共查询到20条相似文献,搜索用时 31 毫秒
1.
Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats. 总被引:9,自引:0,他引:9
Luciana Rossini Pinto Karine Miranda Oliveira Eugênio César Ulian Antonio Augusto Franco Garcia Anete Pereira de Souza 《Génome》2004,47(5):795-804
Sugarcane microsatellites or simple sequence repeats (SSR) were developed in an economical and practical way by mining EST databases. A survey in the SUCEST (sugarcane EST) database revealed a total of 2005 clusters out of 43,141 containing SSRs. Of these, 8.2% were dinucleotide, 30.5% were trinucleotide, and 61.3% were tetranucleotide repeats. Except for dinucleotides, the CG-rich motif types were the most common. Differences in abundance of trinucleotide motif types were observed between EST-SSRs and those isolated from sugarcane genomic libraries. Among the different cDNA libraries used for EST sequencing, SSRs were more frequent in the ones derived from leaf roll (LR). Twenty-three out of 30 tested SSRs produced scorable polymorphisms in 18 sugarcane commercial clones. These EST-SSRs showed a moderate level of polymorphism with some SSRs producing unique fingerprints. The number of alleles observed among the 18 clones evaluated varied from 2 to 15, with an average of 6.04 alleles/locus. The polymorphism information content (PIC) values ranged from 0.28 to 0.90 with a mean of 0.66. The EST-SSRs screened over both parents (SP 80-180; SP 80-4966) and 6 F1 individuals produced 52 segregating markers that could potentially be used for sugarcane mapping. The EST-SSRs were found in clusters that had significant homology to proteins involved in important metabolic pathways such as sugar biosynthesis, proving that EST-SSRs are a valuable tool for the construction of a functional sugarcane map. 相似文献
2.
Chidananda Nagamangala Kanchiswamy Hirotaka Takahashi Stefano Quadro Massimo E Maffei Simone Bossi Cinzia Bertea Simon Atsbaha Zebelo Atsushi Muroi Nobuaki Ishihama Hirofumi Yoshioka Wilhelm Boland Junji Takabayashi Yaeta Endo Tatsuya Sawasaki Gen-ichiro Arimura 《BMC plant biology》2010,10(1):1-10
Background
Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps of these populations have been aligned with each other using publicly available DNA markers, the number of common markers among genetic maps is still low, limiting the ability to compare candidate gene and QTL locations across germplasm.Results
A set of 204 expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers has been assigned to map positions using eight different ryegrass mapping populations. Marker properties of a subset of 64 EST-SSRs were assessed in six to eight individuals of each mapping population and revealed 83% of the markers to be polymorphic in at least one population and an average number of alleles of 4.88. EST-SSR markers polymorphic in multiple populations served as anchor markers and allowed the construction of the first comprehensive consensus map for ryegrass. The integrated map was complemented with 97 SSRs from previously published linkage maps and finally contained 284 EST-derived and genomic SSR markers. The total map length was 742 centiMorgan (cM), ranging for individual chromosomes from 70 cM of linkage group (LG) 6 to 171 cM of LG 2.Conclusions
The consensus linkage map for ryegrass based on eight mapping populations and constructed using a large set of publicly available Lolium EST-SSRs mapped for the first time together with previously mapped SSR markers will allow for consolidating existing mapping and QTL information in ryegrass. Map and markers presented here will prove to be an asset in the development for both molecular breeding of ryegrass as well as comparative genetics and genomics within grass species. 相似文献3.
