David Chagné

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We report a high-quality draft genome sequence of the domesticated apple (Malus × domestica). We show that a relatively recent (>50 million years ago) genome-wide duplication (GWD) has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae. Traces of older GWDs partly support the monophyly of the ancestral paleohexaploidy(More)
Marker-assisted selection (MAS) offers quick and reliable prediction of the phenotypes of seedlings in large populations and thus opens new approaches for selection to breeders of apple (Malus x domestica Borkh.). The development of framework maps enables the discovery of genetic markers linked to desired traits. Although genetic maps have been reported for(More)
Mutations in the genes encoding for either the biosynthetic or transcriptional regulation of the anthocyanin pathway have been linked to color phenotypes. Generally, this is a loss of function resulting in a reduction or a change in the distribution of anthocyanin. Here, we describe a rearrangement in the upstream regulatory region of the gene encoding an(More)
Two unigene datasets of Pinus taeda and Pinus pinaster were screened to detect di-, tri- and tetranucleotide repeated motifs using the SSRIT script. A total of 419 simple sequence repeats (SSRs) were identified, from which only 12.8% overlapped between the two sets. The position of the SSRs within their coding sequences were predicted using FrameD.(More)
The genome sequence of apple (Malus×domestica Borkh.) was published more than a year ago, which helped develop an 8K SNP chip to assist in implementing genomic selection (GS). In apple breeding programmes, GS can be used to obtain genomic breeding values (GEBV) for choosing next-generation parents or selections for further testing as potential commercial(More)
Molecular markers associated with gene coding regions are useful tools for bridging functional and structural genomics. Due to their high abundance in plant genomes, single nucleotide polymorphisms (SNPs) are present within virtually all genomic regions, including most coding sequences. The objective of this study was to develop a set of SNPs for the apple(More)
As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica)(More)
Woolly apple aphid (WAA; Eriosoma lanigerum Hausm.) can be a major economic problem to apple growers in most parts of the world, and resistance breeding provides a sustainable means to control this pest. We report molecular markers for three genes conferring WAA resistance and placing them on two linkage groups (LG) on the genetic map of apple. The Er1 and(More)
Sweet cherry (Prunus avium L.) skin and fruit colors vary widely due to differences in red and yellow pigment profiles. The two major market classes of sweet cherry represent the two color extremes, i.e., yellow skin with red blush and yellow flesh and dark mahogany skin with mahogany flesh. Yet, within these extremes, there is a continuum of skin and flesh(More)
Twenty-three populations of Pinus pinaster (13 Aquitaine populations and 10 Corsican populations) were analysed at three microsatellite loci and 122 AFLP loci. The aims of the study were: (i) to compare levels of within-population and among-population diversity assessed with both kinds of markers; (ii) to compare Aquitaine and Corsican provenances of P.(More)