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1.
Summary Three acrotrisomic lines, Triplo IL1S, 3L3S, and 4L4S, each carrying an extra acrocentric chromosome, were used for cytogenetic linkage mapping of barley chromosomes. The cytological structures of the acrocentric chromosome of the three acrotrisomic lines were studied with an improved Giemsa N-banding technique. The long (1L) and short arm (1S) of chromosome 1 had deficiencies of approximately 38% and 65%, respectively. The percentages of deficiencies were 0 and 77.8% for 3L and 3S, and 31.7 and 59.3% for 4L and 4S, respectively. All three genes tested (br, f c , gs3) in 1S and all three genes tested, f8, n and 1k2 in 1L showed a disomic ratio indicating that they are located in the deficient segments. Two genes (a c , yst2) located in the middle segment of 3S in linkage map showed a trisomic ratio, and two others a n , x s showed a disomic ratio. The only gene(f9) tested in 4L showed a trisomic ratio. Two genes (1g4, g1) located in the proximal segment of 4S in the linkage map showed a trisomic ratio, whereas two genes (br2, g13) located distally in 4S showed a disomic ratio, indicating that the breakage occurred between g1 and br2. This experiment demonstrates a new method for physical localization of genes on chromosome segments in material such as barley in which pachytene analysis can not be effectively used for accurate determination of break points in structural changes. Problems associated with this new technique are discussed.Contribution from the Department of Agronomy and published with the approval of the Director of Colorado State University Experiment Station as Scientific Series Paper No. 2823. Supported by USDA/SEA Competitive Research Grant Nos. 5901-0410-9-0334-0 and 82-CRCR-1-1020 and USDA-CSU Cooperative Research Grant 58-9AHZ-2-265  相似文献   

2.
Generating a contiguous, ordered reference sequence of a complex genome such as hexaploid wheat (2n = 6x = 42; approximately 17 GB) is a challenging task due to its large, highly repetitive, and allopolyploid genome. In wheat, ordering of whole‐genome or hierarchical shotgun sequencing contigs is primarily based on recombination and comparative genomics‐based approaches. However, comparative genomics approaches are limited to syntenic inference and recombination is suppressed within the pericentromeric regions of wheat chromosomes, thus, precise ordering of physical maps and sequenced contigs across the whole‐genome using these approaches is nearly impossible. We developed a whole‐genome radiation hybrid (WGRH) resource and tested it by genotyping a set of 115 randomly selected lines on a high‐density single nucleotide polymorphism (SNP) array. At the whole‐genome level, 26 299 SNP markers were mapped on the RH panel and provided an average mapping resolution of approximately 248 Kb/cR1500 with a total map length of 6866 cR1500. The 7296 unique mapping bins provided a five‐ to eight‐fold higher resolution than genetic maps used in similar studies. Most strikingly, the RH map had uniform bin resolution across the entire chromosome(s), including pericentromeric regions. Our research provides a valuable and low‐cost resource for anchoring and ordering sequenced BAC and next generation sequencing (NGS) contigs. The WGRH developed for reference wheat line Chinese Spring (CS‐WGRH), will be useful for anchoring and ordering sequenced BAC and NGS based contigs for assembling a high‐quality, reference sequence of hexaploid wheat. Additionally, this study provides an excellent model for developing similar resources for other polyploid species.  相似文献   

3.
 The hordeins are the major class of storage proteins in barley and are encoded by multigene families. Two YAC-clones specific for the C-hordein-coding Hor1-locus of barley (Hordeum vulgare L.) were selected. The clones were constructed with DNA from the cultivars ‘Franka’ and ‘Hockey’ and have insert sizes of 330 kb and 350 kb, respectively. Performing partial digestions and hybridizations with vector-specific probes, a restriction analysis was conducted using restriction enzymes with a 8-bp recognition sequence. Both clones cover the complete region of the Hor1-locus, but exhibit a different pattern of restriction sites reflecting the polymorphic nature of the locus on the scale of long-range restriction mapping. The maximal extent of the regions homologous to the Hor1-specific probe, pBSC5, was 105 kb in the ‘Hockey’-derived YAC and 190 kb in the yeast artificial chromosome constructed with ‘Franka’-DNA. Furthermore the high degree of instability observed with the Hor1-specific YAC-clones is discussed in conjunction with the structure of the Hor1-locus. Received: 19 December 1996 / Accepted: 31 January 1997  相似文献   

