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Nucleotide Sequence Diversity and Linkage Disequilibrium of Four Nuclear Loci in Foxtail Millet (Setaria italica).

He SL, Yang Y, Morrell PL, Yi TS - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus

Structure analysis.The median △K for 10 runs for each K estimate are shown. A. median likelihood values. B. Population subdivision and the frequency distribution of foxtail millet population in each inferred clusters. Results from both the K = 2 (C) and K = 7 (D) models are shown. Each accession is shown by a thin vertical line that is partitioned into two or seven colored segments. The accessions in which membership probability is < 50% are classified into a “mixed” group.
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pone.0137088.g002: Structure analysis.The median △K for 10 runs for each K estimate are shown. A. median likelihood values. B. Population subdivision and the frequency distribution of foxtail millet population in each inferred clusters. Results from both the K = 2 (C) and K = 7 (D) models are shown. Each accession is shown by a thin vertical line that is partitioned into two or seven colored segments. The accessions in which membership probability is < 50% are classified into a “mixed” group.

Mentions: Genetic assignment based on the four loci showed moderate genetic structure. Evanno’s [54] ad hoc estimator of the actual number of clusters was used, and the results showed △K indicate modes at △K = 2 & 7 model best fit the data, suggesting that the sample can be divided into 2 or 7 clusters. We examined the geographic distribution using both the K = 2 and K = 7 models (Fig 2).


Nucleotide Sequence Diversity and Linkage Disequilibrium of Four Nuclear Loci in Foxtail Millet (Setaria italica).

He SL, Yang Y, Morrell PL, Yi TS - PLoS ONE (2015)

Structure analysis.The median △K for 10 runs for each K estimate are shown. A. median likelihood values. B. Population subdivision and the frequency distribution of foxtail millet population in each inferred clusters. Results from both the K = 2 (C) and K = 7 (D) models are shown. Each accession is shown by a thin vertical line that is partitioned into two or seven colored segments. The accessions in which membership probability is < 50% are classified into a “mixed” group.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4556640&req=5

pone.0137088.g002: Structure analysis.The median △K for 10 runs for each K estimate are shown. A. median likelihood values. B. Population subdivision and the frequency distribution of foxtail millet population in each inferred clusters. Results from both the K = 2 (C) and K = 7 (D) models are shown. Each accession is shown by a thin vertical line that is partitioned into two or seven colored segments. The accessions in which membership probability is < 50% are classified into a “mixed” group.
Mentions: Genetic assignment based on the four loci showed moderate genetic structure. Evanno’s [54] ad hoc estimator of the actual number of clusters was used, and the results showed △K indicate modes at △K = 2 & 7 model best fit the data, suggesting that the sample can be divided into 2 or 7 clusters. We examined the geographic distribution using both the K = 2 and K = 7 models (Fig 2).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus