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1.
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
2.
Characterization, development and exploitation of EST-derived microsatellites in Porphyra haitanensis Chang et Zheng (Bangiales, Rhodophyta) 总被引:1,自引:0,他引:1
The frequency, type and distribution of simple sequence repeats (SSRs) in Porphyra haitanensis genomes was investigated using expressed sequence tag (EST) data deposited in public databases. A total of 3,489 non-redundant
P. haitanensis ESTs were screened for SSRs using SSRhunter software. From those, 224 SSRs in 210 ESTs were identified; trinucleotides were
the most common type of SSR (64.29%), followed by dinucleotides (33.48%). Tetranucleotides, pentanucleotides, and hexanucleotides
were not common. Among all identified motif types, CGG/CCG had the highest frequency (33.9%), followed by TC/AG (24.6%). From
these EST-SSRs, 37 SSR primer-pairs were designed and tested using common SSR reaction conditions with 15 P. haitanensis DNAs as templates. The results showed that 28 SSR primer-pairs gave good amplification patterns. These were used to conduct
SSR analyses of genetic variations of the 15 germplasm strains of P. haitanensis. A total of 224 alleles were detected, with the number of alleles ranging from 4 to 15. The effective number of alleles,
expected heterozygosity, and polymorphism information content of the 15 germplasm strains of P. haitanensis were 2.81, 0.64, and 0.57, respectively. All of these parameters indicate that the 15 germplasm strains of P. haitanensis harbor rich genetic variation. 相似文献
3.
Characterization of EST-derived microsatellites for gene mapping and evolutionary genomics in turbot
Bouza C Hermida M Millán A Vilas R Vera M Fernández C Calaza M Pardo BG Martínez P 《Animal genetics》2008,39(6):666-670
The detection of microsatellite sequences within expressed sequence tags (ESTs) connects potential markers with specific genes, generating type I markers. We have developed and mapped by linkage analysis a set of EST-derived microsatellites in the turbot, Scophthalmus maximus. One hundred and ninety-one microsatellites were identified from 9256 turbot ESTs. Primer design was possible with 98 microsatellites. After genotyping 25 wild turbot and the parents of two reference families for linkage analysis, 43 EST-derived microsatellites were selected because they met technical and polymorphism criteria. A final set of 31 EST-derived microsatellites could be mapped to 17 linkage groups of the turbot consensus map based on 242 anonymous microsatellites. Twenty-four microsatellite-containing ESTs were functionally annotated, confirming them as type I markers. Nineteen were mapped in the turbot consensus map. These EST-derived microsatellites constitute useful tools for genome scanning of turbot populations, marker-assisted selection programmes and comparative mapping. 相似文献
4.
Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat 总被引:22,自引:0,他引:22
Gupta PK Rustgi S Sharma S Singh R Kumar N Balyan HS 《Molecular genetics and genomics : MGG》2003,270(4):315-323
Nearly 900 SSRs (simple sequence repeats) were identified among 15,000 ESTs (expressed sequence tags) belonging to bread wheat ( Triticum aestivum L.). The SSRs were defined by their minimum length, which ranged from 14 to 21 bp. The maximum length ranged from 24 to 87 bp depending upon the length of the repeat unit itself (1–7 bp). The average density of SSRs was one SSR per 9.2 kb of EST sequence screened. The trinucleotide repeats were the most abundant SSRs detected. As a representative sample, 78 primer pairs were designed, which were also used to screen the dbEST entries for Hordeum vulgare and Triticum tauschii (donor of the D-genome of cultivated wheat) using a cut-off E (expectation) value of 0.01. On the basis of in silico analysis, up to 55.12% of the primer pairs exhibited transferability from Triticum to Hordeum, indicating that the sequences flanking the SSRs are not only conserved within a single genus but also between related genera in Poaceae. Primer pairs for the 78 SSRs were synthesized and used successfully for the study of (1) their transferability to 18 related wild species and five cereal species (barley, oat, rye, rice and maize); and (2) polymorphism between the parents of four mapping populations available with us. A subset of 20 EST-SSR primers was also used to assess genetic diversity in a collection of 52 elite exotic wheat genotypes. This was done with a view to compare their utility relative to other molecular markers (gSSRs, AFLPs, and SAMPL) previously used by us for the same purpose with the same set of 52 bread wheat genotypes. Although only a low level of polymorphism was detected, relative to that observed with genomic SSRs, the study suggested that EST-SSRs can be successfully used for a variety of purposes, and may actually prove superior to SSR markers extracted from genomic libraries for diversity estimation and transferability.Communicated by R. Hagemann 相似文献
5.
