High-resolution mapping of the quantitative trait locus (QTLs) conferring resistance to false smut disease in rice

Abstract Decoding the genetic mechanisms underlying disease resistance is of great importance for crop improvement. Rice false smut (RFS) is a major fungal disease caused by Ustilaginoidea virens that hampers the grain quality and yield of rice worldwide. It causes 2.8-49% global yield loss depending upon disease severity and varieties grown. In India, the severity of yield loss ranged from 2-75%. Keeping the economic importance of this disease, identification of the genes/QTLs governing disease resistance is of prime importance for the development of the linked markers and cloning of the genes. Here, we report mapping of QTLs using a recombinant inbred line (RIL) population derived from a cross between resistant line, RYT2668, and a highly susceptible variety, PR116. The population was evaluated for rice false smut disease under field conditions for three cropping seasons 2013, 2015, and 2016. A total of seven QTLs were mapped on rice chromosomes 2, 4, 5, 7, and 9 of rice using 2326 single nucleotide polymorphism (SNP) markers. Among them, a novel QTL qRFSr9.1 affecting total smut ball (TSB)/panicle on chromosome 9 exhibited the largest phenotypic effect. The prediction of putative candidate genes within the qRFSr9.1 spanned in 994.1Kb revealed four NBS-LRR domain-containing disease resistance proteins. We identified SNPs/Indels associated with the disease resistance which could be used for accelerating breeding programs using marker-assisted selection. In summary, our findings mark the ‘hot-spot’ region on rice chromosomes along with the identification of disease resistance genes in conferring resistance to the rice false smut disease.

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FLYER: A Simple Yet Robust Model for Estimating Yield Loss from Rice False Smut Disease (Ustilaginoidea virens)

American Journal of Agricultural and Biological Sciences ◽

10.3844/ajabssp.2015.41.54 ◽

2015 ◽

Vol 10 (1) ◽

pp. 41-54 ◽

Cited By ~ 7

Author(s):

Bodrun Nessa ◽

Moin U. Salam ◽

A.H.M. Mahfuzul Haque ◽

Jiban K. Biswas ◽

William J. MacLeod ◽

...

Keyword(s):

Yield Loss ◽

Ustilaginoidea Virens ◽

Rice False Smut ◽

Robust Model ◽

False Smut

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Rice false smut detection based on faster R-CNN

Indonesian Journal of Electrical Engineering and Computer Science ◽

10.11591/ijeecs.v19.i3.pp1590-1595 ◽

2020 ◽

Vol 19 (3) ◽

pp. 1590 ◽

Cited By ~ 1

Author(s):

Prabira Kumar Sethy ◽

Nalini Kanta Barpanda ◽

Amiya Kumar Rath ◽

Santi Kumari Behera

Keyword(s):

Object Detection ◽

Paddy Field ◽

Grain Quality ◽

Yield Loss ◽

Causative Pathogen ◽

Convolutional Network ◽

Ustilaginoidea Virens ◽

Rice False Smut ◽

Novel Approach ◽

False Smut

<span lang="EN-IN">Rice false smut is one of the most dangerous diseases in rice at the ripening phase caused by Ustilaginoidea Virens. It is one of the most important grain diseases in rice production worldwide. Its epidemics not only lead to yield loss but also reduce grain quality because of multiple mycotoxins generated by the causative pathogen. The pathogen infects developing spikelets and specifically converts individual grain into rice false smut ball. Rice false smut balls seem to be randomly formed in some grains on a panicle of a plant in the paddy field. In this study, we suggest a novel approach for the detection of rice false smut based on faster R-CNN. The process of faster R-CNN comprises regional proposal generation and object detection. The both tasks are done in same convolutional network. Because of such design it is faster for object detection. The faster R-CNN is able to detect the RFS using rectangular labelling from on-field images. The proposed approach is the initial steps to make a prototype for the automatic detection of RFS.</span>

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A novel transcription factor UvCGBP1 regulates development and virulence of rice false smut fungus Ustilaginoidea virens

Virulence ◽

10.1080/21505594.2021.1936768 ◽

2021 ◽

Vol 12 (1) ◽

pp. 1563-1579

Author(s):

Xiaoyang Chen ◽

Pingping Li ◽

Hao Liu ◽

Xiaolin Chen ◽

Junbin Huang ◽

...

Keyword(s):

Transcription Factor ◽

Smut Fungus ◽

Ustilaginoidea Virens ◽

Rice False Smut ◽

False Smut

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Quantitative Proteomics Analysis Reveals the Function of the Putative Ester Cyclase UvEC1 in the Pathogenicity of the Rice False Smut Fungus Ustilaginoidea virens

International Journal of Molecular Sciences ◽

10.3390/ijms22084069 ◽

2021 ◽

Vol 22 (8) ◽

pp. 4069

Author(s):

Xiaoyang Chen ◽

Zhangxin Pei ◽

Pingping Li ◽

Xiabing Li ◽

Yuhang Duan ◽

...