4.
Whole-genome radiation hybrid mapping has been applied extensively to human and certain animal species, but little to plants. We recently demonstrated an alternative mapping approach in cotton (Gossypium hirsutum L.), based on segmentation by 5-krad γ-irradiation and derivation of wide-cross whole-genome radiation hybrids (WWRHs). However, limitations observed at the 5-krad level suggested that higher doses might be advantageous. Here, we describe the development of an improved second-generation WWRH panel after higher dose irradiation and compare the resulting map to the 5-krad map. The genome of G. hirsutum (n=26) was used to rescue the radiation-segmented genome of G. barbadense (n=26) introduced via 8- and 12-krad γ-irradiated pollen. Viable seedlings were not recovered after 12-krad irradiation, but 8-krad irradiation permitted plant recovery and construction of a 92-member WWRH mapping panel. Assessment of 31 SSR marker loci from four chromosomes revealed that the 8-krad panel has a marker retention frequency of ca. 76%, which is approximately equivalent to the rate of loss in a low-dose animal radiation hybrid panel. Retention frequencies of loci did not depart significantly from independence when compared between the A and D subgenomes, or according to positions along individual chromosomes. WWRH maps of chromosomes 10 and 17 were generated by the maximum likelihood RHMAP program and the general retention model. The resulting maps bolster evidence that WWRH mapping complements traditional linkage mapping and works in cotton, and that the 8-krad panel complements the 5-krad panel by offering higher rates of chromosome breakages, lower marker retention frequency, and more retention patterns. Electronic Supplementary Material Supplementary material is available for this article at  相似文献   

5.
Application of radiation hybrid in gene mapping   总被引:2,自引:0,他引:2  
Radiationhybrid(RH)mappingisasomaticcellgeneticmappingtechniquewitharesolutionofabout500kb.Ithasbecomeageneralwaytoconstructhighresolution,contiguousphysicalmapofhumanchromosomes[1].BasedonearlierstudiesofGossandHarris[2]andmodificationlaterbyCoxandcoworker…  相似文献   

6.
Deletion-based physical mapping of barley chromosome 7H   总被引:1,自引:1,他引:0  
Chromosomal mutations in barley (Hordeum vulgare, 2n=2x=14, HH) chromosome 7H added to the common wheat (Triticum aestivum, 2n=6x=42, AABBDD) cultivar Chinese Spring were induced genetically by the gametocidal activity of certain alien chromosomes derived from wild species of the genus Aegilops. The rearranged barley chromosomes were characterized by C-banding, FISH and GISH. Twenty two deletion or translocation chromosomes in a hemizygous condition were selected for deletion mapping of 17 AFLP and 28 STS markers that are specific to 7H. Of the 22 breakpoints in chromosome 7H, seven involved the short arm (7HS), 12 the long arm (7HL) and three were in the centromeric region. The seven 7HS breakpoints separated all four 7HS-specific AFLP markers and split the 21 STS markers into six groups. One breakpoint occurred between two STS markers formerly occupying the same position in the genetic map. All seven 7HS breakpoints were separated from each other by either the AFLP or STS markers. The 12 breakpoints in 7HL divided the 13 7HL-specific AFLP markers into seven groups, and the seven STS markers into three groups. On the other hand, the 12 breakpoints in 7HL were divided into six groups by the AFLP markers and into two groups by the STS markers. This deletion-based map was in accordance with previously published genetic and physical maps using the same STS markers. The breakpoints, AFLP markers and STS markers were arrayed in a consistent order. Received: 5 February 2001 / Accepted: 19 February 2001  相似文献   

7.

