共查询到20条相似文献,搜索用时 406 毫秒
1.
Mammadov JA Steffenson BJ Maroof MA 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2005,111(8):1651-1660
The rapidly growing expressed sequence tag (EST) resources of species representing the Poacea family and availability of comprehensive sequence information for the rice (Oryza sativa) genome create an excellent opportunity for comparative genome analysis. Extensive synteny between rice chromosome 1 and
barley (Hordeum vulgare L.) chromosome 3 has proven extremely useful for saturation mapping of chromosomal regions containing target genes of large-genome
barley with conserved orthologous genes from the syntenic regions of the rice genome. Rph5 is a gene conferring resistance to the barley leaf rust pathogen Puccinia hordei. It was mapped to chromosome 3HS, which is syntenic with rice chromosome 1S. The objective of this study was to increase
marker density within the sub-centimorgan region around Rph5, using sequence-tagged site (STS) markers that were developed based on barley ESTs syntenic to the phage (P1)-derived artificial
chromosome (PAC) clones comprising the distal region of rice chromosome 1S. Five rice PAC clones were used as queries in a
blastn search to screen 375,187 barley ESTs. Ninety-four non-redundant EST sequences were identified from the EST database
and used as templates to design 174 pairs of primer combinations. As a result, 9 barley EST-based STS markers were incorporated
into the ‘Bowman’ × ‘Magnif 102’ high-resolution map of the Rph5 region. More importantly, six markers, including five EST-derived STS sequences, were found to co-segregate with Rph5. The results of this study demonstrate the usefulness of rice genomic resources for efficient deployment of barley ESTs for
marker saturation of targeted barley genomic regions. 相似文献
2.
Identification and mapping of the leaf stripe resistance gene Rdg1a in Hordeum spontaneum 总被引:2,自引:0,他引:2
Chiara Biselli Simona Urso Letizia Bernardo Alessandro Tondelli Gianni Tacconi Valentina Martino Stefania Grando Giampiero Valè 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2010,120(6):1207-1218
Leaf stripe of barley, caused by Pyrenophora graminea, is an important seed-borne disease in organically grown as well as in conventionally grown Nordic and Mediterranean barley
districts. Two barley segregating populations represented by 103 recombinant inbred lines (RILs) of the cross L94 (susceptible) × Vada
(resistant) and 194 RILs of the cross Arta (susceptible) × Hordeum spontaneum 41-1 (resistant) were analysed with two highly virulent leaf stripe isolates, Dg2 and Dg5, to identify loci for P. graminea resistance. A major gene with its positive allele contributed by Vada and H. spontaneum 41-1 was detected in both populations and for both pathogen isolates on chromosome 2HL explaining 44.1 and 91.8% R
2, respectively for Dg2 and Dg5 in L94 × Vada and 97.8 and 96.1% R
2, respectively for Dg2 and Dg5 in Arta × H. spontaneum 41-1. Common markers in the gene region of the two populations enabled map comparison and highlighted an overlapping for
the region of the resistance locus. Since the map position of the resistance locus identified in this report is the same as
that for the leaf stripe resistance gene Rdg1a, mapped earlier in Alf and derived from the ‘botanical’ barley line H. laevigatum, we propose that leaf stripe resistance in Vada and H. spontaneum 41-1 is governed by the same gene, namely by Rdg1a, and that Rdg1a resistance could be traced back to H. spontaneum, the progenitor of cultivated barley. PCR-based molecular markers that can be used for marker-assisted selection (MAS) of
Rdg1a were identified. An Rdg1a syntenic interval with the rice chromosome arm 4L was identified on the basis of rice orthologs of EST-based barley markers.
Analysis of the rice genes annotated into the syntenic interval did not reveal sequences strictly belonging to the major class
(nucleotide-binding site plus leucine-rich repeat) of the resistance genes. Nonetheless, four genes coding for domains that
are present in the major disease-resistance genes, namely receptor-like protein kinase and ATP/GTP-binding proteins, were
identified together with a homolog of the barley powdery mildew resistance gene mlo. Three (out of five) homologs of these genes were mapped in the Rdg1a region in barley and the mlo homolog map position was tightly associated with the LOD score peak in both populations. 相似文献
3.
