Genome-Wide Linkage Mapping of QTL for Adult-Plant Resistance to Stripe Rust in a Chinese Wheat Population Lantian 25 × Huixianhong

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

There is a lot of scope to improve introduction, methods, results and discussion. 

Comments for author File: Comments.pdf

Author Response

Line 28: Try to mention Huixianhong as a susceptible parent.

Response: Accepted. We have mentioned Huixianhong as the susceptible parent and Lantian 25 as the resistance parent in abstract.

Line 68-69: Try to discuss these APR genes, in terms of their locations, cloning, effectiveness, use, and if any vir rported anywhere; Thirteen APR genes at various loci have been identified, some with pleiotropic effects conferring resistance to other diseases [4].

Response: Accepted. We sincerely appreciate your valuable suggestions on the manuscript. We have supplemented the information on the currently reported APR genes according to your suggestions, as detailed below. We sincerely appreciate your suggestions, which have significantly enhanced the readability of the manuscript.

To date, a total of 86 officially named stripe rust resistance genes have been identified, among which 19 are adult plant resistance genes, including Yr18 (7DS), Yr29 (1BL), Yr30 (3BS), Yr34 (5AL), Yr46 (4DL), Yr48 (5AL), Yr49 (3DS), Yr54 (2DL), Yr56 (2AS), Yr58 (3BS), Yr60 (4AL), Yr68 (4BL), Yr71 (3DL), Yr75 (7AL), Yr77 (6DS), Yr78 (6BS), Yr80 (3BL), Yr83 (6RL), and Yr86 (2AL). In addition, Yr36 (6BS), Yr39 (7BL), Yr52 (7BL), Yr59 (7BL), Yr62 (4BL), and Yr79 (7BL) are high-temperature adult plant (HTAP) resistance genes against stripe rust. Additionally, Yr18/Lr34/Sr57/Pm38, Yr29/Lr46/Sr58/Pm39, Yr30/Lr27/Sr2/Pm70, and Yr46/Lr67/Sr55/Pm46 are pleiotropic genes, which have been widely utilized in breeding alongside all-stage resistance genes such as Yr5, Yr10, Yr15, and Yr24/Yr26/YrCH42. To date, the successfully cloned genes include Yr5 (Marchal et al. 2018), Yr10 (Liu et al. 2014), Yr15 (Klymiuk et al. 2018), YrU1 (Wang et al. 2020), Yr27 (Athiyannan et al., 2022), Yr28 (Zhang et al., 2019), Yr36 (Fu et al. 2009), Yr18 (Krattinger et al. 2009), Yr46 (Moore et al. 2015), and YrNAM (Ni et al., 2023).

10. Liu, Z.; Zhang, H.; Bai, B.; et al. Current Status and Strategies for Utilization of Stripe Rust Resistance Genes in Wheat Breeding Program of China. Scientia Agricultura Sinica 2024, 57(1), 34–51.
11. Kumar, S.; Saini, D.K.; Jan, F.; Jan, S.; Tahir, M.; Djalovic, I.; et al. Comprehensive meta-QTL analysis for dissecting the genetic architecture of stripe rust resistance in bread wheat. BMC Genomics 2023, 24(1), 259.
12. Jan, I.; Saripalli, G.; Kumar, K.; Kumar, A.; Singh, R.; Batra, R.; et al. Meta-QTLs and candidate genes for stripe rust resistance in wheat. Sci. Rep. 2021, 11(1), 22923.
13. Marchal, C.; Zhang, J.; Zhang, P.; Fenwick, P.; Steuernagel, B.; Adamski, N.M.; et al. BED-domain-containing immune receptors confer diverse resistance spectra to yellow rust. Nat. Plants 2018, 4(9), 662–668.
14. Liu, W.; Frick, M.; Huel, R.; Nykiforuk, C.L.; Wang, X.; Gaudet, D.A.; et al. The stripe rust resistance gene Yr10 encodes an evolutionary-conserved and unique CC–NBS–LRR sequence in wheat. Mol. Plant 2014, 7(12), 1740–1755.
15. Klymiuk, V.; Yaniv, E.; Huang, L.; Raats, D.; Fatiukha, A.; Chen, S.; et al. Cloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase family. Nat. Commun. 2018, 9(1), 3735.
16. Wang, H.; Zou, S.; Li, Y.; Lin, F.; Tang, D. An ankyrin-repeat and WRKY-domain-containing immune receptor confers stripe rust resistance in wheat. Nat. Commun. 2020, 11(1), 1353.
17. Fu, D.; Uauy, C.; Distelfeld, A.; Blechl, A.; Epstein, L.; Chen, X.; et al. A kinase-START gene confers temperature-dependent resistance to wheat stripe rust. Science 2009, 323(5919), 1357–1360.
18. Krattinger, S.G.; Lagudah, E.S.; Spielmeyer, W.; Singh, R.P.; Huerta-Espino, J.; McFadden, H.; et al. A putative ABC transporter confers durable resistance to multiple fungal pathogens in wheat. Science 2009, 323(5919), 1360–1363.
19. Moore, J.W.; Herrera-Foessel, S.; Lan, C.; Schnippenkoetter, W.; Ayliffe, M.; Huerta-Espino, J.; et al. A recently evolved hexose transporter variant confers resistance to multiple pathogens in wheat. Nat. Genet. 2015, 47(12), 1494–1498.
20. Zhang, C.; Huang, L.; Zhang, H.; Hao, Q.; Lyu, B.; Wang, M.; et al. An ancestral NB-LRR with duplicated 3′ UTRs confers stripe rust resistance in wheat and barley. Nat. Commun. 2019, 10(1), 4023.
21. Ni, F.; Zheng, Y.; Liu, X.; Yu, Y.; Zhang, G.; Epstein, L.; et al. Sequencing trait-associated mutations to clone wheat rust-resistance gene YrNAM. Nat. Commun. 2023, 14(1), 4353.
22. Athiyannan, N.; Abrouk, M.; Boshoff, W.H.; Cauet, S.; Rodde, N.; Kudrna, D.; et al. Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning. Nat. Genet. 2022, 54(3), 227–231.
23. Wen, W.; He, Z.; Gao, F.; Liu, J.; Jin, H.; Zhai, S.; et al. A high-density consensus map of common wheat integrating four mapping populations scanned by the 90K SNP array. Front. Plant Sci. 2017, 8, 1389.
24. Liu, J.; He, Z.; Wu, L.; Bai, B.; Wen, W.; Xie, C.; Xia, X. Genome-wide linkage mapping of QTL for black point reaction in bread wheat (Triticum aestivum L.). Theor. Appl. Genet. 2016, 129(11), 2179–2190.
25. Meng, L.; Li, H.; Zhang, L.; Wang, J. QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. Crop J. 2015, 3(3), 269–283.

