Hackett Christine A, Milne Linda, Smith Kay, Hedley Pete, Morris Jenny, Simpson Craig G, Preedy Katharine, Graham Julie
Biomathematics and Statistics Scotland, Invergowrie, Dundee, DD25DA, Scotland.
The James Hutton Institute, Invergowrie, Dundee, DD25DA, Scotland.
BMC Genet. 2018 Aug 15;19(1):59. doi: 10.1186/s12863-018-0666-z.
The 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.
In 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.
The 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.
气候变化正在改变关键果实成熟过程的时间，并增加果实缺陷的发生率。为了更好地理解树莓果实发育的遗传控制，我们构建了一个增强的遗传连锁图谱，并用于分析成熟表型数据。
在本研究中，我们利用简化基因组测序（GbS）为树莓品种Glen Moy×Latham参考作图群体构建了一个增强的遗传连锁图谱。与新测序的红树莓品种Glen Moy的参考基因组草图比对，鉴定出8019个单核苷酸多态性（SNP）。经过严格筛选，考虑到所有子代个体的读段覆盖度、与单条染色体的关联、杂合性以及标记回归作图，保留了2348个高可信度SNP，并将其与现有的树莓遗传图谱整合。该连锁图谱中，Latham分离的SNP比Glen Moy多得多。这给使用标准软件进行数量性状位点（QTL）作图带来了困难，因此采用了基于隐马尔可夫模型的新分析方法来改进作图。利用新生成的高密度遗传图谱进行QTL作图，不仅证实了先前确定的遗传位置，还提供了控制树莓果实成熟的其他遗传元件。
高密度的GbS图谱比早期研究更精确地定位了QTL峰值，将QTL与Glen Moy基因组支架对齐，将潜在候选基因的范围缩小到这些区域，这些区域可用于其他群体或基因表达研究以确认其作用，并增加了可用于理解果实成熟性状遗传控制的标记库。
