Genetic associations with resistance to Meloidogyne enterolobii in guava (Psidium sp.) using cross-genera SNPs and comparative genomics to Eucalyptus highlight evolutionary conservation across the Myrtaceae

Carlos Antonio Fernandes Santos; Soniane Rodrigues da Costa; Leonardo Silva Boiteux; Dario Grattapaglia; Orzenil Bonfim Silva-Junior

doi:10.1371/journal.pone.0273959

Peer Review History

Original SubmissionAugust 17, 2022
6 Oct 2022 Decision Letter - Zhenhai Han, Editor PONE-D-22-23102Genetic associations with resistance to Meloidogyne enterolobii in guava (Psidium sp.) using cross-genera SNPs and comparative genomics to Eucalyptus highlight evolutionary conservation across the MyrtaceaePLOS ONE Dear Dr. Grattapaglia, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Nov 20 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. 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Additional Editor Comments: Reviewer #1: The manuscript deals with the identification of genomic loci associated with resistance to Meloidogyne enterolobii in guava, the excellent fruit yielding tree species. It is an important research problem, where in several countries cultivate guava but the trees is routinely getting affected to nematodes. Marker assisted breeding is the suitable approach to produce pest resistant trees. The individuals were genotyped with EUChip60K containing Eucalyptus SNPs. Two SNP loci were found to be associated with nematode resistance. There are two publications available on the use of SNPs in Psidium and authors need to cite these references. However, there is a complete and chromosome scale assembly of Psidium guajava with the coverage of about 95% has already been reported. The authors may utilise this genomic information and analyse SNP data generated to get the genomic coordinates of specific SNP regions identified from guava genome. Interpret the results based on the genomic regions of guava along with eucalypts. The article is well written and reader friendly. There are two publications available on the use of SNPs in guava, which need to be cited 1. Grossi, L.L., Fernandes, M., Silva, M.A. et al. DArTseq-derived SNPs for the genus Psidium reveal the high diversity of native species. Tree Genetics & Genomes 17, 23 (2021). https://doi.org/10.1007/s11295-021-01505-y 2. Diaz‐Garcia, Luis, and José S. Padilla‐Ramírez. "Development of single nucleotide polymorphism markers and genetic diversity in guava (Psidium guajava L.)." Plants, People, Planet (2022). Reviewer #2: In this manuscript an attempt has been made to identify the resistance gene for Meloidogyne enterolobii in Guava using EUChip60K SNPs genotyping and de novo genome assembly of the Psidium guajava. The SNP genotyping could transfer 14,268 SNP probe sets from Eucalyptus to Psidium at the nucleotide level. Two SNPs (EuBR03s29615246 and EuBR03s30383415) on chromosome 3 in a pseudo-assembly of Psidium guajava genome built using a syntenic path approach with the Eucalyptus grandis genome were identified linked to resistance locus for RKN. This contribution should advance the development of new guava cultivars through the development of inexpensive SNP based assays to monitor the introgression of the P. guineense-derived resistance for RKN into guava cultivars and rootstocks. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The manuscript deals with the identification of genomic loci associated with resistance to Meloidogyne enterolobii in guava, the excellent fruit yielding tree species. It is an important research problem, where in several countries cultivate guava but the trees is routinely getting affected to nematodes. Marker assisted breeding is the suitable approach to produce pest resistant trees. The individuals were genotyped with EUChip60K containing Eucalyptus SNPs. Two SNP loci were found to be associated with nematode resistance. There are two publications available on the use of SNPs in Psidium and authors need to cite these references. However, there is a complete and chromosome scale assembly of Psidium guajava with the coverage of about 95% has already been reported. The authors may utilise this genomic information and analyse SNP data generated to get the genomic coordinates of specific SNP regions identified from guava genome. Interpret the results based on the genomic regions of guava along with eucalypts. The article is well written and reader friendly. There are two publications available on the use of SNPs in guava, which need to be cited Reviewer #2: In this manuscript an attempt has been made to identify the resistance gene for Meloidogyne enterolobii in Guava using EUChip60K SNPs genotyping and de novo genome assembly of the Psidium guajava. The SNP genotyping could transfer 14,268 SNP probe sets from Eucalyptus to Psidium at the nucleotide level. Two SNPs (EuBR03s29615246 and EuBR03s30383415) on chromosome 3 in a pseudo-assembly of Psidium guajava genome built using a syntenic path approach with the Eucalyptus grandis genome were identified linked to resistance locus for RKN. This contribution should advance the development of new guava cultivars through the development of inexpensive SNP based assays to monitor the introgression of the P. guineense-derived resistance for RKN into guava cultivars and rootstocks. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: Yes: Ramasamy Yasodha Reviewer #2: Yes: Dr Rakesh Singh ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. 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Revision 1
