Detection of yellow mosaic virus resistance in Soybean (<i>Glycine max</i> L.) genotypes for yield and related traits

Nabila Hoque; Md. Ashraful Haque

doi:10.12688/f1000research.150924.1

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Research Article

Detection of yellow mosaic virus resistance in Soybean (Glycine max L.) genotypes for yield and related traits

[version 1; peer review: 3 approved with reservations, 1 not approved]

Nabila Hoque¹, Md. Ashraful Haque¹

PUBLISHED 30 Aug 2024

Author details Author details

¹ Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Mymensingh Division, 2202, Bangladesh

Nabila Hoque
Roles: Data Curation, Formal Analysis, Methodology, Software, Visualization, Writing – Original Draft Preparation

Md. Ashraful Haque
Roles: Conceptualization, Formal Analysis, Project Administration, Resources, Supervision, Validation, Writing – Review & Editing

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This article is included in the Plant Science gateway.

Abstract

Background

Twenty soybean genotypes were screened for Soybean yellow mosaic virus (YMV) identification which were collected from the Genetics and plant breeding farm laboratory.

Methods

To evaluate genetic studies of the chosen materials, the use of a net house assay upon sap inoculation made it easier to determine the trend of the Area Under Disease Progress Curve (AUDPC) in a controlled environment. Younger leaves from these plants were gathered and used for molecular analysis.

Results

Six genotypes were identified with semi-resistant disease reactions. Yellow mosaic virus-resistant and susceptible soybean genotypes were distinguished using a soybean “Rsv1-h” gene-based primer pair. To discover the existence of the Rsv-1-h gene responsible for YMV resistance, a genetic diversity panel of 15 soybean genotypes was investigated with two simple sequence repeat (SSR) markers. The BARCSOYSSR_13_1115 and BARCSOYSSR_13_1173 primer sets were employed to validate the desired genes in these genotypes.

Conclusion

The genotypes HIHS-WIHS, MINA-HAI, Shohag, G-2120, BRAGG, and BS-3 presented the major gene Rsv1-h, which is said to be essential for yellow mosaic virus resistance and can provide better yield also than other genotypes. The six soybean genotypes with the Rsv1-h gene may be resistant to mosaic virus and could be exploited as a source of improved breeding material in the future.

Keywords

soybean, yellow mosaic virus tolerance, simple sequence repeat marker, genetic resistance, Rsv1-h gene

Corresponding author: Md. Ashraful Haque

Competing interests: No competing interests were disclosed.

Grant information: The author(s) declared that no grants were involved in supporting this work.

Copyright: © 2024 Hoque N and Haque MA. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

How to cite: Hoque N and Haque MA. Detection of yellow mosaic virus resistance in Soybean (Glycine max L.) genotypes for yield and related traits [version 1; peer review: 3 approved with reservations, 1 not approved]. F1000Research 2024, 13:982 (https://doi.org/10.12688/f1000research.150924.1) First published: 30 Aug 2024, 13:982 (https://doi.org/10.12688/f1000research.150924.1) Latest published: 30 Aug 2024, 13:982 (https://doi.org/10.12688/f1000research.150924.1)

Introduction

Soybean (Glycine max) is one of the significant legume crops in today’s world, whose protein content is higher than other legumes.¹^,² 29.7% of the total vegetable oil is produced from soybeans and its major producers are the USA, Brazil, Argentina, and China.³ As it includes 36.6 g of protein, 19.9 g of total fat, 30.2 g of carbohydrates, 9.3 g of dietary fibre, and 15.7 mg of iron per 100 g of seeds, it is nutritious for human and animal consumption.⁴ Soybean is cultivated in 62,870 hectares (ha) of the total cultivable area in Bangladesh, from which we get nearly 96,921 tons of soybean per year.⁵ However, many biotic and abiotic factors adversely affect the growth and productivity of soybeans. Among them, the soybean business faces a severe threat from the soybean yellow mosaic virus (YMV), one of the most notorious agents of yield loss among 100 viruses.⁶ The disease can spread from leaves to seeds during severe infestation which deteriorates the quality of the seeds.⁷ The economic loss caused by this disease is 30-50%; however, it may go up to as high as 80% in extreme cases.⁸ As YMV is a viral disease, its control through chemical or cultural practices is neither effective nor environmentally friendly. So, implementation of genetic resistance can be an ideal option for soybean yellow mosaic virus management. For such an approach to be effective, it is crucial to understand the genetic control of the disease.⁹ The challenge in identifying resistant soybean plants is frequently hampering the progress in the breeding of soybeans in our country. If suitable screening methods are not used, selection may result in picking plants with pseudo-resistance, as YMV is delivered by whiteflies and their distribution in the field may not be uniform.¹⁰

The generation of YMV-resistant genotypes is substantially facilitated by selection using indirect methods, such as gene linked-molecular marker(s), which may help to overcome the limitations of field screening. Microsatellites are among the most widely used molecular markers because of their high degree of polymorphism, co-dominance nature, chromosome specificity, and dependability.¹¹ Simple Sequence Repeat markers, commonly known as SSR markers, have been utilized to locate YMV resistance gene-linked markers in soybean.¹² Field screening and subsequent selection can be made easier by using these marker(s) for YMV resistance. Marker-assisted selection (MAS) is a common strategy in molecular breeding efforts for identifying YMV in soybeans.¹³ The species of soybeans YMV prevalent in Northern Bangladesh differed from those prevalent in Southern Bangladesh.¹⁴ For this reason, the resistance of genotypes may also vary from one region to another region depending upon the strain of the virus prevalent in our country. For the adoption of successful methods for soybean YMV resistance breeding, it is necessary to investigate and unequivocally establish the genetic control of the disease. For this reason, the present experiment was done to evaluate several soybean germplasms to identify YMV disease resistance.

