- Research article
- Open Access
Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas)
© Wang et al; licensee BioMed Central Ltd. 2011
Received: 30 June 2011
Accepted: 20 October 2011
Published: 20 October 2011
Currently there exists a limited availability of genetic marker resources in sweetpotato (Ipomoea batatas), which is hindering genetic research in this species. It is necessary to develop more molecular markers for potential use in sweetpotato genetic research. With the newly developed next generation sequencing technology, large amount of transcribed sequences of sweetpotato have been generated and are available for identifying SSR markers by data mining.
In this study, we investigated 181,615 ESTs for the identification and development of SSR markers. In total, 8,294 SSRs were identified from 7,163 SSR-containing unique ESTs. On an average, one SSR was found per 7.1 kb of EST sequence with tri-nucleotide motifs (42.9%) being the most abundant followed by di- (41.2%), tetra- (9.2%), penta- (3.7%) and hexa-nucleotide (3.1%) repeat types. The top five motifs included AG/CT (26.9%), AAG/CTT (13.5%), AT/TA (10.6%), CCG/CGG (5.8%) and AAT/ATT (4.5%). After removing possible duplicate of published EST-SSRs of sweetpotato, a total of non-repeat 7,958 SSR motifs were identified. Based on these SSR-containing sequences, 1,060 pairs of high-quality SSR primers were designed and used for validation of the amplification and assessment of the polymorphism between two parents of one mapping population (E Shu 3 Hao and Guang 2k-30) and eight accessions of cultivated sweetpotatoes. The results showed that 816 primer pairs could yield reproducible and strong amplification products, of which 195 (23.9%) and 342 (41.9%) primer pairs exhibited polymorphism between E Shu 3 Hao and Guang 2k-30 and among the 8 cultivated sweetpotatoes, respectively.
This study gives an insight into the frequency, type and distribution of sweetpotato EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated sweetpotato. These EST-SSR markers could enrich the current resource of molecular markers for the sweetpotato community and would be useful for qualitative and quantitative trait mapping, marker-assisted selection, evolution and genetic diversity studies in cultivated sweetpotato and related Ipomoea species.
Sweetpotato (Ipomoea batatas) is a hexaploid (2n = 6x = 90) dicot and belongs to the family of Convolvulaceae. Due to its high yielding potential and adaptability under a wide range of environmental conditions, sweetpotato is one of the world's important food crops, especially in developing countries. According to the Food and Agriculture Organization (FAO) statistics, world production of sweetpotato in 2008 was more than 110 million tons, and almost 80% came from China, with a production of around 85 million tons from about 3.7 million hectares . Now sweetpotato is usually used as staple food, animal feed, industrial material and potential raw material for alcohol production. In addition, the high beta carotene content of orange-fleshed sweetpotato plays a crucial role to prevent vitamin A deficiency-related blindness and maternal mortality in many developing countries.
Despite its importance, sweetpotato breeding is constrained by the complexity of the genetics of this hexaploid crop and by the lack of genomic resources. Molecular markers have great potential to speed up the process of developing improved cultivars. Although several sweetpotato genetic maps have been published [2–4], the existing maps do not have sufficient markers to be highly useful for genetic studies. Thus, there is a great need for development of novel markers. With the newly developed high-throughput next generation sequencing technology, a large number of transcribed sequences have been generated for model species as well as economically important non-model plants. In addition to providing an effective approach for gene discovery and transcript profile characterization, these ESTs can be used as a cost-effective, valuable source for molecular marker development, such as single nucleotide polymorphism (SNP) and simple sequence repeats (SSRs).
