An SNP-based saturated genetic map and QTL analysis of fruit-related traits in cucumber using specific-length amplified fragment (SLAF) sequencing.
An SNP-based saturated genetic map and QTL analysis of fruit-related traits in cucumber using specific-length amplified fragment (SLAF) sequencing.
复制标题
利用特定长度扩增片段 (SLAF) 测序对黄瓜果实相关性状进行基于 SNP 的饱和遗传图谱和 QTL 分析
DOI：
10.1186/1471-2164-15-1158
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发表时间：
2014-12-22
期刊：
影响因子：
4.4
通讯作者：
Chen J
中科院分区：
文献类型：
--
作者：
Wei Q;Wang Y;Qin X;Zhang Y;Zhang Z;Wang J;Li J;Lou Q;Chen J
背景黄瓜，黄瓜，是一种经济上重要的蔬菜作物，在世界范围内新鲜加工或消费。然而，黄瓜遗传基础狭窄，难以构建高密度遗传图谱。大规模平行基因分型方法和下一代测序（NGS）技术的发展为开发单核苷酸多态性（SNP）用于园艺性状的连锁图谱构建和QTL分析提供了极好的机会。特异性长度扩增片段测序（SLAF-seq）是一种新的标记开发技术，它允许以合理的成本进行大规模SNP发现和基因分型。在这项研究中，我们构建了一个高密度的SNP图谱，黄瓜使用SLAF-seq和检测果实相关的QTLs.ResultsAnF2群体的148个人之间的品种内杂交CC 3和NC 76。从两个亲本和148个F2代个体中提取基因组DNA，进行高通量测序和SLAF文库构建。总共生成了10.76 GB原始数据和75，024，043个双端读段，以开发52，684个高质量SLAF，其中5，044个是多态的。对4，817个SLAF进行编码，并将其分组为不同的分离模式。为黄瓜构建了包含1，800个SNP的高分辨率遗传图谱，跨度为890.79 cM。相邻标记之间的平均距离为0.50 cM。将183个支架锚定到基于SNP的遗传图谱上，该遗传图谱覆盖黄瓜基因组的46%（168.9 Mb）（367 Mb）。共检测到9个与果实长度和重量相关的QTL，其中1个QTL标记为f13.2，可解释44.60%的表型变异。对齐的SNP标记草图基因组支架显示两个错误组装的支架，通过荧光原位杂交（FISH）进行验证。ConclusionsWe在此报告均匀分散的SNP在黄瓜基因组的发展，并为第一次基于SNP的饱和连锁图谱。这个1,800个位点的图谱可能有助于控制果实产量的复杂QTL位点的遗传作图，以及基因组骨架草图的定位。
BackgroundCucumber,Cucumis sativusL., is an economically important vegetable crop which is processed or consumed fresh worldwide. However, the narrow genetic base in cucumber makes it difficult for constructing high-density genetic maps. The development of massively parallel genotyping methods and next-generation sequencing (NGS) technologies provides an excellent opportunity for developing single nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of horticultural traits. Specific-length amplified fragment sequencing (SLAF-seq) is a recent marker development technology that allows large-scale SNP discovery and genotyping at a reasonable cost. In this study, we constructed a high-density SNP map for cucumber using SLAF-seq and detected fruit-related QTLs.ResultsAn F2population of 148 individuals was developed from an intra-varietal cross between CC3 and NC76. Genomic DNAs extracted from two parents and 148 F2individuals were subjected to high-throughput sequencing and SLAF library construction. A total of 10.76 Gb raw data and 75,024,043 pair-end reads were generated to develop 52,684 high-quality SLAFs, out of which 5,044 were polymorphic. 4,817 SLAFs were encoded and grouped into different segregation patterns. A high-resolution genetic map containing 1,800 SNPs was constructed for cucumber spanning 890.79 cM. The average distance between adjacent markers was 0.50 cM. 183 scaffolds were anchored to the SNP-based genetic map covering 46% (168.9 Mb) of the cucumber genome (367 Mb). Nine QTLs for fruit length and weight were detected, a QTL designatedfl3.2explained 44.60% of the phenotypic variance. Alignment of the SNP markers to draft genome scaffolds revealed two mis-assembled scaffolds that were validated by fluorescencein situhybridization (FISH).ConclusionsWe report herein the development of evenly dispersed SNPs across cucumber genome, and for the first time an SNP-based saturated linkage map. This 1,800-locus map would likely facilitate genetic mapping of complex QTL loci controlling fruit yield, and the orientation of draft genome scaffolds.
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