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Title: Frequency and distribution of single nucleotide polymorphisms detected in an ovary EST database of citrus sinenis and poncirus trifoliata

item Chaparro, Jose
item Bausher, Michael
item Dang, Phat
item Hunter, Wayne
item Niedz, Randall
item Shatters, Robert - Bob

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/29/2003
Publication Date: N/A
Citation: N/A

Interpretive Summary: A citrus cDNA sequence database was mined for the presence of sequence variants. The sequences of seven genes were compared between sweet orange and trifoliate orange. A high level of variation corresponding to one change every 142 bases was found in sweet orange. Variation in trifoliate orange was approximately 3 fold lower. The average frequency of these sequence variants is 7.7 x 10-3 and 2.5 x 10-3 for sweet orange and trifoliate orange respectively. Insertion and or deletion events in the sequence were rare for both species and were approximately 10 fold lower than that of nucleotide substitutions. The validity of the procedure used was confirmed by analyzing small regions of the chalcone synthase and s-adenosylmethionine synthase genes. All the putative SNPs were confirmed and additional variants were detected in the intron sequence of chalcone synthase. The results indicate that sufficient sequence variation exists in sweet orange to easily allow the development of markers based on gene sequence variants. However, this would be more difficult in trifoliate orange due to the lower variation detected.

Technical Abstract: Using an EST sequence database generated from ovaries of sweet orange and trifoliate orange we have examined the nucleotide sequence of seven genes from the two species. Single nucleotide polymorphisms (SNPs) were found at a rate corresponding to 1 every 142 bases in sweet orange and 1 every 400 bases in trifoliate orange. These values corresponded to nucleotide diversity values of 7.7 x 10-3 and 2.5 x 10-3 for sweet orange and trifoliate orange, respectively. Insertions and deletions were found primarily in the 5' and 3' non-coding regions of the cDNA and were approximately an order of magnitude less frequent than SNPs. Small regions of the containing putative SNPs in chalcone synthase and s-adenosylmethionine synthase were analyzed. The diploid sequence data confirmed the SNPs detected in the EST database and indicated the presence of additional SNPs in an intron sequence of chalcone synthase. The results indicate that sufficient sequence polymorphism exists within sweet orange to allow the development of SNP based markers for genome mapping. However, the level of polymorphism is much lower in trifoliate orange and development of a trifoliate orange genome map would be greatly expedited by the use of an interspecific hybrid population.