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Identification and characterization of a genomic region from sugarcane using a QTL for Brix in sorghum

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Luís Paulo dos Santos
Total Authors: 1
Document type: Master's Dissertation
Press: Campinas, SP.
Institution: Universidade Estadual de Campinas (UNICAMP). Instituto de Biologia
Defense date:
Examining board members:
Anete Pereira de Souza; Mirian Perez Maluf; Américo José Carvalho Viana
Advisor: Anete Pereira de Souza

The search for new varieties of sugarcane that present important agronomic characteristics and high sugar content has instigated researchers over the world. Due to the great prestige of culture in the world scenario, fact attributed to its main derivatives of economic importance: sugar and ethanol. The cultivars are interspecific hybrids between "Saccharum officinarum" and "Saccharum spontaneum", resulting in a genome of high genetic complexity, aneuploid and with high ploidy. The sinteny of sugarcane-sorghum is a tool that allows the retrieval of genomic information from sugarcane, using sorghum that is an ancestor with a simpler genome, sequenced and annotated. Therefore, the objective of this work was to study a genomic region of sugarcane with possible influence for Brix trait using a QTL mapped on sorghum. First, a QTL for Brix mapped on chromosome 02 in sorghum (SBI-02) was chosen and all genes present in that region were recovered. The metabolic function of the genes present in this QTL was analyzed to verify possible relationships with genes involved directly or indirectly in sugar production. Comparing sorghum genes from this region with sugarcane transcripts, it was possible to develop 20 pairs of specific primers for sugarcane. The BAC library of the variety IACSP93-3046 was used to recover the corresponding region in the sugarcane genome. It was possible to screen 101.376 clones from the BAC library and obtain 37 clones to recover the region in sugarcane. Twenty two BAC clones were sequenced and annotated. The BACs were compared to the original sorghum region, to the BACs of the R570 variety and to the S. spontaneum genome. A transcriptome of four organs (root, leaf, internode 3 and internode 8) plus meristem was used to observe gene expression. Five genes from the target region were identified in metabolic pathways, including the pathway of starch metabolism and sucrose that may be related to sugar synthesis. Despite the high sinteny observed between sugarcane and sorghum for this region, there were two collinearity breaks, due to inversions of the genes. There are seven sorghum genes that were not found in the genomic region of the sugarcane varieties IACSP93-3046 and R570. Structural differences were observed, such as the presence of duplicated genes only in sorghum or sugarcane or among sugarcane varieties. The observed relationships between genes present in metabolic pathways, tissue specific expression and genes with known functions resulted in four genes candidates for synthesis and accumulation of sugar: orthologous genes to an alpha amylase, a carbonic anhydrase, an uncharacterized protein and a DNAJ. These results are fundamental for the understanding of a complex genomic region in sugarcane, probably related to sugar synthesis (AU)

FAPESP's process: 17/18225-0 - Identification and characterization of a genomic region from sugarcane using QTL for Brix in sorghum
Grantee:Luís Paulo dos Santos
Support type: Scholarships in Brazil - Master