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| Author(s): |
Mariane de Mendonça Vilela
Total Authors: 1
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| Document type: | Doctoral Thesis |
| Press: | Campinas, SP. |
| Institution: | Universidade Estadual de Campinas (UNICAMP). Instituto de Biologia |
| Defense date: | 2015-08-28 |
| Examining board members: |
Michel Georges Albert Vincentz;
Diego Mauricio Riaño Pachón;
Antonio Augusto Franco Garcia;
Gabriel Rodrigues Alves Margarido;
Prianda Rios Laborda
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| Advisor: | Marie Anne Van Sluys; Michel Georges Albert Vincentz |
| Abstract | |
Sugarcane is a grass with global economic importance, responsible for about 80% of the world's sugar production. In addition, it is an important source of renewable energy, which has attracted attention and investments aiming to better understand its genetic and provide subsidies to increase the efficiency of breeding programs. Sugarcane has one of the most complex known plant genomes. Sugarcane cultivars (cv.), such as cv. R570, exhibit two distinct chromosomal organizations, being about 80% originated from 'Saccharum officinarum' (2n = 8x = 80) and 15-25% from 'Saccharum spontaneum' (2n = 5x to 16x = 40 to 128), including a certain degree of aneuploidy. The ancestor genomes are considered as autopolyploids and meiosis is considered bivalent with a polysomic inheritance. However, the processes that shaped the genus 'Saccharum' genomes and how these genomes are evolving and diverging are issues that still need to be better defined. Besides, the regulation of gene expression in this highly redundant genomic context is still poorly understood. For this reason, the present work, which fits in an effort to sequence sugarcane monoploid genome, aimed to analyze three genomic regions of cv. R570 containing probably single-copy genes in sugarcane, the genes LFY ('Leafy'), PHYC ('Phytochrome C') and TOR ('Target of Rapamycin'). Twenty-seven BACs (Bacterial Artificial Chromosome), ten of 'LFY', seven of 'PHYC' and ten of 'TOR', were sequenced, assembled, annotated and compared between themselves and with their sorghum and rice orthologous regions, resulting in seven distinct haplotypes (possible homo/homeologous versions) for 'LFY', four for 'PHYC' and seven for 'TOR'. The haplotypes (possibly alleles) expression for the three genes was evaluated and, with some syntenic transposable elements, the haplotypes were submitted to evolutionary analysis. As expected, the genomic regions of sugarcane have a high degree of conservation with sorghum and rice, regarding gene content and organization. However, sugarcane BACs carry from four to 15 transposable elements each, while, for the other species, only one element was identified in the PHYC genomic region of sorghum, evidence of an expansion of transposable elements in the sugarcane genome. The data also suggests that all the haplotypes are functional, once they are all under purifying selection (dN/dS < 1), however they do not participate equivalently to the gene expression. For TOR haplotypes it was possible to identify two phylogenetic groups, which diverged between 2,5 to 3,5 million years ago probably representing 'S. officinarum' and 'S. spontaneum'. The analysis also revealed that at least one genome duplication event occurred in the lineage that gave rise to 'S. officinarum', after its divergence from 'S. spontaneum'. These results bring advance in knowledge about the evolutionary history of the genus 'Saccharum' and how modern sugarcane cultivars organize their genome and regulate the expression of so many homo/homeologous haplotypes (AU) | |
| FAPESP's process: | 10/02610-2 - Allelic variation in sugarcane: quantification of sequence polymorphism |
| Grantee: | Mariane de Mendonça Vilela |
| Support Opportunities: | Scholarships in Brazil - Doctorate (Direct) |