Large-scale Analysis Of SSR And PIP Markers And Development Of Genetics And Breeding Database In Nicotiana

Tobacco (Nicotiana tabacum L.) is a member of the agriculturally important Solanaceaeplant and is grown as a commercial crop in many different countries. Meanwhile, it was alsoone of the earliest model plant applied in the area of molecular biology and gene engineering.Based on the available sequence data of the tobacco genome and expressed sequence tags(EST), a large scale of simple sequence repeat (SSR) markers and potential intronpolymorphism (PIP) markers had been developed. Aiming at promoting the genetic andbreeding research of tobacco, this study built up a special database for tobacco genetic andbreeding firstly, which was based on the germplasm being collected and stored in TobaccoLab of Shandong Agricultural University, the current genome and EST sequences accessingform the public database, the genetic map, the genetically modified information, and also thedatabase was integrated with the molecular markers above-mentioned. The mainly resultswere as follows:1. A total of66297pairs of Genomic-SSR markers was developed based on the genomesequences of Nicotiaca tabacum, and a total of10551pairs of EST-SSR markers basedon the4types of tobacco EST sequences, and a number of12388pairs of PIP markersbased on the model plant Arabidopsis genome sequence and4types of tobacco ESTsequences.2. A testing of those markers above-mentioned was conducted through e-PCR, and theresults showed that all the primers could obtain the products, and reached to100%ofthe markers. The average of the allelic loci was2.3,1.2, and2.0, separately for theGenomic-SSR, ESR-SSR, and PIP markers.3. The Tobacco Lab paid more attention to the germplasm studies. Based on widelycollecting and properly kept, there had1472accessions with detailed information atpresent, which were classified by the different types and with the BotanicalClassification, plants character, Physiological and biochemical data, tasting character,and resistance information.4. The Tobacco Genetics and Breeding database was firstly set up based on the germplasm, gene sequences, molecular markers, genetic map, and genetically modification. Basingon the LAMP (Linux+Apache+MySQL+PHP) systems, the database contained threeparts: the material database (germplasm and sequences), molecular markers database(Genomic-SSR, EST-SSR, PIP), and the application database (genetic map andgenetically modified).5. TGB was an interactive platform of academic exchanges in the area of tobacco geneticand breeding, and provided the following functions:1) inquiry the germplasm,Genomic-SSR, EST-SSR, and PIP markers;2) develop and download SSR and PIPmarkers online;3) download the tobacco genome and EST sequences;4) the geneticmap based on SSR markers with detailed information; and5) the Perl programs fordeveloping SSR and PIP markers.