Abstract
As domestication and selection have only exploited a small fraction of the existing genetic diversity, reintroducing rare, ancient or wild diversity in breeding schemes is becoming a necessity to face climate change and agroecological constraints. Towards this objective, new multi-species genotyping arrays have been developed and used to characterize genetic diversity available in collections of 4 botanical families in the frame of the AgroDiv project (https://anr.fr/ProjetIA-22-PEAE-0005). One of these arrays includes SNPs for apple and pear, together with SNPs for garden pea, faba bean and white lupin. For apple, SNPs were mostly chosen from previous arrays, i.e. the Illumina 20K and the Axiom 480K and JKI-50K arrays. The choice was based on marker performance in previous genotyping experiments and positions on a genetic map enriched by alignment to the HFTH1 whole genome sequence. The initial choice included the markers from the core 20K-480K compatibility set, known markers targeting traits of interest and markers from the Apple ID SNP set. Markers were then added to fill gaps larger than 1 cM and chosen for high minor allele frequency in available genotypic data. Additional markers were added to potentially fill gaps in a few biparental progenies where genetic mapping for QTL analysis is intended. For pear, SNPs were chosen from the Axiom 70K array in an approach similar to apple. After accommodating for replicates needed for the probesets chosen for each of the five species of the array, a total of 9533 SNPs were tiled for apple and 7663 SNPs for pear. Diversity analysis for 384 apple or pear accessions from the INRAE collection (CRB RosePom) and preliminary genetic mapping results for biparental progenies will be presented.