Data from: Molecular mapping and candidate gene analysis for numerous spines on the fruit of cucumber

Number of spines on the fruit is an important quality trait in cucumber. The inheritance and identification of molecular markers for fruit spine density gene will provide a basis for breeding and lay the foundation for gene cloning. Cucumber inbred lines NCG-122 with numerous spines and NCG-121 with few spines were used for genetic analysis and gene mapping in this study. Genetic analysis showed that numerous spines in NCG-122 was qualitative, and a single recessive nuclear gene (ns) controlled this trait. Few spines trait was dominant over numerous spines trait. In the preliminary genetic mapping of the ns gene, eight SSR markers were found to be linked to ns which was mapped to chromosome 2 (Chr.2) of cucumber. The closest flanking markers SSR22338 and SSR11596 were linked to the ns gene with genetic distances of 10.2 and 1.7cM, respectively. 130 pairs of new SSR primers and 28 pairs of Indel primers were developed based on the sequence information in the preliminary mapping region of ns. Fifteen SSR markers and two Indel markers were identified to be linked to the ns gene after analysis on the F2 mapping population using the new molecular markers. The two closest flanking markers, SSRns-127 and SSR04219, were 0.7 and 2.4 cM from ns, respectively. The physical distance between SSRns-127 and SSR04219 was 266.1Kb containing 27 predicted genes. Csa2G285390 was speculated as the probable candidate gene for numerous spines. The accuracy of the closest linked marker to the ns gene, SSRns-127, for MAS breeding was 95.0%.果实刺数是黄瓜重要的品质性状。对黄瓜果实刺密度基因开展遗传解析与分子标记鉴定，可为黄瓜遗传育种提供理论支撑，亦为后续基因克隆研究奠定基础。本研究以多刺黄瓜自交系NCG-122与少刺黄瓜自交系NCG-121为实验材料，进行遗传分析与基因定位研究。遗传分析结果显示，NCG-122的多刺性状为质量性状，由单个隐性核基因（ns）调控；少刺性状对多刺性状呈显性优势。在ns基因的初步遗传定位阶段，共筛选获得8个与ns基因连锁的简单序列重复（Simple Sequence Repeat，SSR）标记，并将ns基因定位于黄瓜第2号染色体（Chr.2）。其中，距离最近的两侧翼标记SSR22338与SSR11596与ns基因的遗传距离分别为10.2厘摩（cM）和1.7厘摩。基于ns基因初步定位区域的序列信息，本研究开发了130对新型SSR引物与28对插入缺失（Insertion-Deletion，Indel）引物。利用新型分子标记对F2作图群体进行基因型分析后，共鉴定得到15个SSR标记与2个Indel标记与ns基因连锁。其中，距离最近的两侧翼标记SSRns-127与SSR04219与ns基因的遗传距离分别为0.7厘摩和2.4厘摩。SSRns-127与SSR04219之间的物理距离为266.1千碱基对（Kb），该区间共包含27个预测基因。经分析推测，Csa2G285390为调控多刺性状的潜在候选基因。与ns基因连锁最紧密的标记SSRns-127在标记辅助选择（Marker-Assisted Selection，MAS）育种中的应用准确率可达95.0%。