An Integrated Genetic and Cytogenetic Map of the Cucumber Genome

Citation: Ren Y, Zhang Z, Liu J, Staub JE, Han Y, et al. ( An Integrated Genetic and Cytogenetic Map of the Cucumber Genome Yi Ren 0 Zhonghua Zhang 0 Jinhua Liu 0 Jack E. Staub 0 Yonghua Han 0 Zhouchao Cheng 0 Xuefeng Li 0 Jingyuan Lu 0 Han Miao 0 Houxiang Kang 0 Bingyan Xie 0 Xingfang Gu 0 Xiaowu Wang 0 Yongchen Du 0 Weiwei Jin 0 Sanwen Huang 0 Par K. Ingvarsson, University of Umea, Sweden 0 1 Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Sino-Dutch Joint Lab of Horticultural Genomics, Opening Lab of Genetic Improvement of Agricultural Crops of Ministry of Agriculture , Beijing , China , 2 National Maize Improvement Center of China, Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University , Beijing, China, 3 USDA, ARS , Vegetable Crops Research Unit, Department of Horticulture, University of Wisconsin , Madison, Wisconsin , United States of America The Cucurbitaceae includes important crops such as cucumber, melon, watermelon, squash and pumpkin. However, few genetic and genomic resources are available for plant improvement. Some cucurbit species such as cucumber have a narrow genetic base, which impedes construction of saturated molecular linkage maps. We report herein the development of highly polymorphic simple sequence repeat (SSR) markers originated from whole genome shotgun sequencing and the subsequent construction of a high-density genetic linkage map. This map includes 995 SSRs in seven linkage groups which spans in total 573 cM, and defines ,680 recombination breakpoints with an average of 0.58 cM between two markers. These linkage groups were then assigned to seven corresponding chromosomes using fluorescent in situ hybridization (FISH). FISH assays also revealed a chromosomal inversion between Cucumis subspecies [C. sativus var. sativus L. and var. hardwickii (R.) Alef], which resulted in marker clustering on the genetic map. A quarter of the mapped markers showed relatively high polymorphism levels among 11 inbred lines of cucumber. Among the 995 markers, 49%, 26% and 22% were conserved in melon, watermelon and pumpkin, respectively. This map will facilitate whole genome sequencing, positional cloning, and molecular breeding in cucumber, and enable the integration of knowledge of gene and trait in cucurbits. - Funding: The research was supported by Chinese Mininstry of Agriculture (948 Program: 2008-Z42), Ministry of Science and Technology (2006DFA32140), and National Natural Science Foundation (30871707) to S. Huang and by the Program for New Century Excellent Talents in University (NCET-07-0811) to W. Jin. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. . These authors contributed equally to this work. The Cucurbitaceae family comprises about 120 genera and 800 species, including many economically important vegetable and fruit crops such as cucumber (Cucumis sativus L.), melon (C. melo L.), watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai), squash and pumpkin (Cucurbita spp.) [1]. Cucurbits are mostly prostrate or climbing herbaceous annuals that have coiled tendrils and they are characterized by having unisexual flowers and inferior ovaries. Although cucurbits vary in chromosome numbers, their genome sizes have not changed as significantly as in some other botanical families like Brassicaceae and Poaceae (e.g., cucumber: 2n = 2x = 14, 367 Mb; melon: 2n = 2x = 24, 480 Mb; watermelon: 2n = 2x = 22, 430 Mb, and squash and pumpkin: 2n = 2x = 40, 539 Mb) [2]. It seems that chromosome numbers of cucurbits correlate directly with their genome sizes. Differences in cucurbit genome size might be attributable to the structure and position of centromeres and telomeres, and the other repeat-related genomic elements. Genomic resources for cucurbits are scarce, and high density genetic linkage maps have not been reported for cucurbit species. This lack of genomic information seriously hampers genome assembly and genetic analysis in cucurbits. In the genus of Cucumis, cucumber is the only species with a haploid chromosome number of seven (for other Cucumis species, basic number = 12). It is cross-incompatible with other Cucumis species and consequently, cucumber has a narrow genetic basis within domesticated market types [3]. India was thought to be the center of origin and domestication of this species where two botanical varieties C. s. var sativus L. (cultivated) and the feral form C. s. var hardwickii (R.) Alef coexist. Unsaturated cucumber linkage maps have been developed using morphological traits, isozymes, and molecular markers, where markers (,300 loci) were often positioned in more than seven linkage groups [48]. Cytogenetic maps have also been constructed in cucumber using C-banding and fluorescence in situ hybridization (FISH) [911], allowing identification of seven morphologically distinct chromosomes. However, none of the maps ware integrated with cytogenetic map. Marker-trait associations have been effective in achieving selection gain for yield components during marker-assisted backcrossing [12,13], but marker-assisted selection (MAS) of quantitative trait loci seems to be unpredictable due to lack of a high-resolution genetic map [14]. The availability of high-density maps in cucumber would facilitate whole genome sequencing and positional cloning, enhance MAS, and provide opportunities to investigate synteny among cucurbit species (e.g., cucumber and melon). SSRs (simple sequence repeats) or microsatellites are tandem repeats of short DNA sequences ranging in length from one to six base pair (bp), which are abundant and ubiquitous in all eukaryotic genomes [15,16]. Because of their high level of polymorphism, ubiquity, and co-dominance, SSRs have become a valuable source of molecular markers in genetic analysis [17]. Only a limited number of SSR markers, however, have been developed for cucumber through exploiting EST sequences and screening genomic libraries [5,18,19], which has hampered use of molecular markers in genetic analysis and MAS in cucurbits. We present herein the development of a saturated SSR-based cucumber linkage map employing 36 Sanger shotgun sequences. We used FISH to assign linkage groups to a cytogenetic map and to define chromosomal rearrangements between C. sativus var. sativus and var. hardwickii. The integrated genetic-cytogenetic map described herein provides a platform for genetic and genomic analysis that does not currently exist in cucurbits. Materials and Methods Plant and DNA materials Two mapping populations were used for linkage mapping in this study. The first one consisted of 77 F6-F8 recombinant inbred lines (RILs) derived from the inter-subspecific cross between Gy14 and PI 183967 [6]. Gy14 is a (...truncated)