Fwd: Major Revisions requested MOLB-D-22-00163

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kassahunb@gmail.com 7:45 PM (2
hours ago)
to me

Hi Zeleke 

Below is the feedback from Molecular Breeding requesting for major revisions.
Please act carefully and timely.

Regards

---------- Forwarded message ---------

From: Molecular Breeding Editorial Office <em@editorialmanager.com>
Date: Sun, Sep 4, 2022, 5:56 PM
Subject: Major Revisions requested MOLB-D-22-00163
To: Kassahun Bantte <kassahunb@gmail.com>

Dear Prof Bantte,

We have received the reports from our advisers on your manuscript, "Genome-Wide
Association Study Reveals Genomic Loci Influencing Agronomic Traits in Ethiopian
Sorghum [Sorghum bicolor (L.) Moench] Landraces ", which you submitted to Molecular
Breeding.

Based on the advice received, the Editors feel that your manuscript could be
reconsidered for publication should you be prepared to incorporate major revisions.
When preparing your revised manuscript, you are asked to carefully consider the
reviewer comments which are attached. Please also check online for possible reviewer
attachment(s).

In order to submit your revised manuscript, please access the following web site:

https://www.editorialmanager.com/molb/

Your username is: kbantte 

If you forgot your password, you can click the 'Send Login Details' link on the EM Login
page.

We look forward to receiving your revised manuscript before 04 Nov 2022.

Please make sure to submit your editable source files (i. e. Word, TeX).

With kind regards,

Yibo Li, Ph.D

Managing Editor
Molecular Breeding

COMMENTS TO THE AUTHOR:

Reviewer #1: The abstract need to be rewritten as the conclusion made is wrong.  The
authors did not characterized any gene and how come to claim this sentence "This
study contributes to the characterization of genes controlling important agronomic traits
and would serve as a source of markers in sorghum breeding."
Introduction is weak as well several GWAS studies have been conducted in sorghum
please what is difference between the current and the previous please justify this.

The analysis for the GWAS need to be conducted using a specific model since the
authors is dealing with complex traits to be able to identify and or detect minor QTL. 
Please using this package for the GWAS analysis
(https://www.sciencedirect.com/science/article/pii/S1672022920301406) you could
factor in the model different cofactor (such as admixture result, kinship matrix for better
optimization) six different genetic model can be explored.
the LD analysis is wrongly performed and I will suggest authors redo this by estimating
the LD per chromosome using R
For the GWAS analysis as much as authors justify the need to conduct the gwas
analysis per location I will suggest authors use  the blue generated across location
(single blue) to perform the analysis. Author can perform regression analysis to identify
stable QTL.
Please consider add the gene analysis figure to show the correlation between the
identified genes and the SNP region (LD heatmap)

Reviewer #2: Dear Authors,

Thank you for your the manuscript 'Genome-Wide Association Study Reveals Genomic
Loci Influencing Agronomic Traits in Ethiopian Sorghum [Sorghum bicolor (L.) Moench]
Landraces "

First of all, I do apologize for my late response to the review. It is a well-written

manuscript presenting the SNPs important for yield. The work has been carried out very
extensively and with great caution. I strongly think that the paper is technically sound, it
covers all of the aspects of identification of candidate genes for yield. The experiments
have been repeated with good number of biological and technical replicates. The
evidences are reassuring with assumptions made.  The statistical models have been
used well. The availability of the data is very welcoming in the community. The results
are well discussed with supporting literatures from the related crop species. The
manuscript is written very well making the reader very engaging in the subject area. The
tables are decent in presentation. The literature has been wisely cited. 

My comments :
1)      In the field trials, how was the edge effect marginalised? 
2)      How was the phenotype scoring performed? Were the extreme outliers taken in to
account?
3)      I was wondering if the author would also like to include how the statistical tests
related to Phenotypic data analyses were carried out. Were they performed in R? 
4)      Was LD also calculated individually for different populations grown in Kobo and
Mieso regions? If yes, what were the observations?
5)      I would like to see the population structure figure; It is mentioned that germplasm
were collected from diverse locations and then grown in two different regions. Can
authors also demonstrate this by figure? 
6)      I would like to see some figures of phenotypic traits from the experiments. This will
support the analyses and make the manuscript more intriguing for readers.
7)      Have the candidate genes which have been identified in this study been tested in
the all subpopulations and is it stable across them?

Best Wishes