Background

The domestic goat (Capra hircus), an important livestock species, belongs to a clade of Ruminantia, Bovidae, together with cattle, buffalo and sheep. The history of genome evolution and chromosomal rearrangements on a small scale in ruminants remain speculative. Recently completed goat genome sequence was released but is still in a draft stage. The draft sequence used a variety of assembly packages, as well as a radiation hybrid (RH) map of chromosome 1 as part of its validation.

Results

Using an improved RH mapping pipeline, whole-genome dense maps of 45,953 SNP markers were constructed with statistical confidence measures and the saturated maps provided a fine map resolution of approximate 65 kb. Linking RH maps to the goat sequences showed that the assemblies of scaffolds/super-scaffolds were globally accurate. However, we observed certain flaws linked to the process of anchoring chromosome using conserved synteny with cattle. Chromosome assignments, long-range order, and orientation of the scaffolds were reassessed in an updated genome sequence version. We also present new results exploiting the updated goat genome sequence to understand genomic rearrangements and chromosome evolution between mammals during species radiations. The sequence architecture of rearrangement sites between the goat and cattle genomes presented abundant segmental duplication on regions of goat chromosome 9 and 14, as well as new insertions in homologous cattle genome regions. This complex interplay between duplicated sequences and Robertsonian translocations highlights the rearrangement mechanism of centromeric nonallelic homologous recombination (NAHR) in mammals. We observed that species-specific shifts in ANKRD26 gene duplication are coincident with breakpoint reuse in divergent lineages and this gene family may play a role in chromosome stabilization in chromosome evolution.

Conclusions

We generated dense maps of the complete whole goat genome. The chromosomal maps allowed us to anchor and orientate assembled genome scaffolds along the chromosomes, annotate chromosome rearrangements and thereby get a better understanding of the genome evolution of ruminants and other mammals.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-625) contains supplementary material, which is available to authorized users.  相似文献   

8.
Combined mapping of AFLP and RFLP markers in barley   总被引:56,自引:0,他引:56  
AFLP marker technology allows efficient DNA fingerprinting and the analysis of large numbers of polymorphic restriction fragments on polyacrylamide gels. Using the doubled haploids from the F1 of the cross Proctor × Nudinka, 118 AFLP markers were mapped onto a barley (Hordeum vulgare L.) RFLP map, also including five microsatellite and four protein marker loci. The AFLP markers mapped to all parts of the barley chromosomes and filled in the gaps on barley chromosomes 2L, 4L and 6 in which no RFLP loci had been mapped. Interestingly, the AFLP markers seldom interrupted RFLP clusters, but grouped next to them. The combined map covers 1873 cM, with a total of 282 markers. The merging of AFLP and RFLP markers increased the total map length; 402 cM were added to the map at the tips of chromosomes or in regions corresponding to earlier gaps. Another 375 cM resulted from mapping AFLP markers near to RFLP clusters or in between non-clustered RFLP markers.  相似文献   

9.
Variants of the pulsed-field gel electrophoresis technique were used in conjunction with two-dimensional DNA gel electrophoresis (2-DDGE) to determine the ratio of physical to genetic distance in two genetically defined intervals on barley chromosome 1H.2-DDGE analysis demonstrated that two loci that define a 0.3 cM interval, as determined by hybridization with BCD249, reside on a single 450-kbMluI fragment. This result indicates a maximum ratio of physical to genetic distance in this interval of 1500 kb/cM as compared to 3.7–4.2 Mb/cM for the barley genome as a whole. High molecular weight (HMW) DNA restricted withNotI and probed sequentially with MWG068 and BCD249 yield diffuse bands at approximately 2.8 Mb and 3.0 Mb in the C.I. 16151 and C.I. 16155 parental lines, respectively. These results suggest the maximum ratio of physical to genetic distance in the interval defined by these probes is 7.8 Mb/cM. unique HMW DNA restriction fragment length polymorphisms (RFLP) were attributed to the presence of recombination breakpoints. Data from the recombination breakpoint analysis were used to estimate a ratio of physical to genetic distance of 2.5 Mb/cM in theXbcd249.2-Xmwg068 interval and 0.465 Mb/cM in theXbcd249.1-Xbcd249.2 interval. Both physical linkage and recombination breakpoint analysis indicate theXbcd249.1-Xbcd249.2 interval is approximately five-fold smaller, physically, than theXbcd249.2-Xmwg068 interval.Names are necessary to report factually on available data; however the USDA neither guarantees nor warrants the standard of the product and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitable  相似文献   