Characterization of EST-SSRs in loblolly pine and spruce 总被引:3,自引:0,他引:3
Yanik Bérubé Jun Zhuang Dainis Rungis Steven Ralph Jörg Bohlmann Kermit Ritland 《Tree Genetics & Genomes》2007,3(3):251-259
In the first large study of conifer expressed sequence tag-simple sequence repeats (EST-SSRs), two large conifer EST databases
were characterized for EST-SSRs. One database was from “interior spruce” (white and Engelmann spruce in Southern British Columbia)
and Sitka spruce, while the other was from loblolly pine. We found 475 and 629 unique EST-SSRs in loblolly pine and spruce,
respectively. 3′ ESTs contained 14% more SSRs than 5′ EST reads in loblolly pine and 41% more in spruce. Conifer EST-SSRs
differed conspicuously from angiosperm EST-SSRs in several aspects. EST-SSRs were considerably less frequent in conifers (one
EST-SSR every ∼50 kb) than in angiosperms (one EST-SSR every ∼20 kb). Dinucleotide repeats were the most abundant repeat class
in conifers, while in angiosperms, trinucleotides were most common. Finally, the AT motif was the dominant motif recovered
in both conifer species, whereas AG was the most common dinucleotide repeat in angiosperms. Also, as these EST-SSRs in conifers
could be developed into useful genetic markers, our work demonstrates the value of large-scale EST sequencing projects for
in-silico approaches for marker development. 相似文献
6.
Primers were developed for 14 microsatellite or simple sequence repeat (SSR) loci identified from a Prunus avium‘Charger’ genomic DNA library. In a survey of 16 wild cherry accessions 10 of the loci revealed polymorphisms of between two and six alleles. The remaining loci were found to be monomorphic. Seven polymorphic loci identified in this study and four polymorphic loci previously reported in sweet cherry were mapped and found to be unlinked. Two multiplex polymerase chain reactions (PCR) were optimized to enable the characterization of all 11 unlinked, polymorphic SSR loci. 相似文献
7.
Interest in bay scallop conservation has resulted in organized stock enhancement efforts and increased attention to fisheries management issues. Genetic markers can facilitate the monitoring of enhancement efforts, characterization of wild populations, and optimize hatchery practices. We have identified eight polymorphic simple sequence repeat markers including one dinucleotide, six trinucleotide and one compound dinucleotide repeats, in expressed sequence tags generated from multiple bay scallop cDNA libraries. The numbers of alleles range from two to five. The expected and observed heterozygosities range from 0.093 to 0.720 and 0.095 to 0.600, respectively. 相似文献
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10.
Microsatellite DNA markers for rice chromosomes 总被引:44,自引:1,他引:44
H. Akagi Y. Yokozeki A. Inagaki T. Fujimura 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1996,93(7):1071-1077
We found 369 complete microsatellites, of which (CGG/GCC)n was the most frequent, in 11 798 rice sequences in the database. Of these microsatellites, 35 out of 45 could be successfully converted into microsatellite DNA markers using sequence information in their flanking regions. Thus, the time and labor used to develop new microsatellite DNA markers could be saved by using these published sequences. Twenty eight polymorphic markers between Asominori (japonica) and IR24 (indica) have been correctly mapped on the rice genome and microsatellites appear to be randomly distributed in the rice chromosomes. Integration of these markers with the published microsatellite DNA markers showed that about 35% of the rice chromosomes were covered by the 56 microsatellite DNA markers. These microsatellites were hypervariable and were easily to assay by PCR; they were distributed to all chromosomes and therefore, one can easily select plants carrying desired chromosome regions using these microsatellite DNA markers. Thus, microsatellite maps should aid the development of new breeds of rice saving time, labor, and money. 相似文献
11.
? Premise of the study: The redundancies in expressed sequence tags (ESTs) in the National Center for Biotechnology Information sequence database were used to identify and develop polymorphic simple sequence repeat (SSR) markers for pepper (Capsicum annuum). ? Methods and Results: Sixty-eight polymorphic SSR loci were identified in the contigs (containing redundant ESTs) generated by assembling 118060 pepper ESTs from the public sequence database. Thirty-three SSR markers exhibited polymorphism among 31 pepper varieties, with alleles per SSR marker ranging from two to six. The mean observed and expected heterozygosity were 0.28 and 0.39, respectively. There were 18 SSR markers with a motif repeat number of less than five, accounting for 55% of the total. ? Conclusions: We demonstrated the value of mining the redundant sequences in public sequence databases for the development of polymorphic SSR markers, which can be used for marker-assisted breeding in pepper. 相似文献
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13.
