Molecularly Tagged Genes and Quantitative Trait Loci in Cucumber

Since the release of the cucumber draft genomes, significant progress has been made in molecular mapping or cloning of economically important genes and quantitative trait loci (QTLs) in cucumber, which provides the foundation for marker-assisted selection in cucumber breeding. In this paper, I summarized molecularly tagged genes and QTLs for simply inherited traits (total 21), host resistances against the downy mildew, Fusarium wilt, gummy stem blight, powdery mildew, target leaf spot, CYSDV, and ZYMV (54 genes/QTLs), growth and development-related traits (128 genes/QTLs) such as leaf size, shape, color, hypocotyl length, plant architecture (lateral branch number, height, compact, internode length, trichomes, growth habit), traits related with flowers (flowering time and node positions, pistillate flower numbers, sex determination) and fruits (size, shape, number, weight, skin color, flesh color, spine color/ density/number, bitterness), as well as seed-related traits (number, size and weight). The 203 genes/QTLs were placed on a scaffold-based cucumber physical map using the Gy14 draft genome assembly as the reference. These molecularly mapped genes and QTLs were located mainly in chromosomes 1, 5, and 6 with only 4 in Chromosome 7. Compared with field crops, available mutants and characterized genes in cucumber are very limited, but molecular mapping and cloning of more cucumber genes and QTLs is expected in the near future which will greatly facilitate marker-assisted cucumber breeding. 2013). For other types of markers, their physical locations in the Gy14 draft genome scaffolds were inferred with BLASTn sequence alignment or in silico PCR according to Cavagnaro et al. (2010). A Gy14-scaffold based physical map was drawn with the MapChart program (V2.2) (www.wageningenur.nl/en/show/ Mapchart.htm) using their locations in the Gy14 assembly (Version 1.0) as reference. Due to page limit, only references directly reporting molecular markers associated with target traits were cited; literature identifying RAPD or AFLP markers that could not be aligned with the Gy14 or 9930 genome scaffold assemblies was not included. The various factors (marker types, population sizes, genetic backgrounds etc.) may affect the accuracy of the marker locations on a genetic map; therefore, the inferred scaffold locations for the genes or QTLs were, in many cases, only approximations. Results and Discussion Simply inherited genes. Molecular mapping and cloning of 21 simply inherited cucumber genes have been reported (Table 1). Consistent with classic genetic analysis, the F and de genes are linked, and several genes controlling epidermal features D, Fr, H, Tu, u and ss form a cluster in chromosome 5 (Fig. 1). Among the 21 genes, the two sex determining genes m (1-aminocyclopropane1-carboxylic acid synthase-2, ACS2) (Boualem et al, 2009; Li et al, 2009) and F (ACS1g) (Trebitsh et al, 1997) and the tuberculate fruit gene Tu (C2H2 zinc finger transcription factor) (Yang et al, 2014) have been cloned. A β-carotene hydroxylase gene is believed to be a candidate for the orange flesh color locus or (Qi, 2013), and an R2R3-tye MYB transcription factor co-localizes with the Cucumber, Cucumis sativus L. (2n =2x =14) is a diploid species with relatively small genome size (367 Mb), short life cycle (2-3 months from seed to seed) and no inbreeding depression, making it an advantageous crop in genetic and genomics studies. With the release of the cucumber draft genome assemblies and rapid development of cucumber genomics infrastructure such as molecular markers and high density genetic maps (e.g., Huang et al, 2009; Qi et al, 2013; Yang et al, 2012, 2013), significant progress has been made in molecular mapping, gene cloning and QTL mapping for horticulturally important traits in this specialty crop. Among the approximately 145 genes documented in the 2010 cucumber gene list (Call and Wehner, 2011), many have been tagged with molecular markers. Some traits, especially resistances to the downy mildew or powdery mildew pathogens were investigated in multiple QTL mapping studies. On the other hand, many newly mapped genes/QTLs were not listed in the 2010 cucumber gene catalogue. In this paper, recent literature was reviewed, and the cucumber gene list was updated including their physical locations in the cucumber genome. This work could serve as the start point for more systematic characterization and documentation of cucumber genes. Materials and Methods The literature on molecular tagging, gene cloning or QTL mapping in cucumber was reviewed. For most microsatellite markers that are linked with target genes or QTLs, their physical locations in the 9930 or Gy14 cucumber draft genome assemblies are known (Huang et al, 2009; Qi et al, 2013; Yang et al, 2012, *Corresponding author; phone: 608-262-0028; email:[email protected].