DNA simple sequence repeats, also known as microsatellites, are tandem repeats of 2-6 bp DNA core sequences, which are widely distributed in both non-coding and transcribed sequences, commonly known as genomic-SSRs and EST-SSRs . With the advantages of being PCR-based, reliable, co-dominant, multi-allelic, chromosome specific, and highly informative, SSRs are useful for many applications in plant genetics and breeding such as construction of high-density linkage maps, genetic diversity analysis, cultivar identification, and marker-assisted selection. Although genomic SSRs are highly polymorphic and widely distributed throughout the genome [6, 7], and advances in techniques to enrich SSRs have also resulted in the accelerated development of large numbers of genomic SSR markers in many plants [8–14], it is still expensive, labor-intensive and time-consuming to develop genomic SSR markers. In contrast, EST-SSRs can be rapidly developed from EST database at lower cost. Moreover, due to their association with coding sequences, EST-SSRs can also lead to the direct gene tagging for QTL mapping of agronomically important traits and increase the efficiency of marker-assisted selection . In addition, EST-SSRs show a higher level of transferability to closely related species than genomic SSR markers [13, 16–18] and can be served as anchor markers for comparative mapping and evolutionary studies [19, 20].
In sweetpotato, the genomic SSRs were originally developed by Jarret and Bowen  and used in inheritance evaluation and mutation mechanisms of microsatellite markers , paternity analysis  and assessment of genetic diversity and relationship [24, 25] in cultivated sweetpotato and wild species. Later, Hu et al  developed 79 primer pairs from small-insert and enriched library, 27 of which showed length polymorphism among 20 sweetpotato accessions examined. At the same time, they also identified and designed 151 primer pairs from a published EST database, and 75 loci showed length polymorphism among 12 sweetpotato genotypes. Recently, large amount of ESTs were generated using pyrosequencing and Illumina paired end sequencing and provided the opportunity to develop more useful EST-SSRs for sweetpotato [27, 28]. In this study, in order to reduce redundancy we combined and reassembled all these available sequences and screened a large scale of ESTs (181,615) with the objectives: (1) to analyze the frequency and distribution of SSRs in transcribed regions of cultivated sweetpotato genome; (2) to design new PCR primer pairs from these assembled sequences for sweetpotato; (3) to validate and evaluate the designed SSR primer pairs in various cultivated sweetpotato genotypes.
Frequency and distribution of EST-derived SSR markers in sweetpotato
Summary of EST-SSR searching results
Total number of sequences examined
Total size of examined sequences (bp)
Total number of identified SSRs
Number of SSR containing sequences
Number of sequences containing more than 1 SSR
Number of SSRs present in compound formation
Length distribution of EST-SSRs based on the number of repeat units
Primer design and evaluation of EST-SSR markers in cultivated sweetpotato
Polymorphism of EST-derived SSR markers in cultivated sweetpotato
The polymorphism assessment was first examined in E Shu 3 Hao and Guang 2K-30. Among the 816 effective SSR primer pairs, 195 (23.9%) were polymorphic between the two mapping parents. A total of 644 alleles at polymorphic loci were detected and the average number of alleles per SSR marker was 3.30 with a range of 2-10, based on the dominant scoring of the SSR bands characterized by the presence or absence of a particular band (Additional File 1). Polymorphisms could be observed for 45 di-, 72 tri-, 21 tetra-, 29 penta-, 22 hexa-nucleotide repeats and 6 compound formation repeats (Figure 2). The results of a BLASTx search showed that 68.7% (134) of the polymorphic SSR loci could be associated with known or uncharacterized functional genes.
The polymorphism of the 816 EST-derived SSRs was further evaluated in eight diverse accessions of cultivated sweetpotatoes. The results showed that 342 (41.9%) primers were polymorphic, with a total of 1,004 alleles detected (Additional file 1). The average number of alleles per locus was 2.94 with a range of 2-11 alleles. A maximum of 11 alleles was observed for primer GDAAS1073. The PIC values varied from 0.22 to 0.88 with an average value of 0.35. Polymorphisms could be observed for 106 di-, 109 tri-, 28 tetra-, 53 penta-, 36 hexa-nucleotide repeats and 10 compound formation repeats (Figure 2). Among of these 342 polymorphic SSR loci, 266 had BLAST hits to known proteins in the UniProt database.
