Development of cleaved amplified polymorphic sequence markers and a CAPS-based genetic linkage map in watermelon (Citrullus lanatus [Thunb.] Matsum. and Nakai) constructed using whole-genome re-sequencing data.
Development of cleaved amplified polymorphic sequence markers and a CAPS-based genetic linkage map in watermelon (Citrullus lanatus [Thunb.] Matsum. and Nakai) constructed using whole-genome re-sequencing data.
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使用全基因组重测序数据构建西瓜（Citrullus lanatus [Thunb.] Matsum. 和 Nakai）的切割扩增多态性序列标记和基于 CAPS 的遗传连锁图谱
DOI：
10.1270/jsbbs.66.244
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发表时间：
2016-03
期刊：
影响因子：
2.4
通讯作者：
Wang X
中科院分区：
文献类型：
--
作者：
Liu S;Gao P;Zhu Q;Luan F;Davis AR;Wang X
切割扩增多态性序列（CAPS）标记是检测单核苷酸多态性（SNP）的有用工具。本研究基于西瓜高通量重测序数据，检测西瓜SNP位点，并将其转换为CAPS标记，用于西瓜连锁图谱构建和数量性状位点（QTL）分析。利用Perl自编的CAPS标记开发脚本对两个自交系，Cream of Saskatchewan（COS）和LSW-177进行了重新测序和分析。两个亲本材料的组装序列分别有88.7%和78.5%能与参考西瓜基因组定位。比较组装的基因组数据分析提供了两种材料之间的225，693和19，268个SNP和indel。用16种限制性内切酶共设计了532对CAPS标记，其中271对引物经PCR和酶切鉴定，扩增出了预期长度的特异条带，并产生了多态性条带，多态性率为50.94%。利用新的CAPS标记构建了F2群体的初步遗传连锁图谱，图谱跨度为1836.51 cM，包含11个连锁群和301个标记。共检测到12个与果肉颜色、果长、果宽、果形指数和锤度相关的QTL。这些新的CAPS标记将为西瓜育种和遗传研究提供宝贵的资源。
Cleaved amplified polymorphic sequence (CAPS) markers are useful tools for detecting single nucleotide polymorphisms (SNPs). This study detected and converted SNP sites into CAPS markers based on high-throughput re-sequencing data in watermelon, for linkage map construction and quantitative trait locus (QTL) analysis. Two inbred lines, Cream of Saskatchewan (COS) and LSW-177 had been re-sequenced and analyzed by Perl self-compiled script for CAPS marker development. 88.7% and 78.5% of the assembled sequences of the two parental materials could map to the reference watermelon genome, respectively. Comparative assembled genome data analysis provided 225,693 and 19,268 SNPs and indels between the two materials. 532 pairs of CAPS markers were designed with 16 restriction enzymes, among which 271 pairs of primers gave distinct bands of the expected length and polymorphic bands, via PCR and enzyme digestion, with a polymorphic rate of 50.94%. Using the new CAPS markers, an initial CAPS-based genetic linkage map was constructed with the F2 population, spanning 1836.51 cM with 11 linkage groups and 301 markers. 12 QTLs were detected related to fruit flesh color, length, width, shape index, and brix content. These newly CAPS markers will be a valuable resource for breeding programs and genetic studies of watermelon.