Olivier Fouet Mathilde Allegre Xavier Argout M��lanie Jeanneau Arnaud Lemainque Sylvana Pavek Anne Boland Ange Marie Risterucci Gaston Loor Mathias Tahi Xavier Sabau Brigitte Courtois Claire Lanaud 《Tree Genetics & Genomes》2011,7(4):799-817
Theobroma cacao L. is a major cash crop for tropical countries, providing incomes for 14 million small farmers. Establishing sustainable disease resistance and maintaining cocoa qualities are among the major objectives of breeding programs. To enrich the high-density genetic map, useful for all cocoa genetic studies, with gene-based markers, a recently produced large EST resource was mined to develop expressed sequence tag-based simple sequence repeat markers (EST-SSRs) defined in genes with a putative known function. A set of 174 polymorphic EST-SSRs was identified from a selection of 314 non-redundant EST-SSRs with a putative known function. Of them, 115 loci were mapped on the cocoa reference map. This new map contains 582 codominant markers arranged in ten linkage groups corresponding to the haploid number of chromosomes. An average interval between markers of 1.3?cM was found, with approximately one SSR every 2?cM. This new set of EST-SSRs includes 14 candidate genes for plant resistance or cocoa qualities. The percentage of polymorphic SSRs varied depending on the different gene regions from which they originated, with respectively 54%, 69%, and 82% of polymorphic EST-SSRs originating from coding sequences, and from the non-coding untranslated 5??UTR and 3??UTR regions. This new map contains a set of 384 SSR markers that are easily transferable across different mapping populations and useful for all genetic analyses in T. cacao. The new set of EST-SSRs will be a useful tool for studying the functional diversity of populations and for carrying out association mapping studies. 相似文献
4.
Kittipat Ukoskit Ganlayarat Posudsavang Nattapat Pongsiripat Prasert Chatwachirawong Peeraya Klomsa-ard Patthinun Poomipant Somvong Tragoonrung 《Genomics》2019,111(1):1-9
Sugar-related traits are of great importance in sugarcane breeding. In the present study, quantitative trait loci (QTL) mapping validated with association mapping was used to identify expressed sequence tag-simple sequence repeats (EST-SSRs) associated with sugar-related traits. For linkage mapping, 524 EST-SSRs, 241 Amplified Fragment Length Polymorphisms, and 10 genomic SSR markers were mapped using 283 F1 progenies derived from an interspecific cross. Six regions were identified using Multiple QTL Mapping, and 14 unlinked markers using single marker analysis. Association analysis was performed on a set of 200 accessions, based on the mixed linear model. Validation of the EST-SSR markers using association mapping within the target QTL genomic regions identified two EST-SSR markers showing a putative relationship with uridine diphosphate (UDP) glycosyltransferase, and beta-amylase, which are associated with pol and sugar yield. These functional markers can be used for marker-assisted selection of sugarcane. 相似文献
5.
Choudhary S Gaur R Gupta S 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2012,124(8):1449-1462
Well-saturated linkage maps especially those based on expressed sequence tag (EST)-derived genic molecular markers (GMMs)
are a pre-requisite for molecular breeding. This is especially true in important legumes such as chickpea where few simple
sequence repeats (SSR) and even fewer GMM-based maps have been developed. Therefore, in this study, 2,496 ESTs were generated
from chickpea seeds and utilized for the development of 487 novel EST-derived functional markers which included 125 EST-SSRs,
151 intron targeted primers (ITPs), 109 expressed sequence tag polymorphisms (ESTPs), and 102 single nucleotide polymorphisms
(SNPs). Whereas EST-SSRs, ITPs, and ESTPs were developed by in silico analysis of the developed EST sequences, SNPs were identified
by allele resequencing and their genotyping was performed using the Illumina GoldenGate Assay. Parental polymorphism was analyzed
between C. arietinum ICC4958 and C. reticulatum PI489777, parents of the reference chickpea mapping population, using a total of 872 markers: 487 new gene-based markers
developed in this study along with 385 previously published markers, of which 318 (36.5%) were found to be polymorphic and
were used for genotyping. The genotypic data were integrated with the previously published data of 108 markers and an advanced
linkage map was generated that contained 406 loci distributed on eight linkage groups that spanned 1,497.7 cM. The average
marker density was 3.68 cM and the average number of markers per LG was 50.8. Among the mapped markers, 303 new genomic locations
were defined that included 177 gene-based and 126 gSSRs (genomic SSRs) thereby producing the most advanced gene-rich map of
chickpea solely based on co-dominant markers. 相似文献
6.
