Prediction of candidate genes associated with resistance to soybean rust (Phakopsora pachyrhizi) in line UG-5

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.