Line 69-71: Provide reference for this: Over the past two decades, more than 353 Quantitative trait loci (QTL) for YR resistance have been identified across 49 chromosomal regions (Ref.). Authors didn’t cite any study on the methods of SNP genotyping and QTL mapping, which is important for them to understand the methods by going through & citing the related studies. Also, this will improve manuscript for the ease of readers.

Response: Accepted. We have supplemented the relevant references. Firstly, we added references to the reported QTL loci and genes in the introduction section (Liu et al., 2024). Secondly, we included references on genotyping (Wen et al., 2016; Liu et al., 2016) and QTL mapping (Meng et al., 2015) in the methods section. In addition, we reviewed the entire manuscript and addressed related issues in both the introduction and discussion sections. The specific references are as follows. The readability of the paper has been significantly improved after these revisions, and we are particularly grateful for your valuable suggestions.

Line 192: The 3B chromosome is rich in stripe rust resistance gene or genes. Over 15 loci for stripe rust.

Response: Accepted. We have added the references here, many thanks for your kindly reminder.

The reference list:

10. Liu, Z.; Zhang, H.; Bai, B.; et al. Current Status and Strategies for Utilization of Stripe Rust Resistance Genes in Wheat Breeding Program of China. Scientia Agricultura Sinica 2024, 57(1), 34–51.
11. Kumar, S.; Saini, D.K.; Jan, F.; Jan, S.; Tahir, M.; Djalovic, I.; et al. Comprehensive meta-QTL analysis for dissecting the genetic architecture of stripe rust resistance in bread wheat. BMC Genomics 2023, 24(1), 259.
12. Jan, I.; Saripalli, G.; Kumar, K.; Kumar, A.; Singh, R.; Batra, R.; et al. Meta-QTLs and candidate genes for stripe rust resistance in wheat. Sci. Rep. 2021, 11(1), 22923.
13. Marchal, C.; Zhang, J.; Zhang, P.; Fenwick, P.; Steuernagel, B.; Adamski, N.M.; et al. BED-domain-containing immune receptors confer diverse resistance spectra to yellow rust. Nat. Plants 2018, 4(9), 662–668.

Line 201: Sever or seven loci for stripe rust resistance were identified on chromosome 4BL, including. There is no mention of methods used in data collection, at what stage APR data was collected and using which scale? The presence of APR genes Yr18, Yr29, Yr46, Yr78 and Yr80 not ruled out in the resistant parent Lantian 25, using linked available molecular markers. Adding these results will make the study robust and reliable.

Response: Thank you very much for your suggestions. On chromosome 4BL, there are at least 10 or more stripe rust resistance loci in wheat. These loci have all been previously reported and are associated with adult plant resistance. Due to the broad scope of these studies, a variety of materials and methods were employed, including linkage analysis, association analysis, and QTL-seq. Additionally, the criteria for identification varied, such as MDS, AUDPC, or a 0–10 scale. We did not compile a comprehensive table to discuss these loci here, primarily because we were concerned that excessive discussion of these known loci might detract from the reader's experience. Therefore, we chose not to include detailed information. However, we have supplemented the relevant references at the end of the article. If readers are interested in further research on these loci, they can refer to the provided references for additional insights.