11,581 grape (Vitis L.) EST-SSRs were produced and characterized from a total of 381,609 grape ESTs. Among the EST-SSRs, the tri repeat (5,560, 45.4%) represented the most abundant class of microsatellites in grape EST. Most of grape EST-SSR motifs fall within 18-24 bps in length. The EST-SSRs tri-repeats occurred a higher percentage in 5??-end (59.3%) than in 3??-end (48.3%). And EST-SSR tri-repeats had abundant codon repeats for putative amino acid runs as Proline, Arginine in grape ESTs. To better utilizing these markers, 142 of newly developed and validated EST SSR loci as well as 223 linkage map SSR loci were in silico aligned and mapped in grape genome. The orders of these SSR loci in the chromosomal physical locations and in the linkage groups were compared, and about twenty linkage map loci positions were switched or rearranged in grape genome. The EST-SSR markers extended the linkage map in grape genome. The method of in silico mapping reported in this study provided an initial collection for grape mapping resources. This approach offers great opportunities to understand the genetic variations in nucleotide sequences differences in physical map, and genetic recombination in linkage maps, as well as benefits for markers enrichment in a specific grape genome region for fine mapping or QTL mapping. 相似文献
7.
A microsatellite map of white clover 总被引:11,自引:2,他引:9
Barrett B Griffiths A Schreiber M Ellison N Mercer C Bouton J Ong B Forster J Sawbridge T Spangenberg G Bryan G Woodfield D 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2004,109(3):596-608
The white clover (Trifolium repens) nuclear genome (n=2x=16) is an important yet under-characterised genetic environment. We have developed simple sequence repeat (SSR) genetic markers for the white clover genome by mining an expressed sequence tag (EST) database and by isolation from enriched genomic libraries. A total of 2,086 EST-derived SSRs (EST-SSRs) were identified among 26,480 database accessions. Evaluation of 792 EST-SSR primer pairs resulted in 566 usable EST-SSRs. Of these, 335 polymorphic EST-SSRs, used in concert with 30 genomic SSRs, detected 493 loci in the white clover genome using 92 F1 progeny from a pair cross between two highly heterozygous genotypes—364/7 and 6525/5. Map length, as estimated using the joinmap algorithm, was 1,144 cM and spanned all 16 homologues. The R (red leaf) locus was mapped to linkage group B1 and is tightly linked to the microsatellite locus prs318c. The eight homoeologous pairs of linkage groups within the white clover genome were identified using 96 homoeologous loci. Segregation distortion was detected in four areas (groups A1, D1, D2 and H2). Marker locus density varied among and within linkage groups. This is the first time EST-SSRs have been used to build a whole-genome functional map and to describe subgenome organisation in an allopolyploid species, and T. repens is the only Trifolieae species to date to be mapped exclusively with SSRs. This gene-based microsatellite map will enable the resolution of quantitative traits into Mendelian characters, the characterisation of syntenic relationships with other genomes and acceleration of white clover improvement programmes. 相似文献
8.
Woo-Jin Kim Young-Ok Kim Bo-Hye Nam Hee Jeong Kong Eun-Mi Park Jung-Ha Kang Jeong-Ho Lee Kyung-Kil Kim 《Conservation Genetics》2009,10(4):1105-1111
Expressed sequence tags (ESTs) can be used to identify microsatellite markers. We developed 81 polymorphic microsatellite
markers from 4,940 ESTs of the olive flounder, Paralichthys olivaceus. Out of 100 EST-derived microsatellites for which PCR primers were designed, 81 loci were polymorphic in 30 individuals from
a single natural population with 2–28 (mean 10.6) alleles per locus. The observed and expected heterozygosities of these loci
were 0.033–1.000 and 0.033–0.965, respectively. Segregation analysis within a mapping family revealed non-amplifying null
alleles at five loci. These new EST-derived microsatellite markers should be useful for population genetic analyses, pedigree
tracing and constructing a linkage map for olive flounder. 相似文献
9.