10.
Seven biochemical loci, AmpA, Amy1, Amy2, Est-H5, Hor1, Hor2, and Wsp-H1, have been intrachromosomally mapped in the barley genome using a previously published RFLP-based genetic map. In all cases, the map locations confirmed prior chromosome assignments and agreed closely with the map positions of their homoeoloci in hexaploid wheat.  相似文献   

11.
Loci for 9322 equine expressed sequence tags (ESTs) were predicted using the Comparative Mapping by Annotation and Sequence Similarity (Compass) strategy in order to evaluate the programme's ability to make accurate locus predictions in species with comparative gene maps. Using human genome sequence information from Build 35 (May 2004) and published marker information from the radiation hybrid (RH) maps for equine chromosomes (ECA) 17 and X, 162 ESTs were predicted to locations on ECA17 and 328 ESTs to locations on ECAX by selection of the 'top blast hit'. The locations of 30 ESTs were assessed experimentally by RH mapping analysis to evaluate the accuracy of the Compass predictions. The data revealed that 53% (16 of 30) of the ESTs predicted on ECA17 and ECAX mapped to those chromosomes. Analysis of the results suggested the need to identify expressed orthologous sequences in order to generate more accurate predictions for ESTs. Locus predictions were reassessed with three modifications to the Compass strategy's orthologue selection parameters. Selection of the 'top gene hit' improved accuracy to 72% (21 of 29), while selection of the 'top expressed gene hit' improved accuracy to 86% (24 of 28). Using the default Compass parameters with the UniGene database improved prediction accuracy to 96% (22 of 23); however, this level of accuracy came with a substantial decrease in the total number of predictions. When used with optimized prediction parameters, the Compass strategy can be a practical in silico map location prediction tool for large EST sample sets from unsequenced animal genomes.  相似文献   

12.
The 5S rDNA locus on the long arm of barley chromosome 2(2H) was genetically mapped in two crosses in relation to 30 other RFLP loci. Comparison of the genetic maps with the previously published physical position of the 5S rDNA, determined by in-situ hybridization, showed that there was a marked discrepancy between physical and genetic distance in both crosses, with recombination being less frequent in the proximal part of the arm. Pooled information from the present study and other published genetic maps showed that at least 26 of the 44 (59%) RFLPs that have been mapped on 2(2H)L lie distal to the 5S rDNA locus even though this region is only 27% of the physical length of the arm. The distribution of RFLP markers is significantly different from expected (P < 0.01), implying that the low-copy sequences used for RFLP analysis occur more frequently in distal regions of the arm and, or, that sequences in distal regions are more polymorphic.  相似文献   

13.
This work addresses issues around physical maps, in particular, for circular genomes. The overlapping relationship between two fragments obtained by applying two different restriction enzymes, separately, is classified as nonoverlapping, partial overlapping, and total overlapping. A double partial overlapping can also appear in a particular situation. Taking into account DNA fragment lengths and under the assumption that the left-hand endpoints of the two restriction fragments are independent random variables, each of which with a uniform distribution along a circular genome, we present expressions for prior probabilities of those events. This information is combined with hybridization data via Bayes' theorem, in order to evaluate corresponding posterior probabilities. Additionally, we explore a sensitivity analysis to quantify the effect of length variation in the results.  相似文献   

