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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

Frequency distribution of genetic diversity of gene diversity and PIC within the waxy maize, common maize and the entire datasets.
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pone.0142585.g001: Frequency distribution of genetic diversity of gene diversity and PIC within the waxy maize, common maize and the entire datasets.

Mentions: Initially, a total of 220 germplasm accessions in the studied panel that contained 110 waxy maize and 110 common maize germplasms were genotyped with 3072 SNPs. Genetic diversity analysis using PowerMarker 3.25 revealed SNPs with MAF ≥ 5% and missing data ≤ 20%, which were used for subsequent analysis. Based on these criteria, the genotypic dataset of all accessions was reduced to 2811 SNPs, whereas the waxy and common maize datasets were reduced to 2751 and 2835 SNPs, respectively. The diversity among waxy maize, common maize, and entire datasets revealed by the three different sets of SNP greatly varied (Table 1, Fig 1). For the waxy maize set, the average gene diversity was 0.398 with a rang of 0.095–0.500, and the PIC averaged 0.314, ranging from 0.091 to 0.375. The genetic diversity within the waxy maize germplasms was much lower than that in the common maize germplasms (Fig 1), which indicates that waxy maize had substantially lower genetic variability than common maize. For the entire dataset, the gene diversity indices and PIC values were 0.448 and 0.346, respectively.


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)

Frequency distribution of genetic diversity of gene diversity and PIC within the waxy maize, common maize and the entire datasets.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0142585.g001: Frequency distribution of genetic diversity of gene diversity and PIC within the waxy maize, common maize and the entire datasets.
Mentions: Initially, a total of 220 germplasm accessions in the studied panel that contained 110 waxy maize and 110 common maize germplasms were genotyped with 3072 SNPs. Genetic diversity analysis using PowerMarker 3.25 revealed SNPs with MAF ≥ 5% and missing data ≤ 20%, which were used for subsequent analysis. Based on these criteria, the genotypic dataset of all accessions was reduced to 2811 SNPs, whereas the waxy and common maize datasets were reduced to 2751 and 2835 SNPs, respectively. The diversity among waxy maize, common maize, and entire datasets revealed by the three different sets of SNP greatly varied (Table 1, Fig 1). For the waxy maize set, the average gene diversity was 0.398 with a rang of 0.095–0.500, and the PIC averaged 0.314, ranging from 0.091 to 0.375. The genetic diversity within the waxy maize germplasms was much lower than that in the common maize germplasms (Fig 1), which indicates that waxy maize had substantially lower genetic variability than common maize. For the entire dataset, the gene diversity indices and PIC values were 0.448 and 0.346, respectively.

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