Gottwald S Stein N Börner A Sasaki T Graner A 《Molecular genetics and genomics : MGG》2004,271(4):426-436
In this study, comparative high resolution genetic mapping of the GA-insensitive dwarfing gene sdw3 of barley revealed highly conserved macrosynteny of the target region on barley chromosome 2HS with rice chromosome 7L. A rice contig covering the sdw3-orthologous region was identified and subsequently exploited for marker saturation of the target interval in barley. This was achieved by (1) mapping of rice markers from the orthologous region of the rice genetic map, (2) mapping of rice ESTs that had been physically localized on the rice contig, or (3) mapping of barley ESTs that show strong sequence similarity to coding sequences present in the rice contig. Finally, the sdw3 gene was mapped to an interval of 0.55 cM in barley, corresponding to a physical distance of about 252 kb in rice, after employing orthologous EST-derived rice markers. Three putative ORFs were identified in this interval in rice, which exhibited significant sequence similarity to known signal regulator genes from different species. These ORFs can serve as starting points for the map-based isolation of the sdw3 gene from barley.Communicated by R. Hagemann 相似文献
4.
Rice-barley synteny and its application to saturation mapping of the barley Rpg1 region. 总被引:4,自引:0,他引:4 下载免费PDF全文
A Kilian D A Kudrna A Kleinhofs M Yano N Kurata B Steffenson T Sasaki 《Nucleic acids research》1995,23(14):2729-2733
In order to facilitate the map-based cloning of the barley stem rust resistance gene Rpg1, we have demonstrated a high degree of synteny at a micro level between the telomeric region of barley chromosome 1P and rice chromosome 6. We have also developed and applied a simple and efficient method for selecting useful probes from large insert genomic YAC and cosmid clones. The gene order within the most terminal 6.5 cM of barley chromosome 1P was compared with the most terminal 2.7 cM of rice chromosome 6. Nine rice probes, previously mapped in rice or isolated from YAC or cosmid clones from this region, were mapped in barley. All, except one, were in synteny with the rice gene order. The exception, probe Y617R, was duplicated in barley. One copy was located on a different chromosome and the other in a non-syntenic position on barley chromosome 1P. The barley probes from this region could not be mapped to rice, but two of them were inferred to be in a syntenic location based on their position on a rice YAC. This work demonstrates the utility of applying the results of genetic and physical mapping of the small genome cereal rice to map-based cloning of interesting genes from large genome relatives. 相似文献
5.
Comparative mapping of cereals has shown that chromosomes of barley, wheat, and maize can be described in terms of rice "linkage segments." However, little is known about marker order in the junctions between linkage blocks or whether this will impair comparative analysis of major genes that lie in such regions. We used genetic and physical mapping to investigate the relationship between the distal part of rice chromosome 7L, which contains the Hd2 heading date gene, and the region of barley chromosome 2HS containing the Ppd-H1 photoperiod response gene, which lies near the junction between rice 7 and rice 4 linkage segments. RFLP markers were mapped in maize to identify regions that might contain Hd2 or Ppd-H1 orthologs. Rice provided useful markers for the Ppd-H1 region but comparative mapping was complicated by loss of colinearity and sequence duplications that predated the divergence of rice, maize, and barley. The sequences of cDNA markers were used to search for homologs in the Arabidopsis genome. Homologous sequences were found for 13 out of 16 markers but they were dispersed in Arabidopsis and did not identify any candidate equivalent region. The implications of the results for comparative trait mapping in junction regions are discussed. 相似文献
6.
