İpek Ahmet, İpek Meryem, Ercişli Sezai, Tangu Nesrin Aktepe
Faculty of Agriculture, Horticulture Department, Uludag University, Bursa, Turkey.
Faculty of Agriculture, Horticulture Department, Atatürk University, Erzurum, Turkey.
Funct Integr Genomics. 2017 Sep;17(5):493-501. doi: 10.1007/s10142-017-0552-1. Epub 2017 Feb 18.
Molecular markers located in the genic regions of plants are valuable tools for the identification of candidate genes of economically important traits and consequent use in marker-assisted selection (MAS). In the past, simple sequence repeat markers (SSRs) and single-nucleotide polymorphisms (SNPs) located in expressed sequence tags (ESTs) were developed by sequencing RNA derived from different plant tissues, which involves laborious RNA extraction, mRNA isolation, and cDNA synthesis. In order to develop SNP markers located in olive transcriptomes, we used the recently developed genotyping-by-sequencing (GBS) technique. An analysis was done for 125 olive DNA samples (123 DNA samples from a cross-pollinated F mapping population, and two samples from parents). From 45 to 66% of Illumina reads from GBS analysis were aligned to the olive transcriptome. A total of 22,033 transcriptome-based SNP markers were identified, and 3384 of these were mapped in the olive genome. The genetic linkage map constructed in this study consists of 1 cleaved amplified polymorphic sequence (CAPS), 19 SSR, and 3384 transcriptome-based SNP markers. The map covers 3340.8 cM of the olive genome in 23 linkage groups, with the length of the linkage groups ranging from 55.6 to 248.7 cM. Average map distance between flanking markers was 0.98 cM. This genetic linkage map is a saturated genetic map and will be a useful tool for the localization of quantitative trait loci (QTLs) and gene(s) of interest and for the identification of candidate genes for economically important traits.
位于植物基因区域的分子标记是鉴定经济重要性状候选基因并随后用于标记辅助选择（MAS）的宝贵工具。过去，通过对来自不同植物组织的RNA进行测序来开发位于表达序列标签（EST）中的简单序列重复标记（SSR）和单核苷酸多态性（SNP），这涉及繁琐的RNA提取、mRNA分离和cDNA合成。为了开发位于橄榄转录组中的SNP标记，我们使用了最近开发的简化基因组测序（GBS）技术。对125个橄榄DNA样本（123个来自异花授粉F作图群体的DNA样本和2个亲本样本）进行了分析。GBS分析中45%至66%的Illumina读数与橄榄转录组比对。共鉴定出22,033个基于转录组的SNP标记，其中3384个被定位到橄榄基因组中。本研究构建的遗传连锁图谱由1个酶切扩增多态性序列（CAPS）、19个SSR和3384个基于转录组的SNP标记组成。该图谱覆盖了橄榄基因组的3340.8 cM，分布在23个连锁群中，连锁群长度从55.6到248.7 cM不等。侧翼标记之间的平均图距为0.98 cM。这个遗传连锁图谱是一个饱和遗传图谱，将成为定位数量性状基因座（QTL）和感兴趣基因以及鉴定经济重要性状候选基因的有用工具。
