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Identification of Genetic Differentiation between Waxy and Common Maize by SNP Genotyping.

Hao D, Zhang Z, Cheng Y, Chen G, Lu H, Mao Y, Shi M, Huang X, Zhou G, Xue L - PLoS ONE (2015)

Bottom Line: The results revealed abundant genetic diversity in the studied panel and that genetic diversity was much higher in common than in waxy maize germplasms.Subpopulation structure in both waxy and common maize sets were associated with the germplasm origin and corresponding heterotic groups.The information from this study can assist waxy maize breeders by enhancing parental line selection and breeding program design.

View Article: PubMed Central - PubMed

Affiliation: Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China.

ABSTRACT
Waxy maize (Zea mays L. var. ceratina) is an important vegetable and economic crop that is thought to have originated from cultivated flint maize and most recently underwent divergence from common maize. In this study, a total of 110 waxy and 110 common maize inbred lines were genotyped with 3072 SNPs to evaluate the genetic diversity, population structure, and linkage disequilibrium decay as well as identify putative loci that are under positive selection. The results revealed abundant genetic diversity in the studied panel and that genetic diversity was much higher in common than in waxy maize germplasms. Principal coordinate analysis and neighbor-joining cluster analysis consistently classified the 220 accessions into two major groups and a mixed group with mixed ancestry. Subpopulation structure in both waxy and common maize sets were associated with the germplasm origin and corresponding heterotic groups. The LD decay distance (1500-2000 kb) in waxy maize was lower than that in common maize. Fourteen candidate loci were identified as under positive selection between waxy and common maize at the 99% confidence level. The information from this study can assist waxy maize breeders by enhancing parental line selection and breeding program design.

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Related in: MedlinePlus

Plot of the first two PCoA axes using the 2811 SNPs.The red squares correspond to waxy maize germplasms; the blue rhombuses correspond to common maize germplasms.
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pone.0142585.g002: Plot of the first two PCoA axes using the 2811 SNPs.The red squares correspond to waxy maize germplasms; the blue rhombuses correspond to common maize germplasms.

Mentions: A two-dimensional scatter plot that included all 220 accessions revealed that the first two principal components (PCoA1 and PCoA2) explained 12.52 and 6.87%, respectively, of the genetic variation among the studied groups (Fig 2). On the first axis, the majority of the waxy maize germplasms were separated from the common maize, though with some overlap. The PCoA data suggested that the tested germplasms might be grouped into two major groups (waxy group and common group) and a mixed group (mainly including some germplasms with mixed ancestry). The scatter plots of PCoA 1 vs PCoA 3 and PCoA 2 vs PCoA 3 also revealed similar results (S2 and S3 Figs).


Identification of Genetic Differentiation between Waxy and Common Maize by SNP Genotyping.

Hao D, Zhang Z, Cheng Y, Chen G, Lu H, Mao Y, Shi M, Huang X, Zhou G, Xue L - PLoS ONE (2015)

Plot of the first two PCoA axes using the 2811 SNPs.The red squares correspond to waxy maize germplasms; the blue rhombuses correspond to common maize germplasms.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4643885&req=5

pone.0142585.g002: Plot of the first two PCoA axes using the 2811 SNPs.The red squares correspond to waxy maize germplasms; the blue rhombuses correspond to common maize germplasms.
Mentions: A two-dimensional scatter plot that included all 220 accessions revealed that the first two principal components (PCoA1 and PCoA2) explained 12.52 and 6.87%, respectively, of the genetic variation among the studied groups (Fig 2). On the first axis, the majority of the waxy maize germplasms were separated from the common maize, though with some overlap. The PCoA data suggested that the tested germplasms might be grouped into two major groups (waxy group and common group) and a mixed group (mainly including some germplasms with mixed ancestry). The scatter plots of PCoA 1 vs PCoA 3 and PCoA 2 vs PCoA 3 also revealed similar results (S2 and S3 Figs).

Bottom Line: The results revealed abundant genetic diversity in the studied panel and that genetic diversity was much higher in common than in waxy maize germplasms.Subpopulation structure in both waxy and common maize sets were associated with the germplasm origin and corresponding heterotic groups.The information from this study can assist waxy maize breeders by enhancing parental line selection and breeding program design.

View Article: PubMed Central - PubMed

Affiliation: Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China.

ABSTRACT
Waxy maize (Zea mays L. var. ceratina) is an important vegetable and economic crop that is thought to have originated from cultivated flint maize and most recently underwent divergence from common maize. In this study, a total of 110 waxy and 110 common maize inbred lines were genotyped with 3072 SNPs to evaluate the genetic diversity, population structure, and linkage disequilibrium decay as well as identify putative loci that are under positive selection. The results revealed abundant genetic diversity in the studied panel and that genetic diversity was much higher in common than in waxy maize germplasms. Principal coordinate analysis and neighbor-joining cluster analysis consistently classified the 220 accessions into two major groups and a mixed group with mixed ancestry. Subpopulation structure in both waxy and common maize sets were associated with the germplasm origin and corresponding heterotic groups. The LD decay distance (1500-2000 kb) in waxy maize was lower than that in common maize. Fourteen candidate loci were identified as under positive selection between waxy and common maize at the 99% confidence level. The information from this study can assist waxy maize breeders by enhancing parental line selection and breeding program design.

Show MeSH
Related in: MedlinePlus