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Responses to Reviewers’ Comments

Comment
Reviewer #1: The revised version has solved most of the problems of the original version.
There are, however, some questions that are not clearly solved:
- The authors insist on saying that there was a close correspondence between the classification
based on molecular markers and the other two methods (page 1 line 22-23 and line 630) but
actually, only two inbreds are in the same groups across classifications while 10 inbreds were in
a different group for each method.

Response
This statement has been modified.

Comment

- This design does not allow calculation of additive genetic variance (Line 319-326)

Response
The sentences in the whole paragraph have been corrected and modified.

Comment

- GEI effects do not create difficulties in selecting for contrasting environments, they just imply
that selections has to be carried out for specific environments Besides, there are some minor
corrections:

Response
The sentence has been corrected.

Comment
Line 50: Wolfe et al 1988 is 1998 in the references

Response
The year has been corrected in the reference list.

Comment
L115: Makunmbi is Makumbi in the references

Response
“Makunmbi” in L115 has been changed to “Makumbi”.

Comment
L252: insert one space after the point

Response
Space has been inserted.
Comment
L319-326: I cannot see the results reported in this paragraph in table 2

Response
“Table 2” in the paragraph has been changed to “Table 3”.

Comment
L333: TZEEI 1 should be 81

Response
TZEEI 1 has been changed to TZEEI 81.

Comment
L336-338: I cannot see the analysis under low N environment in Table 3 that refers to analysis
combined across environments

Response
“Stay green characteristic” was recorded for only the low-N environments and this has now been
indicated in the materials and methods section.

Comment
L337: remove the "," after "inbreds"

Response
Comma has been delected after inbrdes.

Comment
L357-360: The criteria used for assigning the inbreds to the groups are not clear to me

Response
The criteria used for assigning the inbreds to groups have been expatiated.

Comment
L386: Table 5 should be table 4

Response
The data presented in the paragraph is in Table 5. Therefore, Table 5 is appropriate here.

Comment
L718: fumonium should be fumonisin

Response
“Fumonium” has been change to “fumonisin”.
Comment
References: There are abbreviations of journal names without points (Afr Crop Sci) or with
points (J. Agric Sci.) and many others inconsistencies The reference Badu-Apraku and Oyekunle
(2012) is duplicated; remove the first one because is out of order.

Response
The references have been corrected.

In figures 1 and 3, the lines do not coincide with the names of the inbreds Figure 2 has different
font size than the other two figures Why are there only 18 inbreds in figure 3 instead of 20 as in
the other figures?
Figure 5 is too small and hard to read

Response
Figures 1and 3 have been formatted and have the same front size as figure 2. Figure 5 has also
been properly formatted. Figure 3 has only 18 inbreds because the remaining two inbreds were
excluded in the diversity study due to the poor quality and quantity of the DNA extracted from
two of the inbreds.

Reviewer #2: The authors of the paper entitled "Combining ability, heterotic patterns and genetic
diversity of extra-early yellow inbreds under contrasting environments" (EUPH-D-12-00328R1)
have done a nice work reducing the length of the original manuscript. They have also corrected
most of the faults pointed out in my previous review. There are, however, some points that must
be amended before publication.

Comment
The authors cite three references to support their assertion that "The most commonly used
method for classifying maize inbreds into heterotic groups is the SCA effects of grain yield (Fan
et al. 2009; Akinwale, 2012; Badu-Apraku and Oyekunle 2012)." But one of the references
(Akunwale, 2012) is a PhD thesis very difficult, if not completely impossible, to access to. The
reference Fan et al. (2009) does not support that assertion. What Fan et al. (op cit) say is that a
method called HSGCA is very efficient to classify maize inbred lines into heterotic groups. And
this method, i.e. HSGCA, includes both general and specific combining abilities, not only the
latter, as Badu-Apraku et al. duly explain a little later in the same paragraph. So I cannot
understand the reason to use a reference that does not support their affirmation. The remaining
reference (Badu-Apraku and Oyekunle [2012]) does not say in any place that SCA is the most
commonly used method to assign inbreds to heterotic groups. At most what is said in the latter
paper (page 105) is that "positive SCA effects indicate that lines are in opposite heterotic groups
whereas negative SCA effects indicate that the lines are in the same heterotic group", which is
obviously true, but this is not the same as "SCA is the most commonly used method".

Response
The statement has been corrected.

Comments
Another objection deals with Table 1. With the explanation given in lines 154 through 165 the
meaning of the pedigrees is clear, but still I do not understand why the entries are not ordered in
the table; this lack of order implies additional effort to find a specific inbred. Besides, the
pedigrees must be carefully checked because it seems that there are some obvious errors in, for
instance, lines TZEEI 89 and TZEEI 88. It also seems strange why in some occasions you find
the word "Inb" while in other entries the word seems to be spelled in full, which is "Inbred".
These inconsistencies must be avoided.

Response
The inbreds in Table 1 have now been ordered and pedigrees have been corrected.

Comment
Other minor flaw is the lack of the crop name in the heading of tables 2 through 4. The table
headings must be carefully checked so they are self-explanatory.

Response
Maize has been inserted in the title of Tables 2 to 5.

After making all the corrections the manuscript could be published in EUPHYTICA.

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