Yr18 (7D), Yr29 (1B), Yr46 (4D), Yr78 (6B), Yr26 (1B), Yr30 (3BS), and Yr80 (3B) are important stripe rust resistance genes. We have statistically analyzed the physical locations of these genes. In our experimental work, we collaborated with Professor Lan Caixia (CIMMYT-Huazhong Agricultural University) to test for the presence of these resistance alleles in Lantian 25, but none were detected. Since these genes are not located in the same region as QYr.gaas-4BL or the loci identified in this study, we did not include this information in the original manuscript. In the revised version of the article, we have added relevant content to the discussion section.

In summary, there is a lot of scope to improve introduction, methods, results and discussion.

Response: Accepted. We sincerely appreciate your valuable suggestions on the manuscript. We have made comprehensive revisions to the Introduction, Methods, Results, and Discussion sections based on your suggestions. This includes adding supplementary content and references, revising inappropriate phrasing, correcting grammatical errors, and more. All changes have been marked using the track changes feature for your review. We sincerely appreciate your advice and assistance, as the quality and readability of the manuscript have significantly improved. Thank you once again for your support.

Reviewer 2 Report

Comments and Suggestions for Authors

The article deals with the identification of QTLs for stripe rust in the wheat RIL population. It may be important for introduction of target regions from Lantian 25 wheat or accumulation of advantageous alleles. 

In introduction citations for 160 QTLs and 49 chromosomal regions (line 71) appear to be missing. 

In results section, the number of genes annotated in the QTL region should be given so that we can know how likely the candidate gene is. Figure 1 should be clearer. 

Methods should be supplemented with information:

Is Lantian 25 spring or winter wheat?, description of the source of the expression data and phases/organs selected; description of the phenotyping method of 111 varieties (but some results are shown in Table 3).

Text needs some corrections i.e. Latin species names in italics (lines 23, 24), some editorial errors (lines 114, 195, 201, 219), table numbers changed (132, 162).

Author Response

The article deals with the identification of QTLs for stripe rust in the wheat RIL population. It may be important for introduction of target regions from Lantian 25 wheat or accumulation of advantageous alleles.

1 In introduction citations for 160 QTLs and 49 chromosomal regions (line 71) appear to be missing.

Response: Accepted. We sincerely appreciate your valuable suggestions on the manuscript. We have added relevant references to the revised article. Additionally, we have thoroughly reviewed the entire manuscript, supplemented new content, and included multiple references in the Introduction, Methods, and Discussion sections. Details are as follows. Once again, thank you for your suggestions.

 

2 In results section, the number of genes annotated in the QTL region should be given so that we can know how likely the candidate gene is. Figure 1 should be clearer.

Response: Accepted. Thank you very much for your valuable suggestions. We have supplemented Table S2, which lists all possible candidate genes within the segment. These genes are located within the confidence interval, have annotation information, and may be associated with known fungal disease resistance pathways in wheat. Additionally, we would like to explain that the wheat genome is highly complex, with a chromosome size of approximately 16.8 Gb, containing a large number of repetitive sequences, as well as genetic fragment deletions and inversions. The genetic loci we identified have relatively broad physical segments and are rich in annotated genes. Therefore, it is necessary to construct secondary populations, perform fine mapping, identify genetic differences, and validate transcriptional expression to preliminarily determine the target genes of these loci. Thus, the candidate gene information provided in this study mainly serves as a reference for readers, and substantial work is still required to complete the cloning of the target genes. We have already initiated related work, creating secondary populations F_2:3 and F₃, and developing KASP markers to narrow down the genetic interval. We will report these findings in further researchers. Regarding the results and the cloning of wheat candidate genes, we have made relevant additions to the Results and Discussion sections. Please review these updates.

For Figure 1, this figure is derived from a public database (https://www.wheat-expression.com/) that contains expression data from different wheat organs and developmental stages. We have redrawn the figure in the database, maintaining as high a resolution as possible. Once again, we sincerely appreciate your help and guidance, which have provided us with many highly valuable suggestions.

3 Methods should be supplemented with information:

Response: Accepted. We are especially grateful for your assistance and guidance. We have provided additional information in the Methods section, which mainly includes the following: (1) the sampling time and parts for candidate gene expression analysis; (2) the details and references for genotyping analysis; (3) the details and references for QTL mapping analysis; and (4) the cultivation and data collection information of the validation population. We sincerely appreciate your valuable suggestions, as they have made the manuscript more comprehensive and provided readers with more information about Lantian 25.

4 Is Lantian 25 spring or winter wheat? description of the source of the expression data and phases/organs selected; description of the phenotyping method of 111 varieties (but some results are shown in Table 3).

Response: Lantian 25 is a winter wheat variety, developed by the Wheat Research Institute of the Gansu Academy of Agricultural Sciences. It exhibits moderate resistance to stripe rust and is well-suited for cultivation in the winter wheat regions of northwest and northern China. In the Materials and Methods section, we have added details regarding the cultivation and phenotypic evaluation of the validation panel (comprising 111 accessions). Additionally, we have included specifics related to the sampling of candidate genes in the materials and methods section. For Figure 1, on the right is the expression level of the candidate genes, with darker colors indicating higher expression levels. On the left is information about the organs where the genes are expressed and the physiological and biochemical pathways they are involved in. The expression data are sourced from https://www.wheat-expression.com/. We have added it as the footnote of Fig. 1.

