ESTs as a source for sequence polymorphism discovery in sugarcane: example of the Adh genes.
Expressed sequence tags (ESTs) have proven to be a valuable tool to discover single nucleotide polymorphism (SNP) in human genes but their use for this purpose is still limited in higher plants. Using a database of approximately 250,000 sugarcane ESTs we have recovered 219 sequences encoding alcohol dehydrogenases ( Adh), which tagged 178 distinct cDNAs from 27 libraries, constructed from at least four different cultivars. The partitioning of these ESTs into paralogous genes revealed three Adh genes expressed in sugarcane, one Adh2 and two Adh1. The soundness of the partition was carefully checked by comparison to external data, especially from the closely related sorghum. Analysis of polymorphism in the alignments of EST sequences revealed a total of 37 highly reliable SNPs in the coding and untranslated regions of the three Adh genes. In the coding regions, the mean occurrence of SNPs was one for every 122 base pair. A total of eight insertion-deletions was observed, their occurrence being limited to untranslated regions. These results show that EST data constitute an invaluable source of sequence polymorphism for sugarcane that is worth carefully collecting for the future development of new marker tools.
Grivet
L
L
Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, PO Box 6010, 13083-970 Campinas, SP, Brazil. laurent@unicamp.br
Glaszmann
J-C
JC
Vincentz
M
M
da Silva
F
F
Arruda
P
P
D000426:Alcohol Dehydrogenase / Q000235:genetics*; D001483:Base Sequence; D018076:DNA, Complementary / Q000235:genetics; D020224:Expressed Sequence Tags; D017343:Genes, Plant / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D031786:Saccharum / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
D018076:DNA, Complementary; D000426:Alcohol Dehydrogenase