Methods

The field experiment was conducted at the experimental farm of the Department of Genetics and Plant Breeding, Bangladesh Agricultural University (BAU). It was arranged in a randomized complete block design with three replications. For molecular data analysis, soybean plants were grown in a controlled environment in the Genetics and Plant Breeding net house. The laboratory work has been carried out at the Plant Breeding Division of Bangladesh Institute of Nuclear Agriculture (BINA), Mymensingh, Bangladesh. The whole experiment was done in July 2019-June 2020.

Inoculation of virus in leaves

Nineteen exotic germplasm and one BAU variety were collected for this experiment. In a controlled environment, younger leaves at 3 to 4 stages of soybean were rubbed with inoculation sap (viral solution) for 3 to 4 times at 3 days intervals. The inoculation sap was prepared by homogenizing young leaves with typical mosaic symptoms of virus-infected plants. Leaf inoculation was done to infect younger plants. Individual plants were scored three times for the appearance and type of symptoms at 7-, 10- and 14-days post-inoculation (dpi) with day 0 being the first inoculation date.

Scoring of soybean leaves

Data were recorded for morphological studies and genetic analyses of the selected soybean genotypes. Plants with no symptoms, partial symptoms and systemic mosaic symptoms were rated as 0, 1 and 2 according to the severity of the disease.¹⁵ The scoring of leaves is shown in Table 1.

Table 1. Scoring of soybean leaves.

Rating scale	Description (visual observation)	Reaction
0	No symptoms on any plants	Highly resistant
1	Yellow mottle or necrotic mottle in up to 1-10% of plants	Moderately Susceptible
2	Yellow mottle or necrotic mottle more than 50% of plants	Highly susceptible

Statistical analysis for AUDPC (Area under disease progress curve)

Disease severity data were used to compute the area under disease progress curve (AUDPC) described by Campbell and Madden (1990).

AUDPC = \sum_{n = 0}^{n - 1} (\frac{y_{i} + y_{i + 1}}{2}) (t_{i + 1} - t_{i})

Where, n = number of successive readings,

y_i = disease severity at time i,

t_i = number of days after the observation on assessment date i.

AUDPC was drawn for each plant in each replicate using the mean plot disease score at each rating date.¹⁶ No vector was allowed for any kind of transmission from plant to plant. Mosquito nets were used to cover up the inoculated leaves before taking data for AUDPC.

Molecular marker analysis

Primer used for amplification of soybean yellow mosaic virus

In the net house experiment, leaf inoculation was allowed to infect younger plants as described by Chen et al., 2015.¹⁷ Infected leaves of earlier growth stages were collected from those soybean cultivars and were used as plant materials for molecular analysis. Two sets of primer were selected on the basis of the intensity of bands, presence of smearing, consistency with individuals and potential for population discrimination.

Isolated genomic DNA was tested for quality and quantity following standard procedure. The polymerase chain reaction (PCR) amplification profile consisted of initial denaturation at 94°C for 2 minutes followed by 35 cycles consisting of denaturation, primer annealing and extension at 94°C, 60°C and 72°C, respectively, for 30 seconds to 1 minute each. PCR cocktail made with 5 μL master mixture, 1 μL of template DNA, 1 μL of each forward and reverse primer and 2 μL of Nuclease-free water, which was amplified in a standard thermocycler.

Analysis of SSR data

Gene diversity was calculated using Roldan-Ruiz et al. (2000)’s formula:

{GD}_{i} = {2 f}_{i} (1 - f_{i})

where, GD_i is the gene diversity of marker ‘i’, f_i is the frequency of the amplified allele (band presence), and 1 - f_i is the frequency of the null allele. The GD for a locus can range from 0 to 0.5 using this calculation.

The presence and absence of DNA band were considered for identifying the presence or absence of the gene of interest. Polymorphism information content (PIC) values described for self-pollinated species were calculated as follows:

{PIC}_{i} = 1 - Σ n {p^{2}}_{ij} = 1

Where, P_ij is the frequency of the j^th allele for i^th marker and summed over n alleles.

Results

Molecular marker analysis

We did not obtain high-quality amplification from every soybean genotype. Among all polymorphic markers, polymorphism information content (PIC) was highest (0.61) in BARCSOYSSR_13_1173 and lowest (0.11) in BARCSOYSSR_13_1115 (Table 2). The list of the SSR markers and their PIC values are as follows:

• BARCSOYSSR_13_1115 whose PIC value is 0.11 and major allele frequency is 0.8113
• BARCSOYSSR_13_1173 whose PIC value is 0.61 and major allele frequency is 0.625
Both of these markers’ product size were 299 bp.

Table 2. List of SSR markers.

Name of the SSR marker	Sequence 5’-3’	Major allele frequency	Product size	Gene diversity	PIC
BARCSOYSSR_13_1115	F-CCT CTT TGG GTC AAT AGG TGT T R-ACC CAC CAC AAT CAT GGA TA	0.8113	299 bp	0.306	0.11
BARCSOYSSR_13_1173	F-TTC GGG TTC GAT TGT TTC TC R-TCA GAA CAT GTT TTT GTT TGA AGT T	0.625	299 bp	0.469	0.61

Analysis of SSR data

Performance of soybean genotypes after virus inoculation

Asymptomatic plants were scored as 0; whereas plants with partial symptoms and plants with mosaic symptoms (50-80%) were scored as 1 and 2 accordingly (Figure 1).

