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Integrated Meta-QTL and Genome-Wide Association Study Analyses Reveal Candidate Genes for Maize Yield

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Abstract

Crop yield is of a quantitative nature. Two complementary approaches linkage mapping and genome-wide association study (GWAS) have been employed for the identification of loci influencing maize yield. In previous research, we meta-analyzed QTL for maize yield. Here, we tried to integrate meta-QTL and GWAS analyses to dissect candidate genes for maize yield. A total of seven candidate genes were detected by both meta-QTL and two independent GWAS analyses. Functional annotation indicated that some candidate genes were responsible for the maintenance and differentiation of maize inflorescence meristem that directly affect yield productivity. In addition, well-characterized genes for maize yield-related traits, including SBP-box family member unbranched3 (ub3) for maize ear row number, zea floricaula/leafy1 (zfl1) for maize inflorescence architecture and reproductive transition were detected by the integrated meta-QTL and GWAS analyses. Expression analysis showed that some candidate genes were preferentially expressed in maize rapidly proliferated tissues, including shoot apex, tassel, and ear primordia, which influence maize inflorescence architecture and yield performance. Some candidate genes were hypothesized to be selected during maize domestication and improvement. Results presented here will not only facilitate the cloning of yield-related genes, and provide guidance in breeding of plants with high-yield productivity.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (31571671), the National Key Research and Development Program of China (2016YFD0101002), the Natural Science Foundation of the Jiangsu Higher Education Institutions of China (18KJA210002), the High-end Talents Support Plan of Yangzhou University (18HTYZU12), the Qing Lan Project of Yangzhou University (QLYZU201809), and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

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Author notes

  1. Yijun Wang and Yali Wang contributed equally to this work.

Authors and Affiliations

  1. Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China

    Yijun Wang, Yali Wang & Dexiang Deng

  2. Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China

    Yijun Wang, Yali Wang & Dexiang Deng

  3. College of Agriculture, Anhui Science and Technology University, Fengyang, 233100, China

    Xin Wang

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  1. Yijun Wang
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  2. Yali Wang
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Correspondence to Yijun Wang.

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344_2019_9977_MOESM1_ESM.tif

Supplementary material 1 (TIFF 715 kb). Figure S1 Expression profiles of candidate genes. (A) Expression pattern of candidate gene GRMZM2G377904, homolog of FEA2 for maize inflorescence meristem size and ear row number control. (B) Expression pattern of candidate gene GRMZM2G029242, homolog of bif2 for the initiation of lateral primordia in maize inflorescence

344_2019_9977_MOESM2_ESM.docx

Supplementary material 2 (DOCX 24 kb). Table S1 Candidate genes with GWAS SNPs (Brown et al. 2011) co-localize with meta-QTL interval

344_2019_9977_MOESM3_ESM.docx

Supplementary material 3 (DOCX 19 kb). Table S2 Candidate genes with GWAS SNPs (Yang et al. 2014; Liu et al. 2015) co-localize with meta-QTL interval

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Wang, Y., Wang, Y., Wang, X. et al. Integrated Meta-QTL and Genome-Wide Association Study Analyses Reveal Candidate Genes for Maize Yield. J Plant Growth Regul 39, 229–238 (2020). https://doi.org/10.1007/s00344-019-09977-y

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