syntenic blocks specific to chromosome 1AL, suggesting regions of particular functional interest and targets for future research.     

Comparison of homoeologous group-6 short arm physical maps of wheat and barley reveals a similar distribution of recombinogenic and gene-rich regions

Eighty two new loci, mapped with 51 DNA clones, were added to the earlier deletion maps of the homoeologous group-6 short arms of hexaploid wheat ( Triticum aestivum L. em Thell., 2n = 6 x = 42, AABBDD). There are now 41, 56 and 52 loci mapped on deletion maps of 6AS, 6BS and 6DS, respectively. The linear order of orthologous loci in all three arms appears to be identical. The majority of the loci are located in the distal one-half of the three arms. There seems to be an increased marker/gene density from the centromeric to the telomeric regions in each arm, and the marker density in comparable physical regions is similar on all three maps. Recombination is not uniformly distributed along the chromosome arms; 60% of recombination occurs in the distal one-third of each arm. Recombination increases from the proximal region to the distal end in a nonlinear pattern. The distribution of loci and recombination along each of the three chromosome arms is highly correlated. Comparison of the 6BS deletion map from this study and a 6HS physical map of barley ( Hordeum vulgare L., 2n = 2 x = 14, HH) reveals a remarkably similar distribution of recombinogenic and gene-rich regions between the two chromosome arms, suggesting that the distribution patterns of genes may be conserved in the homoeologous group-6 chromosome short arms of wheat and barley. A consensus map of wheat group-6 short arms containing 46 orthologous loci was constructed. Comparison of the consensus map with published linkage maps of Triticeae group-6 chromosome short arms indicates that the linear order of the loci on the maps has been largely conserved. Evidence from this study does not support the existence of a 2BS-6BS reciprocal terminal translocation.     

Physical distribution of translocation breakpoints in homoeologous recombinants induced by the absence of the Ph1 gene in wheat and triticale

The physical distribution of translocation breakpoints was analyzed in homoeologous recombinants involving chromosomes 1A, 1B, 1D of wheat and 1R of rye, and the long arms of chromosome 7S of Aegilops speltoides and 7A of wheat. Recombination between homoeologues was induced by removal of the Ph1 gene. In all instances, translocation breakpoints were concentrated in the distal ends of the chromosome arms and were absent in the proximal halves of the arms. The relationship between the relative distance from the centromere and the relative homoeologous recombination frequency was best explained by the function f(x)=0.0091e^0.0592x. The pattern of recombination in homoeologous chromosomes was essentially the same as in homologues except that there were practically no double exchanges. Among 313 recombinant chromosomes, only one resulted from a double crossing-over. The distribution of translocation breakpoints in translocated arms indicated that positive chiasma interference operated in homoeologous recombination. This implies that the reduction of the length of alien chromosome segments present in translocations with wheat chromosomes may be more difficult than the production of the original recombinants.     

The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution

Background

The wheat genome sequence is an essential tool for advanced genomic research and improvements. The generation of a high-quality wheat genome sequence is challenging due to its complex 17 Gb polyploid genome. To overcome these difficulties, sequencing through the construction of BAC-based physical maps of individual chromosomes is employed by the wheat genomics community. Here, we present the construction of the first comprehensive physical map of chromosome 1BS, and illustrate its unique gene space organization and evolution.

Results

Fingerprinted BAC clones were assembled into 57 long scaffolds, anchored and ordered with 2,438 markers, covering 83% of chromosome 1BS. The BAC-based chromosome 1BS physical map and gene order of the orthologous regions of model grass species were consistent, providing strong support for the reliability of the chromosome 1BS assembly. The gene space for chromosome 1BS spans the entire length of the chromosome arm, with 76% of the genes organized in small gene islands, accompanied by a two-fold increase in gene density from the centromere to the telomere.

Conclusions

This study provides new evidence on common and chromosome-specific features in the organization and evolution of the wheat genome, including a non-uniform distribution of gene density along the centromere-telomere axis, abundance of non-syntenic genes, the degree of colinearity with other grass genomes and a non-uniform size expansion along the centromere-telomere axis compared with other model cereal genomes. The high-quality physical map constructed in this study provides a solid basis for the assembly of a reference sequence of chromosome 1BS and for breeding applications.     

The human gene encoding acetylcholinesterase is located on the long arm of chromosome 7.

Acetylcholinesterase (AChE) is a secreted enzyme essential for regulating cholinergic neurotransmission at neuronal and neuromuscular synapses. In view of the altered expression of AChE in some central neurological and neuromuscular disorders with a probable genetic basis, we have identified the chromosomal location of the gene encoding AChE. Chromosomal in situ suppression hybridization analysis revealed a single gene to be at 7q22, a result which was confirmed by PCR analysis of genomic DNA from a human/hamster somatic cell hybrid containing a single human chromosome 7. The AChE gene thus maps to the same region in which frequent nonrandom chromosome 7 deletions occur in leukemias of myeloid cell precursors known to express the enzyme during normal differentiation.