Figure 1. (A) Plants with no symptoms of Yellow mosaic virus, (B) yellow mottle up to 1-10% plants, (C) yellow mottle more than 50% plants.

The percent infection and AUDPC for each genotype were calculated from the scores obtained after virus inoculation at 7, 10 and 14 dpi (days post inoculation) and shown in Table 3. The high value of % infection and AUDPC indicated susceptibility, and the low value stated resistance. For this reason, MINA-HAI, Shohag, HIHS-WIHS, BS-3, BRAGG might be considered as highly resistant; Davis, Lokon, G-10180, Asset 93-19-5, G-2120 as moderately susceptible; AGS-66, TAINANS as highly susceptible (Table 3).

Table 3. Performance of soybean genotypes after virus inoculation.

Genotypes	%Infection	AUDPC	Disease reaction
G-10180	55.33	10.83	MS
BS-3	66.77	8.63	HR
Lokon	66.77	8.63	MS
Asset-93-19-5	55.33	6.81	MS
Davis	55.33	5.81	MS
BRAGG	55.33	6.88	HR
MINA- HAI	33.33	4.80	HR
Shohag (PB-1)	44.33	5.80	HR
G-2120	66.66	6.81	MS
Santarosa	66.66	8.63	MS
BS-13	88.66	12.1	HS
HIHS-WIHS	55.33	4.80	HR
AGS-79	55.33	6.88	MS
AGS-278	88.66	10.85	MS
Jayawiyaja	88.66	12.1	HS
SY-35	78.66	11.3	MS
Asset-93-19-1	33.33	4.8	MS
YESOY-4	78.66	11.3	HS
TAINANS	66.66	8.63	HS
AGS-66	78.66	10.77	HS

Five genotypes were found, which showed high resistance of all. The relationship of Area under Disease progress curve (AUDPC) and %Infection in soybean genotypes is shown in Figure 2.

Figure 2. Relationship between Area under Disease progress curve (AUDPC) and %Infection in soybean genotypes.

Here, the highest percent infection (88.66%) was observed for BS-13, AGS-278, and Jayawiyaja and lowest for MINA-HAI and Asset-93-19-1 (33.33%). BS-13 and Jayawiyaja showed the highest AUDPC value (12.1) and MINA-HAI, HIHS-WIHS, and Asset-93-19-1 showed the lowest (4.8).

Molecular detection using specific primer

Though the disappearance and reappearance of viral symptoms often mislead us, pathological identification via AUDPC helped in the virus detection system. We emphasized Rsv1 gene identification, which has a significant role in resistant regulation in soybean. Two sets of primers were used to detect the yellow mosaic virus gene in soybean genotypes which is responsible for yellow mosaic virus resistance. The highly susceptible genotypes were cut down and SSR markers were used to detect desired genes in the 15 soybean genotypes. Individual soybean plants were screened for two simple sequence repeat (SSR) markers named BARCSOYSSR_13_1173 and BARCSOYSSR_13_1115 that flank the Rsv1 locus.

From Figure 3, it was observed that while using the BARCSOYSSR_13_1173 SSR marker, six genotypes namely Mina-hai, Shohag (Pb-1), G-2120, HIHS-WIHS, BS-3 and BRAGG showed fragments at the expected size (299 bp) based on the simple PCR detection system. The viral resistance system is a complex mechanism that provides resistance in a semi-persistent manner, so a certain degree of resistance can be expected if the significant gene is present in a genotype. A remarkable variation was noticed in 15 genotypes (Figure 3). The PCR-based results indicated that a fragment of 300 bp was absent in most of the genotypes as the primers were gene-specific. Mina-hai, Shohag, G-2120, HIHS-WIHS, BS-3, BRAGG carried Rsv1-h gene against Soybean yellow mosaic virus (Table 3). The rest of the genotypes showed the absence of a 299-300 bp fragment, indicating that these genotypes were susceptible to SYMV. Besides this, it was observed that none of the genotypes showed fragments at the expected size (299bp) using the BARCSOYSSR_13_1115 primer.

Figure 3. The banding pattern of 15 soybean genotypes using the BARCSOYSSR_13_1173 SSR marker in SDS-PAGE indicates the presence of the dominant allele of the Rsv1-h gene.

Discussion

Performance of soybean genotypes after virus inoculation

Viral symptom scoring was performed at 7, 10 and 14 days after inoculation of the virus. MINA-HAI, Shohag, HIHS-WIHS, BS-3, BRAGG showed resistance as their infection rate and AUDPC value were low. On the other hand, AGS-66 and TAINANS were highly susceptible because of their high value of % infection rate and AUDPC value. Davis, Lokon, G-10180, Asset 93-19-5, G-2120 was partially susceptible due to their medium level of infection rate and AUDPC value. The phenotypic performance of soybean genotypes regarding yield and yield-contributing traits partially supported this hypothesis. Stewart et al., (2013) inoculated virus to a number of genotypes and calculated % infection and AUDPC at 7, 10 and 14 dpi. They found that the resistant genotype showed 0% infection and the susceptible one showed 100% infection.¹⁵ Molecular work was also performed to ensure the scoring results. The identified resistant genotypes were expected to carry the rsv1-h gene.

