Abstract
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.
Highlights
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]
The number of putatively unique simple sequence repeat (SSR) was reduced to 13,157, from which 1,940 with the longest repeat motifs were selected for polymorphism screening between recombinant inbred lines (RILs) mapping population parental lines (Gy 14 and PI 183967)
We described the development of highly polymorphic SSR markers using whole genome shotgun sequences leading to the construction of the first high-density genetic map in cucumber
Summary
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 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. This lack of genomic information seriously hampers genome assembly and genetic analysis in cucurbits
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