Xu Xuewen, Xu Ruixue, Zhu Biyun, Yu Ting, Qu Wenqin, Lu Lu, Xu Qiang, Qi Xiaohua, Chen Xuehao
Department of Horticulture, School of Horticulture and Plant Protection, Yangzhou University Yangzhou, China.
Front Plant Sci. 2015 Jan 7;5:768. doi: 10.3389/fpls.2014.00768. eCollection 2014.
High-density genetic map provides an essential framework for accurate and efficient genome assembly and QTL fine mapping. Construction of high-density genetic maps appears more feasible since the advent of next-generation sequencing (NGS), which eases SNP discovery and high-throughput genotyping of large population. In this research, a high-density genetic map of cucumber (Cucumis sativus L.) was successfully constructed across an F2 population by a recently developed Specific Length Amplified Fragment sequencing (SLAF-seq) method. In total, 18.69 GB of data containing 93,460,000 paired-end reads were obtained after preprocessing. The average sequencing depth was 44.92 in the D8 (female parent), 42.16 in the Jin5-508 (male parent), and 5.01 in each progeny. 79,092 high-quality SLAFs were detected, of which 6784 SLAFs were polymorphic, and 1892 of the polymorphic markers met the requirements for constructing genetic map. The genetic map spanned 845.87 cm with an average genetic distance of 0.45 cm. It is a reliable linkage map for fine mapping and molecular breeding of cucumber for its high marker density and well-ordered markers.
高密度遗传图谱为准确、高效的基因组组装和QTL精细定位提供了重要框架。自新一代测序（NGS）技术出现以来，构建高密度遗传图谱变得更加可行，因为它简化了单核苷酸多态性（SNP）的发现以及大群体的高通量基因分型。在本研究中，通过最近开发的特异性长度扩增片段测序（SLAF-seq）方法，成功构建了一个跨越F2群体的黄瓜（Cucumis sativus L.）高密度遗传图谱。预处理后，共获得18.69GB的数据，包含93460000对末端测序读段。D8（母本）的平均测序深度为44.92，津5-508（父本）的平均测序深度为42.16，每个子代的平均测序深度为5.01。检测到79092个高质量的SLAF，其中6784个SLAF具有多态性，1892个多态性标记满足构建遗传图谱的要求。该遗传图谱跨度为845.87厘摩（cM），平均遗传距离为0.45厘摩。因其标记密度高且标记排列有序，是黄瓜精细定位和分子育种的可靠连锁图谱。