Liu Fenglou Gupta Sanjiv Zhang Xiao-Qi Jones Michael Loughman Robert Lance Reg Li Chengdao 《Molecular breeding : new strategies in plant improvement》2011,28(4):657-666
Adult plant resistance (APR) is considered potentially more durable for controlling barley leaf rust than seedling Rph (Resistance to Puccinia hordei) genes. A major gene for adult plant resistance to barley leaf rust has been mapped to the telomere region of chromosome
5HS. PCR-based molecular markers were developed for saturation of this region based on previously mapped simple sequence repeat,
restriction fragment length polymorphism and Diversity Arrays Technology markers. In addition, defence gene homologue (DGH)
and wheat expressed sequence tags mapped in specific bins were used to develop new PCR markers. Seventeen PCR-based markers
were mapped to the short arm of chromosome 5H in 292 doubled haploid lines from a cross of Pompadour × Stirling, in which
seven markers were mapped within 5 cM of the APR gene. The closest linked marker was about 0.7 cM from the APR gene. The wheat
deletion bin map together with defence gene homologues was demonstrated to be an efficient tool for development of new molecular
markers associated with the disease resistance gene. Four DGH markers were associated with the APR gene. The new molecular
markers are a useful tool for marker-assisted selection of the APR gene and provided a better understanding of the molecular
mechanism for leaf rust resistance. 相似文献
7.
A number of mutations affecting seed development in barley (Hordeum vulgare L.) have been known for many years; however, to date, no research has been reported that elucidates the molecular structure of the causal genes. As a first step, we initiated the linkage mapping of the two shrunken endosperm genes seg8 and sex1 using microsatellite markers. The recessive gene seg8 was mapped in the centromeric region of chromosome 7H to a 4.6 cM interval flanked by markers GBM1516 and Bmag341. The recessive sex1 gene showed xenia effects and was located in the centromeric region of barley chromosome 6H, which is in accordance to the previously reported chromosomal location in the classical linkage map. It was flanked by markers GBM5012 and GBM1063 in a 4.2 cM interval. EST-derived microsatellite markers were used to establish the syntenic relationships to the genomic rice sequences. Two orthologous sites on rice chromosome 2 flanking a 4.1 Mb sequence had homology to the respective barley markers in the sex1 region. For the markers in the seg8 region orthologous sites on rice chromosome 6 were detected. 相似文献
8.
Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison 总被引:11,自引:0,他引:11
Li C Ni P Francki M Hunter A Zhang Y Schibeci D Li H Tarr A Wang J Cakir M Yu J Bellgard M Lance R Appels R 《Functional & integrative genomics》2004,4(2):84-93
Pre-harvest sprouting results in significant economic loss for the grain industry around the world. Lack of adequate seed dormancy is the major reason for pre-harvest sprouting in the field under wet weather conditions. Although this trait is governed by multiple genes it is also highly heritable. A major QTL controlling both pre-harvest sprouting and seed dormancy has been identified on the long arm of barley chromosome 5H, and it explains over 70% of the phenotypic variation. Comparative genomics approaches among barley, wheat and rice were used to identify candidate gene(s) controlling seed dormancy and hence one aspect of pre-harvest sprouting. The barley seed dormancy/pre-harvest sprouting QTL was located in a region that showed good synteny with the terminal end of the long arm of rice chromosome 3. The rice DNA sequences were annotated and a gene encoding GA20-oxidase was identified as a candidate gene controlling the seed dormancy/pre-harvest sprouting QTL on 5HL. This chromosomal region also shared synteny with the telomere region of wheat chromosome 4AL, but was located outside of the QTL reported for seed dormancy in wheat. The wheat chromosome 4AL QTL region for seed dormancy was syntenic to both rice chromosome 3 and 11. In both cases, corresponding QTLs for seed dormancy have been mapped in rice.C. Li and P. Ni contributed equally to this work 相似文献
9.
10.
11.
《Molecular & general genetics : MGG》1996,253(1-2):225-231
Using a recently developed polymerase chain reaction (PCR)-mediated approach for physical mapping of single-copy DNA sequences
on microisolated chromosomes of barley, sequence-tagged sites of DNA probes that reveal restriction fragment length polymorphisms
(RFLP) localized on the linkage maps of rice chromosomes 5 and 10 were allocated to cytologically defined regions of barley
chromosome 5 (1H). The rice map of linkage group 5, of about 135 cM in size, falls into two separate parts, which are related
to the distal portions of both the short and long arms of the barley chromosome. The markers on the rice map of chromosome
5 were found to be located within regions of the barley chromosome which show high recombination rates. The map of rice chromosome
10, of about 75 cM in size, on the other hand, is related to an interstitial segment of the long arm of chromosome 5 (1H)
which is highly suppressed in recombination activity. For positional cloning of genes of this homoeologous region from the
barley genome, the small rice genome will probably prove to be a useful tool. No markers located on rice chromosomes were
detected within the pericentric Giemsa-positive heterochromatin of the barley chromosome, indicating that these barley-specific
sequences form a block which separates the linkage segments conserved in rice. By our estimate approximately half of the barley-specific
sequences of chromosome 5 (1H) show a dispersed distribution, while the other half separates the conserved linkage segments.
