Molecular Breeding

, 35:146 | Cite as

Genetic properties of 240 maize inbred lines and identity-by-descent segments revealed by high-density SNP markers

  • Changlin Liu
  • Zhuanfang Hao
  • Degui Zhang
  • Chuanxiao Xie
  • Mingshun Li
  • Xiaocong Zhang
  • Hongjun Yong
  • Shihuang Zhang
  • Jianfeng Weng
  • Xinhai Li


Characterization of the genetic properties of maize inbred lines is beneficial not only for increasing knowledge of genetic diversity, but also for maize breeding. In the present study, a panel of 240 maize inbred lines commonly used in China, including three foundation parents Dan340, Mo17, and Huangzao4, and their derivatives, was genotyped using the MaizeSNP50 BeadChip, which contains 56,110 single-nucleotide polymorphism (SNP) markers. As a result, 40,757 SNPs with unique physical positions were successfully recalled in this panel with an average coverage of 50 kb per SNP. Five subgroups including Lan, LRC, PB, Reid, and SPT were inferred using 4000 SNPs with minor allele frequency ≥0.200, a result that was largely consistent with the pedigree information for these 240 inbred lines. With a cutoff value of r 2 < 0.100, linkage disequilibrium (LD) decay distances along the ten chromosomes of maize ranged from 397 to 819 kb, with an average of 643 kb. A subtotal of 26, 35, and 23 identity-by-descent segments, which were longer than both the average LD decay distance on the corresponding chromosomes and the local LD decay distance of r 2 < 0.100, were identified in the Dan340, Huangzao4, and Mo17 derivatives, respectively. Three lower peaks for Tajima’s D overlapped with three major quantitative trait loci (qkrn7, scmv1, and qHS2.09) in these derivatives. Elucidating the genetic properties of this panel provides information for investigating the genetic architecture of agronomic traits and heterotic grouping during maize breeding.


Maize inbred lines Single nucleotide polymorphism Linkage disequilibrium Identity by descent Heterotic grouping 



This research was jointly funded by the National Basic Research Program of China (2014CB138200), the National Natural Science Foundation of China (31201219 and 31471509), and the National High Technology Research and Development Program of China (2012AA101104).

Supplementary material

11032_2015_344_MOESM1_ESM.tif (3.7 mb)
Supplementary Fig. 1 Distributions of MAF, gene diversity, and PIC (TIFF 3776 kb)
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Supplementary Fig. 2 Estimated Ln (the probability of the data) and ΔK in structure analysis (TIFF 866 kb)
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Supplementary Fig. 3 Dendrogram of the 240 maize inbred lines based on genetic distance clustering (TIFF 2186 kb)
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Supplementary Fig. 4 Estimated population structure of the 240 maize inbred lines with values of K from K = 2 to K = 5. Different colors indicate the membership coefficient for each subgroup (TIFF 3325 kb)
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Supplementary Fig. 5 LD decay patterns on the 10 chromosomes of maize. The symbol r 2 represents the LD statistic (TIFF 6070 kb)
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Supplementary Fig. 6 Genetic components transmitted from the foundation parents Dan340, Mo17 and Huangzao4 to their respective derivatives. The foundation parents are charted before their respective derivatives (TIFF 6922 kb)
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Supplementary Fig. 7 Tajima’s D calculated for the three sets of foundation parents and their derivatives, and the entire panel, respectively (TIFF 4226 kb)
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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Changlin Liu
    • 1
  • Zhuanfang Hao
    • 1
  • Degui Zhang
    • 1
  • Chuanxiao Xie
    • 1
  • Mingshun Li
    • 1
  • Xiaocong Zhang
    • 2
  • Hongjun Yong
    • 1
  • Shihuang Zhang
    • 1
  • Jianfeng Weng
    • 1
  • Xinhai Li
    • 1
  1. 1.Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
  2. 2.Northeast Agriculture UniversityHarbinChina

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