Keyword(s):

Quantitative Proteomics ◽

Fungal Pathogens ◽

Protein Localization ◽

Proteomics Data ◽

Ustilaginoidea Virens ◽

Rice False Smut ◽

Oxidative Stresses ◽

Tandem Mass Tag ◽

Cyclase Domain ◽

False Smut

Rice false smut is a fungal disease distributed worldwide and caused by Ustilaginoidea virens. In this study, we identified a putative ester cyclase (named as UvEC1) as being significantly upregulated during U. virens infection. UvEC1 contained a SnoaL-like polyketide cyclase domain, but the functions of ketone cyclases such as SnoaL in plant fungal pathogens remain unclear. Deletion of UvEC1 caused defects in vegetative growth and conidiation. UvEC1 was also required for response to hyperosmotic and oxidative stresses and for maintenance of cell wall integrity. Importantly, ΔUvEC1 mutants exhibited reduced virulence. We performed a tandem mass tag (TMT)-based quantitative proteomic analysis to identify differentially accumulating proteins (DAPs) between the ΔUvEC1-1 mutant and the wild-type isolate HWD-2. Proteomics data revealed that UvEC1 has a variety of effects on metabolism, protein localization, catalytic activity, binding, toxin biosynthesis and the spliceosome. Taken together, our findings suggest that UvEC1 is critical for the development and virulence of U. virens.

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The role of Ustilaginoidea virens sclerotia in increasing incidence of rice false smut disease in the subtropical zone in China

European Journal of Plant Pathology ◽

10.1007/s10658-017-1312-8 ◽

2017 ◽

Vol 150 (3) ◽

pp. 669-677 ◽

Cited By ~ 7

Author(s):

Mingli Yong ◽

Qide Deng ◽

Linlin Fan ◽

Jiankun Miao ◽

Chaohui Lai ◽

...

Keyword(s):

Ustilaginoidea Virens ◽

Subtropical Zone ◽

Rice False Smut ◽

False Smut

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Frequency distribution of sensitivity of Ustilaginoidea virens to four EBI fungicides, prochloraz, difenoconazole, propiconazole and tebuconazole, and their efficacy in controlling rice false smut in Anhui Province of China

Phytoparasitica ◽

10.1007/s12600-013-0288-y ◽

2013 ◽

Vol 41 (3) ◽

pp. 277-284 ◽

Cited By ~ 18

Author(s):

Yu Chen ◽

Yong Zhang ◽

Jian Yao ◽

Yun-Fei Li ◽

Xue Yang ◽

...

Keyword(s):

Frequency Distribution ◽

Anhui Province ◽

Ustilaginoidea Virens ◽

Rice False Smut ◽

False Smut

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Genetic diversity and population structure of the rice false smut pathogen Ustilaginoidea virens in Sichuan-Chongqing region

Plant Disease ◽

10.1094/pdis-04-21-0750-re ◽

2021 ◽

Author(s):

Anfei Fang ◽

Zhuangyuan Fu ◽

Zexiong Wang ◽

Yuhang Fu ◽

Yubao Qin ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Genetic Recombination ◽

Resistance Breeding ◽

Ustilaginoidea Virens ◽

Breeding Lines ◽

Rice False Smut ◽

Geographical Populations ◽

False Smut

Rice false smut caused by Ustilaginoidea virens is currently one of the most devastating fungal diseases of rice panicles worldwide. In this study, two novel molecular markers derived from SNP-rich genomic DNA fragments and a previously reported molecular marker were used for analyzing the genetic diversity and population structure of 167 U. virens isolates collected from nine areas in Sichuan-Chongqing region, China. A total of 62 haplotypes were identified, and a few haplotypes with high frequency were found and distributed in two to three areas, suggesting gene flow among different geographical populations. All isolates were divided into six genetic groups. The groups Ⅰ and Ⅵ were the largest including 61 and 48 isolates, respectively. The pairwise FST values showed significant genetic differentiation among all compared geographical populations. AMOVA showed that intergroup genetic variation accounted for 40.17% of the total genetic variation, while 59.83% of genetic variation came from intragroup. The UPGMA dendrogram and population structure revealed that the genetic composition of isolates collected from ST (Santai), NC (Nanchong), YC (Yongchuan), and WS (Wansheng) dominated by the same genetic subgroup was different from those collected from other areas. In addition, genetic recombination was found in a few isolates. These findings will help to improve the strategies for rice false smut management and resistance breeding, such as evaluating breeding lines with different isolates or haplotypes at different elevations and landforms.

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