Sraphet S Boonchanawiwat A Thanyasiriwat T Boonseng O Tabata S Sasamoto S Shirasawa K Isobe S Lightfoot DA Tangphatsornruang S Triwitayakorn K 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2011,122(6):1161-1170
Simple sequence repeat (SSR) markers provide a powerful tool for genetic linkage map construction that can be applied for identification of quantitative trait loci (QTL). In this study, a total of 640 new SSR markers were developed from an enriched genomic DNA library of the cassava variety 'Huay Bong 60' and 1,500 novel expressed sequence tag-simple sequence repeat (EST-SSR) loci were developed from the Genbank database. To construct a genetic linkage map of cassava, a 100 F(1) line mapping population was developed from the cross Huay Bong 60 by 'Hanatee'. Polymorphism screening between the parental lines revealed that 199 SSRs and 168 EST-SSRs were identified as novel polymorphic markers. Combining with previously developed SSRs, we report a linkage map consisted of 510 markers encompassing 1,420.3?cM, distributed on 23 linkage groups with a mean distance between markers of 4.54?cM. Comparison analysis of the SSR order on the cassava linkage map and the cassava genome sequences allowed us to locate 284 scaffolds on the genetic map. Although the number of linkage groups reported here revealed that this F(1) genetic linkage map is not yet a saturated map, it encompassed around 88% of the cassava genome indicating that the map was almost complete. Therefore, sufficient markers now exist to encompass most of the genomes and efficiently map traits in cassava. 相似文献
10.
P. Ramu B. Kassahun S. Senthilvel C. Ashok Kumar B. Jayashree R. T. Folkertsma L. Ananda Reddy M. S. Kuruvinashetti B. I. G. Haussmann C. T. Hash 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2009,119(7):1193-1204
The sequencing and detailed comparative functional analysis of genomes of a number of select botanical models open new doors
into comparative genomics among the angiosperms, with potential benefits for improvement of many orphan crops that feed large
populations. In this study, a set of simple sequence repeat (SSR) markers was developed by mining the expressed sequence tag
(EST) database of sorghum. Among the SSR-containing sequences, only those sharing considerable homology with rice genomic
sequences across the lengths of the 12 rice chromosomes were selected. Thus, 600 SSR-containing sorghum EST sequences (50
homologous sequences on each of the 12 rice chromosomes) were selected, with the intention of providing coverage for corresponding
homologous regions of the sorghum genome. Primer pairs were designed and polymorphism detection ability was assessed using
parental pairs of two existing sorghum mapping populations. About 28% of these new markers detected polymorphism in this 4-entry
panel. A subset of 55 polymorphic EST-derived SSR markers were mapped onto the existing skeleton map of a recombinant inbred
population derived from cross N13 × E 36-1, which is segregating for Striga resistance and the stay-green component of terminal drought tolerance. These new EST-derived SSR markers mapped across all
10 sorghum linkage groups, mostly to regions expected based on prior knowledge of rice–sorghum synteny. The ESTs from which
these markers were derived were then mapped in silico onto the aligned sorghum genome sequence, and 88% of the best hits corresponded to linkage-based positions. This study demonstrates
the utility of comparative genomic information in targeted development of markers to fill gaps in linkage maps of related
crop species for which sufficient genomic tools are not available. 相似文献
11.
Kanlaya Nirapathpongporn Panida Kongsawadworakul Unchera Viboonjun Kanikar Teerawattanasuk Hervé Chrestin Marc Segiun André Clément-Dement Jarunya Narangajavana 《Molecular breeding : new strategies in plant improvement》2016,36(4):39
Sets of polymorphic expressed sequence tag–simple sequence repeat (EST-SSR) markers from the rubber tree (Hevea brasiliensis) have been published by many researchers, but none has been specifically developed to study latex and wood yield traits. In this study, a total 10,321 rubber tree EST sequences, generated from suppression subtractive hybridization-cDNA libraries of bark and latex of high- and low-yielding clones, were used as sources for SSR searching. A total of 432 EST-SSR loci were identified and it was possible to design primer pairs for a subset of 298 EST-SSRs. The highest proportion of EST-SSRs was represented by dinucleotide repeats (46.6 %), followed by trinucleotide repeats (44.3 %). Based on BLASTX analysis, 234 ESTs (80 %) showed similarity to genes in NCBI databases and could be divided into 120 putative proteins with known function and 114 unknown proteins. To enhance the resolution of an existing linkage map from previous work on a rubber tree RRIM600 × PB217 population, 69 EST-SSR markers from the above set were tested to be integrated into the reference genetic map. The enriched map of 18 linkage groups spanned 2054.2 cM in length, showed an average genetic distance of 4.3 cM between adjacent markers, and included 63 new EST-SSR markers. The enhanced map from this study provides a basis for comparative mapping using PCR-based markers and identification of expressed genes possibly affecting important traits of interest. 相似文献
12.
