共查询到20条相似文献,搜索用时 949 毫秒
1.
Sargent DJ Clarke J Simpson DW Tobutt KR Arús P Monfort A Vilanova S Denoyes-Rothan B Rousseau M Folta KM Bassil NV Battey NH 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2006,112(7):1349-1359
A total of 45 microsatellites (SSRs) were developed for mapping in Fragaria. They included 31 newly isolated codominant genomic SSRs from F. nubicola and a further 14 SSRs, derived from an expressed sequence tagged library (EST-SSRs) of the cultivated strawberry, F. × ananassa. These, and an additional 64 previously characterised but unmapped SSRs and EST-SSRs, were scored in the diploid Fragaria interspecific F2 mapping population (FV×FN) derived from a cross between F. vesca 815 and F. nubicola 601. The cosegregation data of these 109 SSRs, and of 73 previously mapped molecular markers, were used to elaborate an enhanced
linkage map. The map is composed of 182 molecular markers (175 microsatellites, six gene specific markers and one sequence-characterised
amplified region) and spans 424 cM over seven linkage groups. The average marker spacing is 2.3 cM/marker and the map now
contains just eight gaps longer than 10 cM. The transferability of the new SSR markers to the cultivated strawberry was demonstrated
using eight cultivars. Because of the transferable nature of these markers, the map produced will provide a useful reference
framework for the development of linkage maps of the cultivated strawberry and for the development of other key resources
for Fragaria such as a physical map. In addition, the map now provides a framework upon which to place transferable markers, such as genes
of known function, for comparative mapping purposes within Rosaceae. 相似文献
2.
The isolation of polymorphic codominant microsatellite markers in Rubus and in particular red raspberry will provide a tool to investigate gene flow between cultivated and wild raspberries. Microsatellite loci were isolated by screening a PstI size selected genomic library with AC(13) and AG(13). Positive clones were sequenced and primer pairs designed to the sequences flanking identified SSRs. One primer of each pair was fluorescently labelled to facilitate polymerase chain reaction (PCR) product identification on an automated DNA sequencer. We describe 10 polymorphic microsatellite loci developed and demonstrate their usefulness in different Rubus species. 相似文献
3.
An autotetraploid linkage map of rose (Rosa hybrida) validated using the strawberry (Fragaria vesca) genome sequence 总被引:1,自引:0,他引:1
Polyploidy is a pivotal process in plant evolution as it increase gene redundancy and morphological intricacy but due to the complexity of polysomic inheritance we have only few genetic maps of autopolyploid organisms. A robust mapping framework is particularly important in polyploid crop species, rose included (2n = 4x = 28), where the objective is to study multiallelic interactions that control traits of value for plant breeding. From a cross between the garden, peach red and fragrant cultivar Fragrant Cloud (FC) and a cut-rose yellow cultivar Golden Gate (GG), we generated an autotetraploid GGFC mapping population consisting of 132 individuals. For the map we used 128 sequence-based markers, 141 AFLP, 86 SSR and three morphological markers. Seven linkage groups were resolved for FC (Total 632 cM) and GG (616 cM) which were validated by markers that segregated in both parents as well as the diploid integrated consensus map.The release of the Fragaria vesca genome, which also belongs to the Rosoideae, allowed us to place 70 rose sequenced markers on the seven strawberry pseudo-chromosomes. Synteny between Rosa and Fragaria was high with an estimated four major translocations and six inversions required to place the 17 non-collinear markers in the same order. Based on a verified linear order of the rose markers, we could further partition each of the parents into its four homologous groups, thus providing an essential framework to aid the sequencing of an autotetraploid genome. 相似文献
4.
ANDREW KENIRY CLARE J. HOPKINS ERICA JEWELL BRUCE MORRISON GERMAN C. SPANGENBERG DAVID EDWARDS JACQUELINE BATLEY 《Molecular ecology resources》2006,6(2):319-322
The availability of expressed sequence data derived from gene discovery programmes enables mining for simple sequence repeats (SSRs), providing useful genetic markers for crop improvement. These markers are inexpensive, require minimal labour to produce and can frequently be associated with functionally annotated genes. This study reports on the development and characterization of expressed sequence tag (EST)–SSR markers in the cultivated strawberry, Fragaria×ananassa. Fourteen primer pairs were assessed for polymorphism in 13 F.×ananassa genotypes. The markers show reliable amplification and considerable polymorphism, demonstrating the utility of EST–SSRs for genetic analysis of commercial strawberry germplasm. 相似文献
5.
