Advances of QTL Localization and GWAS Application in Crop Resistances Against Plant-Parasitic Nematodes

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The manuscript entitled “Advances of QTL Localization and GWAS Application in Crop Resistances Against Plant-Parasitic Nematodes” addresses an important issue of yield losses caused by plant-parasitic nematodes. Overall, the work is of good; however, several major and minor typographical errors and reference inaccuracies need to be corrected.

Comment 1:

The manuscript does not have a clear purpose. A review manuscript should fill a gap by allowing a reader to access all the relevant information on a topic in one place.

Comment 2:

The text often relies on vague words such as "key," "vital," "crucial," and "essential."

Comment 3:

The manuscript lacks a clear structure. Sentences and topics are introduced without context or transition.

Comment 4: Perhaps the introduction should have a broader perspective, as this manuscript is not focusing on few crops only.

Comment 5: The manuscript should clarify the criteria used for selecting the two nematode species discussed, and provide a rationale for not including the root lesion nematode (Pratylenchus thornei).

Comment 6: The authors are advised to clearly describe the scope of the study, specifying which crops have been covered in this review as you mentioned in abstract “employed in crop resistance breeding”.

Comment 7: Authors missed a number of GWAS and QTL studies which have been published earlier. Some of them mentioned here,

1. Dababat, Abdelfattah, et al. "A GWAS to identify the cereal cyst nematode (Heterodera filipjevi) resistance loci in diverse wheat prebreeding lines." Journal of Applied Genetics 62.1 (2021): 93-98.
2. Singh, Vikas Kumar, et al. "GWAS scans of cereal cyst nematode (Heterodera avenae) resistance in Indian wheat germplasm." Molecular Genetics and Genomics 298.3 (2023): 579-601.

Hence, I ask author to re-evaluate the missing studies and include in manuscript.

Comment 8: I have a major concern regarding Table 1. Genes such as Cre and Rhg1 appear to have been identified using QTL/GWAS approaches? Are you sure? Please correct Table 1. I recommend that the authors divide the current table into two separate tables:

Table 1: Genes identified against PPNs.

Table 2: MTAs/QTLs identified against PPNs using GWAS and QTL mapping.

The legend for Table 1 should be revised accordingly.

Comment 9: All general information should be transferred to Table 1 and removed from the main text. The chromosomal locations and QTL/MTA names should not be mentioned in the text.

Comment 10: Please be more concrete about what novelty and perspectives each of these approaches can bring to the design of crop protection strategies, or how they have or can advance our understanding of plant-nematode interactions.

Comment 11: For each section, the authors sequentially list the findings of each publication they have consulted, but this reads more like a literature compilation that a critical review. Much can be summarised and presented in table form, or just supported by the given tables. Please do write a couple of sentences for each section on what you perceive are key findings or conclusions.

Comment 12: Title of manuscript and objective of manuscript “In this review, we explore the principles and limitations of QTL and GWAS technologies, summarize recent progress in their application to PPNs resistance, and provide a forward-looking perspective on the application of resistance genes in resistance breeding” did not match.

Comment 13: Please define all abbreviations the first time they are used.

 

Based on the manuscript as written and explained, a major concern regarding Table 1 is that it is contradictory, which affects the whole manuscript. Revise the structure of the manuscript, connect each paragraph, be more specific to the objective, do not write general things about QTL and GWAS mapping, be specific to the crops and nematode species, and include root lesion nematode.

I hope the comments provided will help you improve it accordingly. I have also highlighted these points in the attached PDF for your reference.

Comments for author File: Comments.pdf

Author Response

Response to Reviewer 1

Comment 1: The manuscript does not have a clear purpose. A review manuscript should fill a gap by allowing a reader to access all the relevant information on a topic in one place.

Response: We appreciate this important suggestion from the reviewer. The purpose of this review has now been clearly articulated in the abstract and introduction sections, emphasizing its role in integrating recent advances, identifying resistance genes, and applying quantitative trait loci (QTL) and genome-wide association studies (GWAS) for nematode resistance breeding. The revised manuscript this change can be found on page 1, lines 18-24, and page 2, lines 77-88.

lines 18-24 of the revised manuscript:

This review summarizes recent advances in QTL and GWAS applications for enhancing resistance to cyst nematodes (Heterodera glycines, H. filipjevi, and H. avenae), root-knot nematodes (Meloidogyne graminicola and M. incognita), and root-lesion nematodes (Pratylenchus spp.). It also evaluates the commercial deployment of resistance genes, discusses integrated breeding strategies, and highlights future research directions toward developing durable nematode-resistant crops.

lines 77-88 of the revised manuscript:

QTL mapping and GWAS have been applied to resistance breeding research across multiple crops, encompassing major food crops such as soybean, wheat, and rice, as well as numerous other food and cash crop systems. These approaches have identified numerous resistance-associated genes and genetic markers, providing a robust scientific foundation and practical tools for resistance breeding [21]. In this review, we summarize recent advances in the application of QTL mapping and GWAS for resistance to cyst nematodes in soybean, barley and wheat, root-knot nematodes in rice and tomato, and root-lesion nematodes in wheat. We further discuss emerging research directions, including the breeding of nematode-resistant varieties and genome editing approaches, with the aim of providing new strategies and insights for elucidating the genetic mechanisms underlying crop nematode resistance and for advancing resistance breeding.

