Mapping the genomic landscape of peach and almond with PrunusMap

Abstract

High throughput sequencing is accelerating plant breeding. Genotyping, quantitative trait locus or genome-wide association analyses are essential to locate alleles of interest in germplasm collections. These applications require accurately mapping nucleotide markers within growing collections of reference genome sequences. PrunusMap (https://prunusmap.eead.csic.es) is a user-friendly Web application designed to facilitate these tasks to Prunus breeders. It efficiently aligns markers and locates SNPs on peach and almond genomes, providing lists of nearby genes and curated proteins. It can align all markers from a genetic map in one step, producing their physical positions. By searching multiple maps, it can also solve the problem of finding equivalent gene identifiers across different annotations. Three intuitive tools, 'Find markers', 'Align sequences' and 'Locate by position', are available to accelerate mapping analyses, particularly for users with limited bioinformatics expertise. New genomes, annotations or marker sets will be added based on their interest to the community.