Frequency and distribution of sweetpotato EST-SSRs
The frequency of SSRs in SSR containing ESTs can accurately reflect the density of SSRs in the transcribed region of the genome. Using Sanger and next generation sequencing, a large number of EST sequences for sweetpotato have been generated. These sequences offered us an opportunity to discover novel genes, also provided a resource to develop markers. However, there is abundant redundancy in these EST sequences due to the non-normalized cDNA libraries and submission by different researchers. In this study, in order to reduce the redundancy and avoid overestimation of the EST-SSR frequency, SSR searching was performed following redundancy elimination. A total of 87,492 potential unique EST sequences (about 58.7 Mb) were used for SSR searching and 7,163 ESTs (8.2%) contained SSR motifs, generating 8,294 unique SSRs. The result of SSR abundance was in agreement with the report by Hu et al (9.1%) . These two results indicated that the abundance of SSRs for sweetpotato ESTs was relatively higher than that for other species, e.g. peanut (6.8%) , barley (3.4%), maize (1.4%), rice (4.7%), soyghum (3.6%), wheat (3.2%) , Medicago truncatula (3.0%) , Epimudium sagittatum (3.4%) . In this work, the frequency of occurrence for EST-SSRs was one EST-SSR in every 7.1 kb. In previous reports, an EST-SSR occurs every 13.8 kb in Arabidopsis thaliana, 3.4 kb in rice, 8.1 kb in maize, 7.4 kb in soybean, 11.1 kb in tomato, 20.0 kb in cotton and 14.0 kb in poplar . However, a direct comparison of abundance estimation and frequency occurrence of SSR in different reports is difficult due to the fact that the estimates were dependent on the SSR search criteria, the size of the dataset, the database-mining tools and the EST sequence redundancy.
In earlier reports, tri-nucleotide repeats were generally the most common motif found in both monocots  and dicots . In the present investigation, tri-nucleotide repeat was also found to be the most abundant SSRs, followed by di-, tetra-, penta, and hexa-nucleotide (Table 1). As shown in Figure 1, the most dominant di- and tri-nucleotide motif types were AG/CT (26.9%) and AAG/CTT (13.5%), respectively. These were in agreement with recent studies in cultivated peanut (Arachis hypogaea L.) , Epimudium sagittatum , and many dicotyledonous species . The previous studies of arabidopsis  and soybean  also suggested that the tri-nucleotide AAG motif may be common motif in dicots. In contrast, the most frequent tri-nucleotide repeat motifs were (AAC/TTG)n in wheat, (AGG/TCC)n in rice, and (CCG/GGC)n in maize, barley and sorghum [31, 36, 37]. The abundance of the tri-nucleotide CCG repeat motif was favored overwhelmingly in cereal species [31, 36, 38] and also considered as a specific feature of monocot genome, which may be due to the high GC content and consequent codon usage bias [5, 39]. But interestingly, in this study, the second most dominant tri-nucleotide repeat motif was CCG/CGG (5.8%), following AAG/CTT. This result was similar to the previous report in sweetpotao , which also showed CCG repeat was one of high abundant tri-nucleotide motifs.
Validation and polymorphism of sweetpotato EST-SSRs
Repeated SSR loci among published SSR markers in sweetpotato
SSR ID of Wang et al.
SSR ID of Hu et al.
and Schafleitner et al.
SSR sequence ID in this study
At2g03070 [Arabidopsis thaliana]
Transcription factor Myb n = 1
Based on these non-repeat SSR-containing sequences, a total of 1,060 primer pairs were designed and used for validation of the EST-SSR markers in sweetpotato. Of these, 897 primer pairs (84.6%) yielded amplicons in the two parents of our mapping population. This result was similar to EST-SSR amplification rate in sweetpotato [26, 28] and many other studies in which a success rate of 60-90% amplification has also been reported [37, 40–43]. In those studies (except ), they also reported a similar success rate of amplification for both genomic SSRs and EST-SSRs. However, in sweetpotato, the amplification efficiency of EST-SSRs was much higher than that of genomic SSRs [22, 26]. The higher efficiency of PCR amplification of EST-SSRs may be attributed to the reason that sequence data for primer design were from relatively highly conserved transcribed regions, not randomly from total genomic libraries. Just due to the reason that EST-SSRs were from highly conserved transcribed regions, they were reported to be less polymorphic, but have higher transferability and better applicability than genomic SSR markers in crop plants [44–47]. The 816 amplifiable EST-SSR primers will further be used for validation of the amplification and assessment of the polymorphism among wild Ipomoea species.
