Genetic Architecture and Signatures of Selection in the Caqueteño Creole (Colombian Native Cattle)

Round 1

Reviewer 1 Report

The topic of the manuscript is in line with the journal's objectives and of interest to the reader. The manuscript needs extensive English syntax revision because the text is unclear in many parts.

The manuscript describes the genetic structure of the population under study very superficially and this part could also be addressed with other methodologies and not only with a PCA analysis. For example, a classic Admixture analysis could be in this case informative about the relationships between the three farms. Furthermore, the evidence for the presence or absence of differentiation should be detailed in a more comprehensive manner, for example, with a matrix of FSTs across all groups and not just the two found with PCA. In the latter case, the fact that two populations are considered as one only because they are close together in the graph seems to me to be poorly demonstrated evidence.

The discussion should be more centered on initial assumptions made about the population. Why might the genes found under selection have been selected? The author talks about genes related to the environment ... some more details in the discussion would be appreciable.

Here are some more specific remarks in the text

Line 42-43: s,” causing particular situations in somebody's countries” is not clear

Line 43-44: this sentence is not clear, if the author wants to say that these breeds decreased in number, please give a citation or some data

Line 37: Please be more specific about this information. Report some information more about the rearing region, speaking broadly of Amazon it seem that this cattle is reared in the jungle while, as is reported in some article or web pages this breeds is of department of Caquetá with in the “Conca Amazonica”.

Line 74: “footprints the CAQ population” maybe “of” is missing?

Line 86: how many females and male?

Line 87: how and why these farms were chosen?

Line 95: add package version

Line 110-111: this sentence is not clear: the expectation and standard deviation of what?

Line 118: correct reference format (1965)

Line 120: does the authors intend each farm as a population?

Line 122 what is a EHH statistics? Please detail more and justify the need for this new analysis

Line 126: the authors need justify more this affirmation. Normally selection signature without using phenotypes is carried out comparing different structures within a population or among different populations. In this study the authors intend that a selection force exist inside the breeds from an herd to other? What is the hypothesis of this study?

Line 159: correct reference

Line 158-164: this a description of the software and should not be in the results.

Line 164-165: why it is adequate?

Line 168-169: this sentence is not clear

Line 179: probably I lose some detail about the analysis: How the group are defined? Are those defined in PCA analysis? But there the groups were 3… please details the methods

Figure 3: what the colors stand for?

Line 211-212: in the PCA clearly 3 groups are distinguishable. The authors performed all the analysis considering only two. First in the text in my opinion is not very clear how the author chooses these two groups and second, an FST analysis should be carried out among the three groups (for example adding a matrix of pairwise Fst). Authors should take decision also based on the significancy of divergency based on FST, rather than only is values (Than seem to be in line with the other breeds in the region)

Line 238: BON abbreviation was not defined before

Line 287 has

Author Response

REVIEWER 1

Comments and Suggestions for Authors

The topic of the manuscript is in line with the journal's objectives and of interest to the reader. The manuscript needs extensive English syntax revision because the text is unclear in many parts.

The manuscript describes the genetic structure of the population under study very superficially and this part could also be addressed with other methodologies and not only with a PCA analysis. For example, a classic Admixture analysis could be in this

informative about the relationships between the three farms. Furthermore, the evidence for the presence or absence of differentiation should be detailed in a more comprehensive manner, for example, with a matrix of FSTs across all groups and not just the two found with PCA. In the latter case, the fact that two populations are considered as one only because they are close together in the graph seems to me to be poorly demonstrated evidence.

The discussion should be more centered on initial assumptions made about the population. Why might the genes found under selection have been selected? The author talks about genes related to the environment ... some more details in the discussion would be appreciable.