Comment 2: The text often relies on vague words such as "key," "vital," "crucial," and "essential."

Response: We have revised the text to replace vague terms with more specific and descriptive language throughout the manuscript. The phrase “play a key role” has been deleted from line 156 of the revised draft; deleted “essential” in line 190,393 of the revised draft, and deleted “key” in line 361, 399 ,406 ,438 of the revised draft.

Comment 3: The manuscript lacks a clear structure. Sentences and topics are introduced without context or transition.

Response: We have restructured the manuscript to improve logical flow, added transitional sentences, and reorganized sections to enhance clarity and coherence. The revised manuscript this change can be found on page 3, lines 89-143.

lines 89-143 of the revised manuscript:

2. Comparing QTL Mapping and GWAS in PPNs Resistance

2.1. QTL Mapping in PPNs Resistance: Methodology and Constraints

QTL mapping has been applied to dissect the genetic basis of resistance against PPNs. This approach effectively identifies trait-associated genome regions within a specific population, particularly for traits governed by major effect loci or in hybrid populations with known parental lines [24]. Through QTL localization, researchers can identify candidate genes responsible for complex traits, providing valuable resources for developing molecular markers and thereby accelerating the breeding process [21]. In crops such as soybean, rice, wheat, barley, and tomato, QTL mapping has facilitated the identification of genomic regions associated with resistance to cyst nematodes, root-knot nematodes, and root-lesion nematodes (Table 1).

Nevertheless, QTL mapping faces several limitations in breeding crops for resistance to PPNs. The approach is time-consuming and generally offers low resolution due to limited recombination events, often resulting in broad genomic intervals that are challenging to implement directly in marker-assisted selection (Figure 1). In addition, its reliance on allelic variation between two parental lines restricts the detection of resistance alleles present in diverse germplasm. Consequently, although QTL mapping has identified major resistance loci such as Rhg1 and Mi-1, it remains less effective at capturing the polygenic and environmentally influenced nature of PPNs resistance across varied genetic backgrounds [25,26]. Advances in genome sequencing and the development of high-density molecular markers have partially mitigated these limitations, enabling finer mapping of resistance loci and providing more precise tools to support breeding programs.

2.2. GWAS in PPNs Resistance: Opportunities and Challenges

GWAS is a potent tool for identifying single-nucleotide polymorphisms (SNPs) associated with complex traits [21]. In contrast to QTL mapping, which is confined to bi-parental populations, GWAS can identify numerous SNPs associated with nematode resistance across diverse germplasm panels (Figure 1). For instance, GWAS has revealed resistance loci linked to cyst nematodes and root-knot nematodes, providing novel candidate genes and pathways for functional validation [27] (Table 1). These discoveries expand the pool of resistance sources for breeding and provide insights into the polygenic and complex nature of PPNs resistance.

However, GWAS also faces several challenges. Reliable identification of resistance loci requires large sample sizes, accurate phenotyping under nematode-infested conditions, and high-density genome-wide SNP coverage. Moreover, population structure and genetic heterogeneity can produce false-positive associations, necessitating rigorous statistical control. Despite these limitations, GWAS has proven to be a powerful approach for detecting resistance loci across diverse germplasm, complementing QTL mapping and enabling the integration of both methods to accelerate the development of PPNs-resistant cultivars (Figure 2).

Comment 4: Perhaps the introduction should have a broader perspective, as this manuscript is not focusing on few crops only.

Response: We have expanded the introduction to provide a broader context. The revised manuscript this change can be found on page 2, lines 77-88.

lines 77-88 of the revised manuscript:

QTL mapping and GWAS have been applied to resistance breeding research across multiple crops, encompassing major food crops such as soybean, wheat, and rice, as well as numerous other food and cash crop systems. These approaches have identified numerous resistance-associated genes and genetic markers, providing a robust scientific foundation and practical tools for resistance breeding [21]. In this review, we summarize recent advances in the application of QTL mapping and GWAS for resistance to cyst nematodes in soybean, barley and wheat, root-knot nematodes in rice and tomato, and root-lesion nematodes in wheat. We further discusse emerging research directions, including the breeding of nematode-resistant varieties and genome editing approaches, with the aim of providing new strategies and insights for elucidating the genetic mechanisms underlying crop nematode resistance and for advancing resistance breeding.