As is commonly known, polymorphic SSR markers are important for research involving genetic diversity, relatedness, evolution, linkage mapping, comparative genomics, and gene-based association studies. In the present investigation, SSR primer polymorphism was first examined in the two parents of our mapping population. Among the tested primers, 195 were polymorphic between the two mapping parents. These markers would be useful for construction of an SSR-based linkage map. Furthermore, among of these working primer pairs, 342 (41.9%) showed polymorphism in the eight cultivated sweetpotatoes. This value was lower than earlier studies, in which 62.5% and 67.2% SSRs revealed to be polymorphism in different test set [26, 28]. A small number of DNA samples and DNA samples from a different geographic origin may result in a different polymorphism. For example, a relatively high level of polymorphism was reported in cassava when the number of accessions used increased from 38 to over 500 . Additionally, sufficient published data from other plant and animal species have proved that tri-nucleotide SSR loci possess low variability than di-nucleotide containing SSR loci [49–51]. In our results, no correlation was found between the number of nucleotide motif repeats and the level of polymorphism (as shown in Figure 2).
In this study, in addition to the characterization of EST-derived SSR markers in cultivated sweetpotato, we designed and validated 1,060 SSR markers in two parents of our mapping population. Among the effective primers, 41.9% of them showed polymorphism in eight sweetpotato cultivars. These developed SSR markers will provide a valuable resource for genetic diversity, evolution, linkage mapping, comparative genomics, gene-based association studies, and marker-assisted selection in sweetpotato genetic study. Since these markers were developed based on conserved expressed sequences, they may be valuable for functional analysis of candidate genes. To the best of our knowledge, this is the first attempt to exploit EST dababase and develop large numbers of SSR markers in sweetpotato.
Plant materials and DNA extraction
Sweetpotato accessions used for EST-SSR validation and evaluation
E Shu 3 Hao
Improved variety, mapping parent
Improved variety, mapping parent
Sheng Li Bai Hao
Tai Nong 57
Hua Bei 553
Yu Bei Bai
Bao Ting Zhong
Data mining for SSR marker
A total of 181,615 EST sequences including 66,418 (31,685 contigs and 34,733 singletons) from sweetpotato gene index established by Schafleitner et al , 56,516 developed by Wang et al and 58,681 generated in house were used in this study. These ESTs were assembled using the TGICL program . A Perl script known as MIcroSAtellite (MISA http://pgrc.ipk-gatersleben.de/misa/) was used to mine microsatellites. In this work, the search was conducted for sequences that showed at least six repetitions for di-, five repeat units for tri-, and four repetitions for tetra-, penta- and hexa-nucleotides, excluding polyA and polyT repeat. Frequency of SSR refers to kilobase pairs of EST sequences containing one SSR.
Primer design and PCR amplification
In order to remove possible duplicate of published EST-SSRs, comparison was performed using the primers from the published 370 EST-SSR markers (75 , 195 , 100 ) against the 7,163 unique SSR-containing sequences. Each set of sequences was compared by specialized NCBI blast program called bl2seq using default parameters with the exception that the word size algorithmic parameter was changed from 28 to 16 due to the short length of the primers (18-24 bp) .