5 Text needs some corrections i.e. Latin species names in italics (lines 23, 24), some editorial errors (lines 114, 195, 201, 219), table numbers changed (132, 162).

Response: Accepted. Thank you very much for your assistance. We have made all the necessary revisions to the relevant sections and thoroughly reviewed the entire document, including checking for italicization, textual errors, formatting issues, grammatical mistakes, and the ordering of tables. We deeply appreciate your feedback and help, as it has significantly enhanced the readability and overall quality of the manuscript.

Reviewer 3 Report

Comments and Suggestions for Authors

The manuscript reports QTL analysis of true APR to yellow rust in wheat. KASP markers based on the peak markers for four of the six QTL could be developed and validated in an independent cultivar panel. Candidate genes were identified close to the QTL. The discussion covers the comparison with previously identified QTL and the function of the candidate genes.

Major comments:

Please present the genetic map with QTL peaks and support intervals in a supplementary figure, as the results were obtained from a linkage map-based QTL analysis.

Figure 1: It is not clear from which source the expression patterns of the candidate genes were obtained. A clear description for Figure 1 is missing.

Minor comments:

Please present species names in italics.

Please use consistently the term QTL (please avoid using QTLs) throughout the study.

Line 43: KASP markers are also SNP markers. Please omit SNP markers.

Line 142: Please change to “Consequently, four KASP markers…”

Please indicate in Materials and Methods the environments where the validation panel was grown.

Please indicate in Materials and Methods the statistical test used for comparing differences in stripe rust severity of KASP marker classes.

Lines 301-302: “highlighting the complexity of resistance genetics.” This is not clear.

Comments on the Quality of English Language

The language of the manuscript must be improved, especially the chapters “QTL for APR to stripe rust”, “Candidate gene identification and parts of the discussion, i.e. lines 207-224. I have found some issues as following but by no means all of them.

Line 36: Please change “maybe” to “might be”

Lines 53-54: Please improve language “Recent years have seen YR impact approximately 4.2 million hectares annually,”

Line 104: Please change “, and namely as” to “, namely”

Lines 107-108: Please change to “...was flanked by AX-89396432 and AX-111732484 at 665.4-667.9 Mb in Pixian2020, Qingshui 2020 and Pixian 2021,...”. Please use consistently the preposition “in” when you refer to places Pixian and Qingshui.

Lines 158-161: Please omit “This section may be divided by subheadings. It should provide a concise and precise description of the experimental results, their interpretation, as well as the experimental conclusions that can be drawn.”

Lines 173-174: Please change to “Among them, QYrqn.nwafu-2BL (674.0 Mb) and QYraq.cau-2BL (671.0 Mb) overlapped with QYr.gaas-2BL identified in our study.

Line 175-176: Please change to “However, no overlap was observed between QYr.gaas-2BS and previously identified loci on chromosome 2B. Thus, QYr.gaas-2BS might be novel.”

Lines 188-189: Please omit sentence “These APR genes have been reported to account for 5.3-10.3% of the observed 188 phenotypic variance in their respective populations.”

Line 190: Please italicize QYr.gaas-2DS

Line 192: Please change to “The 3B chromosome is rich in stripe rust resistance genes.”

Line 195: Please change to “have shown” and omit “In addition, known”

Line 200: Please change to “is indeed Yr30.”

Line 255: Please change to “: Pixian (30°05′N, 102°54′E) and Qingshui (34°05′N, 104°35′E).

Author Response

The manuscript reports QTL analysis of true APR to yellow rust in wheat. KASP markers based on the peak markers for four of the six QTL could be developed and validated in an independent cultivar panel. Candidate genes were identified close to the QTL. The discussion covers the comparison with previously identified QTL and the function of the candidate genes.

Major comments:

1 Please present the genetic map with QTL peaks and support intervals in a supplementary figure, as the results were obtained from a linkage map-based QTL analysis.

Response: Accepted. Thank you for your kindly reminder. To avoid repeat with the content presented in the tables, we have included the entire QTL linkage map and LOD curve information in Figure S2. Please review it. It was a significant oversight on our part not to include the genetic map and LOD curve information in the manuscript. We sincerely appreciate you pointing out this issue, as it has greatly enhanced the readability of the paper.

2 Figure 1: It is not clear from which source the expression patterns of the candidate genes were obtained. A clear description for Figure 1 is missing.

Response: Accepted. We sincerely appreciate your valuable suggestions on the manuscript. For Figure 1, this figure is derived from a public database (https://www.wheat-expression.com/) that contains expression data from different wheat organs and developmental stages. Currently, the database is experiencing network issues, temporarily preventing queries and plotting. We have contacted the database authors via email and will replace the figure with a high-resolution version as soon as possible. Additionally, we have added the data source and detailed explanation for Figure 1, which has been added as a footnote below the figure. Once again, we sincerely thank you for the significant efforts you have made to improve the quality of the manuscript.