Comment 5: The manuscript should clarify the criteria used for selecting the two nematode species discussed, and provide a rationale for not including the root lesion nematode (Pratylenchus thornei).

Response: We have explaining the selection criteria for the nematode species and included the root lesion nematode (Pratylenchus thornei) to address this gap. The revised manuscript this change can be found on page 1, lines 31-38.

lines 31-38 of the revised manuscript:

 Among the threats to crop production, plant parasitic nematodes (PPNs) present significant challenges to agriculture and global food security [3]. To date, over 4,100 species of PPNs have been identified [4]. PPNs have been classified as sedentary or migratory based on their feeding behavior within the root systems [5]. Among the most destructive PPNs are root-knot nematodes (Meloidogyne spp.) and cyst nematodes (Heterodera spp.), and root-lesion nematodes (Pratylenchus spp.) [6]. Statistically, it is estimated that PPNs cause annual losses of up to $157 billion in global crop yields [7].

Comment 6: The authors are advised to clearly describe the scope of the study, specifying which crops have been covered in this review as you mentioned in abstract “employed in crop resistance breeding”.

Response: We have explicitly defined the scope of the review in the abstract and introduction, listing all crops covered. The revised manuscript this change can be found on page 1, lines 18-24, and page 2, lines 77-88.

lines 18-24 of the revised manuscript:

This review summarizes recent advances in QTL and GWAS applications for enhancing resistance to cyst nematodes (Heterodera glycines, H. filipjevi, and H. avenae), root-knot nematodes (Meloidogyne graminicola and M. incognita), and root-lesion nematodes (Pratylenchus spp.). It also evaluates the commercial deployment of resistance genes, discusses integrated breeding strategies, and highlights future research directions toward developing durable nematode-resistant crops.

lines 77-88 of the revised manuscript:

QTL mapping and GWAS have been applied to resistance breeding research across multiple crops, encompassing major food crops such as soybean, wheat, and rice, as well as numerous other food and cash crop systems. These approaches have identified numerous resistance-associated genes and genetic markers, providing a robust scientific foundation and practical tools for resistance breeding [21]. In this review, we summarize recent advances in the application of QTL mapping and GWAS for resistance to cyst nematodes in soybean, barley and wheat, root-knot nematodes in rice and tomato, and root-lesion nematodes in wheat. We further discusse emerging research directions, including the breeding of nematode-resistant varieties and genome editing approaches, with the aim of providing new strategies and insights for elucidating the genetic mechanisms underlying crop nematode resistance and for advancing resistance breeding.

Comment 7: Authors missed a number of GWAS and QTL studies which have been published earlier.

Response: We sincerely thank the reviewer for pointing out these omissions. We have now included the suggested references by Dababat et al. (2021) and Singh et al. (2023), along with other relevant studies, to provide a more comprehensive review. The revised manuscript this change can be found on citation [51] in Table 1, and page 10, lines 306-310

lines 306-310 of the revised manuscript:

Similarly, Vikas et al. [104] screened 141 Indian wheat genotypes and identified 33 genes like F-box-like domain superfamily, Cytochrome P450 superfamily, Leucine-rich repeat, cysteine-containing subtype Zinc finger RING/FYVE/PHD-type, etc., having a putative role in CCN resistance.

Comment 8: I have a major concern regarding Table 1. Genes such as Cre and Rhg1 appear to have been identified using QTL/GWAS approaches? Are you sure? Please correct Table 1.

Response: We apologize for the inaccuracy. We have corrected Table 1 and split it into two tables in lines :

Table 1: MTAs/QTLs identified against PPNs using GWAS and QTL mapping.

Table 2: Genes identified against PPNs.

The table legends have been revised accordingly.

Comment 9: All general information should be transferred to Table 1 and removed from the main text. The chromosomal locations and QTL/MTA names should not be mentioned in the text.

Response: We have moved general information into the Table 1 and streamlined the text to focus on analysis and interpretation. Deleted “and genetic analyses, localizing them in 1,2,6,7,9 and 11 chromosomes” in line 222-225 of the revised draft, and deleted “on 1AL,2AS,2BL,3AL,3BL,4AS,5AL....” and “on 2A, 3B, 4A, 5A....” in line 293,310 of the revised draft. The same revisions have been made elsewhere in the manuscript.

Comment 10: Please be more concrete about what novelty and perspectives each of these approaches can bring.