Sequences that showed the longest repetitions and flanking regions that quantified primer design were selected for PCR primer design using primer premier 6.0 (PREMIER Biosoft International, Palo Alto, CA). Primers were designed based on the following core criteria: (1) primer length ranging from 18 bp to 24 bp; (2) melting temperature (Tm) between 52°C and 63°C with 60°C as optimum; (3) PCR product size ranging from 100 to 350 bp; (4) GC% content between 40% and 60% with amplification rate larger than 80%. The parameters were modified when unsuitable primer pairs were retrieved by the program. When two distinct microsatellite sequences were present in one EST sequence at distant sites, primer pairs were designed respectively. When two loci were in close proximity in one sequence, the primer pairs were designed outside of these micorsatellites.
PCR analysis was performed in a total volume of 20 μl reaction mixture that contained 40-50 ng template DNA, 1× PCR buffer (20 mM Tris pH 9.0, 100 mM KCl, 2.0 mM MgCl2), 200 μM of each of the four dNTPs, 0.2 μM of each of the forward and reverse primers, and one unit of Taq DNA polymerase with the following cycling profile: 1 cycle of 5 min at 94°C, an annealing temperature of 55-65°C for 35 cycles (1 min at 94°C, 30 s at 55-65°C, 45 s at 72°C) and an additional cycle of 10 min at 72°C. Each of the primer pairs was screened twice to confirm the repeatability of the observed bands in each genotype. PCR products were separated on 6% polyacrylamide denaturing gels. The gels were silver stained for SSR bands detection.
Primer screening, evaluation and data collection
Designed primer pairs were firstly screened using E Shu 3 Hao and Guang 2k-30 for their effectiveness to amplify SSR fragments of the expected size and to detect allele polymorphism. The effective primer pairs from the screening were confirmed and evaluated further on the following eight cultivars. Every PCR reaction was performed twice. The allelic frequencies were calculated for the samples analyzed. The genetic diversity of the samples as a whole was estimated based on the number of alleles per locus (total number of alleles/number of loci), the percentage of polymorphic loci (number of polymorphic loci/total number of loci analyzed) and polymorphism information content (PIC). The polymorphism was determined according to the presence or absence of the SSR locus. The value of PIC was calculated using the formula where Pi is the frequency of an individual genotype generated by a given EST-SSR primer pair and summation extends over n alleles.
We appreciate great advice and assistance on SSR loci searching and comments from Dr. Xiaoping Chen from Crops Research Institute, Guangdong Academy of Agricultural Sciences. This work was supported by the earmarked fund for the National Modern Agro-industry Technology Research System (nycytx-16-B-5), the National Natural Science Foundation of China (No. 31000737), the Natural Science Foundation of Guangdong Province, China (No. 10151064001000018) and the President Foundation of Guangdong Academy of Agricultural Sciences, China (No. 201009).
- The Food and Agriculture Organization. [http://faostat.fao.org/]
- Jim C, G C, Albert K, Kenneth V, Maria A, Robert O, Bryon R: Development of a genetic linkage map and identification of homologous linkage groups in sweetpotato using multiple-dose AFLP markers. Molecular Breeding. 2008, 21 (4): 511-532. 10.1007/s11032-007-9150-6.View ArticleGoogle Scholar