Robert VanBuren Doug Bryant Jill M. Bushakra Kelly J. Vining Patrick P. Edger Erik R. Rowley Henry D. Priest Todd P. Michael Eric Lyons Sergei A. Filichkin Michael Dossett Chad E. Finn Nahla V. Bassil Todd C. Mockler 《The Plant journal : for cell and molecular biology》2016,87(6):535-547
Black raspberry (Rubus occidentalis) is an important specialty fruit crop in the US Pacific Northwest that can hybridize with the globally commercialized red raspberry (R. idaeus). Here we report a 243 Mb draft genome of black raspberry that will serve as a useful reference for the Rosaceae and Rubus fruit crops (raspberry, blackberry, and their hybrids). The black raspberry genome is largely collinear to the diploid woodland strawberry (Fragaria vesca) with a conserved karyotype and few notable structural rearrangements. Centromeric satellite repeats are widely dispersed across the black raspberry genome, in contrast to the tight association with the centromere observed in most plants. Among the 28 005 predicted protein‐coding genes, we identified 290 very recent small‐scale gene duplicates enriched for sugar metabolism, fruit development, and anthocyanin related genes which may be related to key agronomic traits during black raspberry domestication. This contrasts patterns of recent duplications in the wild woodland strawberry F. vesca, which show no patterns of enrichment, suggesting gene duplications contributed to domestication traits. Expression profiles from a fruit ripening series and roots exposed to Verticillium dahliae shed insight into fruit development and disease response, respectively. The resources presented here will expedite the development of improved black and red raspberry, blackberry and other Rubus cultivars. 相似文献
6.
C. L. Govan D. W. Simpson A. W. Johnson K. R. Tobutt D. J. Sargent 《Molecular breeding : new strategies in plant improvement》2008,22(4):649-661
We have identified a reliable set of multiplexed microsatellite (SSR) markers for the genotyping of strawberry cultivars and
their octoploid progenitors. Over 100 SSRs were screened in two F. × ananassa genotypes and from these, 32 that showed promise for genotyping were selected for further analysis. These SSRs were used
to screen a set of 16 strawberry cultivars and a set of fingerprints were produced. Those SSRs that produced reliable, reproducible
and easy to interpret fingerprints, that could also distinguish readily between the 16 strawberry cultivars screened, and
which could be conveniently included in three multiplex reactions, were selected to form the genotyping set. The genotyping
set, consisting of 10 previously-reported SSRs was used to fingerprint a total of 56 cultivated strawberry, and four octoploid
Fragaria species accessions. The SSRs used could reliably distinguish between all 60 genotypes surveyed, including sibling cultivars
derived from the same parental lines. The primers could be combined for multiplex PCR and represent a useful and convenient
genotyping set for Fragaria that will permit fingerprinting data to be shared between laboratories. 相似文献
7.
Fourteen microsatellite primer pairs were developed from a cDNA library of heat‐treated seedlings of Fragaria vesca cv. yellow wonder. Transferability to 13 species of Fragaria ranged from 71% in diploid species F. gracilis Losinsk., F. iinumae Makino, F. nilgerrensis Schltdl. ex J. Gay and F. nipponica Makino, to 100% in octoploid domestic strawberry and its progenitors. Polymorphism was high in polyploid Fragaria species. However, polymorphism and heterozygosity of eight EST‐SSRs (expressed sequence tag–simple sequence repeats) was low in 14 F. vesca genotypes. 相似文献
8.
