Prediction of candidate genes associated with resistance to soybean rust (Phakopsora pachyrhizi) in line UG-5
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Date
2020
Journal Title
Journal ISSN
Volume Title
Publisher
Plant Breed
Abstract
Online databases containing genetic information are crucial to extract new candidate
genes from existing data and web-based resources. The objective of this study was,
therefore, to predict putative candidate genes associated with resistance to SBR in
line UG-5 and understand their functions using different bioinformatics tools from
the online available databases. The physical positions for the flanking markers of the
identified putative QTLs were searched on the SoyBase database genome browser
based on Glyma 1.01 assembly. The putative candidate genes and annotated functions
of the surrounding genes were discovered in the vicinity using SoyBase and
Phytozome databases. A total of 18 putative candidate genes were predicted on approximately
482.7 kb region of QTL-3 (chromosome 18), among which, six putative
candidate genes were found to encode leucine-rich repeat (LRR), Ser/Thr protein
phosphatase, leucine-rich repeat receptor-like protein kinase (LRR-RLK) and chitinase-
related proteins, which are associated with plant defence signalling pathways.
Moreover, F-box and leucine-rich repeat, glycosyltransferase family member and
serine/threonine-protein phosphatase 2A catalytic subunit coding genes were predicted
on the novel putative QTL detected on chromosome 9. This information could,
therefore, be used for further prediction and annotation of candidate genes from
sequenced regions of line UG-5 as these putative candidate genes were predicted
from the Glyma 1.01 assembly.
Description
Keywords
Chitinase, Glycotransferase, Leucine-rich repeat, Phytozome, SoyBase
Citation
Gebremedhn HM, Msiska UM, Weldekidan MB, Odong TL, Rubaihayo P, Tukamuhabwa P. Prediction of candidate genes associated with resistance to soybean rust (Phakopsora pachyrhizi) in line UG-5. Plant Breed. 2020;00:1–7. https://doi.org/10.1111/pbr.12847