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Genome wide association mapping of agro-morphological and disease resistance traits in sugarcane

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Abstract

The objectives of the study were to assess genome wide association study (GWAS) for sugarcane on a panel of 183 accessions and to evaluate the impact of population structure and family relatedness on QTL detection. The panel was genotyped with 3327 AFLP, DArT and SSR markers and phenotyped for 13 traits related to agro-morphology, sugar yield, bagasse content and disease resistances. Marker-trait associations were detected using (i) general linear models that took population structure into account with either a Q matrix from STRUCTURE software or principal components from a principal component analysis added as covariates, and (ii) mixed linear models that took into account both population structure and family relatedness estimated using a similarity matrix K* computed using Jaccard’s coefficient. With general linear models analysis, test statistics were inflated in most cases, while mixed linear models analysis allowed the inflation of test statistics to be controlled in most cases. When only detections in which both population structure and family relatedness were correctly controlled were considered, only 11 markers were significantly associated with three out of the 13. Among these 11 markers, six were linked to the major resistance gene Bru1, which has already been identified. Our results confirm that the use of GWAS is feasible for sugarcane in spite of its complex polyploid genome but also underline the need to take into account family relatedness and not only population structure. The small number of significant associations detected suggests that a larger population and/or denser genotyping are required to increase the statistical power of association detection.

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Acknowledgments

The authors wish to thank T. Dumont, H. Telismart, C. Lallemand, I. Promi, M. Hoarau and R. Tibère for their contributions to field work and phenotypic data acquisition. This study was funded by the eRcane company, by CIRAD (A French research centre working with developing countries to tackle international agricultural and development issues), by an ATP-SEPANG project grant, by the Conseil Régional de la Réunion, by the European Union (European regional development fund—ERDF), by ANR (Agence Nationale de la Recherche) through the Delicas project, grant ANR-08-GENM-001, and by the ANRT (Association Nationale de la Recherche et de la Technologie) through the CIFRE PhD. Grant No.°600/2012 of M. Gouy.

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  1. eRcane, 97494, Sainte-Clotilde, La Réunion, France

    M. Gouy & A. Thong Chane

  2. Cirad, UMR PVBMT, 97410, Saint-Pierre, La Réunion, France

    M. Gouy, Y. Rousselle, A. Anglade, S. Royaert, S. Nibouche & L. Costet

  3. Université de la Réunion, UMR PVBMT, 97410, Saint-Pierre, La Réunion, France

    M. Gouy

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Gouy, M., Rousselle, Y., Thong Chane, A. et al. Genome wide association mapping of agro-morphological and disease resistance traits in sugarcane. Euphytica 202, 269–284 (2015). https://doi.org/10.1007/s10681-014-1294-y

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