- Kriegner A, Cervantes JC, Burg K, Mwanga ROM, Zhang D: A genetic linkage map of sweetpotato [Ipomoea batatas (L.) Lam.] based on AFLP markers. Molecular Breeding. 2003, 11 (3): 169-185. 10.1023/A:1022870917230.View ArticleGoogle Scholar
- Li AX, Liu QC, Wang QM, Zhang LM, Hong Z, Liu SZ: Establishment of Molecular Linkage Maps Using SRAP Markers in Sweet Potato. ACTA AGRONOMICA SINICA. 2010, 36 (8): 1286-1295.Google Scholar
- Morgante M, Hanafey M, Powell W: Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet. 2002, 30 (2): 194-200. 10.1038/ng822.PubMedView ArticleGoogle Scholar
- Taramino G, Tarchini R, Ferrario S, Lee M, Pe ME: Characterization and mapping of simple sequence repeats (SSRs) in Sorghum bicolor. Theoretical and Applied Genetics. 1997, 95: 66-72. 10.1007/s001220050533.View ArticleGoogle Scholar
- La Rota M, Kantety RV, Yu JK, Sorrells ME: Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics. 2005, 6 (1): 23-10.1186/1471-2164-6-23.PubMedPubMed CentralView ArticleGoogle Scholar
- Edwards K, Barker J, Daly A, Jones C, Karp A: Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques. 1996, 20 (5): 758-760.PubMedGoogle Scholar
- Hamilton M, Pincus E, Di-Fiore A, Fleischer R: Universal linker and ligation procedures for construction of genomic DNA libraries enriched for microsatellites. Biotechniques. 1999, 27 (3): 500-507.PubMedGoogle Scholar
- Wen M, Wang H, Xia Z, Zou M, Lu C, Wang W: Developmenrt of EST-SSR and genomic-SSR markers to assess genetic diversity in Jatropha Curcas L. BMC Res Notes. 2010, 3: 42-10.1186/1756-0500-3-42.PubMedPubMed CentralView ArticleGoogle Scholar
- Nunome T, Negoro S, Kono I, Kanamori H, Miyatake K, Yamaguchi H, Ohyama A, Fukuoka H: Development of SSR markers derived from SSR-enriched genomic library of eggplant (Solanum melongena L.). Theor Appl Genet. 2009, 119 (6): 1143-1153. 10.1007/s00122-009-1116-0.PubMedView ArticleGoogle Scholar
- Iniguez-Luy FL, Voort AV, Osborn TC: Development of a set of public SSR markers derived from genomic sequence of a rapid cycling Brassica oleracea L. genotype. Theor Appl Genet. 2008, 117 (6): 977-985. 10.1007/s00122-008-0837-9.PubMedView ArticleGoogle Scholar
- Saha MC, Cooper JD, Mian MA, Chekhovskiy K, May GD: Tall fescue genomic SSR markers: development and transferability across multiple grass species. Theor Appl Genet. 2006, 113 (8): 1449-1458. 10.1007/s00122-006-0391-2.PubMedView ArticleGoogle Scholar
- Wang YW, Samuels TD, Wu YQ: Development of 1,030 genomic SSR markers in switchgrass. Theor Appl Genet. 2011, 122 (4): 677-686. 10.1007/s00122-010-1477-4.PubMedView ArticleGoogle Scholar
- Gupta PK, Rustgi S: Molecular markers from the transcribed/expressed region of the genome in higher plants. Funct Integr Genomics. 2004, 4 (3): 139-162.PubMedView ArticleGoogle Scholar
- Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ: Analysis of SSRs derived from grape ESTs. Theor Appl Genet. 2000, 100: 723-726. 10.1007/s001220051344.View ArticleGoogle Scholar
- Eujayl I, Sledge MK, Wang L, May GD, Chekhovskiy K, Zwonitzer JC, Mian MA: Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp. Theor Appl Genet. 2004, 108 (3): 414-422. 10.1007/s00122-003-1450-6.PubMedView ArticleGoogle Scholar
- Zhang LY, Bernard M, Leroy P, Feuillet C, Sourdille P: High transferability of bread wheat EST-derived SSRs to other cereals. Theor Appl Genet. 2005, 111 (4): 677-687. 10.1007/s00122-005-2041-5.PubMedView ArticleGoogle Scholar
- Varshney RK, Graner A, Sorrells ME: Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 2005, 23 (1): 48-55. 10.1016/j.tibtech.2004.11.005.PubMedView ArticleGoogle Scholar
