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Fine mapping of qKW7, a major QTL for kernel weight and kernel width in maize, confirmed by the combined analytic approaches of linkage and association analysis

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Abstract

Kernel weight (KWEI), a complex quantitative trait that is largely determined by kernel size, is a key component of grain yield in maize. In our previous studies, qKW7, a putative pleiotropic QTL associated with both KWEI and kernel width (KWID), was detected within the 7.02 bin region on chromosome 7 by both F2:3 population and recombinant inbred line (RIL) population from a Ye478 and Huangzaosi cross. Therefore, a series of backcross populations from the same cross have been developed for fine mapping qKW7. By using a large BC3F4 segregation population, the qKW7 QTL was mapped to a physical interval of 647 Kb with several genes. An association panel with 627 diverse inbred lines was used to process the association analysis, and the results indicated that three KWEI- and KWID-related quantitative trait nucleotides (QTNs) were tightly linked to qKW7. Sequence analysis revealed that all three detected QTNs were located within the gene region of GRMZM2G114706, which encodes an ankyrin protein kinase that regulates endosperm development. Finally, the putative genes responsible for qKW7 are discussed.

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Acknowledgments

This work was partially supported by grants provided by the National Natural Science Foundation of China (91335206), the Programmes of MST and MOA of China (2011CB100105, 2014CB138200, 201303007), and the CAAS (Innovation Program). We greatly thank Professor Jinsheng Lai of the China Agricultural University for sharing re-sequence information for marker development in this study.

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  1. Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China

    Xin Li, Yong-xiang Li, Lin Chen, Xun Wu, Weiwei Qin, Yanchun Song, Dengfeng Zhang, Tianyu Wang, Yu Li & Yunsu Shi

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  1. Xin Li
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Correspondence to Yong-xiang Li or Yunsu Shi.

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10681_2016_1706_MOESM1_ESM.tif

Linkage analysis of the major QTL for KWEI and KWID on chromosome 7 in the RIL population of Ye478×HZS. The numbers adjacent markers represent their genetic position (cM). Supplementary material 1 (TIFF 88 kb)

10681_2016_1706_MOESM2_ESM.tif

The comparisons of phenotypic variations of qKW7 alleles between HZS genotype individuals and Ye478 genotype individuals for KWEI (a) and KWID (b) in RIL population. The P-values of the t-test are noted in the right corner below. Supplementary material 2 (TIFF 62 kb)

10681_2016_1706_MOESM3_ESM.tif

Summary statistics of kernel related traits. a), correlation analysis of KWEI among environments across two years. Supplementary material 3 (TIFF 289 kb)

10681_2016_1706_MOESM4_ESM.tif

Summary statistics of kernel related traits. b), correlation analysis of KWID among environments across two years. Supplementary material 4 (TIFF 267 kb)

10681_2016_1706_MOESM5_ESM.tif

Summary statistics of kernel related traits. c), correlation analysis of KWEI and KWID under five environments. In order to picture the simple correlation between environments, missing entries were imputed with average values across all environments. KWEI means the 100-kernel weight. KWID means 10-kernel width. ‘11’ means 2011 year, ‘12’ means 2012 year. BJ is an abbreviation of Beijing, CC is an abbreviation of Changchun in Jilin province, NC is an abbreviation of Nanchong in Sichuan province, TA is an abbreviation of Tai’an in Shandong province, XX is an abbreviation of Xinxiang in Henan province. Histograms show the distribution of KWEI and KWID. Numbers in the up-right triangle are the Pearson Coefficient among different environment pairs. The low-left triangle shows the scatter plots among environment pairs. Supplementary material 5 (TIFF 290 kb)

Supplementary material 6 (DOC 244 kb)

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Li, X., Li, Yx., Chen, L. et al. Fine mapping of qKW7, a major QTL for kernel weight and kernel width in maize, confirmed by the combined analytic approaches of linkage and association analysis. Euphytica 210, 221–232 (2016). https://doi.org/10.1007/s10681-016-1706-2

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