Response: We revised the relevant sections to explore the application of quantitative trait loci (QTL) and genome-wide association studies (GWAS) in screening plant nematode resistance genes. The revised manuscript this change can be found on page 3, lines 89-143.

lines 89-143 of the revised manuscript:

2. Comparing QTL Mapping and GWAS in PPNs Resistance

2.1. QTL Mapping in PPNs Resistance: Methodology and Constraints

QTL mapping has been applied to dissect the genetic basis of resistance against PPNs. This approach effectively identifies trait-associated genome regions within a specific population, particularly for traits governed by major effect loci or in hybrid populations with known parental lines [24]. Through QTL localization, researchers can identify candidate genes responsible for complex traits, providing valuable resources for developing molecular markers and thereby accelerating the breeding process [21]. In crops such as soybean, rice, wheat, barley, and tomato, QTL mapping has facilitated the identification of genomic regions associated with resistance to cyst nematodes, root-knot nematodes, and root-lesion nematodes (Table 1).

Nevertheless, QTL mapping faces several limitations in breeding crops for resistance to PPNs. The approach is time-consuming and generally offers low resolution due to limited recombination events, often resulting in broad genomic intervals that are challenging to implement directly in marker-assisted selection (Figure 1). In addition, its reliance on allelic variation between two parental lines restricts the detection of resistance alleles present in diverse germplasm. Consequently, although QTL mapping has identified major resistance loci such as Rhg1 and Mi-1, it remains less effective at capturing the polygenic and environmentally influenced nature of PPNs resistance across varied genetic backgrounds [25,26]. Advances in genome sequencing and the development of high-density molecular markers have partially mitigated these limitations, enabling finer mapping of resistance loci and providing more precise tools to support breeding programs.

2.2. GWAS in PPNs Resistance: Opportunities and Challenges

GWAS is a potent tool for identifying single-nucleotide polymorphisms (SNPs) associated with complex traits [21]. In contrast to QTL mapping, which is confined to bi-parental populations, GWAS can identify numerous SNPs associated with nematode resistance across diverse germplasm panels (Figure 1). For instance, GWAS has revealed resistance loci linked to cyst nematodes and root-knot nematodes, providing novel candidate genes and pathways for functional validation [27] (Table 1). These discoveries expand the pool of resistance sources for breeding and provide insights into the polygenic and complex nature of PPNs resistance.

However, GWAS also faces several challenges. Reliable identification of resistance loci requires large sample sizes, accurate phenotyping under nematode-infested conditions, and high-density genome-wide SNP coverage. Moreover, population structure and genetic heterogeneity can produce false-positive associations, necessitating rigorous statistical control. Despite these limitations, GWAS has proven to be a powerful approach for detecting resistance loci across diverse germplasm, complementing QTL mapping and enabling the integration of both methods to accelerate the development of PPNs-resistant cultivars (Figure 2).

Comment 11: For each section, the authors sequentially list the findings of each publication they have consulted, but this reads more like a literature compilation that a critical review. Much can be summarised and presented in table form, or just supported by the given tables. Please do write a couple of sentences for each section on what you perceive are key findings or conclusions.

Response: We have revised each section to include critical summaries, key findings, and conclusions, reducing mere listing of studies. The revised manuscript this change can be found on page 5, lines 178-182; page 7, lines 207-213; page 7, lines 230-237; page 9, lines 264-266; page 9, lines 282-288; page 10, lines 306-314; page 10, lines 327-329; page 10, lines 342-344; page 11, lines 362-364; page 11, lines 376-3478; page 11, lines 385-387; page 11, lines 394-396.

lines 178-182 of the revised manuscript:

In summary, the functional characterization of genes such as GmSNAP18, GmSHMT08, GmSNAP11, and GmSNAP02, identified through QTL mapping, has led to substantive progress in elucidating the molecular mechanisms of resistance to SCN. The MTAs or QTLs used in breeding for PPNs resistance are shown in Table 1, and the genes identified against PPNs are shown in Table 2.

lines 207-213 of the revised manuscript:

In summary, nine genes conferring resistance to CCN (Cre1-Cre8, Cre8V) have been characterized, while CreV, CreY, and CreR represent more recent discoveries. By contrast, Rlnn1 remains the sole gene reported for RLN resistance in wheat. Despite the limited genetic diversity of known resistance sources, advances in genomics and the utilization of global wheat germplasm, including wild relatives, provide promising prospects for developing durable resistance to CCN and RLN.

lines 230-237 of the revised manuscript:

Mapping-based cloning and functional analyses demonstrated that MG1 encodes a coiled-coil, nucleotide-binding, and leucine-rich repeat (CC-NB-LRR) protein. Loss-of-function mutations specifically within the LRR domain resulted in a complete loss of resistance, establishing that this domain is indispensable for nematode-resistance [73]. Compared with the QTL mapping of resistance to CCN and SCN, few resistance genes have been identified for RRKN. Only MG1 was identified to confer resistance to RRKN, underscoring the need for further exploration of genetic resources and novel resistance mechanisms.

lines 264-266 of the revised manuscript:

However, resistance conferred by Mi genes is often overcome by high temperatures and SRKN variability, highlighting the need to validate novel QTLs and identify major-effect genes for broader, durable resistance.

lines 282-288 of the revised manuscript:

