Open Access Highly Accessed Research article

The powdery mildew resistance gene REN1 co-segregates with an NBS-LRR gene cluster in two Central Asian grapevines

Courtney Coleman12, Dario Copetti3, Guido Cipriani1, Sarolta Hoffmann4, Pál Kozma4, László Kovács2, Michele Morgante13, Raffaele Testolin13 and Gabriele Di Gaspero13*

Author Affiliations

1 Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100 Udine, Italy

2 Departments of Agriculture and Biology, Missouri State University, Springfield, MO 65897, USA

3 Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100 Udine, Italy

4 University of Pécs, Research Institute of Viticulture and Enology, Pázmány Péter u. 4, 7634 Pécs, Hungary

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BMC Genetics 2009, 10:89  doi:10.1186/1471-2156-10-89

Published: 30 December 2009

Additional files

Additional file 1:

SSR markers across the REN1 locus.

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Additional file 2:

Most informative recombinant genotypes used for mapping REN1. Numbers across the top represent genotypes, with resistant (R) phenotypes on the left and susceptible (S) on the right. The 04-10 individuals are offspring of 'Kishmish vatkana', the 07-12 individuals are 'Dzhandzhal kara' descendents. The most informative individuals are bold faced. Markers are listed on the side according to their genetic order along chr13, with the markers that segregate with REN1 shown in bold. The two markers on top refer to scaffolds 73 and 175, immediately upstream of sc_47, the five markers at the bottom are placed on scaffolds 112 and 84, distal to sc_47. The resistant homologue is indicated in grey, the susceptible homologue in white.

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Additional file 3:

Genes predicted in the REN1 interval in addition to NBS-LRRs.

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Additional file 4:

NBS-LRR genes and pseudogenes predicted in the REN1 interval: structural features, amino acid domains, and similarity with known plant NBS-LRR resistance genes.

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Additional file 5:

Dot plot comparisons between and within the REN1 NBS cluster and paralogous NBS clusters dispersed along the same chromosome. (A) Dot plot comparison between the REN1 interval and the chr13:11.8..12.2 Mb NBS cluster (B) Dot plot self-comparison of the chr13:11.8..12.2 Mb NBS cluster. (C) Dot plot comparison between the REN1 interval and the chr13:21.5..21.9 Mb NBS cluster. (D) Dot plot comparison between the chr13:11.8..12.2 Mb cluster and the chr13:21.5..21.9 Mb NBS cluster. (E) Dot plot self-comparison of the chr13:21.5..21.9 Mb NBS cluster. (F) Dot plot self-comparison of the REN1 interval. Across the panels, diagram of gene content is explained in the corresponding symbol legend. The NJ tree shows the relationship between the NBS genes. The distribution and the percentage of identity of conserved nucleotide sequences is calculated using LAGAN and drawn with VISTA. The cyan bars in (F) indicate 5 gene islands rich in NBS and CAD genes.

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Additional file 6:

Global alignment of 10-kb sequences around each cinnamyl alcohol dehydrogenase (CAD) gene. (A) Comparison between two CAD genes in the locus chr13:11.8..12.2 Mb and CAD paralogues in the REN1 interval. (B) Comparison between the CAD founders in the REN1 interval (CAD8 and CAD9) and other paralogues generated by duplication. Gbrowse tracks for CAD genes in the locus chr13:11.8..12.2 Mb (top of panel A) and the CAD8 and 9 founders in the REN1 interval (top of panel B), displaying annotated transposable elements (TEs) and GAZE gene predictions (red/blue models). The conserved blocks of nucleotide sequences and the corresponding level of identity were calculated using LAGAN and drawn using VISTA.

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Additional file 7:

(A) Genotypic data used for kinship analysis and for UPGMA and NJ clustering. Markers and accessions used for the calculation of relatedness and likelihood ratios are shown in bold. Markers recommended by the European Vitis Database [32] are in italics. Additional markers and accessions included in the cluster analysis conducted using NTSYS are standard font. Markers of the VChr series are described in [56], VrZag series in [57], VVMD series in [58,59], VVS series in [60], SC8_0071_014 is described in [38]. For primer sequences [see Additional file 1]. (B) Kinship analysis of 'Kishmish vatkana' and 'Dzhandzhal kara' with a set of 19 unlinked markers.

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Additional file 8:

Haplotypes of chr13 in 'Kishmish vatkana', 'Dzhandzhal kara', and the offspring 'Dzhandzhal kara' × 'Lasta' (D × L) at 24 loci along chromosome (chr) 13. Kv chr13a, resistant homologue in 'Kishmish vatkana'; Kv chr13b, susceptible homologue in 'Kishmish vatkana', inherited from 'Sultanina'; Dzk chr13a, resistant homologue in 'Dzhandzhal kara'; Dzk chr13b, susceptible homologue in 'Dzhandzhal kara'; D × L chr13a, resistant homologue in the offspring 'Dzhandzhal kara' × 'Lasta', inherited from 'Dzhandzhal kara'; D × L chr13b, susceptible homologue in the offspring 'Dzhandzhal kara' × 'Lasta', inherited from 'Lasta'. SC8_0071_014 cosegregates with REN1.

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Additional file 9:

Principal component analysis (PCA) via covariance matrix with data standardisation of 218 grapevine accessions including 'Kishmish vatkana' and 'Dzhandzhal kara'. Two dimensional projection along the first two coordinates on the x and y axes, explaining 25.6% and 18.3% of the variation, respectively (spreadsheet 'PCA graph'). The list of accessions attributed to the six groups identified in the graph is given in the spreadsheet 'List of accessions, PCA groups'.

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Additional file 10:

Trade routes of the Silk Road, connecting the Eastern Mediterranean basin, the Middle East, Central Asia, and China (top map). The district of Samarqand, at the western foothills of the Pamir Mountains (middle map), and the sites where 'Kishmish vatkana' and 'Dzhandzhal kara' were first discovered by Russian breeders in the 1920's and 1930's (bottom map).

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