Received: 29 February 1996 / Accepted: 28 June 1996 相似文献
12.
A major gene-rich region on the end of the long arm of Triticeae group 2 chromosomes exhibits high recombination frequencies,
making it an attractive region for positional cloning. Traits known to be controlled by this region include chasmogamy/cleistogamy,
frost tolerance at flowering, grain yield, head architecture, and resistance to Fusarium head blight and rusts. To assist
these cloning efforts, we constructed detailed genetic maps of barley chromosome 2H, including 61 polymerase chain reaction
markers. Colinearity with rice occurred in eight distinct blocks, including five blocks in the terminal gene-rich region.
Alignment of rice sequences from the junctions of colinear chromosome segments provided no evidence for the involvement of
long (>2.5 kb) inverted repeats in generating inversions. However, reuse of some junction sequences in two or three separate
evolutionary breakage/fusion events was implicated, suggesting the presence of fragile sites. Sequencing across 91 gene fragments
totaling 107 kb from four barley genotypes revealed the highest single nucleotide substitution and insertion–deletion polymorphism
levels in the terminal regions of the chromosome arms. The maps will assist in the isolation of genes from the chromosome
2L gene-rich region in barley and wheat by providing markers and accelerating the identification of the corresponding points
in the rice genome sequence.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
13.
Targeted mapping of ESTs linked to the adult plant resistance gene Lr46 in wheat using synteny with rice 总被引:1,自引:0,他引:1
Mateos-Hernandez M Singh RP Hulbert SH Bowden RL Huerta-Espino J Gill BS Brown-Guedira G 《Functional & integrative genomics》2006,6(2):122-131
The gene Lr46 has provided slow-rusting resistance to leaf rust caused by Puccinia triticina in wheat (Triticum aestivum), which has remained durable for almost 30 years. Using linked markers and wheat deletion stocks, we located Lr46 in the deletion bin 1BL (0.84–0.89) comprising 5% of the 1BL arm. The distal part of chromosome 1BL of wheat is syntenic
to chromosome 5L of rice. Wheat expressed sequence tags (ESTs) mapping in the terminal 15% of chromosome 1BL with significant
homology to sequences from the terminal region of chromosome 5L of rice were chosen for sequence-tagged site (STS) primer
design and were mapped physically and genetically. In addition, sequences from two rice bacterial artificial chromosome clones
covering the targeted syntenic region were used to identify additional linked wheat ESTs. Fourteen new markers potentially
linked to Lr46 were developed; eight were mapped in a segregating population. Markers flanking (2.2 cM proximal and 2.2 cM distal) and cosegregating
with Lr46 were identified. The physical location of Lr46 was narrowed to a submicroscopic region between the breakpoints of deletion lines 1BL-13 [fraction length (FL)=0.89–1] and
1BL-10 (FL=0.89–3). We are now developing a high-resolution mapping population for the positional cloning of Lr46. 相似文献
14.
A nonsense mutation in a putative sulphate transporter gene results in low phytic acid in barley 总被引:1,自引:0,他引:1
Ye H Zhang XQ Broughton S Westcott S Wu D Lance R Li C 《Functional & integrative genomics》2011,11(1):103-110
Low phytic acid grains can provide a solution to dietary micronutrient deficiency and environmental pollution. A low phytic
acid 1-1 (lpa1-1) barley mutant was identified using forward genetics and the mutant gene was mapped to chromosome 2HL. Comparative genomic
analysis revealed that the lpa1-1 gene was located in the syntenic region of the rice Os-lpa-MH86-1 gene on chromosome 4. The gene ortholog of rice Os-lpa-MH86-1 (designated as HvST) was isolated from barley using polymerase chain reaction and mapped to chromosome 2HL in a doubled haploid population of
Clipper×Sahara. The results demonstrate the collinearity between the rice Os-lpa-MH86-1 gene and the barley lpa1-1 region. Sequence analysis of HvST revealed a single base pair substitution (C→T transition) in the last exon of the gene in lpa1-1 (M422), which resulted in a nonsense mutation. These results will facilitate our understanding of the molecular mechanisms
controlling the low phytic acid phenotype and assist in the development of a diagnostic marker for the selection of the lpa1-1 gene in barley. 相似文献
15.