Molecular detection using specific primer

For the purpose of screening individual soybean plants, we looked for two simple sequence repeat (SSR) markers that border the Rsv1 locus: BARCSOYSSR_13_1173 and BARCSOYSSR_13_1115. This marker was also utilised by Lee et al. (2013) to identify yellow mosaic virus resistance in soybean.¹⁸ The Rsv1 - h gene in cultivar Suweon 97, which confers resistance to SMVs, was found to be mapped to a 97.5-kb location (29,815,195–29,912,667 bp on chromosome 13) in the Rsv1 locus by Ma et al. (2016). This observation gave rise to further questions regarding the molecular basis of variations in resistance alleles in this specific locus.¹⁹ The dominant Rsv1 gene has been assigned to chromosome 13 (molecular linkage group F). While Rsv1 has been the subject of extensive research and discussion among scientists worldwide, as evidenced by the numerous citations, it is important to acknowledge the possibility of the existence of distinct viral strains in Bangladesh that require systematic attention in our local environment.

The six genotypes viz. Mina-hai, Shohag, G-2120, HIHS-WIHS, BS-3, BRAGG having the expected fragment of 299-303 bp using BARCSOYSSR_13_1173 primer sets which were responsible for resistance regulation against soybean yellow mosaic virus. The Rsv1 - h gene enables soybean plants to maintain better stress conditions. Zheng et al. (2014) identified two genomic-simple sequence repeat (SSR) markers, BARCSOYSSR_13_1114 and BARCSOYSSR_13_1136, which are located on either side of the RSC3Q and are associated with the Rsv1 area.²⁰ A quantitative real-time PCR analysis of the candidate genes identified five genes that were possibly implicated in soybean YMV resistance: Glyma13g25730, 25750, 25950, 25970, and 26000. The cloning of the RSC3Q resistance candidate gene and the utilization of marker-assisted selection (MAS) in YMV resistance breeding could both benefit from these findings.

Further extensive molecular and serological studies may be helpful in understanding the Rsv1-h gene-mediated resistance regulation of soybean yellow mosaic virus.

Eventually, six genotypes have been found to be semi-resistant out of twenty genotypes. The genotypes HIHS-WIHS, MINA-HAI, Shohag, G-2120, BRAGG and BS-3 all have the major gene Rsv1-h, which is considered necessary for yellow mosaic virus resistance. They also have produced higher yields than other genotypes. These six soybean genotypes could be used in the future as a source of improved breeding material. During virus indexing at the field level, five genotypes showed highly susceptible expression of the YMV disease. An effort has been made in this research to identify genotypes that are resistant to YMV by using disease indexing and SSR markers. These genotypes could be used as parents in future crossing programs to develop YMV-resistant soybean cultivars through molecular breeding. The improved yellow mosaic virus-resistant genotypes could be used as a barrier against disease transmission to additional locations, perhaps increasing soybean yield in our country.

Ethics and consent

Ethical approval and consent were not required.

Data availability

Underlying/extended data

Figshare: Underlying and extended data for ‘Detection of yellow mosaic virus resistance in Soybean (Glycine max L.) genotypes for yield and related traits’, https://www.doi.org/10.6084/m9.figshare.25918495.v3.²¹

This project contains the following underlying and extended data:

• Scoring of soybean leaves
• List of SSR Markers used for Soybean yellow mosaic virus identification
• Performance of soybean genotypes after virus inoculation
• Figure 01. Symptoms of yellow mosaic virus plants <.jpg format>
• Figure 02. Relationship between Area Under Disease Progress Curve and % Infection in soybean genotypes <.jpg format>
• Figure 3. The banding pattern of 15 soybean genotypes using the BARCSOYSSR_13_1173 SSR marker <.jpg format>

Data are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).

Acknowledgements

We acknowledge the support of the Bangladesh Institute of Nuclear Agriculture for the molecular analysis of the soybean leaf DNA samples.

References

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Author details Author details

¹ Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Mymensingh Division, 2202, Bangladesh

Nabila Hoque
Roles: Data Curation, Formal Analysis, Methodology, Software, Visualization, Writing – Original Draft Preparation

Md. Ashraful Haque
Roles: Conceptualization, Formal Analysis, Project Administration, Resources, Supervision, Validation, Writing – Review & Editing

Competing interests

No competing interests were disclosed.

Grant information

The author(s) declared that no grants were involved in supporting this work.

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https://doi.org/10.12688/f1000research.150924.1

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© 2024 Hoque N and Haque MA. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Hoque N and Haque MA. Detection of yellow mosaic virus resistance in Soybean (Glycine max L.) genotypes for yield and related traits [version 1; peer review: 3 approved with reservations, 1 not approved]. F1000Research 2024, 13:982 (https://doi.org/10.12688/f1000research.150924.1)

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ApprovedThe paper is scientifically sound in its current form and only minor, if any, improvements are suggested

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Reviewer Report 06 Dec 2024

Shridhar Hiremath, CSIR-North East Institute of Science & Technology, Jorhat, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India

Approved with Reservations

https://doi.org/10.5256/f1000research.165538.r338653

This study presents an interesting investigation into the screening of soybean genotypes for resistance to Soybean yellow mosaic virus (YMV) through a combination of phenotypic evaluations and molecular analysis. The use of controlled environment assays, such as the Area Under ... Continue reading

This study presents an interesting investigation into the screening of soybean genotypes for resistance to Soybean yellow mosaic virus (YMV) through a combination of phenotypic evaluations and molecular analysis. The use of controlled environment assays, such as the Area Under Disease Progress Curve (AUDPC) for disease progression monitoring, adds rigor to the findings. The identification of semi-resistant genotypes and the validation of the Rsv1-h gene using SSR markers provide valuable insights into YMV resistance. Below are my detailed comments on the strengths and areas for improvement in this manuscript.