Sargent DJ Passey T Surbanovski N Lopez Girona E Kuchta P Davik J Harrison R Passey A Whitehouse AB Simpson DW 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2012,124(7):1229-1240
The linkage maps of the cultivated strawberry, Fragaria × ananassa (2n = 8x = 56) that have been reported to date have been developed predominantly from AFLPs, along with supplementation with transferrable
microsatellite (SSR) markers. For the investigation of the inheritance of morphological characters in the cultivated strawberry
and for the development of tools for marker-assisted breeding and selection, it is desirable to populate maps of the genome
with an abundance of transferrable molecular markers such as microsatellites (SSRs) and gene-specific markers. Exploiting
the recent release of the genome sequence of the diploid F. vesca, and the publication of an extensive number of polymorphic SSR markers for the genus Fragaria, we have extended the linkage map of the ‘Redgauntlet’ × ‘Hapil’ (RG × H) mapping population to include a further 330 loci,
generated from 160 primer pairs, to create a linkage map for F. × ananassa containing 549 loci, 490 of which are transferrable SSR or gene-specific markers. The map covers 2140.3 cM in the expected
28 linkage groups for an integrated map (where one group is composed of two separate male and female maps), which represents
an estimated 91% of the cultivated strawberry genome. Despite the relative saturation of the linkage map on the majority of
linkage groups, regions of apparent extensive homozygosity were identified in the genomes of ‘Redgauntlet’ and ‘Hapil’ which
may be indicative of allele fixation during the breeding and selection of modern F. × ananassa cultivars. The genomes of the octoploid and diploid Fragaria are largely collinear, but through comparison of mapped markers on the RG × H linkage map to their positions on the genome
sequence of F. vesca, a number of inversions were identified that may have occurred before the polyploidisation event that led to the evolution
of the modern octoploid strawberry species. 相似文献
9.
A set of 41 polymorphic microsatellite markers were developed using a CT/AG‐enriched genomic library of Fragaria vesca cv. Reine des Vallées. Thirty‐five of them were polymorphic in F. vesca and were tested in one accession each of six additional diploid Fragaria species and the octoploid Fragaria× ananassa. A mean of 5.3 alleles per locus and a low level of observed heterozygosity were generally detected in the 32 single‐locus simple sequence repeats of F. vesca. Most of these loci amplify in the other diploid species and in F. × ananassa. 相似文献
10.
Identification,characterisation and mapping of simple sequence repeat (SSR) markers from raspberry root and bud ESTs 总被引:1,自引:0,他引:1
M. Woodhead S. McCallum K. Smith L. Cardle L. Mazzitelli J. Graham 《Molecular breeding : new strategies in plant improvement》2008,22(4):555-563
Raspberry breeding is a long, slow process in this highly heterozygous out-breeder. Selections for complex traits like fruit
quality are broad-based and few simple methodologies and resources are available for glasshouse and field screening for key
pest and disease resistances. Additionally, the timescale for selection of favourable agronomic traits requires data from
different seasons and environmental locations before any breeder selection can proceed to finished cultivar. Genetic linkage
mapping offers the possibility of a more knowledge-based approach to breeding through linking favourable traits to markers
and candidate genes on genetic linkage maps. To further increase the usefulness of existing maps, a set of 25 polymorphic
SSRs derived from expressed sequences (EST-SSRs) have been developed in red raspberry (Rubus idaeus). Two different types of expressed sequences were targeted. One type was derived from a root cDNA library as a first step
in assessing sequences which may be involved in root vigour and root rot disease resistance and the second type were ESTs
from a gene discovery project examining bud dormancy release and seasonality. The SSRs detect between 2 and 4 alleles per
locus and were assigned to linkage groups on the existing ‘Glen Moy’ × ‘Latham’ map following genotyping of 188 progeny and
examined for association with previously mapped QTL. The loci were also tested on a diverse range of Rubus species to determine transferability and usefulness for germplasm diversity studies and the introgression of favourable alleles. 相似文献
11.
Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species 总被引:1,自引:0,他引:1
Ksenija Gasic Yuepeng Han Sunee Kertbundit Vladimir Shulaev Amy F. Iezzoni Ed W. Stover Richard L. Bell Michael E. Wisniewski Schuyler S. Korban 《Molecular breeding : new strategies in plant improvement》2009,23(3):397-411
Genic microsatellites or simple sequence repeat markers derived from expressed sequence tags (ESTs), referred to as EST–SSRs,
are inexpensive to develop, represent transcribed genes, and often have assigned putative function. The large apple (Malus × domestica) EST database (over 300,000 sequences) provides a valuable resource for developing well-characterized DNA molecular markers.
In this study, we have investigated the level of transferability of 68 apple EST–SSRs in 50 individual members of the Rosaceae
family, representing three genera and 14 species. These representatives included pear (Pyrus communis), apricot (Prunus armeniaca), European plum (P. domestica), Japanese plum (P. salicina), almond (P. dulcis), peach (P. persica), sour cherry (P. cerasus), sweet cherry (P. avium), strawberry (Fragaria vesca, F. moschata, F. virginiana, F. nipponica, and F. pentaphylla), and rose (Rosa hybrida). All 68 primer pairs gave an amplification product when tested on eight apple cultivars, and for most, the genomic DNA-derived
amplification product matched the expected size based on EST (in silico) data. When tested across members of the Rosaceae, 75% of these primer pairs produced amplification products. Transferability
of apple EST–SSRs across the Rosaceae ranged from 25% in apricot to 59% in the closely related pear. Besides pear, the highest
transferability of these apple EST–SSRs, at the genus level, was observed for strawberry and peach/almond, 49 and 38%, respectively.
Three markers amplified in at least one genotype within all tested species, while eight additional markers amplified in all
species, except for cherry. These 11 markers are deemed good candidates for a widely transferable Rosaceae marker set provided
their level of polymorphism is adequate. Overall, these findings suggest that transferability of apple EST–SSRs across Rosaceae
is varied, yet valuable, thereby providing additional markers for comparative mapping and for carrying out evolutionary studies. 相似文献
12.
Simple sequence repeats (SSRs) markers were developed for Betula maximowicziana using 2698 expressed sequence tags (ESTs) from the NCBI database. Out of 112 designed primer pairs, 54 showed clear PCR amplification
and 14 of these revealed polymorphism in eight individuals sampled across the species’ range. The number of alleles detected
and the expected heterozygosity ranged from 1 to 3 and 0.000 to 0.570, respectively, when these 14 loci were examined in 49
individuals from a single population. In the cross species transferability test, eight of the 14 loci were also polymorphic
in all four of the diploid, tetraploid and hexaploid Betula species examined. These results showed high transferability of the developed EST-SSRs and that these markers are likely to
be useful in studies of the population genetics of species in the genus Betula. 相似文献
13.
WENDY A BREESE R C SHATTOCK B WILLIAMSON CHRISTINE HACKETT 《The Annals of applied biology》1994,125(1):73-85
The cardinal temperatures for in vitro germination of conidia of imported and indigenous isolates of downy mildew from hosts in the genera Rubus and Rosa were similar. A high percentage of conidia germinated above 2°C and germination remained between 80% and 90% up to 15°C or 20°C, depending on the isolate. The highest incidence of disease on leaf disks of Tummelberry (blackberry × red raspberry) inoculated with an isolate of Peronospora rubi occurred at c. 15°C, with infection over a range from 2°C to 28°C. Tests on leaf disks in vitro, and leaflets of primocane and lateral shoots in plastic tunnels, with three hybrid berry (blackberry x red raspberry), six blackberry and nine red raspberry cultivars showed the hybrid berries to be most susceptible. In a plastic tunnel infected drupelets of red raspberry fruits developed more slowly and failed to ripen evenly compared with uninfected drupelets. Similar malformation of infected fruits occurred in a plantation of Tummelberry. An isolate of P. rubi attacked severely both Tummelberry and rose cv. Can Can. Fluorescence microscopy after staining with aniline blue showed that leaf disks of Tummelberry were extensively colonised by intercellular mycelium of P. sparsa isolated from rose, even though sporulation was sparse or absent. This supports the view that P. rubi and P. sparsa may be conspecific. Oospores of P. rubi were found routinely within leaf disks of Rubus cultivars inoculated in vitro and once in naturally infected leaflets of Tummelberry. 相似文献
14.