Minor comments:

1 Please present species name in italics.

Response: Accepted. We have revised it and check the species names all the whole manuscript.

2 Please use consistently the term QTL (please avoid using QTLs) throughout the study.

Response: Accepted. We have revised it all the whole manuscript. Thank you.

3 Line 43: KASP markers are also SNP markers. Please omit SNP markers.

Response: Accepted. We have revised it in the new version. Thank you.

4 Line 142: Please change to “Consequently, four KASP markers…”

Response: Accepted. We sincerely appreciate your kindly reminder. This was an error in our manuscript, and we have corrected it in the revised version. Many thanks.

5 Please indicate in Materials and Methods the environments where the validation panel was grown.

Response: Accepted. We have added the details for the validation panel in the Methods section. Many thanks for your kindly reminder. The validation panel consisted of 111 wheat accessions, primarily from different wheat-growing regions in China, including modern cultivars, advanced lines, and landraces. All accessions were evaluated for stripe rust resistance during the 2014-2015 and 2015-2016 cropping seasons at the Pixian Experimental Station of the Sichuan Academy of Agricultural Sciences and the Gangu Experimental Station of the Gansu Academy of Agricultural Sciences, as well as during the 2014–2015 cropping season at the Zhongliang Experimental Station of the Tianshui Institute of Agricultural Science in Gansu Province. These three locations are hotspots for stripe rust in China, with environmental conditions conducive to disease development. Field trials were conducted using a randomized complete block design with three replicates, three-row plots, 20 cm row spacing, and 1.5 m row length. Every 10th row was planted with the highly susceptible control cultivar "Huixianhong." Inoculation was performed at the jointing stage by spraying a mixture of prevalent Chinese Puccinia striiformis f. sp. tritici races, including CYR32, CYR33, and CYR34. MDS was recorded 18 to 20 days after flowering. The MDS from each environment and the mean values across the five environments for each accession were used for subsequent validation analysis.

6 Please indicate in Materials and Methods the statistical test used for comparing differences in stripe rust severity of KASP marker classes.

Response: Accepted. Thank you for your valuable suggestions. We have updated the Materials and Methods section to clarify the statistical test used for comparing differences between the marker classes. Specifically, we employed a Student's t test to assess the significance of the differences between the marker classes. The revised text now reads: Differences in stripe rust severity between KASP marker classes were analyzed using a student-test to determine statistical significance.

7 Lines 301-302: “highlighting the complexity of resistance genetics.” This is not clear.

Response: Accepted. Thank you very much for your suggestion. This sentence is not suitable here and could easily lead to misunderstanding. We have deleted it in the new version.

 

Comments on the Quality of English Language

1 The language of the manuscript must be improved, especially the chapters “QTL for APR to stripe rust”, “Candidate gene identification and parts of the discussion, i.e. lines 207-224. I have found some issues as following but by no means all of them.

Response: Accepted. We sincerely appreciate your valuable suggestions on the manuscript. We have carefully read your suggestions and have made revisions to all the issues you pointed out. Additionally, we invited a native speaker to thoroughly review the entire article for language and wording improvements, aiming to minimize grammatical and textual errors as much as possible. Once again, we sincerely thank you for your guidance and valuable advice.

2 Line 36: Please change “maybe” to “might be”

Response: Accepted. We corrected it in the new version.

3 Lines 53-54: Please improve language “Recent years have seen YR impact approximately 4.2 million hectares annually,”

Response: Accepted. We revised it in the new version. Many thanks.

4 Line 104: Please change “, and namely as” to “, namely”

Response: Accepted. We have corrected it in the new version. Many thanks.

5 Lines 107-108: Please change to “...was flanked by AX-89396432 and AX-111732484 at 665.4-667.9 Mb in Pixian2020, Qingshui 2020 and Pixian 2021,...”. Please use consistently the preposition “in” when you refer to places Pixian and Qingshui.

Response: Accepted. We sincerely appreciate your valuable suggestions. We have revised it all the whole manuscript.

6 Lines 158-161: Please omit “This section may be divided by subheadings. It should provide a concise and precise description of the experimental results, their interpretation, as well as the experimental conclusions that can be drawn.”

Response: Accepted. We have corrected it. Many thanks.

7 Lines 173-174: Please change to Among them, QYrqn.nwafu-2BL (674.0 Mb) and QYraq.cau-2BL (671.0 Mb) overlapped with QYr.gaas-2BL identified in our study.

Response: Accepted. Many thanks. We have corrected it in the new version.

8 Line 175-176: Please change to “However, no overlap was observed between QYr.gaas-2BS and previously identified loci on chromosome 2B. Thus, QYr.gaas-2BS might be novel.”

Response: Accepted. We have corrected it in the new version. Thank you.

9 Lines 188-189: Please omit sentence “These APR genes have been reported to account for 5.3-10.3% of the observed 188 phenotypic variance in their respective populations.”

Response: Accepted. Many thanks. We have corrected it in the new version.

10 Line 190: Please italicize QYr.gaas-2DS

Response: Accepted. We have corrected it in the new version. Thank you.