1. The introduction has to be improved, and the taxonomic details of the YMV have to be briefly discussed. Many sentences have to be rephrased.
2. "The species of soybeans YMV prevalent in Northern Bangladesh differed from those prevalent in Southern Bangladesh" Here, instead of species, the "strains" phrase is suitable. Please do correct
3. In M&M: The detailed methodology on inoculation of viruses has to be written
4. Did the authors confirm the virus strain before performing the inoculation? If so, what primers were used for molecular characterization? This has to be discussed thoroughly!
5. The disease scale used in this study seems to be inappropriate. A standard disease scale has to be used, and a proper reference for it has to be cited. Mention if any modifications have been made to the standard disease scale.
8. M&M: Under molecular marker analysis, authors should mention the concentration of PCR components rather than the volumes of aliquots taken. This will help other researchers to reproduce the work.
9. The data presented in Table 3 is bit ambiguous. Davis has same % infection as BRAGG with less AUDPC in comparison to BRAGG but still it is considered as MS. ???How?..even Asset 93-19-1 has low % infection rate and AUDPC but still it is considered as MS??
10. Overall the manuscript has to be revised to provide more details and clarity. The title given is inappropriate. Instead of detection screening phrase suits well and no work has been carried towards yield related trains hence it can be omitted from the title.

Is the work clearly and accurately presented and does it cite the current literature?

Partly
Is the study design appropriate and is the work technically sound?

Partly
Are sufficient details of methods and analysis provided to allow replication by others?

Partly
If applicable, is the statistical analysis and its interpretation appropriate?

Yes
Are all the source data underlying the results available to ensure full reproducibility?

Yes
Are the conclusions drawn adequately supported by the results?

Partly

Competing Interests: No competing interests were disclosed.

Reviewer Expertise: Plant Pathology, Plant Virology, Plant-microbe interaction, Molecular Plant Pathology, Virus Diagnostics.

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

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Reviewer Report 06 Dec 2024

Wanwisa Siriwan, Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand

Not Approved

https://doi.org/10.5256/f1000research.165538.r338651

Title: "Detection of Yellow Mosaic Virus Resistance in Soybean (Glycine max L.) Genotypes for Yield and Related Traits"
However, in the methods and results sections, the authors did not mention yield.

Introduction:

1. ... Continue reading

Title: "Detection of Yellow Mosaic Virus Resistance in Soybean (Glycine max L.) Genotypes for Yield and Related Traits"
However, in the methods and results sections, the authors did not mention yield.

Introduction:

1. "As YMV is a viral disease, its control through chemical or cultural practices is neither effective nor environmentally friendly."
What type of chemicals can control YMV?
2. Authors should include detailed information about YMV, including its genus, species, biology, etc.

Methods:
How many plants were included per replication?

Results:

1. The results should align with the methods to ensure consistency.
2. What was the sample size for calculating the percentage of infection?
3. For disease reactions, the authors should describe how the groups (e.g., HS, MS) were classified.
4. In Table 3, please review and correct errors related to the classification of disease reactions based on AUDPC and percentage of infection.
5. In Figure 2, the figure does not clearly represent the relationship between AUDPC and percentage of infection, leading to confusion for readers. It is recommended to modify the figure for better clarity.
6. In Figure 3, the TAINANS sample appears to show a PCR product at 299 bp as well. Additionally, the quality of the figure is poor and needs improvement.

Discussion:
1. The authors should discuss the integration of AUDPC and molecular markers for screening resistant species.

Is the work clearly and accurately presented and does it cite the current literature?

Yes
Is the study design appropriate and is the work technically sound?

Partly
Are sufficient details of methods and analysis provided to allow replication by others?

No
If applicable, is the statistical analysis and its interpretation appropriate?

Not applicable
Are all the source data underlying the results available to ensure full reproducibility?

Partly
Are the conclusions drawn adequately supported by the results?

Partly

Competing Interests: No competing interests were disclosed.

I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above.

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Reviewer Report 23 Nov 2024

Gabriel Madoglio Favara, Universidade Estadual Paulista (UNESP), São Paulo, Brazil

Approved with Reservations

https://doi.org/10.5256/f1000research.165538.r338654

Title:
The title needs revision because the term "yield" is not appropriate, as this characteristic was not determined in the evaluated genotypes. Additionally, the word "detection" seems unsuitable and should be removed. A more fitting title could be: "Screening ... Continue reading

Title:
The title needs revision because the term "yield" is not appropriate, as this characteristic was not determined in the evaluated genotypes. Additionally, the word "detection" seems unsuitable and should be removed. A more fitting title could be: "Screening for yellow mosaic virus resistance in soybean (Glycine max L.) genotypes." This would better reflect the focus of the study.

Introduction:
The introduction would benefit from the inclusion of essential information regarding Yellow Mosaic Virus (YMV), such as its taxonomic classification (family and genus), particle morphology, genomic structure, and its mode of transmission via insect vectors, to provide readers with a comprehensive understanding of the virus under investigation.

Methods
The term "controlled environment" is somewhat general and could benefit from more specificity. Including details about key environmental parameters, such as temperature and fotoperiod, would strengthen the methodological description and aid reproducibility.

It is unclear whether the inoculum was tested for YMV or other viruses. The authors should clarify if the inoculum was tested for YMV and the absence of other viral infections.

The description of the preparation process for the "inoculation sap" is insufficiently detailed. It is recommended to include the specific buffer used in the preparation, as well as the proportion of plant tissue to buffer volume employed.

