Evolution of Genetics Organisations’ Strategies through the Implementation of Genomic Selection: Learnings and Prospects

Round 1

Reviewer 1 Report

General

This paper covers a very important topic and introduces some very interesting insights that one would not typically find in a traditional journal article. An overview of genomic selection is provided, a rather loosely structured survey approach is presented, and then the responses of the survey are discussed with a high degree of subjectivity.

The key strengths of the paper come from the higher level more holistic perspective on how a new technology (genomic selection) has caused bigger picture changes in the way an incredibly wide diversity of livestock genetic improvement programs have operated. I think it would be very valuable to have some of the key points made formally published in a journal, although many aspects of the paper are not particularly conventional.

I found the prosaic style of writing difficult going, and large sections of the manuscript long winded. I don’t believe that all of the background to genomic selection is necessary, this could be handled a lot more briefly. There was excessive use of bullet points. The paper would be a lot more accessible if there were more section titles, and a greater use of tables.

My greatest concern relates to the subjectivity elements. The respondents to the survey are diverse, but appear to be associates of the Author. The sheep and beef bull and ram breeders all appear to be based in Australia. Most of these respondents have made a significant commitment to genomic selection, it has become a key part of their marketing, and how they define themselves as a business. Many of them have received subsidies via R & D projects to get them started. My reflection when reading through the paper was that we were getting rose tinted perspectives of Genomic Selection with little or no regard to the issue of costs, biases, over prediction, unacceptable fluctuations in genetic improvement predictions, under performance of new method development, and lack of proof that genetic trends have significantly accelerated in a number of adopting industries. I would generally agree with many of the authors conclusions about the holistic and often very positive changes that have come about through adoption of genomic selection. However, in less developed countries, and in industries with quite extensively managed livestock with genetically diverse sub populations and or breed mixing, I am not convinced that genomic selection is as great as what might be interpreted from reading this article.

The description of the survey is very loose, most likely because the survey approach was very loose itself. For example, I could not find a description of how respondents were selected, whether there were potential respondents approached but chose not to participate, was there any attempt made to identify people not using genomic selection and discover why, and also those that have tried and abandoned it. There does not appear to be any way of converting the results into quantitative output. This seems a pity, and highlights my concerns about the approach taken being so subjective.

In summary, the paper has a lot of merit, I think it would draw an interested readership, but quite a bit needs to be done to make the paper sharper, less subjective and more balanced, and with a much more accessible layout.

Specific

Title. This is a general Agricultural Journal, Plant/agronomy focused people might see the title and not realise that this paper is entirely about animals. I think Livestock should be incorporated into the title. There is zero mention of genomic selection in plants. The paper is solely about genomic selection in livestock, and that needs to be clearer throughout the manuscript.

L18 I found the abstract to be great and logical, but then I have a number of concerns about the last sentence starting “Genomic Selection….”. In particular, the sentence is too long, genetics does not collaborate, neither does the genetics discipline, rather it is people that collaborate, and it is not clear to me what is meant by “the genetic improvement algorithm”.

L75 “pecies” should be “species”.

L118 I would drop the statement/implication of 4000 kick in for diminishing returns. It implies that 4000 is enough, but many genomicists are arguing for 20,000. Also, there are diminisihing returns from animal 1.

L124. I doubt that the decay of genomic accuracy over time is limited to populations under selection. Even without selection, over time, the training population becomes less closely related to the selection population, new mutations can appear, genes can be fixed by drift…

L137 suggest “faster genetic change in individual traits”.

L146 1950’s.

L164 these are not the most recent proceedings. Better to avoid this sort of statement, as hopefully readers would still find this paper useful in the future, where recentness will be irrelevant.

L174 unfinished.

L193 to 194. I do not understand the point being made here.

L204 the sentence at the beginning of these bullet points talks about reader interest, so why add wider interest here as a third bullet point?

Table 1 column headers suggest “single enterprise” and “Multiple enterprise”, otherwise reader ahs to hunt back through the text to decipher the table.

L261 seems unnecessary to single out this particular point to provide a detailed example.

L281 to 306 is a direct repetition of material provided above.

L277 to 279 – this constitutes a very loose and subjective methodology.

L439 this idea should not really be attributed to Bijma. Stephen Bishop at Edinburgh and Angela Doechl Wilson have been talking about this for 20 years.

L757 I would advise to reconsider the wording of the statement that genomic selection is a “method of choice”. Genomic selection is an expensive and complicated enhancement to an already complex process of running a genetic improvement program. Would be better to comment on increased rates of adoption of genomic selection, but in my view it is not a method that replaces alternative methods, it is an option to enhance them.

Appendix A. Why have this as an Appendix? Is there a supplementary material option for Appendix B, and the excerpts from responses starting about line 584.

References – there were many 4 digit integers randomly embedded in the citations in the version I reviewed.

Author Response

Please see attached responses

Author Response File: Author Response.pdf

Reviewer 2 Report

This paper reports a survey of organisations involved in genetic improvement, across species, countries, and roles both public and private. With falling costs of genotyping, genomic selection has been implemented in a wide range of species. Both the increased accuracy of breeding values that underpins potentially faster progress, and the re-balancing of genetic change to include real progress in the hard-to-measure traits, have been widely observed. The article is presented in the form of interview, which has a large length and many paragraphs. It is suggested to reorganize the paragraphs and present them in a compact and complete structure, and use serial numbers to divide them when necessary.

Comment 1, lines 23: Please pay attention to the formatting details of the paper. Some text does not need to be bold.

Comment 2, lines 115-125:  Is it divided into 4 segments here? If there are 4 paragraphs, keep each sentence complete. Same goes for the rest of the article.

Comment 3, lines 129-132,173-186: If necessary, the serial number should be used to help section and highlight the structure, instead of using "-".

Comment 4, lines 150: "…et al." pay attention to the correct spelling of words.

Comment 5, lines 169,542: Why are some "…et al." italics and some not?

Comment 6: It is suggested to integrate the paragraphs and maintain the compact structure of the text.

Comment 7, lines 211: Repetition of punctuation marks.

Comment 8, lines 247,254-266: It is recommended to list each item starting with “a”.

Comment 9, lines 315,328,337,343: It is recommended to write after the colon instead of paragraphing. Same goes for the rest of the article.

Comment 10, lines 517: Please keep all references in the same format.

Author Response

Please see attached responses

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

As for the reply given by the author of the review opinion, there are the following points. It is suggested that the article be presented in a compact and complete structure. For example, Comment 2, Lines 115-125: the four main points of the reference, the end of which is ", "and" and "appear, which will give readers the feeling that the sentence is not fully expressed. In addition, there are a large number of sections in the article, which is distinguished by multiple symbols: "-", "ο", "•", numerical sequence number and letter. It is recommended to combine and highlight the article frame appropriately. If the author thinks that the current format is beneficial to improve readability, no objection to this.

Author Response

See attached for response

Author Response File: Author Response.pdf