11 Line 192: Please change to “The 3B chromosome is rich in stripe rust resistance genes.”

Response: Accepted. Many thanks. We have corrected it in the new version.

12 Line 195: Please change to “have shown” and omit “In addition, known”

Response: Accepted. So sorry for the trouble. We have corrected it in the new version. Many thanks.

13 Line 200: Please change to “is indeed Yr30.”

Response: Accepted. We have corrected it in the new version. Many thanks.

14 Line 255: Please change to “: Pixian (30°05′N, 102°54′E) and Qingshui (34°05′N, 104°35′E).

Response: Accepted. We have corrected it in the new version. Thank you.

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Attached.

Comments for author File: Comments.pdf

Author Response

1 Authors are aware that some ARP genes have been widely exploited “lines 90-92, Yr18/Lr34/Sr57/Pm38, Yr29/Lr46/Sr58/Pm39, Yr30/Lr27/Sr2/Pm70, andYr46/Lr67/Sr55/Pm46 are pleiotropic genes, which have been widely utilized in breeding programs alongside all-stage resistance genes” Still they didn’t try to rule out the presence linked markers for these APR gene/s in Lantian 25, though linked markers are available. This was suggested in the previous review as well “The presence of APR genes Yr18, Yr29, Yr46, Yr78 and Yr80 not ruled out in the resistant parent Lantian 25, using linked available molecular markers. Adding these results will make the study robust and reliable.”

Response: Accepted. We apologize that our previous response did not address your concerns. As you mentioned, Yr18, Yr29, Yr30, and Yr46 have good resistance effects against stripe rust and are widely used in Chinese varieties, especially in the Huang-Huai winter wheat region and the southwestern wheat region. We conducted extensive testing for Yr18, Yr29, Yr30, and Yr46 in 2014 and have well-established primers and detection systems (Liu Jindong, Yang Ennian, Xiao Yonggui, Chen Xinmin, Wu Ling, Bai Bin, Li Zaifeng, Xia Xianchun, He Zhonghu. Development, Evaluation and Molecular Detection of Wheat Lines with Durable Adult-Plant Resistance to Stripe Rust. Acta Agronomica Sinica. 2015;41(10):1472-80. In Chinese with English abstract). However, only Yr30 was detected in Lantian25 and maybe QYr.gaas-3BS. Additionally, we sent Lantian25 to Professor Caixia Lan's laboratory (a joint lab of Huazhong Agricultural University and CIMMYT) for testing, and the results also confirmed the absence of Yr18, Yr29 and Yr46. Furthermore, Yr18, Yr29 and Yr46 are located on chromosomes 7DS, 1BL, and 4DL, respectively. In this study, we detected eight loci related to wheat stripe rust resistance in Lantian25, located on chromosomes 2BS, 2BL, 2DS, 2DL, 3BS, and 4BL, none of which are on the same chromosomes as the three important stripe rust resistance genes mentioned above. Therefore, we did not include this part in the results and discussion. In addition to Yr18, Yr29, Yr30, and Yr46, we also tested for Yr17 and Yr26, but none were detected in Lantian25. We sincerely hope this response resolves your concerns. We have supplemented this part of the discussion in the QTL mapping section. We greatly appreciate your help and guidance, which have significantly improved the quality of the paper.

 

2 Secondly, cross refrencing [10-14] in lines 85 to 89 for Yr genes “cluding Yr18 (7DS), Yr29 (1BL), Yr30 (3BS), Yr34 (5AL), Yr46 (4DL), Yr48 (5AL), Yr49 (3DS), Yr54 (2DL), Yr56 (2AS), Yr58 (3BS), Yr60 (4AL), Yr68 (4BL), Yr71 (3DL), Yr75 (7AL), Yr77 (6DS), Yr78 (6BS), Yr80 (3BL), Yr83 (6RL), and Yr86 (2AL) [10-12],and Yr36 (6BS), Yr39 (7BL), Yr52 (7BL), Yr59 (7BL), Yr62 (4BL), and Yr79 (7BL) are high-tempera-ture adult plant (HTAP) resistance genes against stripe rust [10-14]” is not fair for original authors who named these genes. Original work on the publishing of the above said genes should be cited instead of the following references.

Response: We sincerely appreciate your suggestions. In response to your comments regarding the stripe rust resistance genes, we have supplemented references for each of them. Please kindly review the updates.

Yr18 (7DS): Krattinger, S.G.; Lagudah, E.S.; Spielmeyer, W.; Singh, R.P.; Huerta-Espino, J.; McFadden, H.; Bossolini, E.; Selter, L.L.; Keller, B. 2009. A Putative ABC Transporter Confers Durable Resistance to Multiple Fungal Pathogens in Wheat. Science 323, 1360–1363.

Yr29(1BL): Wang, M.H.; Spielmeyer, W.; Lagudah, E.S.; Appels, R. 2006. Characterization of genetic loci conferring adult plant resistance to leaf rust and stripe rust in spring wheat. Genome 49(8), 977–990.

