Skip to main content
SpringerLink
Log in

Development of a Core Collection Based on EST-SSR Markers and Phenotypic Traits in Foxtail Millet [Setaria italica (L.) P. Beauv.]

  • Research Article
  • Published:
Journal of Crop Science and Biotechnology Aims and scope Submit manuscript

Abstract

The germplasm resources of foxtail millet reserve diverse genes for crop improvement which needs to be explored. To comprehend the maximum genetic diversity of this crop, a core collection with minimum number of accessions will facilitate easy access to genetic material. Here we assessed the genetic diversity and population structure in a large germplasm collection of 785 accessions by employing EST-SSR markers and morphological traits. A total of 107 alleles were detected with an average allele number of 4.9 per locus among the 785 accessions based on 22 EST-SSR markers. The number of alleles per locus ranged from 2 to 8. Polymorphism information content and expected heterozygosity ranged from 0.355 to 0.738 (mean = 0.525) and 0.451 to 0.771 (mean = 0.603), respectively. The germplasm collection was separated into three groups based on population structure analysis, whereas principal coordinate analysis (PCoA) could not cluster accessions according to their geographic origin. Subsequently, a core collection with a total of 170 accessions (21.66%) was selected from the whole set of germplasm by combining allelic variations of 22 EST-SSR markers and eight different phenotypic traits. The core collection optimally represented the whole germplasm collection and displayed a similar level of genetic diversity, population structure, and phenotypic variations based on various genetic analyses such as Shannon-Weaver and Nei’s diversity indices and PCoA, while phenotypic traits were analyzed by mean, range, and principal component analysis. This core collection of foxtail millet will be a primary resource for further genetic analysis and development of appropriate breeding strategies.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Ali A, Choi YM, Hyun DY, Lee S, Oh S, Park HJ, Cho YH, Lee MC. 2016. EST–SSR based genetic diversity and population structure among Korean landraces of foxtail millet (Setaria italica L.). Korean J. Plant Res. 29(3): 322–330

    Article  Google Scholar 

  • Ahanchede A, Hamon SP, Darmency H. 2004. Why no tetraploid cultivar of foxtail millet? Genet. Resour. Crop Ev. 51: 227–230

    Article  Google Scholar 

  • Austin DF. 2006. Foxtail millets (Setaria: Poaceae)–Abandoned food in two hemispheres. Econ. Bot. 60: 143–158

    Article  Google Scholar 

  • Balfourier F, Roussel V, Strelchenko P, Exbrayat–Vinson F, Sourdille P, Boutet G, Koenig J, Ravel C, Mitrofanova O, Beckert M, Charmet G. 2007. A worldwide bread wheat core collection arrayed in a 384–well plate. Theor. Appl. Genet. 114: 1265–1275

    Article  PubMed  Google Scholar 

  • Belaj A, Dominguez–Garcia MD, Atienza SG, Urdiroz NM, De la Rosa R, Satovic Z, Martin A, Kilian A, Trujillo I, Valpuesta V, Rio CD. 2012. Developing a core collection of olive (Olea europaea L.) based on molecular markers (DArTs, SSRs, SNPs) and agronomic traits. Tree Genet. Genomes 8(2): 365–378

    Article  Google Scholar 

  • Brown AHD. 1989. Core collections: a practical approach to genetic resources management. Genome, 31: 818–824

    Article  Google Scholar 

  • Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour S. 2000. Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor. Appl. Genet. 100: 713–722

    Article  CAS  Google Scholar 

  • Cho YI, Chung JW, Lee GA, Ma KH, Dixit A, Gwag JG, Park YJ. 2010. Development and characterization of twenty–five new polymorphic microsatellite markers in proso millet (Panicum miliaceum L.). Genes Genom. 32: 267–273

    Article  CAS  Google Scholar 

  • Deb D. 2009. Valuing folk crop varieties for agroecology and food security, Bioscience Resource Project Commentaries. The Bioscience Resource Project, Inc., USA. http://indepen dentsciencenews.org/un–sustainable–farming/valuing–folk–cr op–varieties

    Google Scholar 

  • Dekker J. 2003. Evolutionary biology of the foxtail (Setaria) species–group, In: Weed Biology and Management, Indrjit (ed.). Kluwer Academic Publishers, The Netherlands

    Google Scholar 

  • Dutta S, Kumawat G, Singh BP, Gupta DK, et al. 2011. Development of genic–SSR markers by deep transcriptome sequencing in pigeon pea [Cajanus cajan (L.) Millspaugh]. BMC Plant Biol. 20: 11–17

    Google Scholar 

  • Dwivedi SL, Puppala N, Upadhyaya HD, Manivannan N, Singh S. 2008. Developing a core collection of peanut specific to Valencia market type. Crop Sci. 48: 625–632

    Article  Google Scholar 

  • Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14: 2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Falush D, Stephens M, Pritchard JK. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567–1587

