Genome-Wide Association Mapping of Oil Content and Seed-Related Traits in Shea Tree (Vitellaria paradoxa subsp. nilotica) Populations

Round 1

Reviewer 1 Report

Several issues in this manuscript are listed as follow.

[1] In the study, there are only 7,530 SNPs used for GWAS of oil content and seed related traits in the shea tree population, but far less than those of other GWAS studies. However, how many markers are required for GWAS is an important question. Thus, LD decay analysis should be performed to estimate the number of markers (SNPs) required for GWAS.

[2] In the section 2.1.2 (‘The reads were then aligned to the shea_V1 reference genome publicly available from the ORCAE database (https://bioinformatics.psb.ugent.be/orcae) (accessed on 30 December 2021).’), which mapper (BWA, Bowtie, …?) is used for mapping of reads against reference genome? Add the name and version of the mapper used.

[3] The p-value for Pearson correlation coefficient should be added in Figure 2.

[4] In the Section 3.5, the 2 in ‘R2’ should be superscripted.

The section introduction need further revision. Two paragraphs may be not enough to explain the background and motivation of this manuscript.

Author Response

Response has been attached below

Author Response File: Author Response.docx

Reviewer 2 Report

The manuscript entitled “Genome-wide association mapping of oil content and seed related traits in shea tree (Vitellaria paradoxa Subsp. nilotica) population” proposed to investigate the genome of an important oil-producing species. The work is well structured and presents relevant information that can be applied to the genetic improvement of the species. In addition, the number of genotypes analyzed was very good. 

Author Response

Response  is in attachment

Author Response File: Author Response.docx

Reviewer 3 Report

The manuscript entitled “Genome-wide association mapping of oil content and seed related traits in shea tree (Vitellaria paradoxa Subsp. nilotica) population” describes the identify genomic loci associated with oil content and seed-related traits in the shea tree which is an important economic tree crop known for its oil. Altogether paper is well-written and interesting research has been undertaken. This is among the manuscript which I rate as strong and it just needs some minor revision. With the comments:

1- Introduction is too short so please expand it by adding more information on the botany and breeding of shea tree and other aspects like genome size, feature and structure.

2- The information on how the plant samples have obtained is unclear. Are the trees already in germplasm or you have collected them from those regions? In section 2.1, it has noticed that 180 trees have been used for analyses. Moreover, do not use family for the groups of trees you have exploited. It would be great if you could bring a supplementary table containing all the used genotypes with their information (if available).

3- However, the manuscript has been prepared in a logical way, it needs minor English grammatical and structural polishing.

4- Why the respected authors have not performed a population structure analysis based on the SNP markers?

Based on the above-mentioned comments, in my opinion, the work is worthwhile in the field of shea tree breeding and genomics and I strongly recommend its publication after minor revision.

English quality is good and it just needs a minor revision.

Author Response

The responses are in the attachment below

Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

1) The Figure 2 is ugly. The characters (e.g., Length, Width, Weight, Oil) is so large that overlaps with the data points or curves in the figure.

2) The 'subsp.' in 'Vitellaria paradoxa Subsp. nilotica' should be lowercase.

3) The method for LD decay analysis should be added in the 2.2 'Data analysis' section. 

I have no comments.

Author Response

Response attached as "Round 2" file

Author Response File: Author Response.pdf