- Varshney RK, Sigmund R, Börner A, Korzun V, Stein N, Sorrells ME, Langridge P, Graner A: Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Sci. 2005, 168: 195-202. 10.1016/j.plantsci.2004.08.001.View ArticleGoogle Scholar
- Jarret RL, Bowen N: Simple Sequence Repeats (SSRs) for sweetpotato germplasm characterization. Plant Genet Res Newslett. 1994, 100: 9-11.Google Scholar
- Buteler MI, Jarret RL, LaBonte DR: Sequence characterization of microsatellites in diploid and polyploid Ipomoea. Theor Appl Genet. 1999, 99: 123-132. 10.1007/s001220051216.View ArticleGoogle Scholar
- Buteler MI, Bonte DRL, Jarret RL, Macchiavelli RE: Microsatellite-based paternity analysis in polyploidy sweetpotato. J Am Soc Hort Sci. 2002, 127: 392-396.Google Scholar
- Zhang DP, Carbajulca D, Ojeda L, Rossel G, Milla S, Herrera C, Ghislain M: Microsatellite Analysis of Genetic Diversity in Sweetpotato Varieties from Latin America. "CIP Program Report 1999-2000" International Potato Center, Lima, Peru P295-301. 2001.Google Scholar
- Hwang SY, Tseng YT, Lo HF: Application of simple sequence repeats in determining the genetic relationships of cultivars used in sweet potato polycross breeding in Taiwan. Scientia Horticulturae. 2002, 93 (3-4): 215-224. 10.1016/S0304-4238(01)00343-0.View ArticleGoogle Scholar
- Hu J, Nakatani M, Mizuno K, Fujimura T: Development and Characterization of Microsatellite Markers in Sweetpotato. Breeding Science. 2004, 54: 177-188. 10.1270/jsbbs.54.177.View ArticleGoogle Scholar
- Wang Z, Fang B, Chen J, Zhang X, Luo Z, Huang L, Chen X, Li Y: De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC Genomics. 2010, 11: 726-10.1186/1471-2164-11-726.PubMedPubMed CentralView ArticleGoogle Scholar
- Schafleitner R, Tincopa LR, Palomino O, Rossel G, Robles RF, Alagon R, Rivera C, Quispe C, Rojas L, Pacheco JA, et al: A sweetpotato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers. BMC Genomics. 2010, 11 (1): 604-10.1186/1471-2164-11-604.PubMedPubMed CentralView ArticleGoogle Scholar
- Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, et al: TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics. 2003, 19 (5): 651-652. 10.1093/bioinformatics/btg034.PubMedView ArticleGoogle Scholar
- Liang X, Chen X, Hong Y, Liu H, Zhou G, Li S, Guo B: Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachis wild species. BMC Plant Biol. 2009, 9: 35-10.1186/1471-2229-9-35.PubMedPubMed CentralView ArticleGoogle Scholar
- Kantety RV, La Rota M, Matthews DE, Sorrells ME: Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol. 2002, 48 (5-6): 501-510.PubMedView ArticleGoogle Scholar
- Zeng S, Xiao G, Guo J, Fei Z, Xu Y, Roe BA, Wang Y: Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim. BMC Genomics. 2010, 11: 94-10.1186/1471-2164-11-94.PubMedPubMed CentralView ArticleGoogle Scholar
- Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R: Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics. 2000, 156 (2): 847-854.PubMedPubMed CentralGoogle Scholar
- Kumpatla SP, Mukhopadhyay S: Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome. 2005, 48 (6): 985-998. 10.1139/g05-060.PubMedView ArticleGoogle Scholar
- Gao L, Tang J, Li H, Jia J: Analysis of microsatellites in major crops assessed by computational and experimental approaches. Mol Breed. 2003, 12 (3): 245-261. 10.1023/A:1026346121217.View ArticleGoogle Scholar
- Varshney RK, Thiel T, Stein N, Langridge P, Graner A: In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett. 2002, 7 (2A): 537-546.PubMedGoogle Scholar
- Thiel T, Michalek W, Varshney RK, Graner A: Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet. 2003, 106 (3): 411-422.PubMedGoogle Scholar
