Genetic diversity and population structure of Chinese foxtail millet [Setaria italica (L.) Beauv.] landraces - PubMed (original) (raw)

Genetic diversity and population structure of Chinese foxtail millet [Setaria italica (L.) Beauv.] landraces

Chunfang Wang et al. G3 (Bethesda). 2012 Jul.

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.

Keywords: foxtail millet; landrace; linkage disequilibrium; population structure.

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Figures

Figure 1

Figure 1

The two different methods for determining optimal value of K and inferred population structure of Chinese foxtail millet landrace accessions. (A) The ad hoc procedure described by Pritchard et al. (2000). (B) The second order of statistics (△K) based on Evanno et al. (2005). (C) Optimal population structure (K = 3) and substructuring (K = 2) of Pop2. Each landrace is represented by a single vertical line, each color represents one cluster or subpopulations, and the length of the colored segment shows the landrace’s estimated proportion of membership in that cluster as calculated by STRUCTURE.

Figure 2

Figure 2

Neighbor-jointing (NJ) analysis and principal component analysis (PCA) of Chinese foxtail millet landraces. (A) Unrooted neighbor-jointing tree of 250 landraces; each colored branch represents one accession collected from corresponding inferred subpopulation. (B) NJ tree of inferred subgroups based on Nei’s genetic distance; bootstrap value (out of 1000) is indicated at the branch point. (C) Differentiation of genotypes from subpopulations based on the first three principal components derived from 77 SSR markers diversity analysis.

Figure 3

Figure 3

Map of the collection locations of Chinese foxtail millet landraces grouped by four subpopulations inferred in the investigations. Diverse color spots represent individuals from the various subpopulations. The four eco-regions in China for foxtail millet are illustrated by orange circles and lines.

Figure 4

Figure 4

Scatterplot of linkage disequilibrium (LD) statistics D’ (A) and r2 (B) between SSR pairs vs. intermarker genetic distance (cM) for the whole population. The observed values for interchromosomal markers are compiled in a single file at 350 cM.

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