Abstract Rubus is a large genus of flowering plants in the rose family, Rosaceae, subfamily Rosoideae. The blackberries, as well as various other Rubus species with mounding or rambling growth habits, are often called brambles. Little information is available on the genetic diversity of wild-grown blackberries. The objective of this study was to determine the genetic relationships among nine promising (high-yield capacity, free of pest and diseases, better fruit traits) wild blackberry (Rubus caucasicus L.) selections and the well-known cultivar, “Chester” by using amplified fragment length polymorphism (AFLP) markers. Genotypes were evaluated with three selective primer-enzyme combinations, producing a total of 223 AFLP fragments with 53% polymorphism ratio. Clustering of genotypes using unweighted pair-group method of arithmetic average cluster analysis clearly separated groups of wild blackberry genotypes while the variety “Chester” was clustered independently. Wild selections represented a distinct germplasm source on the basis of the estimated genetic distance among them. Genetic diversity data from this study will be helpful in using and exploiting the wild genetic material for breeding purposes as well as for further research. 相似文献
15.
Kunihisa M Fukino N Matsumoto S 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2005,110(8):1410-1418
Cleavage amplified polymorphic sequence (CAPS) markers of strawberry (Fragaria × ananassa Duch.) can be useful for identifying mislabeled or patent-infringing cultivars in the marketplace. However, CAPS markers in octoploid strawberry tend to give unclear bands because multiple homologous sites are simultaneously amplified by the non-selective PCR. To overcome this problem, we used cluster-specific amplification based on the nucleotide sequences of PCR products and were able to improve the band clarity of 18 CAPS markers. By analyzing the marker segregation ratio, we demonstrated that 13 clarified markers were derived from single diploid loci that were transmitted to progeny in a manner consistent with Mendelian inheritance. We discuss the genomic structure of octoploid strawberry from the viewpoint of cluster and segregation analysis and suggest that it comprises independent genomes. We tested the utility of all of the markers we developed for cultivar identification and confirmed their ability to distinguish among 64 strawberry cultivars. 相似文献
16.
To date, the development of microsatellite (SSR) markers in the genus Fragaria has focused on F. vesca. However, further species are thought to have contributed to the complex allo‐octoploid genome of the cultivated strawberry, F.×ananassa. Here, we present 22 new SSR markers developed from the diploid species F. viridis. Twenty‐one of the primer pairs amplified polymorphisms in six F. viridis accessions, with an average of 4.95 alleles per primer pair and an average expected heterozygosity of 0.68. Fourteen of these primer pairs, and a locus monomorphic in F. viridis, amplified polymorphic alleles in the parents of a F. vesca mapping population. 相似文献
17.
Mourad Mnejja Jordi Garcia-Mas Jean-Marc Audergon Pere Arús 《Tree Genetics & Genomes》2010,6(5):689-700
A total of 145 microsatellite primer pairs from Prunus DNA sequences were studied for transferability in a set of eight cultivars from nine rosaceous species (almond, peach, apricot,
Japanese plum, European plum, cherry, apple, pear, and strawberry), 25 each of almond genomic, peach genomic, peach expressed
sequence tags (EST), and Japanese plum genomic, 22 of almond EST, and 23 of apricot (13 EST and 10 genomic), all known to
produce single-locus and polymorphic simple-sequence repeats in the species where they were developed. Most primer pairs (83.6%)
amplified bands of the expected size range in other Prunus. Transferability, i.e., the proportion of microsatellites that amplified and were polymorphic, was also high in Prunus (63.9%). Almond and Japanese plum were the most variable among the diploid species (all but the hexaploid European plum)
and peach the least polymorphic. Thirty-one microsatellites amplified and were polymorphic in all Prunus species studied, 12 of which, covering its whole genome, are proposed as the “universal Prunus set”. In contrast, only 16.3% were transferable in species of other Rosaceae genera (apple, pear, and strawberry). Polymorphic
Prunus microsatellites also detected lower levels of variability in the non-congeneric species. No significant differences were
detected in transferability and the ability to detect variability between microsatellites of EST and genomic origin. 相似文献
18.
S. Siju K. Dhanya S. Syamkumar B. Sasikumar T. E. Sheeja A. I. Bhat V. A. Parthasarathy 《Molecular biotechnology》2010,44(2):140-147
Expressed sequence tags (ESTs) from turmeric (Curcuma longa L.) were used for the screening of type and frequency of Class I (hypervariable) simple sequence repeats (SSRs). A total
of 231 microsatellite repeats were detected from 12,593 EST sequences of turmeric after redundancy elimination. The average
density of Class I SSRs accounts to one SSR per 17.96 kb of EST. Mononucleotides were the most abundant class of microsatellite
repeat in turmeric ESTs followed by trinucleotides. A robust set of 17 polymorphic EST–SSRs were developed and used for evaluating
20 turmeric accessions. The number of alleles detected ranged from 3 to 8 per loci. The developed markers were also evaluated
in 13 related species of C. longa confirming high rate (100%) of cross species transferability. The polymorphic microsatellite markers generated from this
study could be used for genetic diversity analysis and resolving the taxonomic confusion prevailing in the genus. 相似文献
19.
D. J. GIL‐ARIZA I. AMAYA M. A. BOTELLA J. MU
OZ BLANCO J. L. CABALLERO J. M. L
PEZ‐ARANDA V. VALPUESTA J. F. SNCHEZ‐SEVILLA 《Molecular ecology resources》2006,6(4):1195-1197
Microsatellite or simple sequence repeat markers derived from expressed sequence tags (ESTs) provide genetic markers within potentially functional genes, which could be very useful for breeding programs. To date, the development of microsatellite markers in the genus Fragaria has focused mainly on Fragaria vesca. However, most of the interests of breeding programs relate to specific characteristics of cultivated strawberry. Here, we describe a set of 10 EST‐derived microsatellites from Fragaria × ananassa. These markers showed high levels of polymorphism within strawberry cultivars and among different Fragaria species, indicating their potential for genetic studies not only on strawberry but also in other species within the genus. 相似文献
20.
D. J. Sargent F. Fernandéz-Fernandéz J. J. Ruiz-Roja B. G. Sutherland A. Passey A. B. Whitehouse D. W. Simpson 《Molecular breeding : new strategies in plant improvement》2009,24(3):293-303
The cultivated strawberry, Fragaria × ananassa, is the most economically-important soft-fruit species, but few practical molecular tools for the purpose of marker assisted selection currently exist. As a precursor to the development of such tools, a genetic linkage map was developed from a F1 population comprising 174 seedlings derived from a cross between two F. × ananassa cultivars, ‘Redgauntlet’ × ‘Hapil’. The resultant map is composed of 315 molecular markers—218 microsatellites, 11 gene-specific markers and 86 AFLP and RAPD markers—and spans 3,116 cM. In total, 69 linkage group fragments were recovered, more than the 56 linkage groups expected for the cultivated strawberry, however, all fragments contained a transferable marker that could be associated with one of 56 linkage group scaffolds. The female (Redgauntlet) and male (Hapil) linkage maps are composed, respectively of 170 loci in 32 linkage groups covering 1,675.3 cM and 182 loci in 37 linkage groups covering 1,440.7 cM, with 37 markers common to both maps. The maximum number of markers in one linkage group was 15, the minimum was two. All linkage groups resolved contained at least one transferable marker (SSR or gene-specific) that had been mapped on the diploid Fragaria reference map (FV × FB), and therefore all linkage groups could be identified as homologous to one of the seven diploid Fragaria linkage groups. When marker order was compared to the diploid Fragaria reference map, effectively complete colinearity was observed. However, the occurrence of duplicated loci on homologues of linkage groups FG1 and FG6 provided evidence of a putative chromosomal duplication or translocation event in Fragaria. The development of this linkage map will facilitate the study and dissection of QTL associated with traits of economic importance such as disease resistance and fruit quality, and provides a foundation for the development of markers for the purpose of marker assisted breeding and selection in the cultivated strawberry, F. × ananassa. 相似文献