Abstract
The unavailability of microsatellite markers and saturated genetic linkage map has restricted the genetic improvement of foxtail millet [Setaria italica (L.) P. Beauv.], despite the fact that in recent times it has been documented as a new model species for biofuel grasses. With the objective to generate a good number of microsatellite markers in foxtail millet cultivar ‘Prasad’, 690 clones were sequenced which generated 112.95 kb high quality sequences obtained from three genomic libraries each enriched with different microsatellite repeat motifs. Microsatellites were identified in 512 (74.2%) of the 690 positive clones and 172 primer pairs (pp) were successfully designed from 249 (48.6%) unique SSR-containing clones. The efficacies of the microsatellite containing genomic sequences were established by superior primer designing ability (69%), PCR amplification efficiency (85.5%) and polymorphic potential (52%) in the parents of F2 mapping population. Out of 172 pp, functional 147 markers showed high level of cross-species amplification (~74%) in six grass species. Higher polymorphism rate and broad range of genetic diversity (0.30–0.69 averaging 0.58) obtained in constructed phylogenetic tree using 52 microsatellite markers, demonstrated the utility of markers in germplasm characterizations. In silico comparative mapping of 147 foxtail millet microsatellite containing sequences against the mapping data of sorghum (~18%), maize (~16%) and rice (~5%) indicated the presence of orthologous sequences of the foxtail millet in the respective species. The result thus demonstrates the applicability of microsatellite markers in various genotyping applications, determining phylogenetic relationships and comparative mapping in several important grass species.
References
Bell CJ, Ecker JR (1994) Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics 19:137–144
Bhattramakki D, Dong J, Chhabra K, Hart GE (2000) An integrated SSR and RFLP linkage map of Sorghum bicolor (L.) Moench. Genome 43:988–1002
Bohn M, Utz HF, Melchinger AE (1999) Genetic similarities among winter wheat cultivars determined on the basis of RFLPs, AFLPs, and SSRs and their use for predicting progeny variance. Crop Sci 39:228–237
Chen M, SanMiguel P, de Oliveira AC, Woo SS, Zhang H, Wing RA, Bennetzen JL (1997) Microcollinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. Proc Natl Acad Sci 94:3431–3435
Cordeiro GM, Maguire TL, Edwards KJ, Henry RJ (1999) Optimization of a microsatellite enrichment technique in Saccharum spp. Plant Mol Biol Rep 17:225–229
Depeiges A, Goubely C, Lenoir A et al (1995) Identification of the most represented repeated motifs in Arabidopsis thaliana microsatellite loci. Theor Appl Genet 91:160–168
Devos KM (2005) Updating the crop circle. Curr Opin Plant Biol 8:155–162
Devos KM, Gale MD (2000) Genome relationships: the grass model in current research. Plant Cell 12:637–646
Devos KM, Wang ZM, Beales J, Sasaki T, Gale MD (1998) Comparative genetic maps of foxtail millet (Setaria italica) and rice (Oryza sativa). Theor Appl Genet 96:63–68
Doust AN, Kellogg EA, Devos KM, Bennetzen JL (2009) Foxtail millet: a sequence-driven grass model system. Plant Physiol 149:137–141
Edwards KJ, Barker JHA, Daly A, Jones C, Karp A (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques 20:758–760
Gupta S, Prasad M (2009) Development and characterization of genic SSR markers in Medicago truncatula and their transferability in leguminous and non-leguminous species. Genome 52:761–771
Gupta PK, Varshney RK (2000) The development and use of microsatellites markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:63–185
Gupta S, Kumari K, Das J, Lata C, Puranik S, Prasad M (2011) Development and utilization of novel intron length polymorphic markers in foxtail millet [Setaria italica (L.) P. Beauv.]. Genome 54:586–602
Hamwieh A, Udupa SM, Sarker A, Jung C, Baum M (2009) Development of new microsatellite markers and their application in the analysis of genetic diversity in lentils. Breed Sci 59:77–86
Hernandez P, Dorado G, Laurie DA, Martin A, Snape JW (2001) Microsatellites and RFLP probes from maize are efficient sources of molecular markers for the biomass energy crop Misconstrues. Theor Appl Genet 102:616–622
