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Genetic-genomic studies in tropical forage grasses of the genus Urochloa and Paspalum

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Fernanda Ancelmo de Oliveira
Total Authors: 1
Document type: Doctoral Thesis
Press: Campinas, SP.
Institution: Universidade Estadual de Campinas (UNICAMP). Instituto de Biologia
Defense date:
Examining board members:
Anete Pereira de Souza; Lucimara Chiari; Maria Imaculada Zucchi; Renato Vicentini; Marcelo Mattos Cavallari
Advisor: Bianca Baccili Zanotto Vigna; Anete Pereira de Souza

Brazilian cattle ranching is predominantly based on the use of pasture for livestock feeding. These cover extensive areas, which makes the world's largest commercial herd feasible and the position of the largest beef exporter. U. humidicola is among the exotic forages most cultivated in Brazilian pastures; occurs in humid places, poor drainage or seasonal flooding, which is why it occupies extensive areas in the cerrado and Amazon region. Native species of the genus Paspalum, present forage and ornamental potential, and stand out for the great intra-specific variability to be explored. The launching of new cultivars is an alternative to pasture diversification, and is the main way to mitigate problems arising from monoculture. However, there are few studies about the genetic-molecular-genomic profile in these forage grasses. And knowing the extent of genetic variability contained within germplasm banks helps in planning strategies to maximize genetic gains in breeding programs. In this context, this thesis aimed to contribute to the knowledge on the genetics and genomics of species of these two important genus of tropical forages. Using RNA-seq and de novo assembly, the global transcriptomic profile of U. humidicola leaf and leaf and flower of P. notatum was obtained. For U. humidicola, 35,093 unigenes were obtained, representing the first transcriptome for the species. These were annotated and related to C4 carbon fixation pathways, lignocellulose synthesis and stress response to flooding. The search for potential markers revealed 4,489 microsatellites (SSR) and 560,298 single nucleotide polymorphisms (SNPs). We identified unique and differentially expressed genes, corroborated by qPCR, between the two genotypes of the Embrapa germplasm bank used for analysis, apomictic accession BH16 "BRS Tupi cultivar" (CIAT 26149) and the only sexual genotype of the species, accession BH031 (CIAT 26146). Also the probable hybrid origin for BH031 was suggested. For P. notatum, a highly representative transcriptome was generated from two tissues (leaf and flower) of six genotypes with biological replicates, presenting different ploidy and mode of reproduction (sexual or apomictic), resulting in more than 100,000 unigenes assembled with robust metrics. Differential gene expression approaches between sexual and apomictic, enrichment of GO terms (Gene Ontology) and gene coexpression network, were identified as candidates for apomixia. These can be better investigated to elucidate this intriguing mechanism of reproduction, as well as to develop markers linked to apomixis. Additionally, in the Paspalum study, the first genomic SSR markers for P. plicatulum were developed and transferred to other species that make up the Plicatula botanical group, constituting a valuable tool for the study of the genetic variability of germplasm bank accessions of the species studied. Still, in order to deepen the knowledge about the complex Plicatula group, an expressive set of genomic data was obtained through RAD-seq for the species. So it can be used to aid in the taxonomic classification and species delimitation, as well as in collects, conservation and breeding programs of the Paspalum species (AU)

FAPESP's process: 13/14903-2 - Leaf Transcriptome analysis of Brachiaria humidicola and Paspalum notatum for the development of functional markers for genetic and genomic studies of tropical forage grasses
Grantee:Fernanda Ancelmo de Oliveira
Support Opportunities: Scholarships in Brazil - Doctorate