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Targeted linkage map densification to improve cell wall related QTL detection and interpretation in maize

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Abstract

Several QTLs for cell wall degradability and lignin content were previously detected in the F288 × F271 maize RIL progeny, including a set of major QTLs located in bin 6.06. Unexpectedly, allelic sequencing of genes located around the bin 6.06 QTL positions revealed a monomorphous region, suggesting that these QTLs were likely “ghost” QTLs. Refining the positions of all QTLs detected in this population was thus considered, based on a linkage map densification in most important QTL regions, and in several large still unmarked regions. Re-analysis of data with an improved genetic map (173 markers instead of 108) showed that ghost QTLs located in bin 6.06 were then fractionated over two QTL positions located upstream and downstream of the monomorphic region. The area located upstream of bin 6.06 position carried the major QTLs, which explained from 37 to 59 % of the phenotypic variation for per se values and extended on only 6 cM, corresponding to a physical distance of 2.2 Mbp. Among the 92 genes present in the corresponding area of the B73 maize reference genome, nine could putatively be considered as involved in the formation of the secondary cell wall [bHLH, FKBP, laccase, fasciclin, zinc finger C2H2-type and C3HC4-type (two genes), NF-YB, and WRKY]. In addition, based on the currently improved genetic map, eight QTLs were detected in bin 4.09, while only one QTL was highlighted in the initial investigation. Moreover, significant epistatic interaction effects were shown for all traits between these QTLs located in bin 4.09 and the major QTLs located in bin 6.05. Three genes related to secondary cell wall assembly (ZmMYB42, COV1-like, PAL-like) underlay QTL support intervals in this newly identified bin 4.09 region. The current investigations, even if they were based only on one RIL progeny, illustrated the interest of a targeted marker mapping on a genetic map to improve QTL position.

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Acknowledgments

This work has been funded by the maize breeding companies involved in the PROMAÏS—INRA network on maize cell wall lignification and digestibility (Advanta, Caussade Semences, Limagrain Europe, MaïsAdour, Monsanto SAS, Pioneer Génétique, Pau Euralis, R2n RAGT Semences, SDME KWS France, Syngenta seeds). We thank Christiane Minault, Dominique Denoue and Pascal Vernoux for seed multiplications and plant cropping and sampling at INRA Lusignan. We also thank Jacques Laborde, who managed seed multiplications at INRA, St Martin de Hinx, France. We are grateful to Fabien Mounet for his fruitful criticisms.

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  1. INRA, Unité de Génétique et d’Amélioration des Plantes Fourragères, 86600, Lusignan, France

    Audrey Courtial, Justine Thomas & Yves Barrière

  2. Laboratoire de Recherche en Sciences Végétales, UMR 5546, Université de Toulouse, UPS, BP 42617, Auzeville, 31326, Castanet-Tolosan, France

    Audrey Courtial, Justine Thomas & Jacqueline Grima-Pettenati

  3. CNRS; UMR 5546, BP 42617, 31326, Castanet-Tolosan, France

    Audrey Courtial, Justine Thomas & Jacqueline Grima-Pettenati

  4. INRA, Institut Jean-Pierre Bourgin, 78026, Versailles, France

    Matthieu Reymond & Valérie Méchin

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  1. Audrey Courtial
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Correspondence to Yves Barrière.

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Courtial, A., Thomas, J., Reymond, M. et al. Targeted linkage map densification to improve cell wall related QTL detection and interpretation in maize. Theor Appl Genet 126, 1151–1165 (2013). https://doi.org/10.1007/s00122-013-2043-7

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