Submitted to: Genetics and Molecular Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/9/2003
Publication Date: 11/15/2003
Citation: Santos, C.A., Simon, P.W. 2003. Sequencing of specific AFLP amplicons reveals highly conserved DNA sequences mapping to the same linkage groups in two unrelated F2 populations of carrot. Genetics and Molecular Biology. 25:195-201. Interpretive Summary: Most carrot genetic maps which have been developed used a complex laboratory method called Amplified fragment length polymorphism (AFLP). AFLPs from different maps were compared at the DNA sequence in this study to find out how similar they are. In 26 out of 31 AFLPs compared in this study the DNA sequence was over 90% identical, indicating that these maps were very similar. This information is important for carrot researchers to better understand similarities among different carrot genetic studies.
Technical Abstract: Amplified fragment length polymorphism (AFLP) is a fast and reliable tool to generate a large number of DNA markers. In two unrelated F2 populations of carrot (Daucus carota L.), Brasilia x HCM and B493 x QAL (wild carrot), it was hypothesized that DNA 1) digested with the same restriction endonuclease enzymes and amplified with the same primer combination and 2) sharing the same position in polyacrylamide gels should be conserved sequences. To test this hypothesis AFLP fragments from polyacrylamide gels were eluted, reamplified, separated in agarose gels, purified, cloned and sequenced. Among thirty-one paired fragments from each F2 population, twenty-six had identity greater than 91% and five presented identity of 24% to 44%. Among the twenty-six conserved AFLPs only one mapped to different linkage groups in the two populations while four of the five less-conserved bands mapped to different linkage groups. Of nine SCAR (sequence characterized amplified regions) primers tested, one conserved AFLP resulted in co-dominant markers in both populations. Screening among 14 carrot inbreds or cultivars with three AFLP-SCAR primers revealed clear and polymorphic PCR products, with similar molecular sizes on agarose gels. The development of co-dominant markers based on conserved AFLP fragments will be useful to detect seed mixtures among hybrids, to improve and to merge linkage maps and to study diversity and phylogenetic relationships.