Dissecting expression patterns in the transcriptome of immature sugarcane culms: from methodology to biology

• Autor(a) principal: Pessoa, Victor Hugo de Mello
• Data de Publicação: 2020
• Tipo de documento: Dissertação
• Idioma: eng
• Título da fonte: Biblioteca Digital de Teses e Dissertações da USP
• Texto Completo: https://www.teses.usp.br/teses/disponiveis/11/11137/tde-24112020-162117/
• topic: Saccharum; Saccharum; Biological replicates; Carbon partitioning; Differential expression; Expressão diferencial; Partição de carbono; Réplicas biológicas; RNA-Seq; RNA-Seq

The sugarcane genome is, by all accounts, the most complex among the cultivated crops due to its high ploidy, heterozygosity and history of hybridization events. Despite substantial efforts in the past years to obtain three genomic references by different groups, these sequences still represent incomplete information about sugarcane genomes. The current master thesis presents two core analyses to explore the sugarcane transcriptome, with the goal of bringing both biological insights about gene expression in immature culms as well as methodological considerations for the planning of differential expression experiments. The first chapter presents a methodological comparison of two strategies aiming to illustrate the influence of biological replication for vegetatively propagated plants, such as sugarcane. These analyses compared the use of clones and a diverse set of genotypes as components of contrasting groups of samples. The results indicate that the use of clones yielded an increased number of differentially expressed genes, which likely include genes of actual biological interest amidst genotype-specific significant tests. On the other hand, the use of diverse genotypes provided fewer differentially expressed genes, but the proportion of biologically relevant genes was seemingly higher. This statement was supported by evidence from both functional enrichment tests as well as the set of shared genes detected between the strategies. The second chapter presents a biological inquiry about the genetic mechanics regarding carbon partitioning in apical culms, where the sucrose accumulation process has not yet unfolded. Differentially expressed genes were identified for sucrose metabolism and transport, such as sucrose synthase, invertases, and sucrose transporter. However, the most apparent phenomenon with regard to carbon partitioning was the biosynthesis of cell wall components. These studies could drive new insights into sugarcane genetic investigations, by providing a set of important genes for early fiber and sugar metabolism in sugarcane, as well as aid researchers in making a more careful choice of experimental design for RNA-Seq essays.