JOURNAL BROWSE
Search
Advanced SearchSearch Tips
EST-SSR Based Genetic Diversity and Population Structure among Korean Landraces of Foxtail Millet (Setaria italica L.)
facebook(new window)  Pirnt(new window) E-mail(new window) Excel Download
  • Journal title : Korean Journal of Plant Resources
  • Volume 29, Issue 3,  2016, pp.322-330
  • Publisher : The Plant Resources Society of Korea
  • DOI : 10.7732/kjpr.2016.29.3.322
 Title & Authors
EST-SSR Based Genetic Diversity and Population Structure among Korean Landraces of Foxtail Millet (Setaria italica L.)
Ali, Asjad; Choi, Yu-Mi; Do, Yoon-Hyun; Lee, Sukyeung; Oh, Sejong; Park, Hong-Jae; Cho, Yang-Hee; Lee, Myung Chul;
  PDF(new window)
 Abstract
Understanding the genetic variation among landrace collections is important for crop improvement and utilization of valuable genetic resources. The present study was carried out to analyse the genetic diversity and associated population structure of 621 foxtail millet accessions of Korean landraces using 22 EST-SSR markers. A total of 121 alleles were detected from all accessions with an average of 5.5 alleles per microsatellite locus. The average values of gene diversity, polymorphism information content, and expected heterozygosity were 0.518, 0.594, and 0.034, respectively. Following the unweighted neighbor-joining method with arithmetic mean based clustering using binary data of polymorphic markers, the genotypes were grouped into 3 clusters, and population structure analysis also separated into 3 populations. Principal coordinate analysis (PCoA) explained a variation of 13.88% and 10.99% by first and second coordinates, respectively. However, in PCoA analysis, clear population-level clusters could not be found. This pattern of distribution might be the result of gene flow via germplasm exchanges in nearby regions. The results indicate that these Korean landraces of foxtail millet exhibit a moderate level of diversity. This study demonstrated that molecular marker strategies could contribute to a better understanding of the genetic structure in foxtail millet germplasm, and provides potentially useful information for developing conservation and breeding strategies.
 Keywords
Foxtail millet;Genetic diversity;Population structure;EST-SSR marker;
 Language
English
 Cited by
1.
Effect of Planting Density and Seeding Date on the Tiller Aspect and Growth Characteristics of Proso Millet (Panicum miliaceum L.), Korean Journal of Plant Resources, 2016, 29, 4, 511  crossref(new windwow)
 References
1.
Agrama, H.A., G.C. Eizenga and W. Yan. 2007. Association mapping of yield and its components in rice cultivars. Mol. Breeding 19:341-356. crossref(new window)

2.
Benabdelmouna, A., M. Abirached-Darmency and H. Darmency. 2001. Phylogenetic and genomic relationships in Setaria italica and its close relatives based on the molecular diversity and chromosomal organization of 5S and 18S-5.8S-25S rDNA genes. Theor. Appl. Genet. 103:668-677. crossref(new window)

3.
Camacho-Villa, T., N. Maxted, M. Scholten and B. Ford-Lloyd. 2005. Defining and identifying crop landraces. Plant Genetic Resources: Characterization and Utilization. 3:373-384. crossref(new window)

4.
Cho, Y.G., T. Ishii, S. Temnykh, X. Chen, L. Lipovich, S.R. Mccouch, W.D. Park, N. Ayres and S. Cartinhour. 2000. Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100:713-722. crossref(new window)

5.
Cho, Y.I., J.W. Chung, G.A. Lee, K.H. Ma, A. Dixit, J.G. Gwag and Y.J. Park. 2010. Development and characterization of twenty-five new polymorphic microsatellite markers in proso millet (Panicum miliaceum L.). Genes Genom. 32:267-273. crossref(new window)

