Screening for sugarcane yellow leaf virus in sorghum in Florida revealed its occurrence in mixed infections with sugarcane mosaic virus and a new marafivirus

A viral metagenomics study of the sugarcane virome in Florida was carried out in 2013 to 2014 to analyze occurrence of known and potentially new viruses. In total, 214 sugarcane leaf samples were collected from different commercial sugarcane (Saccharum interspecific hybrids) fields in Florida and from other Saccharum and related species taken from two local germplasm collections. Virion-associated nucleic acids (VANA) metagenomics was used for detection and identification of viruses present within the collected leaf samples. VANA sequence reads were obtained for 204 leaf samples and all four previously reported sugarcane viruses occurring in Florida were detected: Sugarcane yellow leaf virus (SCYLV, 150 infected samples out of 204), Sugarcane mosaic virus (1 of 204), Sugarcane mild mosaic virus (13 of 204), and Sugarcane bacilliform virus (54 of 204). High prevalence of SCYLV in Florida commercial fields and germplasm collections was confirmed by reverse-transcription polymerase chain reaction. Sequence analyses revealed the presence of SCYLV isolates belonging to two different phylogenetic clades (I and II), including a new genotype of this virus. This viral metagenomics approach also resulted in the detection of a new sugarcane-infecting mastrevirus (recently described and named Sugarcane striate virus), and two potential new viruses in the genera Chrysovirus and Umbravirus.

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Improved detection of Sugarcane yellow leaf virus using a real-time fluorescent (TaqMan) RT-PCR assay

Journal of Virological Methods ◽

10.1016/s0166-0934(01)00406-2 ◽

2002 ◽

Vol 103 (2) ◽

pp. 109-120 ◽

Cited By ~ 75

Author(s):

J Korimbocus ◽

D Coates ◽

I Barker ◽

N Boonham

Keyword(s):

Real Time ◽

Yellow Leaf ◽

Rt Pcr ◽

Pcr Assay ◽

Sugarcane Yellow Leaf Virus ◽

Leaf Virus

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Incidence of sugarcane yellow leaf virus in clones maintained in the world collection of sugarcane and related grasses at the United States national repository in Miami, Florida

Sugar Tech ◽

10.1007/bf02956805 ◽

2001 ◽

Vol 3 (4) ◽

pp. 128-133 ◽

Cited By ~ 19

Author(s):

J. C. Comstock ◽

J. D. Miller ◽

R. J. Schnell

Keyword(s):

United States ◽

The United States ◽

Yellow Leaf ◽

Sugarcane Yellow Leaf Virus ◽

World Collection ◽

The World ◽

Leaf Virus

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Detecting Sugarcane yellow leaf virus infection in asymptomatic leaves with hyperspectral remote sensing and associated leaf pigment changes

Journal of Virological Methods ◽

10.1016/j.jviromet.2010.03.024 ◽

2010 ◽

Vol 167 (2) ◽

pp. 140-145 ◽

Cited By ~ 32

Author(s):

Michael P. Grisham ◽

Richard M. Johnson ◽

Paul V. Zimba

Keyword(s):

Remote Sensing ◽

Virus Infection ◽

Hyperspectral Remote Sensing ◽

Yellow Leaf ◽

Sugarcane Yellow Leaf Virus ◽

Leaf Pigment ◽

Leaf Virus

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Sugarcane yellow leaf virus. [Distribution map].

Distribution Maps of Plant Diseases ◽

10.1079/dmpd/20183138502 ◽

2018 ◽

Author(s):

Keyword(s):

Tamil Nadu ◽

Andhra Pradesh ◽

Uttar Pradesh ◽

Saccharum Officinarum ◽

Yellow Leaf ◽

Distribution Map ◽

Sugarcane Yellow Leaf Virus ◽

Leaf Virus ◽

Virus Distribution ◽

New Distribution

Abstract A new distribution map is provided for Sugarcane yellow leaf virus. Luteoviridae: Polerovirus. Hosts: sugarcane (Saccharum officinarum), barley (Hordeum vulgare), sorghum (Sorghum bicolor). Information is given on the geographical distribution in Asia (China, Fujian, Guangdong, Guangxi, Guizhou, Hainan, Jiangxi, Yunnan, India, Andhra Pradesh, Bihar, Haryana, Karnataka, Kerala, Madhya Pradesh, Maharashtra, Punjab, Tamil Nadu, Uttar Pradesh, Uttarakhand, Indonesia, Malaysia, Philippines, Sri Lanka, Taiwan, Thailand), Africa (Egypt, Kenya, Mauritius, Reunion, South Africa, Tunisia), North America (USA, Florida, Hawaii, Louisiana, Texas), Central America & Caribbean (Barbados, Costa Rica, Cuba, Guadeloupe, Guatemala, Martinique, Nicaragua, Puerto Rico), South America (Argentina, Brazil, Colombia, Ecuador, Peru, Venezuela).

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Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance

Scientific Reports ◽

10.1038/s41598-021-95116-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ricardo José Gonzaga Pimenta ◽

Alexandre Hild Aono ◽

Roberto Carlos Villavicencio Burbano ◽

Alisson Esdras Coutinho ◽

Carla Cristina da Silva ◽

...

Keyword(s):

Virus Resistance ◽

Machine Learning Algorithms ◽

Energy Crop ◽

Yellow Leaf ◽

Sugarcane Yellow Leaf Virus ◽

Association Analyses ◽

Sugarcane Breeding ◽

Genetic Base ◽

Genome Wide ◽

Leaf Virus

AbstractSugarcane yellow leaf (SCYL), caused by the sugarcane yellow leaf virus (SCYLV) is a major disease affecting sugarcane, a leading sugar and energy crop. Despite damages caused by SCYLV, the genetic base of resistance to this virus remains largely unknown. Several methodologies have arisen to identify molecular markers associated with SCYLV resistance, which are crucial for marker-assisted selection and understanding response mechanisms to this virus. We investigated the genetic base of SCYLV resistance using dominant and codominant markers and genotypes of interest for sugarcane breeding. A sugarcane panel inoculated with SCYLV was analyzed for SCYL symptoms, and viral titer was estimated by RT-qPCR. This panel was genotyped with 662 dominant markers and 70,888 SNPs and indels with allele proportion information. We used polyploid-adapted genome-wide association analyses and machine-learning algorithms coupled with feature selection methods to establish marker-trait associations. While each approach identified unique marker sets associated with phenotypes, convergences were observed between them and demonstrated their complementarity. Lastly, we annotated these markers, identifying genes encoding emblematic participants in virus resistance mechanisms and previously unreported candidates involved in viral responses. Our approach could accelerate sugarcane breeding targeting SCYLV resistance and facilitate studies on biological processes leading to this trait.

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