Compared with QTL mapping, GWAS has advanced the identification of novel genetic loci beyond the major-effect QTLs Rhg1 and Rhg4, providing valuable molecular markers for breeding. Nevertheless, many associated SNPs account for only minor phenotypic variation and require functional validation. In addition, population structure and allelic heterogeneity often limit the reproducibility of GWAS-identified genes across diverse genetic backgrounds, constraining their direct application in marker-assisted selection.

lines 306-314 of the revised manuscript:

Similarly, Vikas et al. [104] screened 141 Indian wheat genotypes and identified 33 genes like F-box-like domain superfamily, Cytochrome P450 superfamily, Leucine-rich repeat, cysteine-containing subtype Zinc finger RING/FYVE/PHD-type, etc., having a putative role in CCN resistance. Recently, a study utilizing 152K SNP microarrays to perform GWAS on 188 wheat accessions identified 11 resistance markers [105]. Collectively, GWAS have uncovered numerous marker-trait associations for wheat CCN resistance, but genome complexity, population structure, and environmental effects limit reproducibility and necessitate further validation before application in breeding.

lines 327-329 of the revised manuscript:

Overall, GWAS for RRKN have substantially expanded the genetic resource pool for resistance by identifying multiple novel loci and candidate genes.

lines 342-344 of the revised manuscript:

These GWAS have elucidated the complex genetic architecture of SRKN resistance, identifying both novel genomic regions and candidate genes with putative biological functions.

lines 362-364 of the revised manuscript:

The success of Rhg1 and Rhg4, mediated by copy number variation (CNV), highlights the potential of natural genetic variation for SCN resistance in soybean.

lines 376-378 of the revised manuscript:

Distant hybridization of wheat with wild relatives diversifies CCN resistance, enabling gene pyramiding for more durable and broad-spectrum protection against evolving pathogen populations.

lines 385-387 of the revised manuscript:

Cloning of MG1 marks a breakthrough in rice RRKN resistance, but durable protection likely requires pyramiding with minor-effect QTLs to build a resilient genetic barrier.

lines 394-396 of the revised manuscript:

Overall, the successful introgression of the Mi gene into commercial tomato varieties represents a landmark achievement in breeding for nematode resistance.

Comment 12: Title of manuscript and objective of manuscript “In this review, we explore the principles and limitations of QTL and GWAS technologies, summarize recent progress in their application to PPNs resistance, and provide a forward-looking perspective on the application of resistance genes in resistance breeding” did not match.

Response: We have revised the title and objectives to ensure consistency and clarity. The revised manuscript this change can be found on page 3, lines 89-143.

lines 89-143 of the revised manuscript:

2. Comparing QTL Mapping and GWAS in PPNs Resistance

2.1. QTL Mapping in PPNs Resistance: Methodology and Constraints

QTL mapping has been applied to dissect the genetic basis of resistance against PPNs. This approach effectively identifies trait-associated genome regions within a specific population, particularly for traits governed by major effect loci or in hybrid populations with known parental lines [24]. Through QTL localization, researchers can identify candidate genes responsible for complex traits, providing valuable resources for developing molecular markers and thereby accelerating the breeding process [21]. In crops such as soybean, rice, wheat, barley, and tomato, QTL mapping has facilitated the identification of genomic regions associated with resistance to cyst nematodes, root-knot nematodes, and root-lesion nematodes (Table 1).

Nevertheless, QTL mapping faces several limitations in breeding crops for resistance to PPNs. The approach is time-consuming and generally offers low resolution due to limited recombination events, often resulting in broad genomic intervals that are challenging to implement directly in marker-assisted selection (Figure 1). In addition, its reliance on allelic variation between two parental lines restricts the detection of resistance alleles present in diverse germplasm. Consequently, although QTL mapping has identified major resistance loci such as Rhg1 and Mi-1, it remains less effective at capturing the polygenic and environmentally influenced nature of PPNs resistance across varied genetic backgrounds [25,26]. Advances in genome sequencing and the development of high-density molecular markers have partially mitigated these limitations, enabling finer mapping of resistance loci and providing more precise tools to support breeding programs.

2.2. GWAS in PPNs Resistance: Opportunities and Challenges

GWAS is a potent tool for identifying single-nucleotide polymorphisms (SNPs) associated with complex traits [21]. In contrast to QTL mapping, which is confined to bi-parental populations, GWAS can identify numerous SNPs associated with nematode resistance across diverse germplasm panels (Figure 1). For instance, GWAS has revealed resistance loci linked to cyst nematodes and root-knot nematodes, providing novel candidate genes and pathways for functional validation [27] (Table 1). These discoveries expand the pool of resistance sources for breeding and provide insights into the polygenic and complex nature of PPNs resistance.