R/ the manuscript the authors reported to following

For the most significant SNP regions for group 1, candidate genes associated with environmental resistance, immunity, growth, and meat quality were identified. We can highlight the CMPK1 gene in BTA3, which was related to response to stress and thermotolerance between zebu and taurine cattle breeds [26]. Also located in BTA3, the FOXD2 gene was pointed out. That gene was associated with metabolic processes and immune responses in native Korean cattle [30], indicating a possible selection process towards environmental resistance in the CAQ breed. [L231-238]

Finally, related to immunity, we can pinpoint the ULBP (BTA9), which interacts with the NKG2D receptor to activate effector cells in the bovine immune system [38], and the KRTAP9-2 gene (BTA19), associated with tick resistance in Brahman and Angus cattle [39]. [L252-254]

Here are some more specific remarks in the text

Line 42-43: s,” causing particular situations in somebody's countries” is not clear

R/The correction was made in the text [L41-42].

Line 43-44: this sentence is not clear, if the author wants to say that these breeds decreased in number, please give a citation or some data

R/ The correction was made in the text [L49-54].

Line 37: Please be more specific about this information. Report some information more about the rearing region, speaking broadly of Amazon it seem that this cattle is reared in the jungle while, as is reported in some article or web pages this breeds is of department of Caquetá with in the “Conca Amazonica”.

R/ It was inserted in the text [L49-54]. “The Criollo Caqueteño cattle have survived due to rusticity and adaptation traits, which resulted from natural selection against the conditions of the Colombian Amazon, becoming an alternative for livestock in the region. In addition, replacing native vegetation (prairies) with plating grasses sustained the breed's development in that region. Currently, the Criollo Caqueteño cattle have a low number of remaining females in reproductive capacity [6–8]”

Line 74: “footprints the CAQ population” maybe “of” is missing?

R/ The correction was made in the text [L78].

Line 86: how many females and male?

R/ The Caqueteño creole population, there were 18 males and 109 females. The information was added in the material and methods session [L89].

Line 87: how and why these farms were chosen?

R/ The Caqueteño Creole Breed is an autochthonous breed with few specimens (approximately 140). For this reason, the specimens were searched in the department of Caquetá to gather the total population. These were found mainly on three regional farms: Breed nucleus, which belongs to the University of the Amazon, "Villa mery" and "El Pencil" farms. This work is part of a research project aiming to conserve the breed.

Line 95: add package version

R/This information was inserted [L99]

Line 110-111: this sentence is not clear: the expectation and standard deviation of what?

R/ This section was rewritten [L139-140].

Line 118: correct reference format (1965)

R/ The correction was made in the text [L146].

Line 120: does the authors intend each farm as a population?

R/ No, the CAQ population was analyzed as one. However, when we performed the PCA analysis, we identified three clusters, but these were not separated by farm; within each cluster, there were animals from different farms. For this reason, being the first study that addresses the genetic architecture of CAQ, we decided to carry out the DPCA analysis and verify the proximity between the clusters to study the population better.

Line 122 what is a EHH statistics? Please detail more and justify the need for this new analysis

R/ It was inserted into the text [L149-151]. We used the XP-EHH analysis, a robust cross-population statistic, to detect a selection process. It uses extended haplotype homozygosity (EHH) statistics based on specific fixed alleles inside each population.

Line 126: the authors need justify more this affirmation. Normally selection signature without using phenotypes is carried out comparing different structures within a population or among different populations. In this study the authors intend that a selection force exist inside the breeds from an herd to other? What is the hypothesis of this study?

R/ The hypothesis was to identify possible regions in the genome that have been fixed due to a natural selection of the population of the Caqueteño Creole breed raised in the Amazonian environment. To test this hypothesis, we decided to study the genetic architecture first because the breed does not have population information.