Tom Drader Kara Johnson Robert Brueggeman Dave Kudrna Andris Kleinhofs 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2009,118(4):811-820
Approaches utilizing microlinearity between related species allow for the identification of syntenous regions and orthologous
genes. Within the barley Chromosome 7H(1) is a region of high recombination flanked by molecular markers cMWG703 and MWG836.
We present the constructed physical contigs linked to molecular markers across this region using bacterial artificial chromosomes
(BAC) from the cultivar Morex. Barley expressed sequence tags (EST), identified by homology to rice chromosome 6 between the
rice molecular markers C425A and S1434, corresponded to the barley syntenous region of Chromosome 7H(1) Bins 2–5 between molecular
markers cMWG703-MWG836. Two hundred and thirteen ESTs were genetically mapped yielding 267 loci of which 101 were within the
target high recombination region while 166 loci mapped elsewhere. The 101 loci were joined by 43 other genetic markers resulting
in a highly saturated genetic map. In order to develop a physical map of the region, ESTs and all other molecular markers
were used to identify Morex BAC clones. Seventy-four BAC contigs were formed containing 2–102 clones each with an average
of 19 and a median of 13 BAC clones per contig. Comparison of the BAC contigs, generated here, with the Barley Physical Mapping
Database contigs, resulted in additional overlaps and a reduction of the contig number to 56. Within cMWG703-MWG836 are 24
agriculturally important traits including the seedling spot blotch resistance locus, Rcs5. Genetic and physical analysis of this region and comparison to rice indicated an inversion distal of the Rcs5 locus. Three BAC clone contigs spanning the Rcs5 locus were identified.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
16.
Thomas Lüpken Nils Stein Dragan Perovic Antje Habekuß Ilona Krämer Urs Hähnel Burkhard Steuernagel Uwe Scholz Rounan Zhou Ruvini Ariyadasa Stefan Taudien Matthias Platzer Mihaela Martis Klaus Mayer Wolfgang Friedt Frank Ordon 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2013,126(5):1201-1212
Soil-borne barley yellow mosaic virus disease, caused by different strains of Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus (BaMMV), is one of the most important diseases of winter barley (Hordeum vulgare L.) in Europe and East Asia. The recessive resistance gene rym11 located in the centromeric region of chromosome 4HL is effective against all so far known strains of BaMMV and BaYMV in Germany. In order to isolate this gene, a high-resolution mapping population (10,204 meiotic events) has been constructed. F2 plants were screened with co-dominant flanking markers and segmental recombinant inbred lines (RILs) were tested for resistance to BaMMV under growth chamber and field conditions. Tightly linked markers were developed by exploiting (1) publicly available barley EST sequences, (2) employing barley synteny to rice, Brachypodium distachyon and sorghum and (3) using next-generation sequencing data of barley. Using this approach, the genetic interval was efficiently narrowed down from the initial 10.72 % recombination to 0.074 % recombination. A marker co-segregating with rym11 was developed providing the basis for gene isolation and efficient marker-assisted selection. 相似文献
17.
