Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening

Background:The changing climate is altering timing of key fruit ripening processes and increasing the occurrenceof fruit defects. To improve our understanding of the genetic control of raspberry fruit development an enhancedgenetic linkage map was developed and used to examine ripening phenotypic data.
Results:In this study we developed an enhanced genetic linkage map for the raspberry cvs. Glen Moy x Lathamreference mapping population using genotyping by sequencing (GbS). Alignment to a newly sequenced draftreference genome of red raspberry, cultivar (cv.) Glen Moy, identified 8019 single nucleotide polymorphisms (SNPs).After stringent filtering to take account of read coverage over all the progeny individuals, association with a singlechromosome, heterozygosity and marker regression mapping, 2348 high confidence SNPs were retained andintegrated with an existing raspberry genetic map. The linkage map contained many more SNPs segregating inLatham than in Glen Moy. This caused difficulties in quantitative trait loci (QTL) mapping with standard softwareand a novel analysis based on a hidden Markov model was used to improve the mapping. QTL mapping usingthe newly generated dense genetic map not only corroborated previously identified genetic locations but alsoprovided additional genetic elements controlling fruit ripening in raspberry.
Conclusion:The high-density GbS map located the QTL peaks more precisely than in earlier studies, aligned theQTLs with Glen Moy genome scaffolds, narrowed the range of potential candidate genes to these regions that canbe utilised in other populations or in gene expression studies to confirm their role and increased the repertoire ofmarkers available to understand the genetic control of fruit ripening traits