Abstract
Italian millet is a commercially important grain crop. Nineteen polymorphic simple sequence repeat (SSR) markers, developed through construction of an SSR-enriched library from genomic DNA of Italian millet (Setaria italica L., P. Beauv.), were used for assessment of molecular genetic diversity against 40 accessions of S. italica. In total, 85 alleles were detected, with an average of 4.5 alleles per locus. The average gene diversity and polymorphism information content (PIC) values were 0.412 and 0.376, ranging from 0.02 to 0.88 and from 0.02 to 0.87, respectively. Values for observed (H O) and expected (H E) heterozygosities ranged from 0 to 0.73 and from 0.03 to 0.89, respectively. Nine loci deviated from Hardy-Weinberg equilibrium. The mean similarity coefficient among accessions was 0.6593. Based on the UPGMA algorithm, six different groups were successfully identified. In this clustering analysis, all Korean accessions grouped in one cluster, indicating that Korean accessions are genetically quite distinct from other introduced accessions. These newly developed microsatellite markers should be very useful tools for several genetic studies, including an assessment of diversity and population structure in Italian millet.
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Butcher PA, Decroocq S, Gray Y and Moran GF (2000) Development, inheritance and cross-species amplification of microsatellite markers from Acacia mangium. Theor. Appl. Genet. 101: 1282–1290.
Dixit A, Jin MH, Chung JW, Yu JW, Chung HK, Ma KH, Park YJ and Cho EG (2005) Development of polymorphic microsatellite markers in sesame (Sesamum indicum L.). Mol. Ecol. Notes. 5: 736–738.
Doust AN, Devos KM, Gadberry MD, Gale MD and Kellogg EA (2005) Thegenetic basis for inflorescence variation between foxtail and green millet (Poaceae). Genetics. 169: 1659–1672.
Edwards KJ, Barker JH, Daly A, Jones C and Karp A (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques. 20: 758–760.
Ferguson ME, Burow MD, Schultz SR, Bramel PJ, Paterson AH, Kresovich S and Mitchell S (2004) Microsatellite identification and characterization in peanut (A. hypogaea L.). Theor. Appl. Genet. 108: 1064–1070.
Fukunaga K, Ichitani K, Taura S, Sato M and Kawase M (2005) Ribosomal DNA intergenic spacer sequence in foxtail millet, Setaria italica (L.) P. Beauv. and its characterization and application to typing of foxtail millet landraces. Hereditas. 142: 38–44.
Fukunaga K, Wang ZM, Kato K and Kawase M (2002) Geographical variation of nuclear genome RFLPs and genetic differentiation in foxtail millet, Setaria italica (L.) P. Beauv. Genet. Resour. Crop Evol. 49: 95–101.
Gupta PK and Varshney RK (2000) Thedevelopment and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113: 163–185.
He GH, Meng RH, Newman M, Gao GQ, Pittman RN and Prakash CS (2003) Microsatellites as DNA markers in cultivated peanut. BMC Plant Biol. 3: 3–11.
Jia XP, Shi YS, Song YC, Wang GY, Wang TU and Li Y (2007) Development of EST-SSR in foxtail millet (Setaria italica). Genet. Resour. Crop Evol. 54: 233–236.
Jia XP, Zhang ZB, Liu YH, Zhang CW, Shi YS, Song YC, Wang TY and Li Y s(2009) Development and genetic mapping of SSR markers in foxtail millet (Setaria italic (L.) P. Beauv.). Theor. Appl. Genet. 118: 821–829.
Kantety RV, Rota ML, Matthews DE and 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.
Kim KY (2004) Developing one-step program (SSR Manager) for rapid identification of clones with SSRs and primer designing. Master’s thesis, Seoul National University, Seoul, Republic of Korea.
La Rota M, Kantety RV, Yu JK and Sorrells ME (2005) Nonrandom distribution and frequencies of genomic and EST-derived SSR markers in rice, wheat, and barley. BMC Genomics 6: 23–32.
Le Thierry d’Ennequin M, Panaud O, Toupance B and Sarr A (2000) Assessment of genetic relationships between Setaria italica and its wild relative S. viridis using AFLP markers. Theor. Appl. Genet. 100: 1061–1066.
Li Y, Jia J, Wang Y and Wu S (1998) Intraspecific and interspecific variation in Setaria revealed by RAPD analysis. Genet. Res. Crop Evol. 45: 279–285.
Li ZK, Yu SB, Lafitte HR, Huang N, Courtois B, Hittalmani S, Vijayakumar CH, Liu GF, Wang GC, Shashidhar HE, et al(2003) QTL × environment interactions in rice. I. Heading date and plant height. Theor. Appl. Genet. 108: 141–153.
Liu K and Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128–2129.
Ma KH, Jang DH, Dixit A, Chung JW, Lee SY and Park YJ (2007) Characterization of 30 new microsatellite markers, developed from enriched genomic DNA library of zoysia grass Zoysia japonica Steud. Mol. Ecol. Notes 7: 1323–1325.
Morgante M, Hanafey M and Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat. Genet. 30: 194–200.
Moretzsohn MC, Hopkins MS, Mitchell SE, Kresovich S, Valls JFM and Ferreira ME (2004) Genetic diversityof peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hypervariable regions of the genome. BMC Plant Biol. 4: 11.
Mun KH, Kim DJ, Choi HK, Gish J, Debelle F, Mudge J, Denny R, Endre G, Saurat O, Dudez AM, et al. (2006) Distribution of SSRs in the genome of Medicago truncatula: a resource of genetic markers that integrate genetic and physical maps. Genetics 172: 2541–2555.
Pandey M, Gailing O, Fischer D, Hattemer HH and Finkeldey R (2004) Characterization 13 of microsatellite markers in sycamore (Acer pseudoplatanus L.). Mol. Ecol. Notes 4: 253–255.
Powell W, Machray GC and Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci. 1: 215–222.
Sakamoto S (1987) Origin and dispersal of common millet and foxtail millet. Jpn. Agric. Res. Quart. 21: 84–89.
Schontz D and Rether B (1999) Genetic variability in foxtail millet, Setaria italica (L.) P. Beauv.: Identification and classification of lines with RAPD markers. Plant Breeding 118: 190–192.
Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat. Biotechnol. 18: 233–234.
Tamura K, Dudley J, Nei M and Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24: 1596–1599.
Ueno S, Tsumura Y and Washitani I (2003) Development of microsatellite markers in Primula sieboldii E. Morren, a threatened Japanese perennial herb. Conserv. Genet. 4: 809–811.
Wang ZM, Devos KM, Liu CJ, Wang RQ and Gale MD (1998) Construction of RFLPbased maps of foxtail millet, Setaria italica (L.) P. Beauv. Theor. Appl. Genet. 96: 31–36.
Yeh FC, Yang R and Boyle T (1999) POPGENE Version 1.32. Microsoft window-based free ware for population genetic analysis. Computer program and documentation distributed by University of Alberta and Centre for International Forestry Research, Alberta, Canada.
Zane L, Bargelloni L and Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol. Ecol. 11: 1–16.
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Zhao, W., Lee, GA., Kwon, SW. et al. Development and use of novel SSR markers for molecular genetic diversity in Italian millet (Setaria italica L.). Genes Genom 34, 51–57 (2012). https://doi.org/10.1007/s13258-011-0102-5
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DOI: https://doi.org/10.1007/s13258-011-0102-5