However, GWAS also faces several challenges. Reliable identification of resistance loci requires large sample sizes, accurate phenotyping under nematode-infested conditions, and high-density genome-wide SNP coverage. Moreover, population structure and genetic heterogeneity can produce false-positive associations, necessitating rigorous statistical control. Despite these limitations, GWAS has proven to be a powerful approach for detecting resistance loci across diverse germplasm, complementing QTL mapping and enabling the integration of both methods to accelerate the development of PPNs-resistant cultivars (Figure 2).

Comment 13:  Please define all abbreviations the first time they are used.

Response: We have ensured that all abbreviations are defined upon first use throughout the manuscript.

We believe that the revised manuscript has been significantly improved thanks to the reviewers’ valuable comments. We look forward to your positive consideration.

Reviewer 2 Report

Comments and Suggestions for Authors

This is a well-structured review on plant nematode resistance. However, some of the references cited are quite outdated, such as ref # 6, 9, 67 and 77 that would need updating with information that is more recent. QTL mapping involves bi- and multi-parental populations but the latter was not mentioned in the review. Figure 1 therefore should be updated accordingly (such as replacing "biparental populations" with "mapping populations" or "bi- and multi-parent populations"). My other editorial suggestions include:
Line 75: replace "variations" with "variants"
Line 113: replace "genetic background" with "pedigrees"
Line 229: replace "quantitative trait locus (QTL)" with "QTL" because the term QTL was already defined earlier in the MS
Line 397: give a full name for "IoT" 
Table 1: Replace "Cereal Species" with "Plant Species" in the top row.

Author Response

Response to Reviewer 2

Comment 1: Some references are outdated.

Response: We have updated references [3], [5], [6], [7], [14], [16], [19], [20], [21], [22], [23], [24], [40], [92] with more recent and relevant literature.

Comment 2: QTL mapping involves bi- and multi-parental populations but the latter was not mentioned.

Response: We have added a discussion on multi-parent populations and updated Figure 1 accordingly, replacing “biparental populations” with “mapping populations” to be more inclusive. The revised manuscript this change can be found on page 3, lines 99.

Comment 3: Editorial suggestions:

The revised manuscript:

Line 76: we have replaced “variations” with “variants”

Line 128: we have replaced “genetic background” with “pedigrees”

Line 225: we have replaced “quantitative trait locus (QTL)” with “QTL”

Line 418: we have replaced “IoT” with “Long Range-based Internet of Things (LoRa-based IoT) networks”

Table 1 and Table 2: we have replaced “Cereal Species” with “Plant Species”

We believe that the revised manuscript has been significantly improved thanks to the reviewers’ valuable comments. We look forward to your positive consideration.

Reviewer 3 Report

Comments and Suggestions for Authors

Revisions

1. Line 31-32: “ While some plant parasitic nematodes 31 (PPNs), present significant challenges to agriculture and human health”. This sentence seems incomplete.
2. Line 37: The citation [8] is not complete: Genomics and Molecular Genetics of Plant-Nematode Interactions; 2011; pp. 1-557.
3. Line 38: The citation [9] is from 2013 and needs to be more recent.
4. Line 61: Citation [18] Boerma, H.R.; Hussey, R.S. BREEDING PLANTS FOR RESISTANCE TO NEMATODES. Journal of Nematology 1992, 24, 242-252. Change it to appropriate capitalization.
5. Line 123-124 and 132-133: These two sentences are basically same.
6. Line 167: Citation [44] seems incomplete: Liu, S.M.; Kandoth, P.K.; Warren, S.D.; Yeckel, G.; Heinz, R.; Alden, J.; Yang, C.L.; Jamai, A.; El-Mellouki, T.; Juvale, P.S.; et al. A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens. Nature 2012, 492, 256 +.[http://doi.org/10.1038/nature11651]
7. Table 1: On Rice-root-knot-nematode (RRKN) section, some gene names are missing.
8. The citations in the table are not sequential and need to be corrected. Although the table appears in the middle of the text, its references are listed only at the end
9. Line 184-186: “The first 184 gene conferring resistance to CCN was identified in barley [51]. However, relatively few 185 quantitative trait loci (QTL) associated with CCN resistance have been identified in wheat.” This sentence doesn’t make sense.
10. Line 206: globally.. Remove one extra full stop.
11. Line 249: RESISTANCe. Change it to RESISTANCE
12. Line 253-254:” leading to the identification of 84,416 SNP markers associated with resistance”. This doesn’t seem right.
13. Line 314-315:”Similarly, GWAS analysis of SRKN phenotypes in 193 soybean varieties was performed, resulting in the identification and validation of 46,196 SNP markers [83]”. The SNP numbers doesn’t make sense.
14. Line 328: Citation [84]: Tylka, G.L.; Mullaney, M.P. Soybean cyst nematode-resistant soybean varieties for Iowa; Iowa State University, University Extension: 2002. Is the formatting correct.
15. Line 347: Citation [88]: Ogbonnaya, F.C.; Seah, S.; Delibes, A.; Jahier, J.; López-Braña, I.; Eastwood, R.F.; Lagudah, E.S. Molecular-genetic characterisation of a new nematode resistance gene in wheat. Theoretical and Applied Genetics 2001, 102, 623-629.[http://doi.org/10.1007/s001220051689]. Check the formatting.
16. Line 359: the cloning technology for the Mi gene has matured. Change this phrase in understandable way.
17. Line 359: Citation [89]: Aramov, M.K.; Dzhuraeva, L. Breeding Meloidogyne-resistant tomato varieties with a jointless pedicel. 1991, . This citation is incomplete.
18. Line 401: Correct 6. Conclusions
19. Avoid putting citations and new ideas in conclusions section.
20. In figure captions, give full form of abbreviations since the captions should be self-explanatory.