6.
Cordeiro, G.M., R. Casu, C.L. McIntyre, J.M. Manners and R.J. Henry. 2001. Microsatellite markers from sugarcane (Saccharum spp.) EST cross transferable to erianthus and sorghum. Plant Sci. 160:1115-1123. crossref(new window)

7.
da Maia, L.C., D.A. Palmieri, V.Q. de Souza, M.M. Kopp, F.I. de Carvalho and A.C. de Oliveira. 2008. SSR locator: tool for simple sequence repeat discovery integrated with primer design and PCR simulation. Int. J. Plant Genomics. doi:10.1155/2008/412696 crossref(new window)

8.
Deb, D. 2009. Valuing folk crop varieties for agroecology and food security, bioscience resource project commentaries. The Bioscience Resource Project, Inc., USA.

9.
De Campos, V.A.R., T.C. De Oliveira Borba, C. Brondani, P.H.N. Rangel et al. 2008. Genetic analysis of a local population of Oryza glumaepatula using SSR markers: implications for management and conservation programs. Genetica 137:221-231.

10.
de Wet, J.M.J., L.L. Oestry-Stidd and J.I. Cubero. 1979. Origins and evolution of foxtail millets (Setaria italica). J. Agric. Trop. Bot. Appl. 26:53-64.

11.
Evanno, G., S. Regnault and J. Goudet. 2005. Detecting the number of clusters of individuals using the software structure. A simulation study. Molecular Ecology 14:2611-2620.

12.
Fukunaga, K., E. Domon and M. Kawase. 1997. Ribosomal DNA variation in foxtail millet and a survey of variation from Europe and Asia. Theor. Appl. Genet. 95:751-756. crossref(new window)

13.
Fukunaga, K., K. Ichitani and M. Kawase. 2011. rDNA polymorphism of foxtail millet (Setaria italica ssp. italica) landraces in northern Parkistan and Afghanistan and in its wild ancestor (S. italica ssp. viridis). Genet. Resour. Crop Evo. 58:825-830. crossref(new window)

14.
Fukunaga, K., M. Kawase and K. Kato, 2002. Structural variation in the Waxy gene and differentiation in foxtail millet [Setaria italica (L.) P. Beauv.]: implications for multiple origins of the waxy phenotype. Mol. Genet. Genomics. 268:214-222. crossref(new window)

15.
Gupta, S., K. Kumari, P.P. Sahu, S. Vidapu and M. Prasad. 2012. Sequence-based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet [Setaria italica (L.) P. Beauv.] Plant Cell Rep. 31:323-337. crossref(new window)

16.
Hirano, R., K. Naito, K. Fukunaga, K.N. Watanabe, R. Ohsawa and M. Kawase. 2011. Genetic structure of landraces in foxtail millet (Setaria italica (L.) P. Beauv.) revealed with transposon display and interpretation to crop evolution of foxtail millet. Genome 54:498-506. crossref(new window)

17.
Hu, X., J. Wang, P. Lu and H. Zhang. 2009. Assessment of genetic diversity in broomcorn millet (Panicum miliaceum L.) using SSR markers. J. Genet. Genomics 36:491-500. crossref(new window)

18.
Jia, X., Z. Zhang, Y. Liu, C. Zhang, Y. Shi, Y. Song, T. Wang and Y. Li. 2009. Development and genetic mapping of SSR markers in foxtail millet (Setaria italica (L.) P. Beauv.). Theor. Appl. Genet.118: 821-829. crossref(new window)

19.
Jia, X.P., Y.S. Shi, Y.C. Song, G.Y. Wang, T.Y. Wang and Y. Li. 2007. Development of EST-SSR in foxtail millet (Setaria italica). Genet. Resour. Crop Ev. 54:233-236. crossref(new window)

20.
Jin, L., Y. Lu, P. Xiao, M. Sun, H. Corke and J. Bao. 2010. Genetic diversity and population structure of a diverse set of rice germplasm for association mapping. Theor. Appl. Genet. 121:475-487. crossref(new window)

21.
Jusuf, M. and J. Pernes. 1985. Genetic variability of foxtail millet (Setaria italica P Beauv). Theor. Appl. Genet. 71:385-391.

