title: Genetic diversity and population structure of Chinese foxtail millet [Setaria italica (L.) Beauv.] landraces.
abstract: As an ancient cereal of great importance for dryland agriculture even today, foxtail millet (Setaria italica) is fast becoming a new plant genomic model crop. A genotypic analysis of 250 foxtail millet landraces, which represent 1% of foxtail millet germplasm kept in the Chinese National Gene Bank (CNGB), was conducted with 77 SSRs covering the foxtail millet genome. A high degree of molecular diversity among the landraces was found, with an average of 20.9 alleles per locus detected. STRUCTURE, neighbor-jointing, and principal components analyses classify the accessions into three clusters (topmost hierarchy) and, ultimately, four conservative subgroups (substructuring within the topmost clusters) in total, which are in good accordance with eco-geographical distribution in China. The highest subpopulation diversity was identified in the accessions of Pop3 from the middle regions of the Yellow River, followed by accessions in Pop1 from the downstream regions of the Yellow River, suggesting that foxtail millet was domesticated in the Yellow River drainage area first and then spread to other parts of the country. Linkage disequilibrium (LD) decay of less than 20 cM of genetic distance in the foxtail millet landrace genome was observed, which suggests that it could be possible to achieve resolution down to the 20 cM level for association mapping.
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Chunfang
authors.initials: C
authors.lastname: Wang
authors.forename: Guanqing
authors.initials: G
authors.lastname: Jia
authors.forename: Hui
authors.initials: H
authors.lastname: Zhi
authors.forename: Zhengang
authors.initials: Z
authors.lastname: Niu
authors.forename: Yang
authors.initials: Y
authors.lastname: Chai
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Yongfang
authors.initials: Y
authors.lastname: Wang
authors.forename: Haiquan
authors.initials: H
authors.lastname: Li
authors.forename: Ping
authors.initials: P
authors.lastname: Lu
authors.forename: Baohua
authors.initials: B
authors.lastname: Zhao
authors.forename: Xianmin
authors.initials: X
authors.lastname: Diao
mesh_terms: D000483:Alleles; D016000:Cluster Analysis; D017343:Genes, Plant; D014644:Genetic Variation; D005838:Genotype; D015810:Linkage Disequilibrium; D032983:Setaria Plant / Q000235:genetics*