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Association analysis of grapevine bunch traits using a comprehensive approach

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A set of SNP markers associated to bunch compactness and related traits were identified in grapevine.

Abstract

Bunch compactness plays an important role in the sanitary status and perceived quality of table and wine grapes, being influenced by cultural practices and by environmental and genetic factors, which are mostly unknown. In this work, we took advantage of genetic, genomic and bioinformatic advances to analyze part of its molecular basis through a combination of transcriptomic and association analyses. Results from different transcriptomic comparisons between loose and compact grapevine clones were analyzed to select a set of candidate genes likely involved in the observed variation for bunch compactness. Up to 183 genes were sequenced in a grapevine collection, and 7032 single nucleotide polymorphisms (SNPs) were detected in more than 100 varieties with a frequency of the minor allele over 5 %. They were used to test their association in three consecutive seasons with bunch compactness and two of its most influencing factors: total berry number and length of the first ramification of the rachis. Only one SNP was associated with berry number in two seasons, suggesting the high sensitiveness of this trait to seasonal environmental changes. On the other hand, we found a set of SNPs associated with both the first ramification length and bunch compactness in various seasons, in several genes which had not previously related to bunch compactness or bunch compactness-related traits. They are proposed as interesting candidates for further functional analyses aimed to verify the results obtained in this work, as a previous step to their inclusion in marker-assisted selection strategies.

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Acknowledgments

Authors acknowledge R. Aguirrezábal, S. Hernáiz, B. Larreina, M.I. Montemayor and E. Vaquero for their technical assistance, as well as CIDA (Gobierno de la Rioja) for the maintenance of the plant material used in this work. We acknowledge J.M. Martínez-Zapater and N. Diestro for providing unpublished data on QTL mapping. This work was supported by the Spanish Ministerio de Economía y Competitividad (MINECO) through projects AGL2010-15694 and AGL2014-59171-R and grants BES-2011-047041 (JT) and RYC-2011-07791 (JG).

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Authors and Affiliations

  1. Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino (ICVV, CSIC-Universidad de La Rioja-Gobierno de La Rioja), Carretera de Burgos km 6. Finca La Grajera, 26007, Logroño, Spain

    Javier Tello, Rafael Torres-Pérez, Jérôme Grimplet & Javier Ibáñez

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  1. Javier Tello
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  2. Rafael Torres-Pérez
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  3. Jérôme Grimplet
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  4. Javier Ibáñez
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Corresponding author

Correspondence to Javier Ibáñez.

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Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

The authors declare that the experiments comply with the current laws of the country in which they were carried out.

Additional information

Communicated by R. Toepfer.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file 1. Grapevine accessions evaluated in this studySubmitted as a.xlsx file (XLSX 14 kb)

122_2015_2623_MOESM2_ESM.pdf

Supplementary file 2. Phenotypic distribution of the bunch traits analyzed in this study. Submitted as a.pdf file (PDF 154 kb)

Supplementary file 3. Candidate genes selected for next-generation sequencing. Submitted as a.xlsx file (XLSX 34 kb)

122_2015_2623_MOESM4_ESM.pdf

Supplementary file 4. Quantile–quantile (QQ) plots of observed vs expected –log10(P values) for four different association methods (blue line: GLM; violet line:GLM + Q; red line:MLM + K; green line:MLM + Q + K) for bunch compactness (BuComp), first ramification length (1RmLe) and berries per bunch (ToBeBu) in 2011, 2012 and 2013. Observed P values are expected to nearly follow the expected values, which are shown as a black line. Submitted as a.pdf file (PDF 1107 kb)

122_2015_2623_MOESM5_ESM.pdf

Supplementary file 5. Linkage disequilibrium (LD) among called SNPs. Every matrix represents the LD between the SNPs called per linkage group (LG: Unk, 1-12, 14-19). No SNPs were called for LG13. In each LG, first and last SNPs are indicated at the upper left and lower right corners, respectively (see Table 2 and Supplementary file 3). Every matrix is divided into two triangles: the lower one shows LD (r2), and the upper one represents the P value. Values are graphically shown according to the color code. LD matrixes are not shown at the same scale. Submitted as a.pdf file (PDF 649 kb)

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Tello, J., Torres-Pérez, R., Grimplet, J. et al. Association analysis of grapevine bunch traits using a comprehensive approach. Theor Appl Genet 129, 227–242 (2016). https://doi.org/10.1007/s00122-015-2623-9

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  • DOI: https://doi.org/10.1007/s00122-015-2623-9

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