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

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.Electronic supplementary materialThe online version of this article (10.1186/s12863-018-0666-z) contains supplementary material, which is available to authorized users.

Genetic diversity, linkage disequilibrium, and population structure analysis of the tea plant (Camellia sinensis) from an origin center, Guizhou plateau, using genome-wide SNPs developed by genotyping-by-sequencing

“…In this study, we report the first genetic diversity analysis of a tea population using GBS-a simple and cost-effective approach [41–44]. We generated 390.30 Gb clean reads and identified 79,016 high-quality SNPs using stringent filtering criteria.…”

Phenotypic Evaluation of a Hybrid Diploid Blueberry Population for Plant Development and Fruit Quality Traits

“…Genomic resources (mapping populations) have been recently used to map QTL for development and fruit quality traits in other berry crops, like raspberry [19], blackberry [20], cranberry [21][22][23][24] and strawberry [25]. The first genetic linkage maps for red raspberry were generated from a 'Glen Moy' × 'Latham' population [26,27]. This biparental mapping population has been used to identify QTL for several growth stage traits [26,27] and fruit quality traits, including texture [28], color [29], flavor volatiles [30], anthocyanins [31] and fruit softening [28].…”

“…The first genetic linkage maps for red raspberry were generated from a 'Glen Moy' × 'Latham' population [26,27]. This biparental mapping population has been used to identify QTL for several growth stage traits [26,27] and fruit quality traits, including texture [28], color [29], flavor volatiles [30], anthocyanins [31] and fruit softening [28]. Two QTL for the fruit texture disorder in raspberry, called crumbly, have also been identified [32].…”

Peer Review #2 of "Development of core-collections for Guizhou tea genetic resources and GWAS of leaf size using SNP developed by genotyping-by-sequencing (v0.1)"

“…GBS is a cost-efficient and effective genotyping method (Yang et al, 2017;Bhattarai et al, 2018;Hackett et al, 2018). In this study, 390.30 Gb clean reads were generated.…”