title: Principal components analysis--K-means transposon element based foxtail millet core collection selection method.
abstract: BACKGROUND
  Core collections are important tools in genetic resources research and administration. At present, most core collection selection criteria are based on one of the following item characteristics: passport data, genetic markers, or morphological traits, which may lead to inadequate representations of variability in the complete collection. The development of a comprehensive methodology that includes as much element data as possible has been explored poorly. Using a collection of (Setaria italica sbsp. italica (L.) P. Beauv.) as a model, we developed a method for core collection construction based on genotype data and numerical representations of agromorphological traits, thereby improving the selection process.
  
  
  RESULTS
  Principal component analysis allows the selection of the most informative discriminators among the various elements evaluated, regardless of whether they are genetic or morphological, thereby providing an adequate criterion for further K-mean clustering. Overall, the core collections of S. italica constructed using only genotype data demonstrated overall better validation scores than other core collections that we generated. However, core collection based on both genotype and agromorphological characteristics represented the overall diversity adequately.
  
  
  CONCLUSIONS
  The inclusion of both genotype and agromorphological characteristics as a comprehensive dataset in this methodology ensures that agricultural traits are considered in the core collection construction. This approach will be beneficial for genetic resources management and research activities for S. italica as well as other genetic resources.
authors.affiliation: Gene Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba City, 305-8571, Ibaraki, Japan. carbajal.borrayo.gb@u.tsukuba.ac.jp.|Genetc Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannodai, Tsukuba City, 305-8602, Ibaraki, Japan. carbajal.borrayo.gb@u.tsukuba.ac.jp.
authors.forename: Ernesto
authors.initials: E
authors.lastname: Borrayo
authors.affiliation: Gene Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba City, 305-8571, Ibaraki, Japan. machida.ryoko.fm@u.tsukuba.ac.jp.
authors.forename: Ryoko
authors.initials: R
authors.lastname: Machida-Hirano
authors.affiliation: Genetc Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannodai, Tsukuba City, 305-8602, Ibaraki, Japan. katu@affrc.go.jp.
authors.forename: Masaru
authors.initials: M
authors.lastname: Takeya
authors.affiliation: Gene Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba City, 305-8571, Ibaraki, Japan. kawase.makoto.gf@u.tsukuba.ac.jp.
authors.forename: Makoto
authors.initials: M
authors.lastname: Kawase
authors.affiliation: Gene Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba City, 305-8571, Ibaraki, Japan. nabechan@gene.tsukuba.ac.jp.
authors.forename: Kazuo
authors.initials: K
authors.lastname: Watanabe
mesh_terms: D000483:Alleles; D016000:Cluster Analysis; D004251:DNA Transposable Elements; D030541:Databases, Genetic; D005819:Genetic Markers; D005838:Genotype; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D032983:Setaria Plant / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D005819:Genetic Markers