Research article
Sugarcane genes associated with sucrose content
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* Corresponding author: Glaucia M Souza glmsouza@iq.usp.br
1 Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
2 BIOINFO-USP Núcleo de Pesquisas em Bioinformática, Universidade de São Paulo, São Paulo, SP, Brazil
3 Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
4 Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
5 Centro de Tecnologia Canavieira, Piracicaba, São Paulo, SP, Brazil
6 Monsanto do Brasil Ltda, São Paulo, SP, Brazil
BMC Genomics 2009, 10:120 doi:10.1186/1471-2164-10-120
Published: 21 March 2009Additional files
Additional file 1:
Brix degree and sugar content of populations. Brix degree, sucrose, glucose and fructose were determined from 10-month old plants of Population 1 and 11-month old plants of Population 2. The measurements were made from juice extracted from the 9th internode. Brix measurements of these populations have been previously described [33]
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Additional file 2:
SAS showing differential expression when high and low Brix plants were compared or when mature and immature internodes were compared using cDNA microarrays. The table also shows differential expression of the same SAS as seen in [31] for plants submitted to drought and ABA treatment. The table lists a SAS whose expression was enriched or decreased as determined by the Outliers Search Method in two technical replicates for each biological sample. The expression ratio for each technical replicate is in brackets.
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Additional file 3:
P value of qRT-PCR. Genes associated with sucrose content, drought, ABA and sugars were validated by qRT-PCR. The tables indicate all the genes evaluated and the values of P for differential expression.
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Additional file 4:
Sugarcane and Arabidopsis orthologues similarly regulated by sucrose and glucose. Orthologies between Sugarcane and Arabidopsis were assigned using the Neighbor-Joining method [94]. The Arabidopsis orthologues were compared with the set of Arabidopsis genes regulated by glucose [30] and/or sucrose [34].
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Additional file 5:
Inferred phylogenetic relationships among tblastx hits using the sugarcane SAS as queries. The amino acid alignments were performed with ClustalX. The distances were obtained by p-distance and topography inferred with Neighbor-Joining (NJ) using only the aligned blocks (complete deletion). Analysis were conducted in MEGA4. The continuous blocks show regulation by sucrose and the pointed blocks show regulation by glucose (in both cases red for induction and green for repression). A – SCRFLR2037F09.g (Calreticulin 2); B – SCEQRT1024E12.g (Phenylalanine ammonia-lyase); C – SCCCRZ1001G10.g (IAA16); D – SCACLR2007G02.g and SCRFLR1034G06.g (canePKABA1-1 and canePKABA1-3); E – SCQGLR1085F11.g (Dehydrin). The sequences names correspond to those present in the protein data sets showed in Material & Methods: AT – Arabidopsis thaliana; Gm – Glycine max (soybean); jgi|Poptr1 – Populus trichocarpa; LOC Os – Oryza sativa (rice); Sb – Sorghum bicolor (sorghum); jgi|Selmo1 – Selaginella moellendorffii; jgi|Phypa1_1 – Physcomitrella patens patens; jgi|MicpuC2 – Micromonas pusilla CCMP1545, jgi|MicpuN2 – Micromonas strain RCC299; jgi|Volca1 – Volvox carteri; jgi|Chlre3 – Chlamydomonas reinhardtii.
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