Therefore, principal component analysis (PCA) and discriminant principal component analysis (DAPC) are used using the adegenet package for R software Jombart et al. (2010). The PCA approach allows individuals to be classified based on the reduced number of important orthogonal principal components (PC). This genomic analysis is used because it indicates the total genetic variability represented by the PC. The DAPC was applied to select the optimal number of clusters (K) among all the PCA output clusters. DAPC uses PC clustering of K-means to infer the actual number of populations (Jombart et al., 2010). Therefore, when we obtained the results of DAPC, which showed two groups, we decided to study the population in group 1 and group 2. Subsequently, with groups 1 and 2, we analyzed the selection footprints between populations (Fst and XPHH). Maiorano et al. (2018) analyzed the IHS, Fst, and XPHH selection tracks in the Gyr breed, studying two populations within the same breed.

Jombart T, Devillard S, Balloux F. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics. 2010;11: 94 10.1186/1471-2156-11-94.

Maiorano, A. M., Lourenco, D. L., Tsuruta, S., Ospina, A., Stafuzza, N. B., Masuda, Y., Filho, A., Cyrillo, J., Curi, R. A., & Silva, J. (2018). Assessing genetic architecture and signatures of selection of dual purpose Gir cattle populations using genomic information. PloS one, 13(8), e0200694. https://doi.org/10.1371/journal.pone.0200694

 

Line 159: correct reference 24

R/ The correction was made in the text [L99].

Line 158-164: this a description of the software and should not be in the results.

R/ This section is inserted now in Methods [L96-104].

Line 168-169: this sentence is not clear

R/ This section was rewritten and inserted now in Methods [130-131].

Line 179: probably I lose some detail about the analysis: How the group are defined? Are those defined in PCA analysis? But there the groups were 3… please details the methods

R/ To better understand the text, the analysis and results of the genetic architecture of the Caqueteño Creole were added in the methods session to clarify how the groups later used in the signatures selection were defined [L119-131].

Figure 3: what the colors stand for?

R/ It was corrected in the figure legend [L111-118]

Line 211-212: in the PCA clearly 3 groups are distinguishable. The authors performed all the analysis considering only two. First in the text in my opinion is not very clear how the author chooses these two groups and second, an FST analysis should be carried out among the three groups (for example adding a matrix of pairwise Fst). Authors should take decision also based on the significancy of divergency based on FST, rather than only is values (Than seem to be in line with the other breeds in the region).

R/ Yes, in the PCA are shown three clusters. The DAPC analysis (Figure 1c) points out two separate groups based on the genetic distance, where group 1 (blue) is distant from group 2 (overlapping red and yellow). Therefore, only two groups were considered to explain the Caqueteño Creole cattle better and perform the signature selection analyses; Group 1 (n =24) and Group 2 (n = 96) [L128-131].

Line 238: BON abbreviation was not defined before

R/ It was inserted into the text [L44].

Reviewer 2 Report

Dear authors

Thank you for submitting an interesting manuscript. However, I have some issues that need to be addressed - detailed comments are given in the form of sticky notes on the pdf version.

I would appreciate clarification regarding:

1. The selection strategy (or lack thereof) that is followed for this breed.

2. Why these specific methodologies for selection signatures were applied (intra- and inter population approaches).

3. How the statistically significant SNP and genes were identified.

Regards

Comments for author File: Comments.pdf

Author Response

REVIEWER 2

Dear authors

Thank you for submitting an interesting manuscript. However, I have some issues that need to be addressed - detailed comments are given in the form of sticky notes on the pdf version.

I would appreciate clarification regarding:

1. The selection strategy (or lack thereof) that is followed for this breed.

R/ It would be a lack of selection. The Caqueteño Creole was declared a genetic resource of Caquetá, and its conservation is beeing promoted. However, this conservation was not based on population parameters or directed selection to conserve and improve the breed. During these years, they have adopted an extensive grazing system with males and females without any specific control. This management was the same for the three farms participating in the study.

