Potential targets for evaluation of sugarcane yellow leaf virus resistance in sugarcane cultivars: in silico sugarcane miRNA and target network prediction

被引:9
作者
Ashraf, Muhammad Aleem [1 ,2 ]
Ashraf, Fakiha [1 ]
Feng, Xiaoyan [1 ,3 ]
Hu, Xiaowen [4 ]
Shen, Linbo [1 ]
Khan, Jallat [5 ]
Zhang, Shuzhen [1 ,3 ]
机构
[1] Chinese Acad Trop Agr Sci, Key Lab Biol & Genet Resources Trop Crops, Minist Agr, Inst Trop Biosci & Biotechnol,Sugarcane Res Ctr, Haikou, Hainan, Peoples R China
[2] Khwaja Fareed Univ Engn & Informat Technol, Dept Biosci & Technol, Rahim Yar Khan, Pakistan
[3] Chinese Acad Trop Agr Sci, Hainan Acad Trop Agr Resources, Haikou, Hainan, Peoples R China
[4] Chinese Acad Trop Agr Sci, Zhanjiang Expt Stn, Zhanjiang, Peoples R China
[5] Khwaja Fareed Univ Engn & Informat Technol, Dept Chem, Rahim Yar Khan, Pakistan
关键词
Host-virus interaction; RNA interference; Saccharum officinarum; sugarcane yellow leaf virus; target prediction; ARTIFICIAL MICRORNAS;
D O I
10.1080/13102818.2022.2041483
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
The Sugarcane yellow leaf virus (SCYLV) is associated with sugarcane yellow leaf disease (SCYLD) and is considered to be the most economically deleterious emerging pathogen that represents a potential threat and danger to sugarcane cultivation in China. Over the last two decades, high genetic diversity in the SCYLV genotypes was observed worldwide, with a greater chance of YLD incidence for sugarcane injury. SCYLV infection has significantly damaged its economic traits and is responsible for substantial losses in biomass production in sugarcane cultivars. This study aims to identify and analyse sugarcane microRNAs (miRNAs) as therapeutic targets against SCYLV using plant miRNA prediction tools. Mature sugarcane miRNAs are retrieved and are used for hybridisation of the SCYLV. A total of seven common sugarcane miRNAs were selected based on consensus genomic positions. The biologically significant, top ranked ssp-miR528 was consensually predicted to have a potentially unique hybridisation site at nucleotide position 4162 for targeting the ORF5 of the SCYLV genome; this was predicted by all the algorithms used in this study. Then, the miRNA-mRNA regulatory network was generated using the Circos algorithm, which was used to predict novel targets. There are no acceptable commercial SCYLV-resistant sugarcane varieties available at present. Therefore, the predicted biological data offer valuable evidence for the generation of SCYLV-resistant sugarcane plants.
引用
收藏
页码:1990 / 2001
页数:12
相关论文
共 38 条
[1]   Artificial microRNA-mediated resistance against the monopartite begomovirus Cotton leaf curl Burewala virus [J].
Ali, Irfan ;
Amin, Imran ;
Briddon, Rob W. ;
Mansoor, Shahid .
VIROLOGY JOURNAL, 2013, 10
[2]   Prevalence of Sugarcane yellow leaf virus in Sugarcane-Producing Regions in Kenya Revealed by Reverse-Transcription Loop-Mediated Isothermal Amplification Method [J].
Amata, Ruth L. ;
Fernandez, Emmanuel ;
Filloux, Denis ;
Martin, Darren P. ;
Rott, Philippe ;
Roumagnac, Philippe .
PLANT DISEASE, 2016, 100 (02) :260-268
[3]   A novel computational approach to the silencing of Sugarcane Bacilliform Guadeloupe A Virus determines potential host-derived MicroRNAs in sugarcane (Saccharum officinarum L.) [J].
Ashraf, Fakiha ;
Ashraf, Muhammad Aleem ;
Hu, Xiaowen ;
Zhang, Shuzhen .
PEERJ, 2020, 8
[4]  
Ashraf MA., 2022, PLOS ONE, V17
[5]   RNA silencing in plants [J].
Baulcombe, D .
NATURE, 2004, 431 (7006) :356-363
[6]   Partition function and base pairing probabilities of RNA heterodimers [J].
Bernhart, Stephan H. ;
Tafer, Hakim ;
Mueckstein, Ulrike ;
Flamm, Christoph ;
Stadler, Peter F. ;
Hofacker, Ivo L. .
ALGORITHMS FOR MOLECULAR BIOLOGY, 2006, 1 (1)
[7]   Principles of MicroRNA-target recognition [J].
Brennecke, J ;
Stark, A ;
Russell, RB ;
Cohen, SM .
PLOS BIOLOGY, 2005, 3 (03) :404-418
[8]   Widespread translational inhibition by plant miRNAs and siRNAs [J].
Brodersen, Peter ;
Sakvarelidze-Achard, Lali ;
Bruun-Rasmussen, Marianne ;
Dunoyer, Patrice ;
Yamamoto, Yoshiharu Y. ;
Sieburth, Leslie ;
Voinnet, Olivier .
SCIENCE, 2008, 320 (5880) :1185-1190
[9]  
Carbonell A, 2019, METHODS MOL BIOL, V2028, P231, DOI 10.1007/978-1-4939-9635-3_13
[10]  
Comstock J. C., 1998, Sugar Cane, P21