22.
Kapila, R.K., R.S. Yadav, P. Plaha, K.N. Rai et al. 2007. Genetic diversity among pearl millet maintainers using microsatellite markers. Plant Breeding 127:33-37.

23.
Kim, C.Y., G.T. Cho, J. Lee, J.S. Sung, Y.W. Na, M.S. Yoon, H.J. Baek, H.C. Ko and Y.H. Cho. 2012. Introduction and significance on reintroduction of Korean native plant genetic resources from foreign countries. Korean J. Intl. Agri. 24(1):22-31.

24.
Kim, E.J, K.J. Sa, K.C. Park and J.K. Lee. 2012. Study of genetic diversity and relationship among accessions of foxtail millet [Setaria italica (L.) P. Beauv] in Korea, China and Pakistan using SSR markers. Genes & Genomics. 34:529-538. crossref(new window)

25.
Kim, E.J., K.J. Sa and J.K. Lee. 2011. Genetic variation of foxtail millet [Setaria italica (L.) P. Beauv.] among accessions collected from Korea revealed by AFLP markers. Korean J. Crop Sci. 56:322-328. crossref(new window)

26.
Kumari, K., M. Muthamilarasan, G. Misra, S. Gupta, A. Subramanian, S.K. Parida, D. Chattopadhyay and M. Prasad. 2013. Development of eSSR-markers in Setaria italica and their applicability in studying genetic diversity, cross-transferability and comparative mapping in millet and non-millet species. PLoS ONE 8:e67742. crossref(new window)

27.
Le Thierry d’Ennequin, M., O. Panaud, B. Toupance and A. Sarr. 2000. Assessment of geneticrelationships between Setaria italica and its wild relatives S. viridis using AFLP marker. Theor. Appl. Genet. 100:1061-1066. crossref(new window)

28.
Lee, J.K. and N.S. Kim. 2007. Genetic diversity and relationships of cultivated and weedy types of Perilla frutescens collected from East Asia revealed by SSR markers. Korean J. Breed. Sci. 39(4):491-499.

29.
Li, Y., J. Jia, Y. Wang and W. Shuzhi. 1998. Intraspecific and interspecific variation in Setaria revealed by RAPD analysis. Genet. Resour. Crop Ev. 45(3):279-285. crossref(new window)

30.
Li, Y., Y.S. Cao, S.Z. Wu and X.Z. Zhang. 1995. A phenotypic diversity analysis of foxtail millet (Setaria italica (L.) P. Beauv.) landraces of Chinese origin. Genet. Resour. Crop Ev. 43:377-389.

31.
Lin, H.S., G.I. Liao, C.Y. Chiang, C.S. Kuoh and S.B. Chang. 2012. Genetic diversity in the foxtail millet (Setaria italica) germplasm as determined by agronomic traits and microsatellite markers. Aust. J. Crop Sci. 6(2):342-349.

32.
Liu, K. and S.V. Muse. 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128-2129. crossref(new window)

33.
Liu, Z., G. Bai, D. Zhang, C. Znu, X. Xia, Z. Cheng and Z. Shi. 2011. Genetic diversity and population structure of elite foxtail millet (Setaria italica (L.) P. Beauv.) germplasm in China. Crop Sci. 51:1655-1663. crossref(new window)

34.
Mondini, L., A. Noorani and M.A. Pagnotta. 2009. Assessing plant genetic diversity by molecular tools. Diversity 1:19-35. crossref(new window)

35.
Peakall, R. and P. Smouse. 2006. Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes. 6:288-295. crossref(new window)

36.
Pejic, I., P. Ajmone-Marsan, M. Morgante, V. Kozumplick, P. Castiglioni, G. Taramino and M. Motto. 1998. Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs. Theor. Appl. Genet. 97:1248-1255. crossref(new window)

37.
Perrier X. and J.P. Jacquemoud-Collet. 2006. DARwin software http://darwin.cirad.fr/

38.
Prasada Rao, K.E., J.M.J. de Wet, D.K. Brink and M.H. Mengesha. 1987. Intraspecific variation and systematics of cultivated Setaria italica, foxtail millet (Poaceae). Econ. Bot. 41:108-116. crossref(new window)

39.
Pritchard, J.K., M. Stephens and P. Donnelly. 2000 Inference of population structure using multilocus genotype data. Genetics 155:945-959.