Yr30 (3BS): Wang, X.; Xu, M.; Lin, H.; Cheng, P.; Bucher, J.; Li, T.; Wang, C.; et al. 2024. High-density mapping of durable and broad-spectrum stripe rust resistance gene Yr30 in wheat. Theor. Appl. Genet. 137, 152.

Yr34 (5AL): Bariana, H.S.; Parry, N.; Barclay, I.R.; Brown, G.N.; McLean, R.J.; Shankar, M.; Cakir, M.; et al. 2006. Identification and characterization of stripe rust resistance gene Yr34 in common wheat. Theor. Appl. Genet. 112, 1143–1148.

Yr46 (4DL): Moore, J.W.; Herrera-Foessel, S.; Lan, C.; Schnippenkoetter, W.; Ayliffe, M.; Huerta-Espino, J.; Lillemo, M.; et al. 2015. A recently evolved hexose transporter variant confers resistance to multiple pathogens in wheat. Nat. Genet. 47, 1494–1498.

Yr48 (5AL): Lowe, I.; Jankuloski, L.; Chao, S.; Chen, X.; See, D.; Dubcovsky, J. 2011. Mapping and validation of QTL which confer partial resistance to broadly virulent post-2000 North American races of stripe rust in hexaploid wheat. Theor. Appl. Genet. 123, 143–157.

Yr49 (3DS): McIntosh, R.A.; Dubcovsky, J.; Rogers, W.J.; Morris, C.; Appels, R.; Xia, X.C. 2012. Catalogue of gene symbols. KOMUGI Integr. Wheat Sci. Database 2012.

Yr54 (2DL): Basnet, B.R.; Singh, R.P.; Ibrahim, A.M.H.; Herrera-Foessel, S.A.; Huerta-Espino, J.; Lan, C.; Rudd, J.C. 2014. Characterization of Yr54 and other genes associated with adult plant resistance to yellow rust and leaf rust in common wheat Quaiu 3. Mol. Breed. 33, 385–399.

Yr56 (2AS): McIntosh, R.A.; Dubcovsky, J.; Rogers, J. 2014. Catalogue of gene symbols for wheat: 2013-2014 supplement. 2014.

Yr58 (3BS): Chhetri, M.; Bariana, H.; Kandiah, P.; Bansal, U. 2016. Yr58: a new stripe rust resistance gene and its interaction with Yr46 for enhanced resistance. Phytopathology 106, 1530–1534.

Yr60 (4AL): Herrera-Foessel, S.A.; Singh, R.P.; Lan, C.X.; Huerta-Espino, J.; Calvo-Salazar, V.; Bansal, U.K.; Bariana, H.S.; Lagudah, E.S. 2015. Yr60, a gene conferring moderate resistance to stripe rust in wheat. Plant Dis. 99, 508–511.

Yr68 (4BL): McIntosh, R.A.; Dubcovsky, J.; Rogers, W.J.; Morris, C.; Appels, R.; Xia, X.C. 2016. Catalogue of gene symbols for wheat: 2015–2016 Supplement. 2016.

Yr71 (3DL): Bariana, H.; Forrest, K.; Qureshi, N.; Miah, H.; Hayden, M.; Bansal, U. 2016. Adult plant stripe rust resistance gene Yr71 maps close to Lr24 in chromosome 3D of common wheat. Mol. Breed. 36, 98.

Yr75 (7AL): Kanwal, M.; Qureshi, N.; Gessese, M.; Forrest, K.; Babu, P.; Bariana, H.; Bansal, U. 2021. An adult plant stripe rust resistance gene maps on chromosome 7A of Australian wheat cultivar Axe. Theor. Appl. Genet. 134, 2213–2220.

Yr77 (6DS): Chugunkova, T.V.; Pastukhova, N.L.; Pirko, Y.V.; Blume, Y.B. 2025. Genetic Basis of Resistance to Wheat Yellow Rust. Cytol. Genet. 59, 186–196.

Yr78 (6BS): Dang, C.; Zhang, J.; Dubcovsky, J. 2022. High‐resolution mapping of Yr78, an adult plant resistance gene to wheat stripe rust. Plant Genome 15, e20212.

Yr80 (3BL): Nsabiyera, V.; Bariana, H.S.; Qureshi, N.; Wong, D.; Hayden, M.J.; Bansal, U.K. 2018. Characterization and mapping of adult plant stripe rust resistance in wheat accession Aus27284. Theor. Appl. Genet. 131, 1–9.

Yr83 (6RL): Li, J.; Dundas, I.; Dong, C.; Li, G.; Trethowan, R.; Yang, Z.; Hoxha, S.; Zhang, P. 2020. Identification and characterization of a new stripe rust resistance gene Yr83 on rye chromosome 6R in wheat. Theor. Appl. Genet. 133, 1095–1107.

Yr86 (2AL): Zhu, Z.; Cao, Q.; Han, D.; Wu, J.; Wu, L.; Tong, J.; Xu, X.; Yan, J.; Zhang, Y.; Xu, K.; Wang, F. 2023. Molecular characterization and validation of adult-plant stripe rust resistance gene Yr86 in Chinese wheat cultivar Zhongmai 895. Theor. Appl. Genet. 136, 142.