14.
In many cropping regions of the world, yield is limited by the availability of micronutrients, and micronutrient-efficient cultivars provide a yield advantage. Traditional methods of testing cultivars for micronutrient efficiency are time-consuming and laborious. Molecular markers linked to loci controlling micronutrient efficiency will allow more rapid and efficient selection and introgression of these traits than is currently possible. Using a pot-based bioassay and bulked segregant analysis of an F2 population, we have identified several RFLPs (grouped distally on chromosome 4HS) linked to a locus for manganese efficiency in barley. This manganese efficiency locus has been designated Mel1. Pot bioassay analysis of intercrosses suggests that three useful sources of manganese efficiency are likely to be allelic at the Mel1 locus. Field evaluation of marker selected F4 progeny supports the major role of Mel1 in the genetic control of manganese efficiency. Adoption of marker assisted selection for this trait in the Southern Australian barley breeding program has occurred. This has been facilitated by the demonstration that the Mel1 allele of Amagi Nijo can be distinguished from 95 other locally useful varieties and breeder’s lines on the basis of RFLPs identified by just two molecular markers. Received: 20 October 1999 / Accepted: 18 February 2000  相似文献   

15.
Xu Z  Sun S  Covaleda L  Ding K  Zhang A  Wu C  Scheuring C  Zhang HB 《Genomics》2004,84(6):941-951
Genome physical mapping with large-insert clones by fingerprint analysis is becoming an active area of genomics research. Here, we report two new capillary electrophoresis-based fingerprinting methods for genome physical mapping and the effects of different fingerprinting methods and source clone genome coverage on quality physical map construction revealed by computer simulations and laboratory experiments. It was shown that the manual sequencing gel-based two-enzyme fingerprinting method consistently generated larger and more accurate contigs, followed by the new capillary electrophoresis-based three-enzyme method, the new capillary electrophoresis-based five-enzyme (SNaPshot) method, the agarose gel-based one-enzyme method, and the automatic sequencing gel-based four-enzyme method, in descending order, when 1% or fewer questionable clones were allowed. Analysis of clones equivalent to 5x, 8x, 10x, and 15x genomes using the fingerprinting methods revealed that as the number of clones increased from 5x to 10x, the contig length rapidly increased for all methods. However, when the number of clones was increased from 10x to 15x coverage, the contig length at best increased at a lower rate or even decreased. The results will provide useful knowledge and strategies for effective construction of quality genome physical maps for advanced genomics research.  相似文献   

16.
The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC‐by‐BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high‐resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high‐resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome‐scale analysis of repetitive sequences and revealed a ~800‐kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone‐by‐clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC‐contig physical map and validate sequence assembly on a chromosome‐arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome‐by‐chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules.  相似文献   

17.
Recent genomic projects reveal that about half of the gene repertoire in plant genomes is made up by multigene families. In this paper, a set of structural and phylogenetic analyses have been applied to compare the differently sized nicotianamine synthase (NAS) gene families in barley and rice. Nicotianamine acts as a chelator of iron and other heavy metals and plays a key role in uptake, phloem transport and cytoplasmic distribution of iron, challenging efforts for the breeding of iron-efficient crop plants. Nine barley NAS genes have been mapped, and co-linearity of flanking genes in barley and rice was determined. The combined analyses reveal that the NAS multigene family members in barley originated through at least one duplication event that occurred before the divergence of rice and barley. Additional duplications appear to have occurred within each of the species. Although we detected no evidence for positive selection of recently duplicated genes within species, codon-based tests revealed evidence for positive selection having contributed to the divergence of some amino acids. The integrated comparative and phylogenetic analysis improved our current view of NAS gene family evolution, might facilitate the functional characterization of individual members and is applicable to other multigene families. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.  相似文献   

