High-density genetic map construction and gene mapping of pericarp color in wax gourd using specific-locus amplified fragment (SLAF) sequencing.
High-density genetic map construction and gene mapping of pericarp color in wax gourd using specific-locus amplified fragment (SLAF) sequencing.
复制标题
利用特定位点扩增片段（SLAF）测序技术构建冬瓜果皮颜色高密度遗传图谱及基因定位
DOI：
10.1186/s12864-015-2220-y
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发表时间：
2015-12-09
期刊：
影响因子：
4.4
通讯作者：
Liang Z
中科院分区：
文献类型：
--
作者：
Jiang B;Liu W;Xie D;Peng Q;He X;Lin Y;Liang Z
高密度图谱是遗传和基因组分析的一种有价值的工具。冬瓜虽然是葫芦科中分布广泛的蔬菜，且具有重要的药用和保健价值，但由于缺乏有效的标记，尚未构建出遗传图谱。特异位点扩增片段测序（SLAF - seq）是一种新开发的用于大规模单核苷酸多态性（SNP）发现和基因分型的高通量策略。
在我们目前的研究中，我们利用SLAF - seq构建了一个高密度遗传图谱，并确定了冬瓜中一个控制果皮颜色的位点。对140个F2个体及其两个亲本进行了SLAF - seq。共产生了1.4338亿对末端读长。母本（B214）的平均测序深度为26.51，父本（B227）为27.01，每个F2个体为5.11。在过滤低深度SLAF标签时，共检测到142653个高质量SLAF，其中22151个具有多态性，多态率为15.42%。最后，选择了4607个多态性标记用于构建遗传图谱，并产生了12个连锁群（LGs）。该图谱跨度为2172.86 cM，相邻标记间的平均距离为0.49 cM。还对果皮颜色的遗传进行了研究，结果表明果皮颜色由一个单基因控制。并且基于新构建的高密度图谱，在5号染色体上确定了一个控制冬瓜果皮颜色的单一位点。
这是冬瓜高密度遗传图谱构建和基因定位的首次报道，它将成为冬瓜基因定位、标记辅助育种、基于图谱的基因克隆、比较图谱绘制和基因组草图组装的极有价值的工具。
本文的网络版（doi:10.1186/s12864 - 015 - 2220 - y）包含补充材料，授权用户可获取。
High-density map is a valuable tool for genetic and genomic analysis. Although wax gourd is a widely distributed vegetable of Cucurbitaceae and has important medicinal and health value, no genetic map has been constructed because of the lack of efficient markers. Specific-locus amplified fragment sequencing (SLAF-seq) is a newly developed high-throughput strategy for large-scale single nucleotide polymorphism (SNP) discovery and genotyping. In our present study, we constructed a high-density genetic map by using SLAF-seq and identified a locus controlling pericarp color in wax gourd. An F2 population of 140 individuals and their two parents were subjected to SLAF-seq. A total of 143.38 M pair-end reads were generated. The average sequencing depth was 26.51 in the maternal line (B214), 27.01 in the parental line (B227), and 5.11 in each F2 individual. When filtering low-depth SLAF tags, a total of 142,653 high-quality SLAFs were detected, and 22,151 of them were polymorphic, with a polymorphism rate of 15.42 %. And finally, 4,607 of the polymorphic markers were selected for genetic map construction, and 12 linkage groups (LGs) were generated. The map spanned 2,172.86 cM with an average distance between adjacent markers for 0.49 cM. The inheritance of pericarp color was also studied, which showed that the pericarp color was controlled by one single gene. And based on the newly constructed high-density map, a single locus locating on chromosome 5 was identified for controlling the pericarp color of wax gourd. This is the first report of high-density genetic map construction and gene mapping in wax gourd, which will be served as an invaluable tool for gene mapping, marker assisted breeding, map-based gene cloning, comparative mapping and draft genome assembling of wax gourd. The online version of this article (doi:10.1186/s12864-015-2220-y) contains supplementary material, which is available to authorized users.