Yr36 (6BS): Uauy, C.; Brevis, J.C.; Chen, X.; Khan, I.; Jackson, L.; Chicaiza, O.; Distelfeld, A.; Fahima, T.; Dubcovsky, J. 2005. High-temperature adult-plant (HTAP) stripe rust resistance gene Yr36 from Triticum turgidum ssp. dicoccoides is closely linked to the grain protein content locus *Gpc-B1*. Theor. Appl. Genet. 112, 97–105.

Yr39 (7BL): Coram, T.E.; Settles, M.L.; Chen, X. 2008. Transcriptome analysis of high‐temperature adult‐plant resistance conditioned by Yr39 during the wheat–Puccinia striiformis f. sp. tritici interaction. Mol. Plant Pathol. 9, 479–493.

Yr52 (7BL): TaoHong, F.A.; Zhang, M.; ChunHua, M.A.; Zheng, X.; WenJing, T.A.; Ran, T.I.; Qiong, Y.A.; XinLi, Z.H.; Xin, L.I.; SuiZhuang, Y.A.; Huang, K. 2022. Application of Yr52 gene in wheat improvement for stripe rust resistance. Sci. Agric. Sin. 55, 2077–2091.

Yr59 (7BL): Zhou, X.L.; Wang, M.N.; Chen, X.M.; Lu, Y.; Kang, Z.S.; Jing, J.X. 2014. Identification of Yr59 conferring high-temperature adult-plant resistance to stripe rust in wheat germplasm PI 178759. Theor. Appl. Genet. 127, 935–945.

Yr62 (4BL): Lu, Y.; Wang, M.; Chen, X.; See, D.; Chao, S.; Jing, J. 2014. Mapping of Yr62 and a small-effect QTL for high-temperature adult-plant resistance to stripe rust in spring wheat PI 192252. Theor. Appl. Genet. 127, 1449–1459.

Yr79 (7BL): 2018. Characterization of novel gene Yr79 and four additional QTL for all-stage and high-temperature adult-plant resistance to stripe rust in spring wheat PI 182103. Phytopathology 108, 737–747.

Reviewer 3 Report

Comments and Suggestions for Authors

I only have a few minor comments left.

Please change the following lines to:

Line 29 “(resistant…”

Lines 132-133 “…, indicating that stripe rust resistance is influenced by both genetic and environmental factors.”

Line 142 “..., namely Qyr.gaas-2BS,…”

Line 174 “A total of 707 annotated genes were present in the QTL regions for wheat stripe rust identified in this study and are listed in Table S2.” Please improve language in the following lines: 175 to 184.

Line 211 “…linked SNP markers…”

Line 230: It appears that the number of “353” includes only QTL for stripe rust as indicated in line 96. If you want to have all-stage resistance genes also included in the number, you have to adapt the number.

Author Response

Comments and Suggestions for Authors

I only have a few minor comments left.

Please change the following lines to:

Line 29 “(resistant…”

Response: Accepted. Many thanks.

Lines 132-133 “…, indicating that stripe rust resistance is influenced by both genetic and environmental factors.”

Response: Accepted.

Line 142 “..., namely Qyr.gaas-2BS,…”

Response: Accepted.

Line 174 “A total of 707 annotated genes were present in the QTL regions for wheat stripe rust identified in this study and are listed in Table S2.” Please improve language in the following lines: 175 to 184.

Response: Accepted.

Line 211 “…linked SNP markers…”

Response: Accepted.

Line 230: It appears that the number of “353” includes only QTL for stripe rust as indicated in line 96. If you want to have all-stage resistance genes also included in the number, you have to adapt the number.

Response: Accepted. Thank you very much for your suggestions. As you mentioned, 353 is the number of QTL loci for adult-plant resistance to wheat stripe rust mentioned in the review literature. Since this literature could not possibly cover all stripe rust QTL loci, and there may be cases where multiple QTL loci are linked or represent the same locus, we revised this sentence to avoid potential misunderstanding by omitting the specific number and instead emphasizing the distribution regions across the 21 chromosomes. We greatly appreciate your valuable advice.

Round 3

Reviewer 1 Report

Comments and Suggestions for Authors

Double check the citations and references list. Correct the following reference;

37 Characterization of novel gene Yr79 and four additional QTL for all-stage and high-temperature adult-plant resistance to 599 stripe rust in spring wheat PI 182103. Phytopathology 2018, 108, 737–747.

Author Response

Double check the citations and references list. Correct the following reference;

37 Characterization of novel gene Yr79 and four additional QTL for all-stage and high-temperature adult-plant resistance to 599 stripe rust in spring wheat PI 182103. Phytopathology 2018, 108, 737–747.

Response: Thank you very much for your reminder. We have revised the reference format according to your suggestions. Additionally, we have thoroughly checked and modified all references throughout the manuscript. Due to the extensive revisions, we will carefully review and finalize all references once the article revisions are fully accepted. Once again, we sincerely appreciate your continuous guidance on this manuscript. Your suggestions have significantly improved the readability of the paper.