Abstract Detail



Comparative Genomics/Transcriptomics

Allasi Canales , Nataly Olivia [1].

Genome-wide identification of resistant genes in domesticated and wild rice varieties (Oryza spp; Poaceae).

Background: Rice is the staple food for a large part of human population in the world. Rice plants are threatened by pathogens, however they have developed two defense mechanisms to resist pathogens. In this study, we focused on the resistant (R) proteins in different rice varieties that are encoded by NBS-LRR genes. It has been found that some motifs in the LRR domain are under strong positive selection in cultivated rice and other grass species. In this study we aimed to find out if this feature was also present in wild rice varieties and to what extent. Material and Methods: The genome data of nine rice varieties were used as materials, including Oryza sativa japonica, Oryza sativa indica as cultivated rice and Oryza barthii, Oryza brachyantha, Oryza glumaepatula, Oryza meridionalis, Oryza nivara, Oryza punctata and Oryza rufipogon as wild rice varieties. R gene identification was performed with BLAST searches and HMM approaches through PRGDB, then annotated with InterProScan, HMMPam and Pepcoil. Ortholog analysis was done by two approaches, phylogeny and sequences based (Orthofinder). The phylogenetic analysis was performed through Fasttree using the CC-MHD region. Finally, positive selection analysis was performed with PAML’s yn00. Results: We identified the number of R genes ranging from 204 (O. meridionalis) to 551 (O. sativa indica). A common distribution trend of NBS-LRR encoding genes on chromosomes in all varieties was found; chromosome 11 and 12 held from 26% to 40% of the total R gene amount. Additionally, we obtained 405 clades of ortholog R genes, spanning the CC-MHD region, in all varieties, suggesting a rapid conserved evolution and a window to improve resistance in cultivated varieties from wild ones. The results in the phylogenomic analysis confirmed previous results, showing that O. rufipogon and O. nivara are highly related to O. sativa cultivars. Oryza barthii was closely related to O. glumaepatula, while O. brachyantha was more divergent from the others. Selection pressure analyses in LRR domains among the R gene ortholog groups showed that an ortholog R gene group, related to signal transduction, was also found to be under positive selection (Ka/Ks=1.22). Additionally, its core region (xxLxLxx) was under strong positive selection (Ka/Ks=2.11) showing that R genes evolve rapidly not only in domesticated Oryza but also in wild varieties and might also be the key sites under selection in the process of rice domestication.


1 - Fujian Agriculture and Forestry U., Natural History Museum of Denmark

Keywords:
NBS-LRR
Oryza
positive selection
R gene phylogeny.

Presentation Type: Poster
Number: PGT005
Abstract ID:114
Candidate for Awards:None


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