    CAS  PubMed  PubMed Central  Google Scholar 

  • Frankel OH. 1984. Genetic perspectives of germplasm conservation. In: W Arber, K Illmensee, WJ Peacock, and P Starlinger, eds., Genetic manipulation: impact on man and society, pp: 161–170. Cambridge University Press, Cambridge, UK

    Google Scholar 

  • Fukunaga K, Kawase M, Kato K. 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

    CAS  PubMed  Google Scholar 

  • Glaszmann JC, Kilian B, Upadhyaya HD, Varshney RK. 2010. Accessing genetic diversity for crop improvement. Curr. Opin. Plant Biol. 13: 1–7

    Article  CAS  Google Scholar 

  • Gupta S, Kumari K, Muthamilarasan M, Parida SK, Prasad M. 2014. Population structure and association mapping of yield contributing agronomic traits in foxtail millet. Plant Cell Rep. 33: 881–893

    Article  CAS  PubMed  Google Scholar 

  • Gupta S, Kumari K, Sahu PP, Vidapu S, Prasad M. 2012. Sequence–based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet [Setaria italic (L.) P. Beauv.]. Plant Cell Rep. 31: 323–337

    Article  CAS  PubMed  Google Scholar 

  • Hammer Ø, Harper DAT, Ryan RD. 2001. PAST: paleontological statistics software package for education and data analysis. Palaeontol. Electronica 4: 1–9

    Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Jia XP, Shi YS, Song YC, Wang GY, Wang TY, Li Y. 2007. Development of EST–SSR in foxtail millet (Setaria italica). Genet. Resour. Crop Ev. 54: 233–236

    Article  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Kapila RK, Yadav RS, Plaha P, Rai KN, Yadav OP, Hash CT, Howarth CJ. 2007. Genetic diversity among pearl millet maintainers using microsatellite markers. Plant Breed. 127: 33–37

    Google Scholar 

  • Kim EJ, Sa KJ, Park JC, Lee JK. 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 Genom.. 34: 529–538

    CAS  Google Scholar 

  • Kim EJ, Sa KJ, Yu CY, Lee JK. 2010. Morphological variation of foxtail millet (Setaria italica (L.) P. Beauv.) germplasm collected in Korea, China, Pakistan. Korean J. Breed. Sci. 42: 181–187

    Google Scholar 

  • Kim KW, Chung HK, Cho GT, Ma KH, Chandrabalan D, Gwag JD, Kim TS, Cho EG, Park YJ. 2007. Power Core: A program applying the advanced M strategy with a heuristic search for establishing core sets. Bioinformatics 23: 2155–2162

    Article  CAS  PubMed  Google Scholar 

  • Kumari K, Muthamilarasan M, Misra G, Gupta S, Subramanian A, Parida SK, Chattopadhyay D, Prasad M. 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 doi: 10.1371/journal.pone.0067742

    Book  Google Scholar 

  • Le Thierry D’ennequin M, Panaud O, Toupance B. 2000. Assessment of genetic relationships between Setaria italica and its wild relatives S. viridis using AFLP marker. Theor. Appl. Genet. 100: 1061–1066

    Article  Google Scholar 

  • Li H, Li C, Pao W. 1945. Cytological and genetic studies of the interspecific cross of the cultivated foxtail millet, Setaria italica P. Beauv., and the green foxtail millet, S. viridis L. J. Amer. Soc. Agron. 9: 32–54

    Article  Google Scholar 

  • Li Y, Wu SZ, Cao YS. 1995. Cluster analysis of an international collection of foxtail millet (Setaria italica (L.) P. Beauv). Genet. Res. Crop Evol. 45: 279–285

    Article  Google Scholar 

  • Li Y, Wu SZ, Ji YF. 1991. Agronomic performances of foxtail millet germplasm from abroad and their prospect for utilization in China. Millet Crops 3: 15–19 (In Chinese)

    CAS  Google Scholar 

  • Lin HS, Liao GI, Chiang CY, Kuoh CS, Chang SB. 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

    Google Scholar 

  • Liu K, Muse M. 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128–2129

    Article  CAS  PubMed  Google Scholar 

  • Masud MAT, Chowdhury MAZ, Hossain MA, Hossain SMM. 1995. Multivariate analysis in pumpkin (Cucurbita moschata Dueh ex Poir). Bangladesh J. P1ant Breed. Genet. 8: 45–50

    Google Scholar 

  • Mondini L, Noorani A, Pagnotta MA. 2009. Assessing plant genetic diversity by molecular tools. Diversity 1: 19–35

    Article  CAS  Google Scholar 

  • Nicot N, Chiquet V, Gandon B, Amilhat L, Legeai F, Leroy P, Bernard M, Sourdille P. 2004. Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). Theor. Appl. Genet. 109: 800–805

    Article  CAS  PubMed  Google Scholar 

  • Ning N, Yuan X, Dong S, Wen Y, Gao Z, Guo M, Guo P. 2015. Grain yield and quality of foxtail millet (Setaria italica L.) in response to Tribenuron–methyl. PLoS One doi:10.1371/journal.pone.0142557

    Book  Google Scholar 

  • Peakall R, Smouse PE. 2006. GENEALEX 6; Genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes 6: 288–295