Abundance, marker development and genetic mapping of microsatellites from unigenes in Brassica napus
Fang Wang Xiaofeng Wang Xun Chen Yingjie Xiao Haitao Li Shunchang Zhang Jinsong Xu Jie Fu Lei Huang Chao Liu Jiangsheng Wu Kede Liu 《Molecular breeding : new strategies in plant improvement》2012,30(2):731-744
Rapeseed (Brassica napus) is the second most important oil crop in the world after soybean. The repertoire of simple sequence repeat (SSR) markers for rapeseed is limited and warrants a search for a larger number of polymorphic SSRs for germplasm characterization and breeding applications. In this study, a total of 5,310 SSR-containing unigenes were identified from a set of 46,038 B. napus unigenes with an average density of one SSR every 5.75?kb. A set of 1,000 expressed sequence tag (EST)-SSR markers with repeat length ??18?bp were developed and tested for their ability to detect polymorphism among a panel of six rapeseed varieties. Of these SSR markers, 776 markers detected clear amplification products, and 511 displayed polymorphisms among the six varieties. Of these polymorphic markers, 195 EST-SSR markers, corresponding to 233 loci, were integrated into an existing B. napus linkage map. These EST-SSRs were randomly distributed on the 19 linkage groups of B. napus. Of the mapped loci, 166 showed significant homology to Arabidopsis genes. Based on the homology, 44 conserved syntenic blocks were identified between B. napus and Arabidopsis genomes. Most of the syntenic blocks were consistent with the duplication and rearrangement events identified previously. In addition, we also identified three previously unreported blocks in B. napus. A subset of 40 SSRs was used to assess genetic diversity in a collection of 192 rapeseed accessions. The polymorphism information content of these markers ranged from 0.0357 to 0.6753 with an average value of 0.3373. These results indicated that the EST-SSR markers developed in this study are useful for genetic mapping, molecular marker-assisted selection and comparative genomics. 相似文献
13.
14.
Nirala Ramchiary Van Dan Nguyen Xiaonan Li Chang Pyo Hong Vignesh Dhandapani Su Ryun Choi Ge Yu Zhong Yun Piao Yong Pyo Lim 《DNA research》2011,18(5):305-320
Genic microsatellite markers, also known as functional markers, are preferred over anonymous markers as they reveal the variation in transcribed genes among individuals. In this study, we developed a total of 707 expressed sequence tag-derived simple sequence repeat markers (EST-SSRs) and used for development of a high-density integrated map using four individual mapping populations of B. rapa. This map contains a total of 1426 markers, consisting of 306 EST-SSRs, 153 intron polymorphic markers, 395 bacterial artificial chromosome-derived SSRs (BAC-SSRs), and 572 public SSRs and other markers covering a total distance of 1245.9 cM of the B. rapa genome. Analysis of allelic diversity in 24 B. rapa germplasm using 234 mapped EST-SSR markers showed amplification of 2 alleles by majority of EST-SSRs, although amplification of alleles ranging from 2 to 8 was found. Transferability analysis of 167 EST-SSRs in 35 species belonging to cultivated and wild brassica relatives showed 42.51% (Sysimprium leteum) to 100% (B. carinata, B. juncea, and B. napus) amplification. Our newly developed EST-SSRs and high-density linkage map based on highly transferable genic markers would facilitate the molecular mapping of quantitative trait loci and the positional cloning of specific genes, in addition to marker-assisted selection and comparative genomic studies of B. rapa with other related species. 相似文献
15.
Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat 总被引:39,自引:0,他引:39
Eujayl I Sorrells ME Baum M Wolters P Powell W 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2002,104(2-3):399-407
Genetic variation present in 64 durum wheat accessions was investigated by using three sources of microsatellite (SSR) markers:
EST-derived SSRs (EST-SSRs) and two sources of SSRs isolated from total genomic DNA. Out of 245 SSR primer pairs screened,
22 EST-SSRs and 20 genomic-derived SSRs were polymorphic and used for genotyping. The EST-SSR primers produced high quality
markers, but had the lowest level of polymorphism (25%) compared to the other two sources of genomic SSR markers (53%). The
42 SSR markers detected 189 polymorphic alleles with an average number of 4.5 alleles per locus. The coefficient of similarity
ranged from 0.28 to 0.70 and the estimates of similarity varied when different sources of SSR markers were used to genotype
the accessions. This study showed that EST-derived SSR markers developed in bread wheat are polymorphic in durum wheat when
assaying loci of the A and B genomes. A minumum of ten EST-SSRs generated a very low probability of identity (0.36×10−12) indicating that these SSRs have a very high discriminatory power. EST-SSR markers directly sample variation in transcribed
regions of the genome, which may enhance their value in marker-assisted selection, comparative genetic analysis and for exploiting
wheat genetic resources by providing a more-direct estimate of functional diversity.
Received: 19 December 2000 / Accepted: 17 April 2001 相似文献
16.
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
17.
Garcia AA Kido EA Meza AN Souza HM Pinto LR Pastina MM Leite CS Silva JA Ulian EC Figueira A Souza AP 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2006,112(2):298-314
Sugarcane (Saccharum spp.) is a clonally propagated outcrossing polyploid crop of great importance in tropical agriculture. Up to now, all sugarcane
genetic maps had been developed using either full-sib progenies derived from interspecific crosses or from selfing, both approaches
not directly adopted in conventional breeding. We have developed a single integrated genetic map using a population derived
from a cross between two pre-commercial cultivars (‘SP80-180’ × ‘SP80-4966’) using a novel approach based on the simultaneous
maximum-likelihood estimation of linkage and linkage phases method specially designed for outcrossing species. From a total
of 1,118 single-dose markers (RFLP, SSR and AFLP) identified, 39% derived from a testcross configuration between the parents
segregating in a 1:1 fashion, while 61% segregated 3:1, representing heterozygous markers in both parents with the same genotypes.
The markers segregating 3:1 were used to establish linkage between the testcross markers. The final map comprised of 357 linked
markers, including 57 RFLPs, 64 SSRs and 236 AFLPs that were assigned to 131 co-segregation groups, considering a LOD score
of 5, and a recombination fraction of 37.5 cM with map distances estimated by Kosambi function. The co-segregation groups
represented a total map length of 2,602.4 cM, with a marker density of 7.3 cM. When the same data were analyzed using JoinMap
software, only 217 linked markers were assigned to 98 co-segregation groups, spanning 1,340 cM, with a marker density of 6.2 cM.
The maximum-likelihood approach reduced the number of unlinked markers to 761 (68.0%), compared to 901 (80.5%) using JoinMap.
All the co-segregation groups obtained using JoinMap were present in the map constructed based on the maximum-likelihood method.
Differences on the marker order within the co-segregation groups were observed between the two maps. Based on RFLP and SSR
markers, 42 of the 131 co-segregation groups were assembled into 12 putative homology groups. Overall, the simultaneous maximum-likelihood
estimation of linkage and linkage phases was more efficient than the method used by JoinMap to generate an integrated genetic
map of sugarcane.
E.A. Kido, A.N. Meza and H.M.B. Souza contributed equally to this work. 相似文献
18.
