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Patterns of genomic variation in Chinese maize inbred lines and implications for genetic improvement

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Genetic relationships among Chinese maize germplasms reveal historical trends in heterotic patterns from Chinese breeding programs and identify line Dan340 as a potential genome donor for elite inbred line Zheng58.

Abstract

The characterization of the genetic relationships, heterotic patterns and breeding history of lines in maize breeding programs allows breeders to efficiently use maize germplasm for line improvement over time. In this study, 269 temperate inbred lines, most of which have been widely used in Chinese maize breeding programs since the 1970s, were genotyped using the Illumina MaizeSNP50 BeadChip, which contains 56,110 single-nucleotide polymorphisms. The STRUCTURE analysis, cluster analysis and principal coordinate analysis results consistently revealed seven groups, of which five were consistent with known heterotic groups within the Chinese maize germplasm—Domestic Reid, Lancaster, Zi330, Tang SPT and Tem-tropic I (also known as “P”). These genetic relationships also allowed us to determine the historical trends in heterotic patterns during the three decades from 1970 to 2000, represented by Mo17 from Lancaster, HuangZaoSi (HZS) from Tang SPT, Ye478 from Domestic Reid and P178 from Tem-tropic I heterotic groups. Mo17-related commercial hybrids were widely used in the 1970s and 1980s, followed by the release of HZS- and Ye478-related commercial hybrids in the 1980s and 1990s, and the introduction of Tem-tropic I group in the 1990s and 2000s. Additionally, we identified inbred line Dan340 as a potential genome donor for Zheng58, which is the female parent of the most widely grown commercial hybrid ZhengDan958 in China. We also reconstructed the recombination events of elite line HZS and its 14 derived lines. These findings provide useful information to direct future maize breeding efforts.

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Acknowledgements

We greatly appreciate Dr. Qing Li at Huazhong Agricultural University for manuscript language improvement. This research was supported by the National Science and Technology Support Program (Grant number 2014BAD01B02) and the National Key Research and Development Program of China (Grant number 2016YFD0101803 and 2016YFD0100303).

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  1. Renyu Zhang and Gen Xu contributed equally to this work.

Authors and Affiliations

  1. National Maize Improvement Center of China, MOA Key Laboratory of Maize Biology, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing, 100193, China

    Renyu Zhang, Gen Xu, Jiansheng Li & Xiaohong Yang

  2. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China

    Jianbing Yan

  3. Institute of Crop Sciences and CIMMYT China Office, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Huihui Li

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  1. Renyu Zhang
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Correspondence to Huihui Li or Xiaohong Yang.

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Communicated by Benjamin Stich.

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Zhang, R., Xu, G., Li, J. et al. Patterns of genomic variation in Chinese maize inbred lines and implications for genetic improvement. Theor Appl Genet 131, 1207–1221 (2018). https://doi.org/10.1007/s00122-018-3072-z

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