Would be useful to specify the exact "standard procedure" for testing the quality and quantity of genomic DNA for reproducibility.

PCR Protocol Details: It may be helpful to state the total reaction volume of the PCR or the concentration of each component in the cocktail for better methodological clarity.

Results:
Figure 2 is difficult to interpret, and there is no explanation for it in the text. Additionally, the legend appears to have the labels for AUDPC and virus infection reversed.

Table 3 requires revision. For example, the genotypes BS-3 Lokon show the same values for percentage of infection and AUDPC, yet one is classified as HR (highly resistant) and the other as MS (moderately susceptible). This discrepancy should be addressed and clarified. Additionally, I disagree with the rationale suggesting that a genotype is considered resistant to YMV when the percentage of infection is as high as 50%, as seen for other genotypes in the table. The authors should reconsider the classification criteria or provide stronger justification for these classifications.

Could the authors confirm whether the information regarding amplification in only 6 genotypes is correct? In the gel image, it is possible to observe the amplification of the 299 bp fragment in the Davis, Lokon, and SY-35 genotypes. This should be clarified to ensure consistency between the results presented in the figure and the text.

This study addresses an important topic regarding yellow mosaic virus resistance in soybean genotypes, but there are several areas where the methodology and presentation could be clarified. Strengthening the descriptions of experimental conditions, providing more detailed methodological information, and ensuring consistency between figures, tables, and the text would greatly improve the overall clarity and reproducibility of the study. Furthermore, the classification criteria for resistance should be more robustly justified. With these revisions, the manuscript would be significantly strengthened and offer a clearer contribution to the field.

Is the work clearly and accurately presented and does it cite the current literature?

Partly
Is the study design appropriate and is the work technically sound?

Partly
Are sufficient details of methods and analysis provided to allow replication by others?

No
If applicable, is the statistical analysis and its interpretation appropriate?

I cannot comment. A qualified statistician is required.
Are all the source data underlying the results available to ensure full reproducibility?

Partly
Are the conclusions drawn adequately supported by the results?

Partly

Competing Interests: No competing interests were disclosed.

Reviewer Expertise: Plant Virology

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

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Reviewer Report 30 Sep 2024

Karupiah Eraivan Arutkani Aiyanathan, Professor (Retd.), Department of Plant Pathology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, Tamil Nadu, India

Approved with Reservations

https://doi.org/10.5256/f1000research.165538.r322673

Detection of yellow mosaic virus resistance in Soybean (Glycine max L.) genotypes for yield and related traits.

Title:
The article title needs to be changed because the word “Detection” is not relevant to screening and identifying resistance ... Continue reading

Detection of yellow mosaic virus resistance in Soybean (Glycine max L.) genotypes for yield and related traits.

Title:
The article title needs to be changed because the word “Detection” is not relevant to screening and identifying resistance to the virus.

Introduction :
The importance of the YMV problem in soybeans needs to be emphasized in detail. Also, indicate the previously published information/references on molecular approaches for the confirmation of YMV resistance.

Methods:
The manuscript indicated that the virus was not confirmed as YMV before screening, so molecular confirmation is necessary.
Only 20 soybean genotypes/lines were screened, which is insufficient for testing disease resistance. Additionally, no standard scoring technique was followed for the assessment of YMV, and proper references for the scoring were not cited.
Resistance should be proved through vector transmission in addition to sap inoculation.
Only two markers were used. More SSR markers should have been included to obtain polymorphism.

Results:
The presence of resistance in the genotypes should also be further confirmed by PCR using Rsv1-h gene-specific primers.

Discussion:
The discussion does not address the relationship of YMV infection with AUDPC.
A more detailed discussion with recent supporting literature is necessary.

References require corrections as per Journal specification.
General Comments:
1. The English language is poor and needs improvement in sentence formation.
2. Consider outsourcing (language editing) to rewrite the article. This article requires substantial revisions to become academically valid.

Therefore, I recommend revising the manuscript to improve the language and include more relevant results and elaborate critical discussion. The mentioned shortcomings in the manuscript led me to consider it only for a "Research Note”.

Is the work clearly and accurately presented and does it cite the current literature?

Partly
Is the study design appropriate and is the work technically sound?

Partly
Are sufficient details of methods and analysis provided to allow replication by others?

No
If applicable, is the statistical analysis and its interpretation appropriate?

I cannot comment. A qualified statistician is required.
Are all the source data underlying the results available to ensure full reproducibility?

Partly
Are the conclusions drawn adequately supported by the results?

Partly

Competing Interests: No competing interests were disclosed.

Reviewer Expertise: Host Plant Resistance to Pathogens, Biological Control of plant diseases

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

CITE

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VERSION 1 PUBLISHED 30 Aug 2024

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Karupiah Eraivan Arutkani Aiyanathan, Tamil Nadu Agricultural University, Madurai, India
Gabriel Madoglio Favara, Universidade Estadual Paulista (UNESP), São Paulo, Brazil
Wanwisa Siriwan, Kasetsart University, Bangkok, Thailand
Shridhar Hiremath, CSIR-North East Institute of Science & Technology, Jorhat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India

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Reviewer Report

9 Views

06 Dec 2024 | for Version 1

Shridhar Hiremath, CSIR-North East Institute of Science & Technology, Jorhat, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India

9 Views Cite this report Responses(0)

Approved With Reservations

This study presents an interesting investigation into the screening of soybean genotypes for resistance to Soybean yellow mosaic virus (YMV) through a combination of phenotypic evaluations and molecular analysis. The use of controlled environment assays, such as the Area Under Disease Progress Curve (AUDPC) for disease progression monitoring, adds rigor to the findings. The identification of semi-resistant genotypes and the validation of the Rsv1-h gene using SSR markers provide valuable insights into YMV resistance. Below are my detailed comments on the strengths and areas for improvement in this manuscript.