Hirata M, Cai HW, Inoue M, Yuyama N, Miura Y, Komatsu T, Takamizo T, Fujimori M (2006) Development of simple sequence repeat (SSR) markers and construction of an SSR-based linkage map in Italian ryegrass (Lolium multiflorum Lam.). Theor Appl Genet 113:270–279
Hokanson SC, Szewc-Mcfadden AK, Lamboy WF, Mcferson JR (1998) Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus domestica borkh. core subset collection. Theor Appl Genet 67:671–683
Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877
Hüttel B, Winter P, Weising K, Choumane W, Weigand F, Kahl G (1999) Sequencetagged microsatellite markers for chickpea (Cicer arietinum L.). Genome 42:210–217
Ince AG, Karaca M, Onus AN (2010) CAPS-microsatellites: use of CAPS method to convert non-polymorphic microsatellites into useful markers. Mol Breed 25:491–499
Jaccard P (1908) Nouvelle recherches sur la distribution florale. Bulletin de la Société Vaudoise des Sciences Naturelles 44:223–270
Jia XP, Shi YS, Song YC, Wang GY, Wang TY, Li Y (2007) Development of EST-SSR in foxtail millet (Setaria italica). J Genet Resour Crop Evol 54(2):233–236
Jia X, Zhang Z, Liu Y, Zhang C, Shi Y, Song Y, Wang T, Li Y (2009) Development and genetic mapping of SSR markers in foxtail millet [Setaria italica (L.) P. Beauv.]. Theor Appl Genet 118:821–829
Jones ES, Dupal MP, Kolliker R, Drayton MC, Forster JW (2001) Development and characterization of simple sequence repeat (SSR) markers for perennial ryegrass (Lolium perenne L.). Theor Appl Genet 102:405–415
Jones KC, Levine KF, Banks JD (2002) Characterization of 11 polymorphic tetra-nucleotide microsatellites for forensic applications in California elk (Cervus elaphus canadensis). Mol Ecol Notes 2:425–427
Kalia RK, Rai MK, Kalia S, Singh R, Dhawan AK (2011) Microsatellites markers: an overview of the recent progress in plants. Euphytica 177:309–334
Kantety RV, La Rota M, Matthews DE, Mark E, Sorrells ME (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501–510
Koelliker R, Jones ES, Drayton MC, Dupal MP, Forster JW (2001) Development and characterization of simple sequence repeat (SSR) markers for white clover (Trifolium repens L.). Theor Appl Genet 102:416–424
Kubik C, Meyer WA, Gaut BS (1999) Assessing the abundance and polymorphism of simple sequence repeats in perennial ryegrass. Crop Sci 39:1136–1141
Lagercrantz U, Ellegren H, Andersson L (1993) The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res 21:1111–1115
Lata C, Jha S, Dixit V, Sreenivasulu N, Prasad M (2011a) Differential antioxidative responses to dehydration-induced oxidative stress in core set of foxtail millet cultivars [Setaria italica (L.)]. Protoplasma. doi:10.1007/s00709-010-0257-y
Lata C, Bhutty S, Bahadur RP, Majee M, Prasad M (2011b) Association of an SNP in a novel DREB2-like gene SiDREB2 with stress tolerance in foxtail millet [Setaria italica (L.)]. J Exp Bot 62:3387–3401
Lichtenzveig J, Scheuring C, Dodge J, Abbo S, Zhang H (2005) Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, Cicer arietinum L. Theor Appl Genet 110:492–510
Liu Z, Bai G, Zhang D, Zhu C, Xia X, Cheng R, Shi Z (2011) Genetic diversity and population structure of elite foxtail millet [Setaria italica (L.) P. Beauv.] germplasm in China. Crop Sci 51:1655–1663
Nei M (1973) Analysis of genetic diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323
Panaud O, Chen SR, McCouch R (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 252:597–607
Parida SK, Kalia SK, Kaul S, Dalal V, Hemaprabha G, Selvi A, Pandit A, Singh A, Gaikwad K, Sharma TR, Srivastava PS, Singh NK, Mohapatra T (2009) Informative genomic microsatellite markers for efficient genotyping applications in sugarcane. Theor Appl Genet 118:327–338
Pejic I, Ajmone-Marsan P, Morgante M, Kozumplick V, Castiglioni P, Taramino G, Motto M (1998) Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs. Theor Appl Genet 97:1248–1255
Pestova F, Ganal MW, Roder MS (2000) Isolation and mapping of microstallite markers specific for the D-genome of bread wheat. Genome 43:689–697
Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222
Prasad M, Varshney RK, Roy JK, Balyan HS, Gupta PK (2000) The use of microsatellites for detecting DNA polymorphism, genotype identification and genetic diversity in wheat. Theor Appl Genet 100:584–592
Rajendrakumar P, Biswal AK, Balachandran SM, Srinivasarao K, Sundaram RM (2007) Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intercoding regions. Bioinformatics 23:1–4