18.
Molecular mapping of the photoperiod response gene ea7 in barley   总被引:1,自引:0,他引:1  
 The gene ea 7 determining photoperiod insensitivity under short day length was mapped on the short arm of chromosome 6H near the centromere. The gene was linked to the two flanking markers Xmwg2264 and Xmwg916 by 6.7 and 13.0 cM, respectively. Compared to Ppd-H1 (chromosome 2H) and Ppd-H2 (chromosome 1H), ea 7 determines the strongest effect on flowering time with 55 and 18 days difference compared to photoperiod sensitive genotypes grown under short and long photoperiods, respectively. Allelic and homoeologous relationships to major genes and quantitative trait loci controlling flowering time in barley and wheat are discussed. Received: 10 March 1998 / Accepted: 7 April 1998  相似文献   

19.
We present the first radiation hybrid (RH) map of river buffalo (Bubalus bubalis) chromosome 6 (BBU6) developed with a recently constructed river buffalo whole-genome RH panel (BBURH(5000)). The preliminary map contains 33 cattle-derived markers, including 12 microsatellites, 19 coding genes and two ESTs, distributed across two linkage groups. Retention frequencies for markers ranged from 14.4% to 40.0%. Most of the marker orders within the linkage groups on BBU6 were consistent with the cattle genome sequence and RH maps. This preliminary RH map is the starting point for comparing gene order between river buffalo and cattle, presenting an opportunity for the examination of micro-rearrangements of these chromosomes. Also, resources for positional candidate cloning in river buffalo are enhanced.  相似文献   

20.
Summary A total of 37 genetic markers located in chromosomes 2, 3, 4 and 5 were associated with specific arms by means of telotrisomic analysis in five telotrisomics (Triplo 2 L, 2 S, 3 S, 4 S, 5 L) of barley (Hordeum vulgare L.). The genes v, gp (= gp 2), li, gs 5, tr and msg2 showed a trisomic ratio with Triplo 2 L indicating that these genes were on the long arm of chromosome 2. A disomic ratio was obtained for genes wst 4, gs 5, and v with Triplo 2 S, confirming that these genes were on the long arm of chromosome 2(2 L). A disomic ratio was observed for genes e, f(= lg), sk, and gs6 with Triplo 2 L. Two genes, f(= lg) and gs6 showed a trisomic ratio with Triplo 2S. These results indicated that genes e, f(= lg), sk, and gs 6 are on the short arm of chromosome 2 (2S). Since only one telocentric chromosome was available for chromosome 3, 4 and 5, most of the well-mapped marker genes were tested with those telocentric chromosomes. The genes cu 2, uz, wst, als, gs 2, zb,f2, and cer-zn 348 showed trisomic ratio with the telocentric for chromosome 3. These genes were located on the short arm of chromosome 3 (Robertson 1971). This indicated that the telocentric chromosome is for the short arm of chromosome 3(3 S). A disomic ratio was obtained for genes yst, x c, al, yst2, a n, ari-a 6 and x s, indicating that these genes are on the long arm of chromosome 3. Two genes, f9 and K, showed trisomic ratio with the telocentric chromosome for 4, while genes gl(= gl2), br2, yh, lg 3, lg 4 and lk 5 showed disomic ratios. This indicated that the telocentric chromosome is for the short arm of chromosome 4. Two genes, fs 2 and g, were studied with Triplo 5 L. Both showed trisomic ratio, indicating that fs 2 and g are located on Triplo 5 L. The centromere position (C) on chromosome 2, 3 and 4 was thus located as (the left side of C is the short arm and the right is the long arm): chromosome 2: fskgs6e — C — gs5msg2wst4vgplitr; chromosome 3: f2cer-zn 348uzgs2alscu2wstzb — C — ystx calyst2a nari-a 6x s; chromosome 4: f9KClg4lg 3gl2br2lk5yh. The centromere position on chromosome 5 was not precisely located.Contribution from the Department of Agronomy, Published with the approval of the director of the Colorado State University Experiment Station as Scientific Series Paper No. 2606. This research was supported in part by by NSF Grant GB 4482X and GB 30 493 to T. Tsuchiya and Colorado State University Experiment Station Hatch Project  相似文献   

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