2. Why these specific methodologies for selection signatures were applied (intra- and inter population approaches).

R/ These intra- and inter-population methodologies were carried out due to the results of the genomic architecture analysis of the CAQ breed. In the analysis, two groups were identified within the breed, which generated curiosity to identify what occurred in each group and point out similarities between the two groups. Thus, to better understand the Creole breed, we separated the CAQ into two groups and performed the IHS analysis on each group to identify differences and the Fst and XP-HH analyses to identify similar regions.

3. How the statistically significant SNP and genes were identified.

R/ HIS and XP-EHH  ≥ 5 (p < 0.01)

Reviewer 3 Report

 

Major issues

1. The Fst and XP-EHH methods for detecting selection signatures are suitable for comparisons between populations, not for a single population. The authors applied the two methods to the same cattle population,  in spite of using two groups within CAQ population. Thus, I would recommend the authors apply other methods such as pcadapt (https://bcm-uga.github.io/pcadapt/articles/pcadapt.html), composite likelihood ratio (CLR) to detect signatures of selection in CAQ population.

2. After quality control, how many samples kept for subsequent analysis should clearly stated. 

Minor issues

3. line 17, "genomic structure" should be "genomic Architecture".

4. line 43, "somebody's countries" should be "some countries".

Author Response

REVIEWER 3

Major issues

1. The Fst and XP-EHH methods for detecting selection signatures are suitable for comparisons between populations, not for a single population. The authors applied the two methods to the same cattle population,  in spite of using two groups within CAQ population. Thus, I would recommend the authors apply other methods such as pcadapt (https://bcm-uga.github.io/pcadapt/articles/pcadapt.html), composite likelihood ratio (CLR) to detect signatures of selection in CAQ population.

R/ The genetic architecture analysis was previously carried out to identify whether the Caqueteño Creole breed had any subdivision. For this reason, principal component analysis (PCA) and discriminant principal component analysis (DAPC) were performed using the adegenet package for the R software Jombart et al. (2010). The PCA approach allows individuals to be classified based on the reduced number of important orthogonal principal components (PC). This genomic analysis is used because it indicates the total genetic variability that PC represents. The DAPC was applied to select the optimal number of clusters (K) among all PCA output clusters. DAPC uses PC clustering of K-means to infer the actual number of populations (Jombart et al., 2010). Therefore, obtaining the results of DAPC, which showed two groups, we decided to study the population in group 1 and group 2. Subsequently, with groups 1 and 2, we analyzed the selection fingerprints between populations (Fst and XPHH). Maiorano et al. (2018) analyzed the IHS, Fst, and XPHH selection tracks in the Gyr breed, studying two populations within the same breed.           

2. After quality control, how many samples kept for subsequent analysis should clearly stated. 

R/The genotypic database included 127 individuals genotyped after quality control.

 

Minor issues

2. line 17, "genomic structure" should be "genomic Architecture".

R/ The correction was made in the text [L18].

4. line 43, "somebody's countries" should be "some countries".

R/ The correction was made in the text [L42].

 

Round 2

Reviewer 1 Report

Dear Author, thank you to accept the revisions and submit a new version of the manuscript. In my opnion no addicionals correction are needed.

Author Response

Thanks for the suggestions to improve the manuscript.

Reviewer 2 Report

Dear authors

Thank you for submitting a much improved version. I suggested a few minor corrections and comments in the current version.

Comments for author File: Comments.pdf

Author Response

REVIEWER 2

Thanks for the suggestions to improve the manuscript.

Please revise the title (suggestion given in previous revision)

R/ was revised the title and modified

 

This sentence still does not have a verb.

R/The correction was made in the text

 

I don't think this is a word. Do you mean "robustness" or "hardiness"?

R/The correction was made in the text

 

planted pastures?

R/The correction was made in the text

 

These are Results, not M&M.

R/ were inserted section in Results

 

And these could even be Discussion.

R/ were inserted in the text

Reviewer 3 Report

The authors addressed all concerns and thus I recommend accepting the manuscript.

Author Response

Thanks for the suggestions to improve the manuscript.