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ORIGINAL RESEARCH article

Front. Genet.
Sec. Genomics of Plants and the Phytoecosystem
Volume 15 - 2024 | doi: 10.3389/fgene.2024.1431043

Genetic Architecture of Kernel-related Traits in Sweet and Waxy Maize Revealed by Genome-Wide Association Analysis

Provisionally accepted
Jingtao Qu Jingtao Qu 1Diansi Yu Diansi Yu 1Wei Gu Wei Gu 1*Muhammad Hayder Bin Khalid Muhammad Hayder Bin Khalid 2Huiyun Kuang Huiyun Kuang 1*Dongdong Dang Dongdong Dang 1Hui Wang Hui Wang 1*Prasanna Boddupalli Prasanna Boddupalli 3Xuecai Zhang Xuecai Zhang 4Ao Zhang Ao Zhang 5Hongjian Zheng Hongjian Zheng 1*Yuan Guan Yuan Guan 1*
  • 1 Shanghai Academy of Agricultural Sciences, Shanghai, China
  • 2 National Research Center of Intercropping, Islamia University of Bahawalpur, Bahawalpur, Punjab, Pakistan
  • 3 The International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
  • 4 International Maize and Wheat Improvement Center (Mexico), Texcoco, Tabasco, Mexico
  • 5 Shenyang Key Laboratory of Maize Genome Selective Breeding, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning Province, China

The final, formatted version of the article will be published soon.

    Maize (Zea mays L.) is one of the most important crops worldwide, the kernel size-related traits are the major components of maize grain yield. To dissect the genetic architecture of four kernel-related traits of100-kernel weight, kernel length, kernel width, and kernel diameter, a genome-wide association study (GWAS) was conducted in the waxy and sweet maize panel comprising of 447 maize inbred lines re-sequenced at the 5× coverage depth. GWAS analysis was carried out with the mixed linear model using 1,684,029 high-quality SNP markers. In total, 49 SNPs significantly associated with the four kernel-related traits were identified, including 46 SNPs on chromosome 3, two SNPs on chromosome 4, and one SNP on chromosome 7. Haplotype regression analysis identified 338 haplotypes that significantly affected these four kernel-related traits. These significant SNPs and important haplotypes provide valuable information for developing functional markers for the implementation of marker-assisted selection in breeding. Genomic selection (GS) results revealed that a set of 10,000 SNPs and a training population size of 30% are sufficient for the application of GS in waxy and sweet maize breeding for kernel weight and kernel size. Forty candidate genes associated with the four kernel-related traits were identified, including both Zm00001d000707 and Zm00001d044139 expressed in the kernel development tissues and stages with unknown functions. The molecular mechanism of Zm00001d000707 and Zm00001d044139 regulating these kernel-related traits needs to be investigated further.

    Keywords: Kernel size, Kernel weight, NGS, GWAS, GS

    Received: 11 May 2024; Accepted: 17 Sep 2024.

    Copyright: © 2024 Qu, Yu, Gu, Khalid, Kuang, Dang, Wang, Boddupalli, Zhang, Zhang, Zheng and Guan. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Wei Gu, Shanghai Academy of Agricultural Sciences, Shanghai, China
    Huiyun Kuang, Shanghai Academy of Agricultural Sciences, Shanghai, China
    Hui Wang, Shanghai Academy of Agricultural Sciences, Shanghai, China
    Hongjian Zheng, Shanghai Academy of Agricultural Sciences, Shanghai, China
    Yuan Guan, Shanghai Academy of Agricultural Sciences, Shanghai, China

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