 

 

 

 

 

Author Response

Response to Reviewer 3

Comment 1: Line 31-32: “ While some plant parasitic nematodes 31 (PPNs), present significant challenges to agriculture and human health”. This sentence seems incomplete.

Response: We have rephrased the sentence for clarity and completeness. The revised manuscript this change can be found on page 1, lines 31-38.

lines 31-38 of the revised manuscript:

Among the threats to crop production, plant parasitic nematodes (PPNs) present significant challenges to agriculture and global food security [3]. To date, over 4,100 species of PPNs have been identified [4]. PPNs have been classified as sedentary or migratory based on their feeding behavior within the root systems [5]. Among the most destructive PPNs are root-knot nematodes (Meloidogyne spp.) and cyst nematodes (Heterodera spp.), and root-lesion nematodes (Pratylenchus spp.) [6]. Statistically, it is estimated that PPNs cause annual losses of up to $157 billion in global crop yields [7].

Comment 2: Line 37: The citation [8] is not complete: Genomics and Molecular Genetics of Plant-Nematode Interactions; 2011; pp. 1-557.

Response: We apologize for the oversight. All reference has be completed according to the required journal style.

Comment 3: Line 38: The citation [9] is from 2013 and needs to be more recent.

Response: We have updated references [3], [5], [6], [7], [9], [14], [16], [19], [20], [21], [22], [23], [24], [40], [92] with more recent and relevant literature. All reference has be completed according to the required journal style.

Comment 4: Line 61: Citation [18] Boerma, H.R.; Hussey, R.S. BREEDING PLANTS FOR RESISTANCE TO NEMATODES. Journal of Nematology 1992, 24, 242-252. Change it to appropriate capitalization.

Response: Agreed. All reference has be completed according to the required journal style.

Comment 5: Line 123-124 and 132-133: These two sentences are basically same.

Response: Thank you for catching this duplication. This is an important edit. We have removed the redundant sentence and rephrased the paragraph to ensure clarity and avoid repetition. The revised manuscript this change can be found on page 4, lines 136-138.

Comment 6: Line 167: Citation [44] seems incomplete: Liu, S.M.; Kandoth, P.K.; Warren, S.D.; Yeckel, G.; Heinz, R.; Alden, J.; Yang, C.L.; Jamai, A.; El-Mellouki, T.; Juvale, P.S.; et al. A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens. Nature 2012, 492, 256 +.[http://doi.org/10.1038/nature11651]

Response: Agreed. All reference has be completed according to the required journal style.

Comment 7: Table 1: On Rice-root-knot-nematode (RRKN) section, some gene names are missing.

Response: Thank you. We have reviewed the primary literature and filled in all missing gene names in the Table 1.

Comment 8: The citations in the table are not sequential and need to be corrected. Although the table appears in the middle of the text, its references are listed only at the end

Response: We have ensured that all citation numbers in the tables remain updated and consistent with the final reference list in the main text. These numbers will undergo cross-checking during the final proofreading stage.

Comment 9: Line 184-186: “The first 184 gene conferring resistance to CCN was identified in barley [51]. However, relatively few 185 quantitative trait loci (QTL) associated with CCN resistance have been identified in wheat.” This sentence doesn’t make sense.

Response: We have rephrased the sentence for clarity and completeness. The revised manuscript this change can be found on page 7, lines 193-194.

lines 193-194 of the revised manuscript:

Few QTL associated with CCN/RLN resistance have been identified in wheat (Table 1).

Comment 10: Line 206: globally.. Remove one extra full stop.

Response: We have made the necessary modifications. The revised manuscript this change can be found on page 7, lines 216.

Comment 11: Line 249: RESISTANCe. Change it to RESISTANCE

Response: We have made the necessary modifications. The revised manuscript this change can be found on page 9, lines 267.

Comment 12: Line 253-254:” leading to the identification of 84,416 SNP markers associated with resistance”. This doesn’t seem right.

