PGRFA Management of Outcrossing Plants Propagated by Seed: From On-Farm to Ex Situ Conservation and Some Italian Maize Case Studies

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Comments to ms agronomy-2954659 by Landoni et al

The ms is a review article on management of plant genetic resources of cross pollinating-species used for agriculture. General concepts of in situ and ex situ conservation is described, population genetics and molecular markers briefly discussed and some examples on conservation and utilization of maize genetic resources in Italy are given.

The text is overall clear and the the English language is mostly fine. The ms would benefit for some more subheadings.

The description of on farm-conservation is interesting and I appreciate the discussion of various challeges with this conservation strategy. On the other hand, the section on genebank management is rather basic and the sections on population genetics and molecular marker very elementary. The case studies are not very well described. Overall, I think the ms would benefit from more focus on the specific scope, e.g. conservation of Italian corn PGRs.

Specific comments:

Line 50. "... landraces were collected ex situ between.." Was the material found in other genebanks?

Line 51. "monolineal varietis". Do you mean "pure lines".

Line 52. I think "genetic erosion" is a more approriate term than "genetic flow" here. (gene flow is something else)

Line 58. Check and cite Casañas, Francesc, et al. "Toward an evolved concept of landrace." Frontiers in plant science 8 (2017): 245305.

Line 68-70. How are these figures calculated. What years are compared? "Since 1900s" is very unspecific.

75-76. I would already here meantion the importance of co-evolution with cultural practices.

Line 139-140. High genetic diversity within and among populations is not specific for outcrossing species. Landraces on self-pollinationg species can also have very high genetic diversity. Among populations diversity is often higher for self-pollinators than for outcrossing species.

Line 206-208. Please provide some PGRFA species examples for the different groups.

Line 225-226. "...and to set a number of seeds to be sampled..." The meaning of this sentence is unclear. Please explain better.

Line 241. Is there a risk of loss of genetic diversity during cleaning? For example if some genotypes in the population are small seeded or late maturing. Please discuss.

Line 288- cont. It would be valuable with a better description on the management of maize at the Bergamo gene bank. How is cross-pollination between accessions avoided? How many plnts are used during regeneration? How is genetic drift and unintentional selection avoided? 

Line 357-cont. This section is very basic and poorly referenced. I do not agree the SSR marker systems necessarily is the most economical option any longer, when sequencing costs are rapidly decreasing. I would also discuss the problem of ascertainment bias for different marker systems.

Line 383-cont. This section is partly very general and redundant with previous text. I recommend to expand the text discribing the case studies instead.

Figure 3. The figure is not full clear. What is the difference between solid and dashed lines? Following the lines it looks like that heterogenous material (e.g. a landrace) should either the discarded or subjection to selection. That cannot be the true case? It is also unclear how molecular analysis aid in the desicion making in the figure.   

Line 407-413. Does this only concern maize?

 

 

Author Response

The ms is a review article on management of plant genetic resources of cross pollinating-species used for agriculture. General concepts of in situ and ex situ conservation is described, population genetics and molecular markers briefly discussed and some examples on conservation and utilization of maize genetic resources in Italy are given.

The text is overall clear and the the English language is mostly fine. The ms would benefit for some more subheadings.

We added some more subheadings as suggested.

The description of on farm-conservation is interesting and I appreciate the discussion of various challeges with this conservation strategy. On the other hand, the section on genebank management is rather basic and the sections on population genetics and molecular marker very elementary. The case studies are not very well described. Overall, I think the ms would benefit from more focus on the specific scope, e.g. conservation of Italian maize PGRs.

We added more information regarding the reviewer’s suggestions and modified the title as suggested from:

 “PGRFA management of outcrossing plants propagated by seed: from on-farm to ex situ conservation and some case studies”

To

“ PGRFA management of outcrossing plants propagated by seed: from on-farm to ex situ conservation and some Italian maize case studies “

 

Specific comments:

 

Line 50. "... landraces were collected ex situ between.." Was the material found in other genebanks?

We modified the text from :

“In fact, in developed countries, most landraces were collected ex situ between the 1950s and 1970s.”

to

“ Indeed, in developed nations, the majority of landraces were gathered ex situ between the 1950s and 1970s, coinciding with the establishment of modern genebanks in various countries, following the example set by the USA [104].”

 

Line 51. "monolineal varietis". Do you mean "pure lines".

Yes,  we modified the text as suggested

Line 52. I think "genetic erosion" is a more approriate term than "genetic flow" here. (gene flow is something else)

OK,  we modified the text as suggested

Line 58. Check and cite Casañas, Francesc, et al. "Toward an evolved concept of landrace." Frontiers in plant science 8 (2017): 245305.

We added this citation and some consideration

Line 68-70. How are these figures calculated. What years are compared? "Since 1900s" is very unspecific.

The citation is part of Training Manual “Building on Gender,Agrobiodiversity and Local Knowledge”. FAO, 2004.

However we modified the text from:

 “Since the 1900s, a lot of of plant genetic diversity has diminished, driven by global farmers abandoning their local varieties and landraces in favour of genetically uniform, high-yielding varieties [11]”

To

“Since the 1900s, a significant portion of plant genetic diversity has diminished due to global farmers forsaking their local varieties and landraces in favor of genetically uniform, high-yielding varieties. [13]”

 

75-76. I would already here meantion the importance of co-evolution with cultural practices.