40.
Reddy, M.T., H. Begum, N. Sunil, P.S. Rao, N. Sivaraj and S. Kumar. 2014. Preliminary characterization and evaluation of landraces of Indian spinach (Basella spp. L.) for agro-economic and quality traits. Plant Breed. Biotech. 2(1):48-63.

41.
Schontz, D. and B. Reather. 1999. Genetic variability in foxtail millet, Setaria italica P. Beauv.: Identification and classification of lines with RAPD markers. Plant Breeding 118:190-192. crossref(new window)

42.
Seo, D.H., K.M. Jung, S.J. Kim and K.M. Kim. 2013. Development of EST-SSR markers and analysis of genetic diversity using persimmon (Diospyros kaki Thunb) cultivars collecting from domestic. Korean J. Plant Res. 26(4): 491-502 (in Korean). crossref(new window)

43.
Shehzad, T., H. Iwata and K. Okuno. 2009. Genome-wide association mapping of quantitative traits in sorghum (Sorghum bicolor (L.) Moench) by using multiple models. Breeding Science 59:217-227. crossref(new window)

44.
Song, J.Y., J.R. Lee, S. Oh, C.Y. Kim, C.H. Bae, G.A. Lee, K.H. Ma, Y.M. Choi, H.J. Park and M.C. Lee. 2012. Assessment of genetic diversity and fatty acid composition of perilla (Perilla frutescens var. frutescens) germplasm. Korean J. Plant Res. 25(6):762-772. crossref(new window)

45.
Upadhyaya, H.D., S.L. Dwivedi, M. Baum, R.K. Varshney, S.M. Udupa and C.L.L. Gowda. 2008. Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.) BMC Plant Biol. 8: 106. DOI: 10.1186/1471-2229-8-106. crossref(new window)

46.
Varshney, R.K., A. Graner and M.E. Sorrells. 2005. Genic microsatellite markers in plants, features and applications. Trends Biotechnol. 23:48-55. crossref(new window)

47.
Vavilov, N.I. 1926. Studies on the origin of cultivated plants. Inst Appl. Bot. Plant Breed., Leningrad, USSR.

48.
Wright, S.I. and B.S. Gaut. 2005. Molecular population genetics and the search for adaptive evolution in plants. Molecular biology and evolution 22(3):506-519.

49.
Wang, M.L., C. Zhu, N.A. Barkley, Z. Chen, J.E. Erpelding, S.C. Murray, M.R. Tuinstra, T. Tesso, G.A. Pederson and J. Yu. 2009. Genetic diversity and population structure analysis of accessions in the US historic sweet sorghum. Theor. Appl. Genet. 120:13-23. crossref(new window)

50.
Wang, R.L., J. Wendell and J. Dekker. 1995. Weedy adaptation in Setaria spp.: I. Isozyme analysis of the genetic diversity and population genetic structure in S. viridis. Amer. J. Bot. 82:308-317. crossref(new window)

51.
Yang, X., J. Yan, T. Shah, M.L. Warburton, Q. Li, L. Li, Y. Chai, Z. Fu, Y. Zhou, S. Xu, G. Bai, Y. Meng, Y. Zheng and J. Li. 2010. Genetic analysis and characterization of a new maize association mapping panel for quantitative trait loci dissection. Theor. Appl. Genet. 121:417-431. crossref(new window)