Journal of Crop Science and Biotechnology

, Volume 21, Issue 4, pp 395–405 | Cite as

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

  • Yu-Mi Choi
  • Kyung-Min Kim
  • Sukyeung Lee
  • Sejong Oh
  • Myung-Chul LeeEmail author
Research Article


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.

Key words

Foxtail millet core collection genetic diversity EST-SSR population structure 


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Copyright information

© Korean Society of Crop Science (KSCS) and Springer Nature B.V. 2018

Authors and Affiliations

  • Yu-Mi Choi
    • 1
  • Kyung-Min Kim
    • 2
  • Sukyeung Lee
    • 1
  • Sejong Oh
    • 1
  • Myung-Chul Lee
    • 1
    Email author
  1. 1.National Agrobiodiversity CenterNational Institute of Agricultural Science, RDAJeollabuk-doKorea
  2. 2.School of Applied BiosciencesKyungpook National UniversityDaeguKorea

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