Tools

Thanks to information generated by our genome sequencing projects and resequencing of intraspecific diversity, we produced and released SNP databases.

We also have used SNP and InDel databases for developing and validating SNP arrays and InDel markers and for generating SNP-based genetic maps.

 

SNP chips

SNP arrays have been developed for black poplar, wheat, peach, and grape.

Faivre-Rampant et al (2016) New resources for genetic studies in Populus nigra: genome wide SNP discovery and development of a 12k Infinium array. Molecular Ecology Resources doi: 10.1111/1755-0998.12513

Wang et al (2014) Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. Plant Biotechnology Journal 12:787-796.

Le Paslier et al (2014) The GrapeReSeq 18k Vitis genotyping chip. IX International Symposium of Grapevine Physiology and Biotechnology. Chile 21-26 April 2013. https://urgi.versailles.inra.fr/Species/Vitis/GrapeReSeq_Illumina_20K

Verde et al (2012) Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm. PLoS One 7(4):e35668. doi: 10.1371/journal.pone.0035668

 

SNP datasets

We have released validated SNP datasets for durum wheat, black poplar and maize

Vendramin et al (2019) Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm.​ BMC Genomics 20:278

Scaglione et al (2019) Single primer enrichment technology as a tool for massive genotyping: a benchmark on black poplar and maize. Annals of Botany 124:543-552

 

SNP and InDel markers

We have released validated InDel markers for grapevine.

Foria et al (2018) InDel markers for monitoring the introgression of downy mildew resistance from wild relatives into grape varieties. Molecular Breeding 38:124

 

Genetic maps

Genetic maps have been developed for wheat and Norway spruce.

Maccaferri et al (2015) A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. Plant Biotechnology Journal 13:648-663

Lind et al (2014) A Picea abies linkage map based on SNP markers identifies QTLs for four aspects of resistance to Heterobasidion parviporum infection. PLoS One 9(7):e101049. doi: 10.1371/journal.pone.0101049