Zhang Guoyu, Ren Yi, Sun Honghe, Guo Shaogui, Zhang Fan, Zhang Jie, Zhang Haiying, Jia Zhangcai, Fei Zhangjun, Xu Yong, Li Haizhen
Beijing Vegetable Research Center, BAAFS, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, 100097, P.R. China.
Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA.
BMC Genomics. 2015 Dec 24;16:1101. doi: 10.1186/s12864-015-2312-8.
Pumpkin (Cucurbita maxima Duch.) is an economically important crop belonging to the Cucurbitaceae family. However, very few genomic and genetic resources are available for this species. As part of our ongoing efforts to sequence the pumpkin genome, high-density genetic map is essential for anchoring and orienting the assembled scaffolds. In addition, a saturated genetic map can facilitate quantitative trait locus (QTL) mapping.
A set of 186 F2 plants derived from the cross of pumpkin inbred lines Rimu and SQ026 were genotyped using the genotyping-by-sequencing approach. Using the SNPs we identified, a high-density genetic map containing 458 bin-markers was constructed, spanning a total genetic distance of 2,566.8 cM across the 20 linkage groups of C. maxima with a mean marker density of 5.60 cM. Using this map we were able to anchor 58 assembled scaffolds that covered about 194.5 Mb (71.7%) of the 271.4 Mb assembled pumpkin genome, of which 44 (183.0 Mb; 67.4%) were oriented. Furthermore, the high-density genetic map was used to identify genomic regions highly associated with an important agronomic trait, dwarf vine. Three QTLs on linkage groups (LGs) 1, 3 and 4, respectively, were recovered. One QTL, qCmB2, which was located in an interval of 0.42 Mb on LG 3, explained 21.4% phenotypic variations. Within qCmB2, one gene, Cma_004516, encoding the gibberellin (GA) 20-oxidase in the GA biosynthesis pathway, had a 1249-bp deletion in its promoter in bush type lines, and its expression level was significantly increased during the vine growth and higher in vine type lines than bush type lines, supporting Cma_004516 as a possible candidate gene controlling vine growth in pumpkin.
A high-density pumpkin genetic map was constructed, which was used to successfully anchor and orient the assembled genome scaffolds, and to identify QTLs highly associated with pumpkin vine length. The map provided a valuable resource for gene cloning and marker assisted breeding in pumpkin and other related species. The identified vine length QTLs would help to dissect the underlying molecular basis regulating pumpkin vine growth.
南瓜（Cucurbita maxima Duch.）是葫芦科一种具有重要经济价值的作物。然而，该物种可用的基因组和遗传资源非常少。作为我们正在进行的南瓜基因组测序工作的一部分，高密度遗传图谱对于锚定和定向组装的支架至关重要。此外，饱和遗传图谱有助于数量性状位点（QTL）定位。
利用简化基因组测序方法对由南瓜自交系Rimu和SQ026杂交产生的186个F2植株进行基因分型。利用我们鉴定出的单核苷酸多态性（SNP），构建了一个包含458个bin标记的高密度遗传图谱，跨越南瓜20个连锁群，总遗传距离为2566.8厘摩（cM），平均标记密度为5.60 cM。利用该图谱，我们能够锚定58个组装支架，这些支架覆盖了271.4 Mb组装南瓜基因组的约194.5 Mb（71.7%），其中44个（183.0 Mb；67.4%）被定向。此外，该高密度遗传图谱用于鉴定与重要农艺性状矮化藤蔓高度相关的基因组区域。分别在连锁群（LG）1、3和4上发现了三个QTL。位于LG 3上0.42 Mb区间的一个QTL，qCmB2，解释了21.4%的表型变异。在qCmB2内，一个基因Cma_004516，编码赤霉素（GA）生物合成途径中的GA 20-氧化酶，在丛生型品系的启动子中有一个1249 bp的缺失，其表达水平在藤蔓生长期间显著增加，且在蔓生型品系中高于丛生型品系，支持Cma_004516作为控制南瓜藤蔓生长的一个可能候选基因。
构建了一个高密度南瓜遗传图谱，该图谱成功用于锚定和定向组装的基因组支架，并鉴定与南瓜藤蔓长度高度相关的QTL。该图谱为南瓜及其他相关物种的基因克隆和分子标记辅助育种提供了宝贵资源。鉴定出的藤蔓长度QTL将有助于剖析调控南瓜藤蔓生长的潜在分子基础。
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