Full text
| |
| Author(s): |
Danilo Augusto Sforça
Total Authors: 1
|
| Document type: | Doctoral Thesis |
| Press: | Campinas, SP. |
| Institution: | Universidade Estadual de Campinas (UNICAMP). Instituto de Biologia |
| Defense date: | 2019-02-05 |
| Examining board members: |
Anete Pereira de Souza;
Gabriel Rodrigues Alves Margarido;
Maria Lucia Carneiro Vieira;
Américo José Carvalho Viana;
Rodrigo Gazaffi
|
| Advisor: | Anete Pereira de Souza |
| Abstract | |
Sugarcane is mainly used in the production of sugar and ethanol. The contemporaneous cultivars originate from a series of natural and artificial hybridizations and backcrossing. The process of domestication and breeding resulted in a complex genome with high levels of ploidy, aneuploidy and approximately 10Gb genome. In addition, Sorghum has high sintenia with sugarcane and it is the closest ancestor with genome completely sequenced and annotated. The aim of this thesis was to study the genetic architecture, genomic and gene expression of a region in sugarcane, as well as generate molecular tools involving sugarcane genome. Single copy genes were searched in rice, maize and sorghum transcripts and the result compared to expressed sequences of sugarcane. Thirteen candidates¿ genes were found, which the HP600 gene (in sorghum Sobic.003G221600) was in silgle copy and also located in a QTL in sorghum for Brix. A BAC library was constructed for the sugarcane SP80-3280 variety and another for IACSP93-3046 with the objective of accessing the sugarcane genome. Two methods of clone selection were developed: macroarrays (developed for both libraries) and orderly clone mixing (Pool3D - developed for half of the SP80-3280 library). The BAC libraries construction of the varieties SP80-3280 and IACSP93-3046 resulted in 221,184 and 165,888 clones, both with an average size of 110 kb, representing approximately 2.4 x and 1.8 x the sugarcane genome, respectively. The thirteen genes were used to select BACs from both libraries using macroarrays and the Pool3D selection of the SP80-3280 library. The BACs of the SP80-3280 library resulting from the two selections for the HP600 gene were used to study the genomic architecture and transcripts of the gene to study the genic expression in sugarcane. The gene of Centromeric Protein C (CENP-C) was found side-by-side the HP600 gene in sugarcane and sorghum, and both were used to exemplify allelic expression and genomic and genetic behavior. The HP600 and CENP-C genes were found in two homeologue chromosomic groups. The first group (Region01), with ploidy eight, represents the synthenic region of Sorghum bicolor, with all the haplotypes of the two genes expressed, but the HP600 haplotypes exhibited differential expression. The second group of homoelogues (Region02), with ploidy ten, is a region formed from different non-collinear genes with sorghum containing duplications of the HP600 and CENP-C genes (paralogues). This duplication occurred after sorghum and sugarcane separation, resulting in an HP600 pseudogene and a fused and recombined version of CENP-C with a third gene (ortholog of Sobic.003G299500), with at least two expressed chimeric haplotypes. The genetic map evidenced that markers in duplicate regions are mapped in linkage groups with bias in the genetic distance, affecting the genetic mapping. This thesis presents the complexity involved in genetics, genomics and gene expression of sugarcane and in genomic and allelic dynamics, which may be useful for understanding other polyploid genomes (AU) | |