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Fine genetic characterization of elite maize germplasm using high-throughput SNP genotyping

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Abstract

To investigate the genetic structure of Chinese maize germplasm, the MaizeSNP50 BeadChip with 56,110 single nucleotide polymorphisms (SNPs) was used to genotype a collection of 367 inbred lines widely used in maize breeding of China. A total of 41,819 informative SNPs with minor allele number of more than 0.05 were used to estimate the genetic diversity, relatedness, and linkage disequilibrium (LD) decay. Totally 1,015 SNPs evenly distributed in the genome were selected randomly to evaluate the population structure of these accessions. Results showed that two main groups could be determined i.e., the introduced germplasm and the local germplasm. Further, five subgroups corresponding to different heterotic groups, that is, Reid Yellow Dent (Reid), Lancaster Sure Crop (Lancaster), P group (P), Tang Sipingtou (TSPT), and Tem-tropic I group (Tem-tropic I), were determined. The genetic diversity of within subgroups was highest in the Tem-Tropic I and lowest in the P. Most lines in this panel showed limited relatedness with each other. Comparisons of gene diversity showed that there existed some conservative genetic regions in specific subgroups across the ten chromosomes, i.e., seven in the Lancaster, seven in the Reid, six in the TSPT, five in the P, and two in the Tem-Tropical I. In addition, the results also revealed that there existed fifteen conservative regions transmitted from Huangzaosi, an important foundation parent, to its descendants. These are important for further studies since the outcomes may provide clues to understand why Huangzaosi could become a foundation parent in Chinese maize breeding. For the panel of 367 elite lines, average LD distance was 391 kb and varied among different chromosomes as well as in different genomic regions of one chromosome. This analysis uncovered a high natural genetic diversity in the elite maize inbred set, suggesting that the panel can be used in association study, esp. for temperate regions.

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Acknowledgments

This work was partly supported by the Ministry of Science and Technology of China (2011CB100100, 2011DFA30450), National Natural Science Foundation (U1138304), CAAS (Innovation Program) and the Ministry of Agriculture of China (2011-G15, Baozhong Project). We are grateful to Dr. Alain Charcosset for language correcting and suggestions on data analyses. We also thank anonymous reviewers for suggestions to improve the quality of this manuscript.

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Authors and Affiliations

  1. Maize Institute, Sichuan Agricultural Unversity, Ya’an, 625014, Sichuan, China

    Xun Wu & Yubi Huang

  2. Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Xun Wu, Yongxiang Li, Yunsu Shi, Yanchun Song, Tianyu Wang & Yu Li

  3. Nanchong Academy of Agricultural Sciences, Nanchong, 637000, Sichuan, China

    Xun Wu

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  1. Xun Wu
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  2. Yongxiang Li
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  3. Yunsu Shi
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  5. Tianyu Wang
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  7. Yu Li
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Correspondence to Yubi Huang or Yu Li.

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Communicated by A. Charcosset.

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Wu, X., Li, Y., Shi, Y. et al. Fine genetic characterization of elite maize germplasm using high-throughput SNP genotyping. Theor Appl Genet 127, 621–631 (2014). https://doi.org/10.1007/s00122-013-2246-y

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