Xiao-Qi Zhang Chengdao Li Amy Tay Reg Lance Daryl Mares Judy Cheong Mehmet Cakir Junhong Ma Rudi Appels 《Molecular breeding : new strategies in plant improvement》2008,22(2):227-236
Pre-harvest sprouting (PHS) is a complex trait controlled by multiple genes with strong interaction between environment and
genotype that makes it difficult to select breeding materials by phenotypic assessment. One of the most important genes for
pre-harvest sprouting resistance is consistently identified on the long arm of chromosome 4A. The 4AL PHS tolerance gene has
therefore been targeted by Australian white-grained wheat breeders. A new robust PCR marker for the PHS QTL on wheat chromosome
4AL based on candidate genes search was developed in this study. The new marker was mapped on 4AL deletion bin 13-0.59-0.66
using 4AL deletion lines derived from Chinese Spring. This marker is located on 4AL between molecular markers Xbarc170 and Xwg622 in the doubled-haploid wheat population Cranbrook × Halberd. It was mapped between molecular markers Xbarc170 and Xgwm269 that have been previously shown to be closely linked to grain dormancy in the doubled haploid wheat population SW95-50213 × Cunningham
and was co-located with Xgwm269 in population Janz × AUS1408. This marker offers an additional efficient tool for marker-assisted selection of dormancy for
white-grained wheat breeding. Comparative analysis indicated that the wheat chromosome 4AL QTL for seed dormancy and PHS resistance
is homologous with the barley QTL on chromosome 5HL controlling seed dormancy and PHS resistance. This marker will facilitate
identification of the gene associated with the 4A QTL that controls a major component of grain dormancy and PHS resistance. 相似文献
18.
Tian-su Zhou Iimure Takashi Kanatani Ryouichi Hirota Naohiko Kihara Makoto Hoki Takehiro Sato Kazuhiro 《Molecular breeding : new strategies in plant improvement》2012,30(1):103-112
A high-density map consisting of 550 markers was constructed based on the segregation data of 95 doubled-haploid lines (DHLs) derived from the cross between a Japanese barley cultivar, Mikamo Golden and a North American barley cultivar, Harrington (MH-DHLs). Quality traits of malt extract (EX), total nitrogen (TN), soluble nitrogen (SN), Kolbach index (KI), diastatic power (DP), wort beta-glucan (WG) and viscosity (VS) were determined in three site/year crops. Quantitative trait loci (QTL) analyses were performed with these quality data sets, using the linkage map. Major QTL controlling EX, SN and KI were mapped on terminal region of 5H with Harrington as effective allele. Another QTL controlling EX was mapped on 2H with Mikamo Golden as effective allele. QTL controlling TN, DP, WG and VS were detected variably in terms of flanking markers and chromosomes depending on site/year. Cleaved amplified polymorphic sequences (CAPS) markers for EX based on the QTL detected on 2H and 5H were developed. Analysis of EX and genotypes of 33 malting barley cultivars from around the world as well as MH-DHLs revealed that the two CAPS marker on 2H and 5H affect EX by a significant difference, suggesting that the two CAPS markers were valuable for marker-assisted selection in malting barley breeding. 相似文献
19.
The maize rp1 rust resistance gene identifies homologues in barley that have been subjected to diversifying selection 总被引:1,自引:0,他引:1
M.A. Ayliffe N.C. Collins J.G Ellis A. Pryor 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,100(7):1144-1154
A number of agronomically important grasses (sorghum, wheat, panicum, sugar cane, oats, rice and barley) are shown to contain
sequences homologous to rp1, a maize gene that confers race-specific resistance to the rust fungus Puccinia sorghi. Mapping of rp1-related sequences in barley identified three unlinked loci on chromosomes 1HL, 3HL and 7HS. The locus located on chromosome
7HS comprises a small gene family of at least four members, two of which were isolated and are predicted to encode nucleotide
binding site-leucine-rich repeat (NBS-LRR) proteins that are respectively 58% and 60% identical to the maize rp1 protein. Evidence of positive selection for sequence diversification acting upon these two barley genes was observed; however,
diversifying selection was restricted to the carboxy terminal half of the LRR domain. One of these rp1 homologous genes cosegregated with the barley Rpg1 stem rust resistance gene amongst 148 members of the Steptoe × Morex double haploid mapping family. Three other unrelated
resistance gene-like sequences, potentially encoding NBS-LRR proteins, are also shown to be linked to the Rpg1 locus but not cosegregating with the gene.
Received: 2 August 1999 / Accepted: 28 September 1999 相似文献
20.
V. M. Koladia J. D. Faris J. K. Richards R. S. Brueggeman S. Chao T. L. Friesen 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2017,130(1):163-173