- Gao LF, Jing RL, Huo NX, Li Y, Li XP, Zhou RH, Chang XP, Tang JF, Ma ZY, Jia JZ: One hundred and one new microsatellite loci derived from ESTs (EST-SSRs) in bread wheat. Theor Appl Genet. 2004, 108 (7): 1392-1400. 10.1007/s00122-003-1554-z.PubMedView ArticleGoogle Scholar
- La Rota M, Kantety RV, Yu JK, Sorrells ME: Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics. 2005, 6: 23-10.1186/1471-2164-6-23.PubMedPubMed CentralView ArticleGoogle Scholar
- Saha MC, Mian MA, Eujayl I, Zwonitzer JC, Wang L, May GD: Tall fescue EST-SSR markers with transferability across several grass species. Theor Appl Genet. 2004, 109 (4): 783-791. 10.1007/s00122-004-1681-1.PubMedView ArticleGoogle Scholar
- Cordeiro GM, Casu R, McIntyre CL, Manners JM, Henry RJ: Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum. Plant Sci. 2001, 160 (6): 1115-1123. 10.1016/S0168-9452(01)00365-X.PubMedView ArticleGoogle Scholar
- Yu JK, Dake TM, Singh S, Benscher D, Li W, Gill B, Sorrells ME: Development and mapping of EST-derived simple sequence repeat markers for hexaploid wheat. Genome. 2004, 47 (5): 805-818. 10.1139/g04-057.PubMedView ArticleGoogle Scholar
- Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, Balyan HS: Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genomics. 2003, 270 (4): 315-323. 10.1007/s00438-003-0921-4.PubMedView ArticleGoogle Scholar
- Rungis D, Berube Y, Zhang J, Ralph S, Ritland CE, Ellis BE, Douglas C, Bohlmann J, Ritland K: Robust simple sequence repeat markers for spruce (Picea spp.) from expressed sequence tags. Theor Appl Genet. 2004, 109 (6): 1283-1294. 10.1007/s00122-004-1742-5.PubMedView ArticleGoogle Scholar
- Russell J, Booth A, Fuller J, Harrower B, Hedley P, Machray G, Powell W: A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley genome. Genome. 2004, 47 (2): 389-398. 10.1139/g03-125.PubMedView ArticleGoogle Scholar
- Aggarwal RK, Hendre PS, Varshney RK, Bhat PR, Krishnakumar V, Singh L: Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theor Appl Genet. 2007, 114 (2): 359-372. 10.1007/s00122-006-0440-x.PubMedView ArticleGoogle Scholar
- Guo W, Wang W, Zhou B, Zhang T: Cross-species transferability of G. arboreum-derived EST-SSRs in the diploid species of Gossypium. Theor Appl Genet. 2006, 112 (8): 1573-1581. 10.1007/s00122-006-0261-y.PubMedView ArticleGoogle Scholar
- Chavarriaga-Aguirre PP, Maya MM, Bonierbale MW, Kresovich S, Fregene MA, Tohme J, G K: Microsatellites in Cassava (Manihot esculenta Crantz): discovery, inheritance and variability. Theoretical and Applied Genetics. 1998, 97 (3): 493-501. 10.1007/s001220050922.View ArticleGoogle Scholar
- Wang YW, Samuels TD, Wu YQ: Development of 1,030 genomic SSR markers in switchgrass. Theor Appl Genet. 2010.Google Scholar
- Chakraborty R, Kimmel M, Stivers DN, Davison LJ, Deka R: Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci. Proc Natl Acad Sci USA. 1997, 94 (3): 1041-1046. 10.1073/pnas.94.3.1041.PubMedPubMed CentralView ArticleGoogle Scholar
- Schug MD, Hutter CM, Wetterstrand KA, Gaudette MS, Mackay TF, Aquadro CF: The mutation rates of di-, tri- and tetranucleotide repeats in Drosophila melanogaster. Mol Biol Evol. 1998, 15 (12): 1751-1760.PubMedView ArticleGoogle Scholar
- Stewart CN, Via LE: A rapid CTAB DNA isolation technique useful for RAPD fingerprinting and other PCR applications. Biotechniques. 1993, 14 (5): 748-750.PubMedGoogle Scholar
- Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25 (17): 3389-3402. 10.1093/nar/25.17.3389.PubMedPubMed CentralView ArticleGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.