Data_Sheet_1_Identification of an Allelic Variant of the CsOr Gene Controlling Fruit Endocarp Color in Cucumber (Cucumis sativus L.) Using Genotyping-By-Sequencing (GBS) and Whole-Genome Sequencing.pdf

The cucumber is a major vegetable crop around the world. Fruit flesh color is an important quality trait in cucumber and flesh color mainly depends on the relative content of β-carotene in the fruits. The β-carotene serves as a precursor of vitamin A, which has dietary benefits for human health. Cucumbers with orange flesh contain a higher amount of β-carotene than white fruit flesh. Therefore, development of orange-fleshed cucumber varieties is gaining attention for improved nutritional benefits. In this study, we performed genotyping-by-sequencing (GBS) based on genetic mapping and whole-genome sequencing to identify the orange endocarp color gene in the cucumber breeding line, CS-B. Genetic mapping, genetic sequencing, and genetic segregation analyses showed that a single recessive gene (CsaV3_6G040750) encodes a chaperone DnaJ protein (DnaJ) protein at the Cucumis sativus(CsOr) locus was responsible for the orange endocarp phenotype in the CS-B line. The Or gene harbored point mutations T13G and T17C in the first exon of the coding region, resulting in serine to alanine at position 13 and isoleucine to threonine at position 17, respectively. CS-B line displayed increased β-carotene content in the endocarp tissue, corresponding to elevated expression of CsOr gene at fruit developmental stages. Identifying novel missense mutations in the CsOr gene could provide new insights into the role of Or mechanism of action for orange fruit flesh in cucumber and serve as a valuable resource for developing β-carotene-rich cucumbers varieties with increased nutritional benefits.

黄瓜是全球范围内的重要蔬菜作物。果实果肉颜色是黄瓜重要的品质性状，其主要取决于果实中β-胡萝卜素的相对含量。β-胡萝卜素作为维生素A的前体物质，对人体健康具有膳食益处。果肉呈橙色的黄瓜，其β-胡萝卜素含量高于果肉呈白色的黄瓜。因此，培育兼具更高营养益处的橙色果肉黄瓜品种正受到广泛关注。本研究结合遗传作图与全基因组测序，采用测序分型（genotyping-by-sequencing, GBS）技术，在黄瓜（Cucumis sativus）育种品系CS-B中鉴定出调控橙色内果皮颜色的基因。遗传作图、基因测序与遗传分离分析结果显示，位于CsOr基因座上的单个隐性基因CsaV3_6G040750，编码分子伴侣DnaJ蛋白（DnaJ），该基因正是导致CS-B品系出现橙色内果皮表型的原因。该Or基因在编码区第一外显子区域存在T13G和T17C两处点突变，分别导致第13位丝氨酸突变为丙氨酸、第17位异亮氨酸突变为苏氨酸。CS-B品系的内果皮组织中β-胡萝卜素含量显著升高，这与果实发育阶段CsOr基因的表达上调相一致。本研究鉴定出的CsOr基因全新错义突变，可为解析黄瓜橙色果肉性状的作用机制提供新视角，同时也为培育高β-胡萝卜素含量、营养更丰富的黄瓜品种提供了宝贵的遗传资源。