Ok, we added a consideration and definition citing some papers.

Line 139-140. High genetic diversity within and among populations is not specific for outcrossing species. Landraces on self-pollinationg species can also have very high genetic diversity. Among populations diversity is often higher for self-pollinators than for outcrossing species.

Yes, it was a general affirmation.

We modified the sentence from:

“A specific issue for outcrossing species is the high genetic diversity within and among populations, which conflicts with the uniformity criterion required for registration. “

To

“Although in some cases genetic diversity is high even in self-pollinating plants [17], a specific challenge to face managing outcrossing species is the high genetic diversity within and among populations. This conflicts with the uniformity criterion required for registration”

 

Line 206-208. Please provide some PGRFA species examples for the different groups.

We provided some examples as suggested

 

Line 225-226. "...and to set a number of seeds to be sampled..." The meaning of this sentence is unclear. Please explain better.

 

We explain better the concept adding another sentence.

Line 241. Is there a risk of loss of genetic diversity during cleaning? For example if some genotypes in the population are small seeded or late maturing. Please discuss.

We explain better the concept discussing the problem.

Line 288- cont. It would be valuable with a better description on the management of maize at the Bergamo gene bank. How is cross-pollination between accessions avoided? How many plnts are used during regeneration? How is genetic drift and unintentional selection avoided?

 

We added a better description on the management of maize at Bergamo gene bank.

 

Line 357-cont. This section is very basic and poorly referenced. I do not agree the SSR marker systems necessarily is the most economical option any longer, when sequencing costs are rapidly decreasing. I would also discuss the problem of ascertainment bias for different marker systems.

We restructured the text adding the suggested consideration

 

Line 383-cont. This section is partly very general and redundant with previous text. I recommend to expand the text discribing the case studies instead.

We expanded the case studies as suggested and deleted some redundancies.

Figure 3. The figure is not full clear. What is the difference between solid and dashed lines? Following the lines it looks like that heterogenous material (e.g. a landrace) should either the discarded or subjection to selection. That cannot be the true case? It is also unclear how molecular analysis aid in the desicion making in the figure.  

We modified the figure to better explain this scheme

 

Line 407-413. Does this only concern maize?

Yes, we modified the title:

From : “PGRFA management of outcrossing plants propagated by seed: from on-farm to ex situ conservation and some case studies”

To: “PGRFA management of outcrossing plants propagated by seed: from on-farm to ex situ conservation and some Italian maize case studies”

We have used maize as a model since the challenges in managing other outcrossing plants are the same."

Reviewer 2 Report

Comments and Suggestions for Authors

 

The article is an interesting and well-prepared look at plant genetic resources. The chapter titles and contents proposed by the authors allow the reader to systematically explore the analyzed topics. The entire manuscript is aptly complemented by an example of the practical use of corn genetic resources. Only the text in lines 78 to 83 should be supported by appropriate literature. Since rice is an autogamous species, it would be good to justify this statement with an example of an allogamous species.

Author Response

Reviewer  2.

The article is an interesting and well-prepared look at plant genetic resources. The chapter titles and contents proposed by the authors allow the reader to systematically explore the analyzed topics. The entire manuscript is aptly complemented by an example of the practical use of maize genetic resources. Only the text in lines 78 to 83 should be supported by appropriate literature. Since rice is an autogamous species, it would be good to justify this statement with an example of an allogamous species.

We have replaced the example about rice with an example about maize.

Reviewer 3 Report

Comments and Suggestions for Authors

The conservation concerning outcrossing plants poses a significant challenge, starting from in situ sampling, collection in germplasm banks, and conservative reproductive methods.

The study under this heading is very useful and worthwhile, but it has many weaknesses that need to be improved and detailed.

- First, it was displayed on the Journal's website as an article, not a review.

- More than one plant type should be used for comparison in this study ( Zea mays is not enough).

- Clarification and explanation should be made using more than one variety within the same plant type.

- Use some statistical analyses such as multivariate analyses and then interpret and explain the results.

- The same with part of molecular markers work comparisons, analyses, and interpretation of outputs.

 

Author Response

Reviewer 3.

The conservation concerning outcrossing plants poses a significant challenge, starting from in situ sampling, collection in germplasm banks, and conservative reproductive methods.

The study under this heading is very useful and worthwhile, but it has many weaknesses that need to be improved and detailed.

- First, it was displayed on the Journal's website as an article, not a review.

Yes, it was a mistake. We modified the word

- More than one plant type should be used for comparison in this study ( Zea mays is not enough).

- Clarification and explanation should be made using more than one variety within the same plant type.

We have modified the title as requested by reviewer 1.

From: “PGRFA management of outcrossing plants propagated by seed: from on-farm to ex situ conservation and some case studies”

To: “PGRFA management of outcrossing plants propagated by seed: from on-farm to ex situ conservation and some Italian maize case studies ”

We have used maize as a model since the challenges in managing other outcrossing plants are the same.

- Use some statistical analyses such as multivariate analyses and then interpret and explain the results.

It is a review

- The same with part of molecular markers work comparisons, analyses, and interpretation of outputs.

It is a review

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Author´s have provided good response to all issues raised. The ms has improved significantly from the previous version and could be accepted in present form.

Reviewer 3 Report

Comments and Suggestions for Authors

The review has improved and does not prevent its publication