Development of crop-specific transposable element (SINE) markers for studying gene flow from oilseed rape to wild radish

• Published in: Theoretical and applied genetics Vol. 111; no. 3; pp. 446 - 455
• Main Authors: Prieto, J.L, Pouilly, N, Jenczewski, E, Deragon, J.M, Chevre, A.M
• Format: Journal Article
• Language: English
• Published: Heidelberg Springer 01.08.2005; Berlin Springer Nature B.V; Springer Verlag
• Subjects: Biological and medical sciences; Brassica napus; Brassica napus - drug effects; Brassica napus - genetics; chromosome mapping; Classical genetics, quantitative genetics, hybrids; DNA Transposable Elements - genetics; Fundamental and applied biological sciences. Psychology; gene flow; Genes, Plant; Genetic Markers; genetic polymorphism; Genetics; Genetics of eukaryotes. Biological and molecular evolution; Genetics, Population; Genic rearrangement. Recombination. Transposable element; Genomics; intergeneric hybridization; introgression; Life Sciences; linkage groups; Molecular and cellular biology; Molecular genetics; polymerase chain reaction; Population Dynamics; Pteridophyta, spermatophyta; rapeseed; Raphanus - genetics; Raphanus raphanistrum; sequence specific amplified polymorphism; Short Interspersed Nucleotide Elements - genetics; short-interspersed element; transposons; Vegetals; wild plants; wild relatives; Gene flow; Brassica napus var. oleifera; Cruciferae; Dicotyledones; Angiospermae; Development; Genetics; Spermatophyta; Agriculture; Transposable element; Raphanus raphanistrum
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-005-2017-5

The screening of wild populations for evidence of gene flow from a crop to a wild related species requires the unambiguous detection of crop genes within the genome of the wild species, taking into account the intraspecific variability of each species. If the crop and wild relatives share a common ancestor, as is the case for the Brassica crops and their wild relatives (subtribe Brassiceae), the species-specific markers needed to make this unambiguous detection are difficult to identify. In the model oilseed rape (Brassica napus, AACC, 2n=38)-wild radish (Raphanus raphanistrum, RrRr, 2n=18) system, we utilized the presence or absence of a short-interspersed element (SINE) at a given locus to develop oilseed rape-specific markers, as SINE insertions are irreversible. By means of sequence-specific amplified polymorphism (SINE-SSAP) reactions, we identified and cloned 67 bands specific to the oilseed rape genome and absent from that of wild radish. Forty-seven PCR-specific markers were developed from three combinations of primers anchored either in (1) the 5'- and 3'-genomic sequences flanking the SINE, (2) the 5'-flanking and SINE internal sequences or (3) the SINE internal and flanking 3'-sequences. Seventeen markers were monomorphic whatever the oilseed rape varieties tested, whereas 30 revealed polymorphism and behaved either as dominant (17) or co-dominant (13) markers. Polymorphic markers were mapped on 19 genomic regions assigned to ten linkage groups. The markers developed will be efficient tools to trace the occurrence and frequency of introgressions of oilseed rape genomic region within wild radish populations.