Molecularly tagged genes and quantitative trait loci in cucumber - and recommendation of controlled vocabulary for QTL mapping

Authors: WANG, YUHUI - University Of Wisconsin; BO, KAILIANG - Chinese Academy Of Agricultural Sciences; GU, XINGFANG - Chinese Academy Of Agricultural Sciences; PAN, JUNSONG - Shanghai Jiaotong University; LI, YUHONG - Northwest A&f University; CHEN, JINFENG - Nanjing Agricultural University; WEN, CHANGLONG - Beijing Academy Of Agricultural Sciences; REN, ZHONGHAI - Shandong Agricultural University; REN, HUAZHONG - China Agricultural University; GRUMET, REBECCA - Michigan State University; Weng, Yiqun

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/18/2019
Publication Date: 1/1/2020
Citation: Wang, Y., Bo, K., Gu, X., Pan, J., Li, Y., Chen, J., Wen, C., Ren, Z., Ren, H., Chen, X., Grumet, R., Weng, Y. 2020. Molecularly tagged genes and quantitative trait loci in cucumber with recommendations for QTL nomenclature. Horticulture Research. 7:3. https://doi.org/10.1038/s41438-019-0226-3.
DOI: https://doi.org/10.1038/s41438-019-0226-3

Interpretive Summary: Cucumber is an important vegetable crop worldwide, and a favorite model for study sex expression and vascular biology in plants. Cucumber was the first specialty crop with a publicly available draft genome. Its relatively small genome size, short life cycle, and a high-degree of homozygosity offer advantages for genetic studies. In the last decade, significant progress has been made in molecular mapping and gene/QTL cloning in cucumber. Here we conducted an extensive literature review on mutants, genes and QTL that have been molecularly mapped or cloned in cucumber. In total, we documented 80 simply inherited genes that have been cloned or fine mapped, as well as 295 QTL for various quantitative traits including 102 for disease resistances against seven pathogens. By aligning these genes/QTL against the newest cucumber draft genome, consensus QTL across multiple studies were established, which provided insights into inheritance correlations among different traits. To facilitate their use in molecular breeding, information on markers tagging the target genes/QTL, and polymorphism within cloned causal genes was included for the target traits. In order to establish consistency and reduce confusion in QTL naming, we worked with public and private cucumber researchers to develop a standard vocabulary for quantitative traits, and recommended naming rules for future cucumber QTL mapping studies. This is the first attempt to systematically summarize, analyze and inventory cucumber mutants, cloned or mapped genes and QTL, which should be a valuable resource for the cucumber breeders as well as the more-broad cucurbit research community.

Technical Abstract: Cucumber, Cucumis sativus L. (2n=2x=14) is an important vegetable crop worldwide, and a favorite model for study sex expression and vascular biology in plants. Cucumber was the first specialty crop with a publicly available draft genome. Its relatively small genome size (~400 Mbp), short life cycle (2-3 months seed to seed), and high-degree of homozygosity offer advantages for genetic studies. In the last decade, significant progress has been made in molecular mapping and gene/QTL cloning in cucumber. Here we conducted an extensive literature review on mutants, genes and QTL that have been molecularly mapped or cloned in cucumber. In total, we documented 80 simply inherited genes that have been cloned or fine mapped, as well as 295 QTL for various quantitative traits including 102 for disease resistances against seven pathogens. By aligning these genes/QTL against the newest cucumber draft genome, consensus QTL across multiple studies were established, which provided insights into inheritance correlations among different traits. To facilitate their use in molecular breeding, information on markers tagging the target genes/QTL, and polymorphism within cloned causal genes was included for the target traits. In order to establish consistency and reduce confusion in QTL naming, we worked with public and private cucumber researchers to develop a standard vocabulary for quantitative traits, and recommended naming rules for future cucumber QTL mapping studies. This is the first attempt to systematically summarize, analyze and inventory cucumber mutants, cloned or mapped genes and QTL, which should be a valuable resource for the cucurbit research community.