Oliver Gailing Catherine Bodénès Reiner Finkeldey Antoine Kremer Christophe Plomion 《Tree Genetics & Genomes》2013,9(5):1361-1367
The availability of genomic resources such as expressed sequence tag-derived simple sequence repeat (EST-SSR) markers in adaptive genes with high transferability across related species allows the construction of genetic maps and the comparison of genome structure and quantitative trait loci (QTL) positions. In the present study, genetic linkage maps were constructed for both parents of a Quercus robur × Q. robur ssp. slavonica full-sib pedigree. A total of 182 markers (61 AFLPs, 23 nuclear SSRs, 98 EST-SSRs) and 172 markers (49 AFLPs, 21 nSSRs, 101 EST-SSRs, 1 isozyme) were mapped on the female and male linkage maps, respectively. The total map length and average marker spacing were 1,038 and 5.7 cM for the female map and 998.5 and 5.8 cM for the male map. A total of 68 nuclear SSRs and EST-SSRs segregating in both parents allowed to define homologous linkage groups (LG) between both parental maps. QTL for leaf morphological traits were mapped on all 12 LG at a chromosome-wide level and on 6 LG at a genome-wide level. The phenotypic effects explained by each single QTL ranged from 4.0 % for leaf area to 15.8 % for the number of intercalary veins. QTL clusters for leaf characters that discriminate between Q. robur and Quercus petraea were mapped reproducibly on three LG, and some putative candidate genes among potentially many others were identified on LG3 and LG5. Genetic linkage maps based on EST-SSRs can be valuable tools for the identification of genes involved in adaptive trait variation and for comparative mapping. 相似文献
19.
Cassava (Manihot esculenta) is an economically important crop that is grown in tropical and sub-tropical regions. Use of molecular technology for genetic
improvement of cassava has been limited by the lack of a large set of DNA markers and a genetic map. Therefore, the aims here
were to develop additional simple sequence repeat (SSR) markers from the public expressed sequence tags (ESTs), and to construct
a genetic linkage map. In this study, we designed 425 EST-SSR markers from sequences obtained from the cassava EST database
in GenBank, and integrated them with 667 SSR markers from a microsatellite-enriched genomic sequence received from the International
Center for Tropical Agriculture (CIAT). Of these, 107 EST-SSR and 500 genomic SSR primer pairs showed polymorphic patterns
when screened in two cassava varieties, Hauy Bong 60 and Hanatee, which were used as female and male parental lines, respectively.
Within the 107 and 500 primer pairs, 81 and 226 EST-SSR and SSR primer pairs were successfully genotyped with 100 samples
of F1 progeny, respectively. The results showed 20 linkage groups consisting of 211 markers—56 EST-SSR and 155 SSR markers—spanning
1,178 cM, with an average distance between markers of 5.6 cM and about 11 markers per linkage group. These novel EST-SSR markers
provided genic PCR-based co-dominant markers that were useful, reliable and economical. The EST-SSRs were used together with
SSR markers to construct the cassava genetic linkage map which will be useful for the identification of quantitative trait
loci controlling the traits of interest in cassava breeding programs. 相似文献
20.
Shigeki Moriya Hiroshi Iwanami Nobuhiro Kotoda Takashi Haji Kazuma Okada Shingo Terakami Naozumi Mimida Toshiya Yamamoto Kazuyuki Abe 《Tree Genetics & Genomes》2012,8(4):709-723
Identification of markers associated with genes of interest and quantitative trait loci (QTLs), combined with high-density genetic linkage maps, can help reduce labor and costs by enabling marker-assisted selection (MAS). In this study, a dwarfing apple rootstock cultivar ??JM7?? (Malus prunifolia × Malus pumila ??Malling 9??) and wild apple Malus sieboldii ??Sanashi 63?? (section Sorbomalus) were used for constructing genetic linkage maps. Here, a species from section Sorbomalus was used for the first time as a target species in a genome-wide mapping study. We also developed and mapped 137 novel-expressed sequence tag-simple sequence repeat (EST-SSR) markers. The genetic linkage maps of ??JM7?? and ??Sanashi 63?? consisted of 415 and 310 loci and spanned 998.0 and 981.8?cM, respectively, comparable to the reference map of Malus × domestica ??Discovery??. A BLASTN search revealed that all of the EST-SSR sequences used in this study exhibited very high homology to one or more previously characterized apple genome contigs. Although the most homologous contigs of 89 EST-SSRs were located within the same linkage groups (LGs) identified by mapping analysis, the other 48 EST-SSRs were aligned into contigs positioned in different LGs than those identified by mapping. When search criteria were expanded to include the five most homologous contigs of each EST-SSR, at least one of the top five contigs for 15 of these 48 EST-SSRs corresponded to the LG obtained by mapping. The maps of ??JM7?? and ??Sanashi 63?? may be useful for analyzing important rootstock characteristics and identifying markers for MAS. 相似文献