Public data

Grapevine / Vitis vinifera

Nicolas et al, 2016
Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies.

In this study we designed a method to select a panel of 279 cultivars representing the three main genetic pools, including the founding cultivars, and with reduced relatedness. We then assessed within this panel, diversity, linkage disequilibrium in four genomic regions, and the power achieved by this panel to detect associations with traits of interest. The Association panel consists in three subgroups of 93 cultivars, characteristic of fruit use (table vs wine) and geographical origin (Eastern vs Western Europe). The panel is representative of the whole French grapevine germplasm collection for both genetic and phenotypic diversity and structure. It was genotyped with Illumina GoldenGate technology for 501 SNPs previously discovered by sequencing in a core collection of 30 accessions. Linkage disequilibrium was measured as the correlation between these SNPs corrected by kinship and/or structure.

Bacilieri et al, 2016
Potential of combining morphometry and archeo-DNA information to investigate grapevine domestication.

The goal of this work was to study DNA variation on archeological grape pips and to compare it to polymorphisms in modern cultivated varieties (Vitis vinifera L.) and wild grapes (Vitis spp.). The archeological material was composed of waterlogged seeds originating from three Roman and one Medieval archaeological sites in France. We studied 842 SNPs in several genes, including two genes related to sex, over four archaeological pips, and compared them to a dataset of 73 modern Vitis. Phylogeny analisys indicated that the three pips from the Roman period were females and close to modern wild grapevines, while the only Medieval pip was close to the modern cultivated group and hermaphrodite. Morphogeometrical results based on a 3D methodology on the same pips were in agreement with these findings. We conclude that the combined use of SNP markers and morphogeometry is promising to decipher the intricate history of grapevine domestication.

Cassava / Manihot esculenta

Soto et al, 2015
A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes

In this study we present the first study reported so far of an integrated high density genetic map using SNPs obtained from GBS with integrated genetic and physical localization of 569 annotated immunity related genes in cassava. The map contains 2,141 SNPs from a total of 78,854 SNP, on average, to one SNP every 1,763 base pairs. They are distributed across 3,450 scaffolds from 12,977 constituting the current cassava genome sequence draft, corresponding to 87% (463.2 Mb) of the genome. The size of the genome sequence draft aligned to the genetic map is increased to 344Mb corresponding to 64% of total cassava genome. These data build a solid basis for future studies to map and associate markers with single loci or quantitative trait loci for agronomical important traits and molecular cloning of genes controlling these traits

Cotton / Gossypium

Lacape et al, 2012
Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton.

In this study we characterized the fiber transcriptomes of the two species, Gossypium hirsutum and Gossypium barbadense, that were parental genotypes of a RIL mapping population used previously for phenotypic QTL and expression QTL mapping. We used 454 deep pyrosequencing to characterize cDNAs from developing fibers at two key developmental time-points; 10 and 22 days post anthesis. A unigene set was assembled and annotated, and differential digital gene expression was assessed from the different time-point and genotype representations of the reads within assembled contigs.
Contigs were mined for the presence of microsatellite repeats and SNPs that will be useful markers for mapping and marker-assisted selection in cotton improvement.

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