Nucleotide Sequence Diversity and Linkage Disequilibrium of Four Nuclear Loci in Foxtail Millet (Setaria italica).
Foxtail millet (Setaria italica (L.) Beauv) is one of the earliest domesticated grains, which has been cultivated in northern China by 8,700 years before present (YBP) and across Eurasia by 4,000 YBP. Owing to a small genome and diploid nature, foxtail millet is a tractable model crop for studying functional genomics of millets and bioenergy grasses. In this study, we examined nucleotide sequence diversity, geographic structure, and levels of linkage disequilibrium at four nuclear loci (ADH1, G3PDH, IGS1 and TPI1) in representative samples of 311 landrace accessions across its cultivated range. Higher levels of nucleotide sequence and haplotype diversity were observed in samples from China relative to other sampled regions. Genetic assignment analysis classified the accessions into seven clusters based on nucleotide sequence polymorphisms. Intralocus LD decayed rapidly to half the initial value within ~1.2 kb or less.
China Southwestern Germplasm Bank of Wild Species, the Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China; Landscape and Horticulture College, Yunnan Agriculture University, Kunming, Yunnan, China.
Shui-Lian
SL
He
China Southwestern Germplasm Bank of Wild Species, the Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
Yang
Y
Yang
Department of Agronomy & Plant genetics, 411 Borlaug Hall, 1991 Upper Buford Circle, University of Minnesota, Saint Paul, Minnesota, United States of America.
Peter L
PL
Morrell
China Southwestern Germplasm Bank of Wild Species, the Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
Ting-Shuang
TS
Yi
D002467:Cell Nucleus / Q000235:genetics*; D015810:Linkage Disequilibrium; D000066928:Millets / Q000235:genetics*; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic