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Analysis of the genetic architecture of maize ear and grain morphological traits by combined linkage and association mapping

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Abstract

Key message

Using combined linkage and association mapping, 26 stable QTL and six stable SNPs were detected across multiple environments for eight ear and grain morphological traits in maize. One QTL, PKS2, might play an important role in maize yield improvement.

Abstract

In the present study, one bi-parental population and an association panel were used to identify quantitative trait loci (QTL) for eight ear and grain morphological traits. A total of 108 QTL related to these traits were detected across four environments using an ultra-high density bin map constructed using recombinant inbred lines (RILs) derived from a cross between Ye478 and Qi319, and 26 QTL were identified in more than two environments. Furthermore, 64 single nucleotide polymorphisms (SNPs) were found to be significantly associated with the eight ear and grain morphological traits (−log10(P) > 4) in an association panel of 240 maize inbred lines. Combining the two mapping populations, a total of 17 pleiotropic QTL/SNPs (pQTL/SNPs) were associated with various traits across multiple environments. PKS2, a stable locus influencing kernel shape identified on chromosome 2 in a genome-wide association study (GWAS), was within the QTL confidence interval defined by the RILs. The candidate region harbored a short 13-Kb LD block encompassing four SNPs (SYN11386, PHM14783.16, SYN11392, and SYN11378). In the association panel, 13 lines derived from the hybrid PI78599 possessed the same allele as Qi319 at the PHM14783.16 (GG) locus, with an average value of 0.21 for KS, significantly lower than that of the 34 lines derived from Ye478 that carried a different allele (0.25, P < 0.05). Therefore, further fine mapping of PKS2 will provide valuable information for understanding the genetic components of grain yield and improving molecular marker-assisted selection (MAS) in maize.

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Abbreviations

KL:

Kernel length

KW:

Kernel width

KT:

Kernel thickness

KV:

Kernel volume (KL × KW × KT)

KS:

Kernel shape (KL:KW:KT)

HKW:

Hundred-kernel weight

KRN:

Kernel row number

KNPR:

Kernel number per row

CIM:

Composite interval mapping

QTL:

Quantitative trait loci

SNP:

Single nucleotide polymorphisms

MAS:

Marker-assisted selection

GWAS:

Genome-wide association studies

LD:

Linkage disequilibrium

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Acknowledgements

This research was jointly funded by the National Basic Research Program of China (2014CB138200), the National Natural Science Foundation of China (31471509), and the Chinese Academy of Agricultural Sciences (CAAS) Innovation Project.

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    Authors and Affiliations

    1. College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, 150030, Heilongjiang, China

      Chaoshu Zhang, Xiaochong Zhang, Fangjun Zhang & Zhenhua Wang

    2. Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China

      Chaoshu Zhang, Zhiqiang Zhou, Hongjun Yong, Xiaochong Zhang, Zhuanfang Hao, Fangjun Zhang, Mingshun Li, Degui Zhang, Xinhai Li & Jianfeng Weng

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    1. Chaoshu Zhang
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    2. Zhiqiang Zhou
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    3. Hongjun Yong
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    4. Xiaochong Zhang
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    5. Zhuanfang Hao
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    6. Fangjun Zhang
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    7. Mingshun Li
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    8. Degui Zhang
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    9. Xinhai Li
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    10. Zhenhua Wang
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    11. Jianfeng Weng
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    Correspondence to Zhenhua Wang or Jianfeng Weng.

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    We claim that the experiments described herein comply with the ethical standards in China.

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    C. Zhang and Z. Zhou are equal contributors.

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    Cite this article

    Zhang, C., Zhou, Z., Yong, H. et al. Analysis of the genetic architecture of maize ear and grain morphological traits by combined linkage and association mapping. Theor Appl Genet 130, 1011–1029 (2017). https://doi.org/10.1007/s00122-017-2867-7

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    • DOI: https://doi.org/10.1007/s00122-017-2867-7

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