11 Oct 2022 Author Response Below we respond to the reviewers’ comments. Reviewer #1 REVIEWER COMMENT: The manuscript deals with the identification of genomic loci associated with resistance to Meloidogyne enterolobii in guava, the excellent fruit yielding tree species. It is an important research problem, where in several countries cultivate guava but the trees is routinely getting affected to nematodes. Marker assisted breeding is the suitable approach to produce pest resistant trees. The individuals were genotyped with EUChip60K containing Eucalyptus SNPs. Two SNP loci were found to be associated with nematode resistance. There are two publications available on the use of SNPs in Psidium and authors need to cite these references. RESPONSE: Thank you for pointing out those two papers. We have now included the two references in the manuscript. In the interest of the readership, we added a comment regarding the fact that these two SNP genotyping experiments were carried out using genotyping by sequencing methods based on genome complexity reduction by digestion with restriction enzymes. Although such methods do offer advantages as far as no upfront cost and simultaneous SNPs discovery and genotyping, they are well known to have low reproducibility across independent experiments and laboratories, and suffer with large proportions of missing data. As such, although SNPs are genotyped, they do not constitute a legacy genomic resource for future widespread and continuous use by the community, nor they allow consolidation of data across studies in the same manner as the chip-based SNPs data we have used in our work. REVIEWER COMMENT: However, there is a complete and chromosome scale assembly of Psidium guajava with the coverage of about 95% has already been reported. The authors may utilize this genomic information and analyze SNP data generated to get the genomic coordinates of specific SNP regions identified from guava genome. Interpret the results based on the genomic regions of guava along with eucalypts. RESPONSE: We are fully aware of the chromosome scale assembly of the Psidium guajava genome. In fact, we have cited that paper already in the introduction when presenting the available genomic resources for the species. As the reviewer might have noticed, in our work we have generated a de novo assembly of the Psidium guajava genome for a different Psidium guajava tree than the one for which the genome had been published. We did exactly what the reviewer is suggesting, i.e., we used the genome assembly we generated to transfer a large number of SNP probesets that had been developed for Eucalyptus to the Psidium genome at the nucleotide level providing the exact genomic coordinates. Please also note that we have deposited our genome assembly at DDBJ/ENA/GenBank under the accession JAGHRR000000000. The version described in this article is JAGHRR010000000. These resources were deposited under the BioProject ID PRJNA713343. The entire presentation of results, their interpretation and discussion were therefore based on a detailed mapping of the SNP probesets on the Psidium genome we have generated, which is fully syntenic to the previously published Psidium genome. Therefore, all the necessary genomic address information for the SNPs is made available to the readership for future use of the publicly available EUCHIP60K to further genotype Psidium genetic resources. Reviewer #2: REVIEWER COMMENT: In this manuscript an attempt has been made to identify the resistance gene for Meloidogyne enterolobii in Guava usingEUChip60K SNPs genotyping and de novo genome assembly of the Psidium guajava. The SNP genotyping could transfer 14,268 SNP probe sets from Eucalyptus to Psidium at the nucleotide level. Two SNPs (EuBR03s29615246 andEuBR03s30383415) on chromosome 3 in a pseudo-assembly of Psidium guajava genome built using a syntenic path approach with the Eucalyptus grandis genome were identified linked to resistance locus for RKN. This contribution should advance the development of new guava cultivars through the development of inexpensive SNP based assays to monitor the introgression of the P. guineense-derived resistance for RKN into guava cultivars and rootstocks. RESPONSE: We thank the reviewer for the positive comment. Attachments Attachment Submitted filename: Responses_to_reviewers_PONE-D-22-23102.docx https://doi.org/10.1371/journal.pone.0273959.r002
17 Oct 2022 Decision Letter - Zhenhai Han, Editor Genetic associations with resistance to Meloidogyne enterolobii in guava (Psidium sp.) using cross-genera SNPs and comparative genomics to Eucalyptus highlight evolutionary conservation across the Myrtaceae PONE-D-22-23102R1 Dear Dr. Grattapaglia, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Zhenhai Han, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0273959.r003
Formally Accepted
20 Oct 2022 Acceptance Letter - Zhenhai Han, Editor PONE-D-22-23102R1 Genetic associations with resistance to Meloidogyne enterolobii in guava (Psidium sp.) using cross-genera SNPs and comparative genomics to Eucalyptus highlight evolutionary conservation across the Myrtaceae Dear Dr. Grattapaglia: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Zhenhai Han Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0273959.r004

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