    Google Scholar 

  • Perrier X, Jacquemoud–Collet JP. 2006. Darwin software, http://darwin.cirad.fr/darwin

    Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945–959

    CAS  PubMed  Google Scholar 

  • Saha MC, Mian MA, Eujayl I, Zwonitzer JC, Wang L, May GD. 2004. Tall fescue EST–SSR markers with transferability across several grass species. Theor. Appl. Genet. 109: 783–79

    Article  PubMed  Google Scholar 

  • Schontz D, Rether B. 1999. Genetic variability in foxtail millet, Setaria italica (L.) P. Beauv: identification and classification of lines with RAPD markers. Plant Breed. 118: 190–192

    Google Scholar 

  • Song J, Lee G, Yoon M, Choi Y, Lee J, Jung Y, Park H, Kim C, and Lee M. 2011. Analysis of genetic diversity and population structure of buckwheat (Fagopyrum esculentum) landraces of Korea using SSR markers. Korean J. Plant Res. 24: 702–711

    Article  Google Scholar 

  • Tatineni V, Cantrell RG, Davis DD. 1996. Genetic diversity in elite cotton germplasm determined by morphological characteristics and RAPDs. Crop Sci. 36: 186–192

    Article  Google Scholar 

  • Thiel T, Michalek W, Varshney RK, Graner A. 2003. Exploiting EST databases for the development of cDNA derived microsatellite markers in barley (Hordeum vulgare L.). Theor. Appl. Genet. 106: 411–422

    Article  CAS  PubMed  Google Scholar 

  • Upadhyaya HD, Pundir RPS, Gowda CLL, Reddy VG, Singh S. 2008. Establishing a core collection of foxtail millet to enhance the utilization of the germplasm of an underutilized crop. Plant Genet. Resour. 7: 177–184

    Article  Google Scholar 

  • Upadhyaya HD, Pundir PRS, Dwivedi SL, Gowda CLL, Reddy VG, Singh S. 2009. Developing a mini core collection of sorghum for diversified utilization of germplasm. Crop Sci. 49: 1769–1780

    Article  Google Scholar 

  • van Hintum THJL, Brown AHD, Spillane C, and T Hodgkin. 2000. Core collections of plant genetic resources. IPGRI Tech. Bull. 3: 48

    Google Scholar 

  • Varshney RK, Graner A, Sorrells ME. 2005. Genic microsatellite markers in plants, features and applications. Trends Biotechnol. 23: 48–55

    Article  CAS  PubMed  Google Scholar 

  • Victoria FC, Da Maia LC, De Oliveira AC. 2011. In silico comparative analysis of SSR markers in plants. BMC Plant Boil 11: 15. doi: 10.1186/1471–2229–11–15

    Article  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Wilson PJ, Thompson K, Hodgson JG. 1999. Specific leaf area and leaf dry matter content as alternative predictors of plant strategies. New Phytol. 143: 155–162

    Article  Google Scholar 

  • Yan W, Rutger JN, Bryant RJ, Bockelman HE, Fjellstrom RG, Chen MH, Tai TH, McClung AM. 2007. Development and evaluation of a core subset of the USDA rice germplasm collection. Crop Sci. 47: 869–878

    Article  Google Scholar 

  • Zhang B, Ye W, Ren D, Tian P, Peng Y, Gao Y, Ruan B, Wang L, Zhang G, Guo L, Qian Q, Z Gao. 2015. Genetic analysis of flag leaf size and candidate genes deteremination of a major QTL for flag leaf width in rice. Rice 8(1): 39. doi: 10.1186/s12284–014–0039–9

    Article  PubMed  Google Scholar 

  • Zhang YF, Zhang QL, Yang Y, Luo ZR. 2009. Development of Japanese persimmon core collection by genetic distance sampling based on SSR markers. Biotechnol. Biotechnol. Equipment 23: 1474–1478

    Article  CAS  Google Scholar 

  • Zhao WG, Lee GA, Kwon SW, Ma KH, Lee MC, Park YJ 2012. Development and use of novel SSR markers for molecular genetic diversity in Italian millet (Setaria italica L.). Genes Genom. 34: 51–57

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. National Agrobiodiversity Center, National Institute of Agricultural Science, RDA, 370 Nongsaengmyeong-ro, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54874, Korea

    Yu-Mi Choi, Sukyeung Lee, Sejong Oh & Myung-Chul Lee

  2. School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Korea

    Kyung-Min Kim

Authors
  1. Yu-Mi Choi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kyung-Min Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sukyeung Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sejong Oh
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Myung-Chul Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Myung-Chul Lee.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Choi, YM., Kim, KM., Lee, S. et al. Development of a Core Collection Based on EST-SSR Markers and Phenotypic Traits in Foxtail Millet [Setaria italica (L.) P. Beauv.]. J. Crop Sci. Biotechnol. 21, 395–405 (2018). https://doi.org/10.1007/s12892-018-0189-0

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12892-018-0189-0

Key words

Search

Navigation