1. The introduction has to be improved, and the taxonomic details of the YMV have to be briefly discussed. Many sentences have to be rephrased.
2. "The species of soybeans YMV prevalent in Northern Bangladesh differed from those prevalent in Southern Bangladesh" Here, instead of species, the "strains" phrase is suitable. Please do correct
3. In M&M: The detailed methodology on inoculation of viruses has to be written
4. Did the authors confirm the virus strain before performing the inoculation? If so, what primers were used for molecular characterization? This has to be discussed thoroughly!
5. The disease scale used in this study seems to be inappropriate. A standard disease scale has to be used, and a proper reference for it has to be cited. Mention if any modifications have been made to the standard disease scale.
8. M&M: Under molecular marker analysis, authors should mention the concentration of PCR components rather than the volumes of aliquots taken. This will help other researchers to reproduce the work.
9. The data presented in Table 3 is bit ambiguous. Davis has same % infection as BRAGG with less AUDPC in comparison to BRAGG but still it is considered as MS. ???How?..even Asset 93-19-1 has low % infection rate and AUDPC but still it is considered as MS??
10. Overall the manuscript has to be revised to provide more details and clarity. The title given is inappropriate. Instead of detection screening phrase suits well and no work has been carried towards yield related trains hence it can be omitted from the title.

Is the work clearly and accurately presented and does it cite the current literature?

Partly
Is the study design appropriate and is the work technically sound?

Partly
Are sufficient details of methods and analysis provided to allow replication by others?

Partly
If applicable, is the statistical analysis and its interpretation appropriate?

Yes
Are all the source data underlying the results available to ensure full reproducibility?

Yes
Are the conclusions drawn adequately supported by the results?

Partly

Competing Interests

No competing interests were disclosed.

Reviewer Expertise

Plant Pathology, Plant Virology, Plant-microbe interaction, Molecular Plant Pathology, Virus Diagnostics.

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

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Reviewer Report

3 Views

06 Dec 2024 | for Version 1

Wanwisa Siriwan, Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand

3 Views Cite this report Responses(0)

Not Approved

Title: "Detection of Yellow Mosaic Virus Resistance in Soybean (Glycine max L.) Genotypes for Yield and Related Traits"
However, in the methods and results sections, the authors did not mention yield.

Introduction:

1. "As YMV is a viral disease, its control through chemical or cultural practices is neither effective nor environmentally friendly."
What type of chemicals can control YMV?
2. Authors should include detailed information about YMV, including its genus, species, biology, etc.

Methods:
How many plants were included per replication?

Results:

1. The results should align with the methods to ensure consistency.
2. What was the sample size for calculating the percentage of infection?
3. For disease reactions, the authors should describe how the groups (e.g., HS, MS) were classified.
4. In Table 3, please review and correct errors related to the classification of disease reactions based on AUDPC and percentage of infection.
5. In Figure 2, the figure does not clearly represent the relationship between AUDPC and percentage of infection, leading to confusion for readers. It is recommended to modify the figure for better clarity.
6. In Figure 3, the TAINANS sample appears to show a PCR product at 299 bp as well. Additionally, the quality of the figure is poor and needs improvement.

Discussion:
1. The authors should discuss the integration of AUDPC and molecular markers for screening resistant species.

Is the work clearly and accurately presented and does it cite the current literature?

Yes
Is the study design appropriate and is the work technically sound?

Partly
Are sufficient details of methods and analysis provided to allow replication by others?

No
If applicable, is the statistical analysis and its interpretation appropriate?

Not applicable
Are all the source data underlying the results available to ensure full reproducibility?

Partly
Are the conclusions drawn adequately supported by the results?

Partly

Competing Interests

No competing interests were disclosed.

I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above.

Respond to this report

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Reviewer Report

4 Views

23 Nov 2024 | for Version 1

Gabriel Madoglio Favara, Universidade Estadual Paulista (UNESP), São Paulo, Brazil

4 Views Cite this report Responses(0)

Approved With Reservations

Title:
The title needs revision because the term "yield" is not appropriate, as this characteristic was not determined in the evaluated genotypes. Additionally, the word "detection" seems unsuitable and should be removed. A more fitting title could be: "Screening for yellow mosaic virus resistance in soybean (Glycine max L.) genotypes." This would better reflect the focus of the study.

Introduction:
The introduction would benefit from the inclusion of essential information regarding Yellow Mosaic Virus (YMV), such as its taxonomic classification (family and genus), particle morphology, genomic structure, and its mode of transmission via insect vectors, to provide readers with a comprehensive understanding of the virus under investigation.

Methods
The term "controlled environment" is somewhat general and could benefit from more specificity. Including details about key environmental parameters, such as temperature and fotoperiod, would strengthen the methodological description and aid reproducibility.

It is unclear whether the inoculum was tested for YMV or other viruses. The authors should clarify if the inoculum was tested for YMV and the absence of other viral infections.

The description of the preparation process for the "inoculation sap" is insufficiently detailed. It is recommended to include the specific buffer used in the preparation, as well as the proportion of plant tissue to buffer volume employed.

Would be useful to specify the exact "standard procedure" for testing the quality and quantity of genomic DNA for reproducibility.