Response: We have rephrased the sentence for clarity and completeness. The revised manuscript this change can be found on page 9, lines 270-272.

lines 270-272 of the revised manuscript:

For instance, Wen et al. [99] genotyped 363 accessions, with association mapping revealing resistance-linked markers and a homozygous gene cluster at the soybean Rhg1 locus.

Comment 13: Line 314-315:”Similarly, GWAS analysis of SRKN phenotypes in 193 soybean varieties was performed, resulting in the identification and validation of 46,196 SNP markers [83]”. The SNP numbers doesn’t make sense.

Response: We have rephrased the sentence for clarity and completeness. The revised manuscript this change can be found on page 10, lines 338-342.

lines 338-342 of the revised manuscript:

Similarly, GWAS analysis of SRKN phenotypes in 193 soybean varieties was performed [109]. Among these, three most significant SNPs were all localized within Glyma10g017100, which encodes a bifunctional protein containing two distinct structural domains: a pectin esterase (PEC)-like domain and a pectin methyl esterase inhibitor (PMI) domain. Notably, these resistance loci were all localized within a small (3.4 kb) region of chromosome 10.

Comment 14: Line 328: Citation [84]: Tylka, G.L.; Mullaney, M.P. Soybean cyst nematode-resistant soybean varieties for Iowa; Iowa State University, University Extension: 2002. Is the formatting correct.

Response: Agreed. All reference has be completed according to the required journal style.

Comment 15: Line 347: Citation [88]: Ogbonnaya, F.C.; Seah, S.; Delibes, A.; Jahier, J.; López-Braña, I.; Eastwood, R.F.; Lagudah, E.S. Molecular-genetic characterisation of a new nematode resistance gene in wheat. Theoretical and Applied Genetics 2001, 102, 623-629.[http://doi.org/10.1007/s001220051689]. Check the formatting.

Response: Agreed. All reference has be completed according to the required journal style.

Comment 16: Line 359: the cloning technology for the Mi gene has matured. Change this phrase in understandable way.

Response: We have rephrased the sentence for clarity and completeness. The revised manuscript this change can be found on page 11, lines 389-390.

lines 389-390 of the revised manuscript:

Advances in molecular biology will broaden the application of Mi gene cloning in the development of resistant varieties. 

Comment 17: Line 359: Citation [89]: Aramov, M.K.; Dzhuraeva, L. Breeding Meloidogyne-resistant tomato varieties with a jointless pedicel. 1991, . This citation is incomplete.

Response: Agreed. All reference has be completed according to the required journal style.

Comment 18: Line 401: Correct 6. Conclusions

Response: We have made the necessary modifications. The revised manuscript this change can be found on page 14, line 435.

Comment 19: Avoid putting citations and new ideas in conclusions section.

Response: We have revised the conclusion section to ensure it only summarizes the key findings presented in the manuscript without introducing new concepts or citations. The revised manuscript this change can be found on page 14, line 436-453.

lines 436-453 of the revised manuscript:

In crop breeding strategies, the identification of gene loci or potential candidate genes is considered for optimizing traits. Pinpointing gene loci and cloning QTLs have helped to reveal the functional basis of plant phenotypes over the last decade. Additionally, GWAS has successfully identified thousands of genetic loci associated with agronomic traits and other characteristics of crops, and multiple methods have been developed to improve resolving power and computational efficiency. By integrating identified QTL with GWAS results, PPNs resistance research can be more effectively advanced, thus achieving more efficient resistance breeding goals. Future work should aim to integrate transcriptomic, proteomic, and metabolomic data to comprehensively analyze plant defense mechanisms against parasitic nematodes. By comparing gene expression patterns under different environmental conditions, researchers can screen for more potent resistance markers and candidate genes. The continued advancement of genomic technologies, combined with interdisciplinary approaches integrating multiple omics platforms, will undoubtedly accelerate the development of crop varieties with enhanced resistance to plant-parasitic nematodes. These developments will contribute significantly to sustainable agricultural practices and global food security in the face of increasing population pressure and environmental challenges.

Comment 20: In figure captions, give full form of abbreviations since the captions should be self-explanatory.

Response: We have made the necessary modifications. The revised manuscript this change can be found on page 3, line 101-102; page 4,line 126-127; page 13, line 423.

lines 101-102 of the revised manuscript:

Figure 1. Comparison of quantitative trait loci mapping and genome-wide association study analysis in plant-parasitic nematodes resistance.

lines 126-127 of the revised manuscript:

Figure 2. The principles of quantitative trait loci mapping and genome-wide association study analysis in plant-parasitic nematodes resistance.

line 423 of the revised manuscript:

Figure 3. New strategies in breeding crops for resistance to plant-parasitic nematodes.

We believe that the revised manuscript has been significantly improved thanks to the reviewers’ valuable comments. We look forward to your positive consideration.