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Analysis of recombination QTLs, segregation distortion, and epistasis for fitness in maize multiple populations using ultra-high-density markers

Theoretical and Applied Genetics volume 129, pages 1775–1784 (2016)Cite this article

Abstract

Key message

Using two nested association mapping populations and high-density markers, some important genomic regions controlling recombination frequency and segregation distortion were detected.

Abstract

Understanding the maize genomic features would be useful for the study of genetic diversity and evolution and for maize breeding. Here, we used two maize nested association mapping (NAM) populations separately derived in China (CN-NAM) and the US (US-NAM) to explore the maize genomic features. The two populations containing 36 families and about 7000 recombinant inbred lines were evaluated with genotyping-by-sequencing. Through the comparison between the two NAMs, we revealed that segregation distortion is little, whereas epistasis for fitness is present in the two maize NAM populations. When conducting quantitative trait loci (QTL) mapping for the total number of recombination events, we detected 14 QTLs controlling recombination. Using high-density markers to identify segregation distortion regions (SDRs), a total of 445 SDRs were detected within the 36 families, among which 15 common SDRs were found in at least ten families. About 80 % of the known maize gametophytic factors (ga) genes controlling segregation distortion were overlapped with highly significant SDRs. In addition, we also found that the regions with high recombination rate and high gene density usually tended to have little segregation distortion. This study will facilitate population genetic studies and gene cloning affecting recombination variation and segregation distortion in maize, which can improve plant breeding progress.

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Acknowledgments

This work was partly supported by the Ministry of Science and Technology of China (2011DFA30450, 2011CB100100), China National Natural Science Foundation (91335206), CAAS (Innovation Program), US National Science Foundation under the Plant Genome Research Program (PGRP) (Grant Nos DBI-0820619 and IOS-1238014) and the Basic Research to Enable Agricultural Development (BREAD) project (ID: IOS-0965342), as well as by the USDA-ARS.

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Affiliations

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

    Chunhui Li, Yongxiang Li, Yunsu Shi, Yanchun Song, Dengfeng Zhang, Yu Li & Tianyu Wang

  2. Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA

    Edward S. Buckler & Zhiwu Zhang

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  1. Chunhui Li
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  2. Yongxiang Li
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  3. Yunsu Shi
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  4. Yanchun Song
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  5. Dengfeng Zhang
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  6. Edward S. Buckler
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  7. Zhiwu Zhang
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  8. Yu Li
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  9. Tianyu Wang
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Correspondence to Yu Li or Tianyu Wang.

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Communicated by N. de Leon.

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Li, C., Li, Y., Shi, Y. et al. Analysis of recombination QTLs, segregation distortion, and epistasis for fitness in maize multiple populations using ultra-high-density markers. Theor Appl Genet 129, 1775–1784 (2016). https://doi.org/10.1007/s00122-016-2739-6

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  • DOI: https://doi.org/10.1007/s00122-016-2739-6

Keywords

  • Quantitative Trait Locus
  • Recombination Event
  • Segregation Distortion
  • Inclusive Composite Interval Mapping
  • Segregation Distortion Locus