PCR Protocol Details: It may be helpful to state the total reaction volume of the PCR or the concentration of each component in the cocktail for better methodological clarity.

Results:
Figure 2 is difficult to interpret, and there is no explanation for it in the text. Additionally, the legend appears to have the labels for AUDPC and virus infection reversed.

Table 3 requires revision. For example, the genotypes BS-3 Lokon show the same values for percentage of infection and AUDPC, yet one is classified as HR (highly resistant) and the other as MS (moderately susceptible). This discrepancy should be addressed and clarified. Additionally, I disagree with the rationale suggesting that a genotype is considered resistant to YMV when the percentage of infection is as high as 50%, as seen for other genotypes in the table. The authors should reconsider the classification criteria or provide stronger justification for these classifications.

Could the authors confirm whether the information regarding amplification in only 6 genotypes is correct? In the gel image, it is possible to observe the amplification of the 299 bp fragment in the Davis, Lokon, and SY-35 genotypes. This should be clarified to ensure consistency between the results presented in the figure and the text.

This study addresses an important topic regarding yellow mosaic virus resistance in soybean genotypes, but there are several areas where the methodology and presentation could be clarified. Strengthening the descriptions of experimental conditions, providing more detailed methodological information, and ensuring consistency between figures, tables, and the text would greatly improve the overall clarity and reproducibility of the study. Furthermore, the classification criteria for resistance should be more robustly justified. With these revisions, the manuscript would be significantly strengthened and offer a clearer contribution to the field.

Is the work clearly and accurately presented and does it cite the current literature?

Partly
Is the study design appropriate and is the work technically sound?

Partly
Are sufficient details of methods and analysis provided to allow replication by others?

No
If applicable, is the statistical analysis and its interpretation appropriate?

I cannot comment. A qualified statistician is required.
Are all the source data underlying the results available to ensure full reproducibility?

Partly
Are the conclusions drawn adequately supported by the results?

Partly

Competing Interests

No competing interests were disclosed.

Reviewer Expertise

Plant Virology

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

Respond to this report

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Reviewer Report

11 Views

30 Sep 2024 | for Version 1

Karupiah Eraivan Arutkani Aiyanathan, Professor (Retd.), Department of Plant Pathology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, Tamil Nadu, India

11 Views Cite this report Responses(0)

Approved With Reservations

Detection of yellow mosaic virus resistance in Soybean (Glycine max L.) genotypes for yield and related traits.

Title:
The article title needs to be changed because the word “Detection” is not relevant to screening and identifying resistance to the virus.

Introduction :
The importance of the YMV problem in soybeans needs to be emphasized in detail. Also, indicate the previously published information/references on molecular approaches for the confirmation of YMV resistance.

Methods:
The manuscript indicated that the virus was not confirmed as YMV before screening, so molecular confirmation is necessary.
Only 20 soybean genotypes/lines were screened, which is insufficient for testing disease resistance. Additionally, no standard scoring technique was followed for the assessment of YMV, and proper references for the scoring were not cited.
Resistance should be proved through vector transmission in addition to sap inoculation.
Only two markers were used. More SSR markers should have been included to obtain polymorphism.

Results:
The presence of resistance in the genotypes should also be further confirmed by PCR using Rsv1-h gene-specific primers.

Discussion:
The discussion does not address the relationship of YMV infection with AUDPC.
A more detailed discussion with recent supporting literature is necessary.

References require corrections as per Journal specification.
General Comments:
1. The English language is poor and needs improvement in sentence formation.
2. Consider outsourcing (language editing) to rewrite the article. This article requires substantial revisions to become academically valid.

Therefore, I recommend revising the manuscript to improve the language and include more relevant results and elaborate critical discussion. The mentioned shortcomings in the manuscript led me to consider it only for a "Research Note”.

Is the work clearly and accurately presented and does it cite the current literature?

Partly
Is the study design appropriate and is the work technically sound?

Partly
Are sufficient details of methods and analysis provided to allow replication by others?

No
If applicable, is the statistical analysis and its interpretation appropriate?

I cannot comment. A qualified statistician is required.
Are all the source data underlying the results available to ensure full reproducibility?

Partly
Are the conclusions drawn adequately supported by the results?

Partly

Competing Interests

No competing interests were disclosed.

Reviewer Expertise

Host Plant Resistance to Pathogens, Biological Control of plant diseases

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

Respond to this report

Responses (0)

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Detection of yellow mosaic virus resistance in Soybean (Glycine max L.) genotypes for yield and related traits

Abstract

Background

Methods

Results

Conclusion

Keywords

Introduction

Methods

Inoculation of virus in leaves

Scoring of soybean leaves

Table 1. Scoring of soybean leaves.

Statistical analysis for AUDPC (Area under disease progress curve)

Molecular marker analysis

Results

Molecular marker analysis

Table 2. List of SSR markers.

Analysis of SSR data

Figure 1. (A) Plants with no symptoms of Yellow mosaic virus, (B) yellow mottle up to 1-10% plants, (C) yellow mottle more than 50% plants.

Table 3. Performance of soybean genotypes after virus inoculation.

Figure 2. Relationship between Area under Disease progress curve (AUDPC) and %Infection in soybean genotypes.

Figure 3. The banding pattern of 15 soybean genotypes using the BARCSOYSSR_13_1173 SSR marker in SDS-PAGE indicates the presence of the dominant allele of the Rsv1-h gene.

Discussion

Performance of soybean genotypes after virus inoculation

Molecular detection using specific primer

Ethics and consent

Data availability

Underlying/extended data

Acknowledgements

References

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