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

Christine A Hackett,Craig G Simpson,Julie Graham,Jenny Morris,Pete Hedley,Kay Smith,Katharine Preedy,Linda Milne

doi:10.1186/s12863-018-0666-z

Christine A Hackett, Craig G Simpson + Show 6 more

Open Access

https://doi.org/10.1186/s12863-018-0666-z

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Abstract

BackgroundThe changing climate is altering timing of key fruit ripening processes and increasing the occurrence of fruit defects. To improve our understanding of the genetic control of raspberry fruit development an enhanced genetic linkage map was developed and used to examine ripening phenotypic data.ResultsIn this study we developed an enhanced genetic linkage map for the raspberry cvs. Glen Moy x Latham reference mapping population using genotyping by sequencing (GbS). Alignment to a newly sequenced draft reference 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 single chromosome, heterozygosity and marker regression mapping, 2348 high confidence SNPs were retained and integrated with an existing raspberry genetic map. The linkage map contained many more SNPs segregating in Latham than in Glen Moy. This caused difficulties in quantitative trait loci (QTL) mapping with standard software and a novel analysis based on a hidden Markov model was used to improve the mapping. QTL mapping using the newly generated dense genetic map not only corroborated previously identified genetic locations but also provided additional genetic elements controlling fruit ripening in raspberry.ConclusionThe high-density GbS map located the QTL peaks more precisely than in earlier studies, aligned the QTLs with Glen Moy genome scaffolds, narrowed the range of potential candidate genes to these regions that can be utilised in other populations or in gene expression studies to confirm their role and increased the repertoire of markers available to understand the genetic control of fruit ripening traits.

Highlights

The changing climate is altering timing of key fruit ripening processes and increasing the occurrence of fruit defects
Latham are associated with Fragaria linkage groups (FLG) FLGVII, FLGIII, FLGVI, FLGII, FLGV and FLG1 and nearly 90% of the sequences of red raspberry markers tested aligned to the recent black raspberry genome assembly [19, 21]
Glen Moy draft genome reference To facilitate reference sequence-based assembly of genotyping by sequencing (GbS) sequence tags, a draft genome sequence was established for the raspberry cultivar Glen Moy

Summary

Introduction

The changing climate is altering timing of key fruit ripening processes and increasing the occurrence of fruit defects. Unpredictable phenotypic variation in a range of developmental traits directly impacts yield across a range of crops [1,2,3,4,5,6]. In raspberry, this has been evident in increased occurrence of crumbly fruit [4], lack of evenness and variable timings of bud break [7], flowering and fruiting [8], variations in yield, modification of primocane (annual) and biennial behaviour Latham are associated with Fragaria linkage groups (FLG) FLGVII, FLGIII, FLGVI, FLGII, FLGV and FLG1 and nearly 90% of the sequences of red raspberry markers tested aligned to the recent black raspberry genome assembly [19, 21]

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