Rohlf FJ (1997) NTSYS-pc. Numerical taxonomy and multivariance analysis system version 2.02e. Exeter Software, New York, USA. http://www.exetersoftware.com/cat/ntsyspc/ntsyspc.html
Roldán-Ruiz I, Van Eeuwijk FA, Gilliland TJ, Dubreuil P, Dillmann J, Lalemand M, De Loose M, Baril CP (2001) A comparative study of molecular and morphological methods of describing relationships between perennial ryegrass (Lolium perenne L.) varieties. Theor Appl Genet 103:1138–1150
Russel J, Fuller J, Young G, Thomas B, Taramino G, Macaulay M, Waugh R, Powell W (1997) Discriminating between barley genotypes using microsatellite markers. Genome 40:442–450
Saghai-Maroof MA, Biyaschev RM, Yang GP, Zhang Q, Allard RW (1994) Extaordinary polymorphism microsatellite DNA in barley: species diversity, chromosomal location and population dynamics. Proc Natl Acad Sci USA 91:5466–5470
Saha MC, Cooper JD, Rouf Mian MA, Chekhovskiy K, May GD (2006) Tall fescue genomic SSR markers: development and transferability across multiple grass species. Theor Appl Genet 113:1449–1458
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbour Laboratory, Cold Spring Harbour
Sharopova N, McMullen MD, Schultz L, Schroeder S, Sanchez-Villeda H, Gardiner J, Bergstrom D, Houchins K, Melia-Hancock S, Musket T et al (2002) Development and mapping of SSR markers for maize. Plant Mol Biol 48:463–481
Shokeen B, Sethy NK, Kumar S, Bhatia S (2007) Isolation and characterization of microsatellite markers for analysis of molecular variation in the medicinal plant Madagascar periwinkle (Catharanthus roseus (L.) G. Don.). Plant Sci 172:441–451
Smith DN, Devey ME (1994) Occurrence and inheritance of microsatellites in Pinus radiata. Genome 37:977–983
Srinivasachary DidaMM, Gale MD, Devos KM (2007) Comparative analyses reveal high levels of conserved colinearity between the finger millet and rice genomes. Theor Appl Genet 115:489–499
Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations and genetic marker potential. Genome Res 11:1441–1452
Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes survey and analysis. Genome Res 10:967–981
Tsuruta SI, Hashiguchi M, Ebina M, Matsuo T, Yamamoto T, Kobayashi M, Takahara M, Nakagawa H, Akashi R (2005) Development and characterization of simple sequence repeat markers in Zoysia japonica Steud. Grassland Sci 51:249–257
Varshney RK, Kumar A, Balyan HS, Roy JK, Prasad M, Gupta PK (2000) Characterization of microsatellites and development of chromosome specific STMS markers in bread wheat. Plant Mol Biol Rep 18:5–16
Wang ZM, Devos KM, Liu CJ, Wang RQ, Gale MD (1998) Construction of RFLP-based maps of foxtail millet, Setaria italica (L.) P. Beauv. Theor Appl Genet 96:31–36
Wang ML, Barkley NA, Yu JK, Dean RE, Newman ML, Sorrells ME, Pederson GA (2005) Transfer of simple sequence repeat (SSR) markers from major cereal crops to minor grass species for germplasm characterization and evaluation. Plant Genet Resour 3:45–57
Wang YW, Samuels TD, Wu YQ (2011) Development of 1,030 genomic SSR markers in switchgrass. Theor Appl Genet 122:677–686
Yeh FC, Boyle TJB (1997) Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belgian J Botany 129:157
Yu F, Wang B-H, Feng S-P, Wang J-Y, Li W-G, Wu Y–Y (2011) Development, characterization, and cross-species/genera transferability of SSR markers for rubber tree (Hevea brasiliensis). Plant Cell Rep 30:335–344
Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11:1–16
Acknowledgments
We are grateful to the Director, National Institute of Plant Genome Research (NIPGR) for providing facilities. Dr. Sarika Gupta acknowledges the award of DST-Young Scientist fellowship (SR/FT/LS-152/2008) from the Department of Science & Technology (DST), Government of India. The study was supported by DST, DBT and NIPGR core grant. We acknowledge Dr. Swarup K Parida and Mr. Kamlesh K Sahu of NIPGR for helpful discussions.
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Communicated by P. Lakshmanan.
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Gupta, S., Kumari, K., Sahu, P.P. et al. Sequence-based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet [Setaria italica (L.) P. Beauv.]. Plant Cell Rep 31, 323–337 (2012). https://doi.org/10.1007/s00299-011-1168-x
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DOI: https://doi.org/10.1007/s00299-011-1168-x