Submit to this Journal Review for this Journal Propose a Special Issue

Article Menu

Share Help Cite Discuss in SciProfiles

Open AccessArticle

Peer-Review Record

Genome-Wide Association Studies for Flesh Color and Intramuscular Fat in (Duroc × Landrace × Large White) Crossbred Commercial Pigs

Genes 2022, 13(11), 2131; https://doi.org/10.3390/genes13112131

by Hao Li^1,2,†

, Cineng Xu^1,†, Fanming Meng^2,†, Zekai Yao^1,2, Zhenfei Fan¹, Yingshan Yang¹, Xianglun Meng¹, Yuexin Zhan¹, Ying Sun¹, Fucai Ma¹, Jifei Yang¹, Ming Yang³, Jie Yang^1,4

, Zhenfang Wu^1,4,5, Gengyuan Cai^1,4,* and Enqin Zheng^1,*

Reviewer 1: Anonymous

Reviewer 2:

Ioan Hutu

Genes 2022, 13(11), 2131; https://doi.org/10.3390/genes13112131

Submission received: 29 October 2022 / Revised: 12 November 2022 / Accepted: 12 November 2022 / Published: 16 November 2022

(This article belongs to the Section Animal Genetics and Genomics)

Round 1

Reviewer 1 Report

This is an interesting manuscript focused to detect SNPs associated with flesh color and intramuscular fat at 45 minutes and 12 hours (45mFC, 45hIMF, 12hFC, 12hIMF) in crossbred commercial pigs using GWAS analyses. The methodology is well described, but some additional results appear to be needed to enhance the discussion.

I suggest considering next minor comments to improve the manuscript:

1) Abstract: According to guidelines described in “Instructions for authors”, this section should include a brief description of the main methods or treatments applied.

2) Introduction: The objective does not match with the one described in the Introduction.

3) Results: I suggest including Manhattan plots for GWAS analyses, as well as gene ontology graphs, in order to show the results more clearly.

Minor grammar comments:

- Line 28= Insert the words “after slaughter” before the bracket.

- Line 28= Replace the word “45hIMF” by “45mIMF”.

- Line 29= Remove the word “respectively”.

- Line 30= Replace the semicolon by a period sign.

- Line 31= Replace the semicolon by a period sign.

- Line 31= Remove the word “four”.

- Line 32= Replace “is” by “was”.

- Line 32= Remove the period after “0.178”.

- Line 32= It is not clear with which traits the 7 and 3 SNPs were associated.

- Line 37= Replace “pigmentation, skeletal” by “pigmentation and skeletal”.

- Line 47= Replace “etc” by “etc.”

- Line 48= Replace “Which” by “It”.

- Lines 70-72= This sentence is confuse, please rewrite.

- Line 72= Separate the bracket from the period sign.

- Lines 93-95= This sentence is confuse, please rewrite.

- Lines 101-102= Move “Genotype” sentence 5 lines forward.

- Line 128= Remove the semicolon.

- Line 139= Replace “is” by “was”.

- Line 140= Replace “According to the Gebriel…” by “According to Gabriel…”.

- Line 141= Insert the word “was” after “search for genes”.

- Line 150= Remove the word “And”.

- Line 152= Replace “are” by “were”.

- Lines 153-157= Very long paragraph, please separate in two shorter paragraphs.

- Line 158= Replace “is” by “was”.

- Line 168= Replace “may cause” by “may be caused”.

- Line 183= Insert the word “respectively” after the scores.

- Lines 214-218= This sentence is confuse, please rewrite.

- Line 224= Replace “in12hFC” by “in 12hFC”.

- Line 228= Replace the semicolon by a period sign.

- Line 255= Remove “S. M”.

- Line 256= Replace the comma by a semicolon.

Author Response

Reviewer #1

I suggest considering next minor comments to improve the manuscript:

Response: We sincerely thank the editor and all reviewers for their valuable feedback that we have used to improve the quality of our manuscript. The reviewer comments are laid out below in normal font and specific concerns have been numbered. Our response is given in italicized font and changes/additions to the manuscript are given in the red text.

Q1: Abstract: According to guidelines described in “Instructions for authors”, this section should include a brief description of the main methods or treatments applied.

Response: Thank you for your suggestion, we added the description of the main methods, added content is "In this study, we determined the flesh color and intramuscular fat at 45 minutes and 12 hours after slaughter (45mFC, 45mIMF, 12hFC, 12hIMF) of 1,518 commercial Duroc × Landrace × Large White (DLY) pigs. We performed single nucleotide polymorphism (SNP) Genome-wide association study (GWAS) analysis with 28,066 SNPs." and "Furthermore, GO and KEGG analysis revealed that these genes are involved in the regulation of apoptosis and are implicated in functions such as pigmentation and skeletal muscle metabolism.". Please see Page 1 Lines 26-30 and Lines 36-38 in the revision

Q2: Introduction: The objective does not match with the one described in the Introduction.

Response: Thank you for this point. We changed it to "we used a 1,518 Duroc × Landrace × Large White (DLY) crossbred pigs population to analyzed the four traits (45mFC, 12hFC, 45mIMF, 12hIMF) through GWAS, combined with the actual character correlation and heritability, we expect provide a new sight for the identification of candidate genes for flesh color and IMF, molecular breeding of pigs.". Please see Page 2 Lines 81-84.

Q3: Results: I suggest including Manhattan plots for GWAS analyses, as well as gene ontology graphs, in order to show the results more clearly.

Response: Thank you for your suggestions on the results. We have redrawn the Manhattan plot (as shown in Figure 1 in the revision), and the gene ontology enrichment analysis result plot has been uploaded to supplement Figure S2.

Q4: Minor grammar comments:

Line 28 = Insert the words "after slaughter" before the bracket.