Martin WJ McCallum J Shigyo M Jakse J Kuhl JC Yamane N Pither-Joyce M Gokce AF Sink KC Town CD Havey MJ 《Molecular genetics and genomics : MGG》2005,274(3):197-204
The Poales (which include the grasses) and Asparagales [which include onion (Allium cepa L.) and other Allium species] are the two most economically important monocot orders. Enormous genomic resources have been developed for the grasses;
however, their applicability to other major monocot groups, such as the Asparagales, is unclear. Expressed sequence tags (ESTs)
from onion that showed significant similarities (80% similarity over at least 70% of the sequence) to single positions in
the rice genome were selected. One hundred new genetic markers developed from these ESTs were added to the intraspecific map
derived from the BYG15-23×AC43 segregating family, producing 14 linkage groups encompassing 1,907 cM at LOD 4. Onion linkage
groups were assigned to chromosomes using alien addition lines of Allium fistulosum L. carrying single onion chromosomes. Visual comparisons of genetic linkage in onion with physical linkage in rice revealed
scant colinearity; however, short regions of colinearity could be identified. Our results demonstrate that the grasses may
not be appropriate genomic models for other major monocot groups such as the Asparagales; this will make it necessary to develop
genomic resources for these important plants.
Electronic Supplementary Material Supplementary material is available for this article at 相似文献
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15.
Physical molecular maps of wheat chromosomes 总被引:5,自引:0,他引:5
Goyal A Bandopadhyay R Sourdille P Endo TR Balyan HS Gupta PK 《Functional & integrative genomics》2005,5(4):260-263
In bread wheat, a set of 527 simple sequence repeats (SSRs) were tried on 164 deletion lines, leading to a successful mapping of 270 SSRs on 313 loci covering all 21 chromosomes. A maximum of 119 loci (38%) were located on B subgenome, and a minimum of 90 loci (29%) mapped on D subgenome. Similarly, homoeologous group 7 carried a maximum of 61 loci (19%), and group 4 carried a minimum of 22 loci (7%). Of the cited 270 SSRs, 39 had multiple loci, but only eight of these detected homoeologous loci. Linear order of loci in physical maps largely corresponded with those in the genetic maps. Apparently, distances between each of only 26 pairs of loci significantly differed from the corresponding distances on genetic maps. Some loci, which were genetically mapped close to the centromere, were physically located distally, while other loci that were mapped distally in the genetic maps were located in the proximal bins in the physical maps. This suggested that although the linear order of the loci was largely conserved, variation does exist between genetic and physical distances.Electronic Supplementary Material Supplementary material is available for this article at . 相似文献
16.
Kurt Weising Raymond W. M. Fung D. Jeannette Keeling Ross G. Atkinson Richard C. Gardner 《Molecular breeding : new strategies in plant improvement》1996,2(2):117-131
We have identified a set of informative microsatellite markers for genome analysis in kiwifruit and related Actinidia species. A small-insert genomic library was constructed from Actinidia chinensis DNA, and screened for microsatellites. About 1.2% of the total colonies hybridised to a (GA)8 probe, 0.4% to (GT)8, and 0.1% to a mixture of three different trinucleotide repeat probes, (CAA)5, (GAA)5 and (CTA)5. From the DNA sequences of 35 hybridising clones, 18 primer pairs were designed, and used to amplify genomic DNA from 38 individual plants, representing 30 different accessions of ten Actinidia species. The banding patterns for most of the dinucleotide repeats showed a high degree of polymorphism in the diploid and tetraploid A. chinensis, and in the hexaploid A. deliciosa (kiwifruit). Heterozygosity levels of up to 100% were found among eight diploid accessions of A. chinensis examined, and the number of different-sized bands among all the species varied from 3 to 36 for each microsatellite. One simple CT microsatellite gave 21 bands with sizes suggesting that the number of repeats ranged from 9 to 37. The highest number of bands (36) and the largest size variation (>100 bp) were observed with a complex microsatellite harbouring four different repeat motifs. The majority of primer pairs amplified bands from most of the ten Actinidia species tested. The most polymorphic primer pairs were used successfully to fingerprint a range of closely related varieties of kiwifruit (A. deliciosa).Abbreviations PCR
polymerase chain reaction
- RFLP
restriction fragment length polymorphism
- VNTR
variable number of tandem repeats 相似文献
17.
EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome 总被引:2,自引:0,他引:2
Kota R Varshney RK Prasad M Zhang H Stein N Graner A 《Functional & integrative genomics》2008,8(3):223-233
In a panel of seven genotypes, 437 expressed sequence tag (EST)-derived DNA fragments were sequenced. Single nucleotide polymorphisms
(SNPs) that were polymorphic between the parents of three mapping populations were mapped by heteroduplex analysis and a genome-wide
consensus map comprising 216 EST-derived SNPs and 4 InDel (insertion/deletion) markers was constructed. The average frequency of SNPs amounted to 1/130 bp and 1/107.8 bp for a set of randomly selected
and a set of mapped ESTs, respectively. The calculated nucleotide diversities (π) ranged from 0 to 40.0 × 10−3 (average 3.1 × 10−3) and 0.52 × 10−3 to 39.51 × 10–3 (average 4.37 × 10−3) for random and mapped ESTs, respectively. The polymorphism information content value for mapped SNPs ranged from 0.24 to
0.50 with an average of 0.34. As expected, combination of SNPs present in an amplicon (haplotype) exhibited a higher information
content ranging from 0.24 to 0.85 with an average of 0.50. Cleaved amplified polymorphic sequence assays (including InDels) were designed for a total of 87 (39.5%) SNP markers. The high abundance of SNPs in the barley genome provides avenues for
the systematic development of saturated genetic maps and their integration with physical maps.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
Both R. Kota and R.K. Varshney contributed equally to this work. 相似文献
18.
Zun-Zheng Wei Lai-Bo Luo Hua-Li Zhang Min Xiong Xian Wang Di Zhou 《American journal of botany》2012,99(12):e493-e497
• Premise of the study: A new set of microsatellite or simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) was developed for arum lily (Zantedeschia aethiopica), which is one of the most iconic and widely recognized ornamental plants in the world. • Methods and Results: Using 2175 unigenes derived from 4283 random ESTs in arum lily, 166 primer pairs were designed and tested for amplification in 24 accessions from Asia, Europe, and Africa. A total of 43 loci were polymorphic, with the number of alleles per locus ranging from two to 10. The observed heterozygosity, expected heterozygosity, and polymorphism information content ranged from 0.2313 to 0.8480, 0.3034 to 0.8648, and 0.1015 to 0.7364, respectively. • Conclusions: These novel polymorphic EST-SSR markers will facilitate future studies of genetic variation and molecular-assisted breeding systems in arum lily. 相似文献
19.
Jon-Ivar Westgaard Tekle Tafese Mette Serine Wesmajervi Frank Nilsen Kjersti Turid Fjalestad Børge Damsgård Madjid Delghandi 《Conservation Genetics》2007,8(6):1503-1506
Ten polymorphic microsatellite markers were developed from approximately 1,300 expressed sequence tags (ESTs) of Atlantic
cod (Gadus morhua L.). Thirty two primer pairs were designed for EST sequences containing perfect di- tri- tetra- and pentanucleotide motifs
and characterised in 96 unrelated fish. Ten markers were successfully amplified with number of alleles from 2 to 13 per locus
and observed and expected heterozygosity ranging from 0.03 to 0.69 and 0.03 to 0.74, respectively. Loci Gmo-C131, C132 and C136 deviated from Hardy-Weinberg equilibrium. Genetic linkage disequilibrium analysis between all pairs of
the loci showed significant departure from the null hypothesis between loci Gmo-C131 and Gmo-C132 and C128 and Gmo-C133. The gene identity was determined at five of the loci, confirming the associated microsatellites as Type I markers.
The new microsatellites reported in this work can be used for conservation and enhancement of wild stocks for commercial harvesting.
Jon-Ivar Westgaard and Tekle Tafese have contributed equally to the work. 相似文献
20.
Amir Mohammad Naji Mohammad Moghaddam Mohammad Reza Ghaffari Hashem Pour Irandoost Laleh Karimi Farsad Seyed Mostafa Pirseyedi Seyed Abolghasem Mohammadi Behzad Ghareyazie Mohsen Mardi 《遗传学报》2008,35(10)
A few EST-derived STS markers localized on Qfhs.ndsu-3BS, a major QTL for resistance to Fusarium head blight (FHB) in wheat, have been previously identified in the 'Sumai 3'/'Stoa' population. In this study, we used a 'Wangshuibai' (resistant)/'Seri82' (susceptible) derived population, linkage group, QTL, and quantitative gene expression analysis to assess the genetic background dependence and stability of the EST-derived STS markers for use in marker aided selection to improve FHB resistance in wheat. Based on our results, a QTL in the map interval of Xsts3B-138_1-Xgwm493 on chromosome 3BS was detected for FHB resistance, which accounted for up to 16% of the phenotypic variation. BLASTN analysis indicated that Xsts3B-138_1 sequence had significant similarity with the resistance gene analogue. Real-time quantitative PCR showed that the relative expression of Xsts3B-1381 in 'Wangshuibai' at 96 h after inoculation was 2.6 times higher than 'Seri82'. Our results underlined that EST-derived STS3B-138 markers could be predominantly used in marker aided selection to improve FHB resistance in wheat. 相似文献