Quantitative Trait Loci for Horticulturally Important Traits Defining the Sikkim Cucumber, Cucumis sativus var. sikkimensis

Authors: WANG, YUHUL - University Of Wisconsin; JIHANG, BIAO - University Of Wisconsin; DYMERSKI, RONALD - University Of Wisconsin; XU, XUEWEN - University Of Wisconsin; Weng, Yiqun

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/18/2020
Publication Date: 9/30/2020
Citation: Wang, Y., Jihang, B., Dymerski, R., Xu, X., Weng, Y. 2020. Quantitative Trait Loci for Horticulturally Important Traits Defining the Sikkim Cucumber, Cucumis sativus var. sikkimensis. Theoretical and Applied Genetics. (2021) 134:229–247. https://doi.org/10.1007/s00122-020-03693-y.
DOI: https://doi.org/10.1007/s00122-020-03693-y

Interpretive Summary: The Sikkim cucumber is featured with some morphological traits like black spine, brown fruit with fine and heavy netting, as well as large hollow in mature fruit. Despite of its establishment as a botanical variety ~150 years ago, and its wide use as an important source of disease resistances in cucumber breeding, little is known about its taxonomic status and genetic basis of those characteristic traits. In this study, we investigated the genetic basis of horticulturally important traits by QTL mapping with segregating populations derived from two Sikkim-type inbred lines, WI7088D and WI7120. We identified 48 QTL underlying phenotypic variation for 18 traits. We found that the fruit spine and skin colors in the two populations were controlled by the previously cloned gene B (for black spine). The fruit netting in WI7088D and WI7120 was controlled by the well-known H (for heavy netting) on chromosome 5 and a new gene Rs (for Russet skin) on chromosome 1, respectively. One large effect QTL was detected for flowering time in each population. Fifteen, 6 and 5 QTL were identified for fruit size, hollow size, and flesh thickness variation in the two populations, respectively. No major structural changes were found between the Sikkim and cultivated cucumbers. In addition, there were no unique genes or QTL identified from this study. We concluded that the Sikkim cucumber should be treated as an ecotype of cultivated cucumber that is not worthy of formal taxonomic recognition.

Technical Abstract: The Sikkim cucumber, Cucumis sativus var. sikkimensis is featured with some morphological traits like black spine, brown fruit with fine and heavy netting, as well as large hollow in mature fruit. Despite of its establishment as a botanical variety ~150 years ago, and its wide use as an important source of disease resistances in cucumber breeding, little is known about its taxonomic status and genetic basis of those characteristic traits. Here we reported QTL mapping with segregating populations derived from two Sikkim-type inbred lines, WI7088D and WI7120, and identification of 48 QTL underlying phenotypic variation for 18 horticulturally important traits. We found that the fruit spine and skin colors in the two populations were controlled by the previously cloned pleiotropic B (black spine) locus. The fruit netting in WI7088D and WI7120 was controlled by the well-known H (heavy netting) and a novel Rs (Russet skin) locus, which was delimited to a 271-kb region on Chr5, and ~736-kb region on Chr1, respectively. A single major-effect QTL was detected for flowering time in each population (ft1.1 for WI7088D and ft6.2 for WI7120). Fifteen, 6 and 5 QTL were identified for fruit size, hollow size, and flesh thickness variation in the two populations, respectively. No major structural changes were found between the Sikkim and cultivated cucumbers. Except for the rare allele at the Rs locus, there seem no private QTL/alleles identified from this study supporting the Sikkim cucumber as an ecotype of C. sativus, not worthy of formal taxonomic recognition.