|Tipo di tesi||Tesi di dottorato di ricerca|
|Titolo||Mappaggio fine di due QTL per la resistenza alla ruggine fogliare Puccinia brachypodii nella pianta modello Brachypodium distachyon (L.)|
|Titolo in inglese||Fine mapping of two QTLs for resistance to the leaf rust Puccinia brachypodii in the model grass Brachypodium distachyon (L.)|
|Settore scientifico disciplinare||AGR/07 - GENETICA AGRARIA|
|Corso di studi||Scuola di D.R. in SCIENZE, TECNOLOGIE E BIOTECNOLOGIE AGRO-ALIMENTARI|
|Data inizio appello||2016-03-18|
|Disponibilità||Accessibile via web (tutti i file della tesi sono accessibili)|
Il patosistema Brachypodium-Puccinia brachypodii è un utile modello per la genomica traslazionale delle interazioni tra le ruggini e i loro cereali ospiti.
The Brachypodium-Puccinia brachypodii pathosystem is a useful model for translational genomics of rust interactions with their cereal hosts. Three quantitative trait loci (QTL) Rpbq1, Rpbq2 and Rpbq3, for resistance to the H-Ki isolate of the leaf rust pathogen, were previously mapped on Brachypodium chromosomes 2,3 and 4, in a segregating population derived from the cross between the inbred lines Bd3-1 and Bd1-1. For validation of the three QTLs, F3 to F7 families derived from single F2 plants, and harbouring single QTLs at homozygosous state, were selected by genotyping of flanking markers, and phenotyped with the H-Ki isolate. Rpbq2 and Rpbq3 were confirmed and prioritized for further research. The main aim of this study is to fine map the two genomic regions associated to the leaf rust resistance in order to obtain a precise targeting of candidate genes towards the cloning of the two QTLs. To reach this aim, two large segregating populations composed of 497 individuals for Rpbq3 and 434 for Rpbq2 were developed. Sequences of the QTL regions of the two parental lines were then aligned and searched for the discovery of gene-based single nucleotide polymorphisms (SNP) and Insertion-deletions (InDel). SNPs and sequence tagged sites (STSs) markers have been designed in order to find recombinant individuals. Thanks to these markers, eleven recombinant individuals for Rpbq2 and 12 for Rpbq3 were found and multiplied by selfing to stabilize the recombinations at homozygosity; a second round of genotyping was thus necessary to select homozygous recombinant individuals. To refine the position of the two QTLs, the recombinants were phenotyped with the H-Ki isolate of Puccinia brachypodii. Their progenies were phenotyped one year later as to validate the experiment. Thanks to the recombinant identification and screening the Rpbq3 interval was reduced, and the chromosome segment comprised between Bradi4g10017 and Bradi4g10230 was identified as the most linked with the resistance. The Rpbq2 interval was reduced as well, to the segment comprised between bradi3g16020 and bradi3g16140. Subsequently a functional protein domain analysis using NCBI Conserved Domain Database (http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) and InterPro: protein sequence analysis & classification (http://www.ebi.ac.uk/interpro) was performed for all genes residing at the two refined intervals for the two QTLs. Comparing the results obtained from the bioinformatics analysis and the fine mapping study , a first list of most promising candidate genes for the false brome rust resistance in B. distachyon composed of 6 genes for Rpbq2 3 for Rpbq3 was obtained. These candidate genes might lead to the cloning of the two QTLs. Moreover an evaluation of isolate-specificity of the resistance genes was performed via inoculations of the developed pseudo-RILs with other 4 different isolates of Puccinia brachypodii: NL-De, NL-Vij, F-Fl and F-Co. As a complementary approach a diversity panel of 54 different accessions of Brachypodium distachyon collected around the world, resequenced by JGI (USA), was screened for response to Puccinia brachypodii. This study represents the first fine mapping for the QTL cloning of the resistance genes to leaf rust pathogen Puccinia brachypodii in the model plant Brachypodium distachyon, for translational genomics to the economically relevant cereals.