From 0e5cfba224789311dc10c4446432c7427d578595 Mon Sep 17 00:00:00 2001
From: Mekhrona Mirzoeva <memir101@hhu.de>
Date: Fri, 27 Sep 2024 13:09:48 +0200
Subject: [PATCH 1/7] README.md wo picture
---
.gitattributes | 1 +
README.md | 23 +++++++++++++++++++++++
_publication/erae198_fig1.jpeg | 3 +++
3 files changed, 27 insertions(+)
create mode 100644 README.md
create mode 100644 _publication/erae198_fig1.jpeg
diff --git a/.gitattributes b/.gitattributes
index 67fdbe3..951e266 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,2 +1,3 @@
**/dataset/** filter=lfs diff=lfs merge=lfs -text
/_publication/Gao[[:space:]]et[[:space:]]al.[[:space:]]-[[:space:]]2024[[:space:]]-[[:space:]]Exploring[[:space:]]natural[[:space:]]genetic[[:space:]]variation[[:space:]]in[[:space:]]photosynthe.pdf filter=lfs diff=lfs merge=lfs -text
+_publication/erae198_fig1.jpeg filter=lfs diff=lfs merge=lfs -text
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..d51593e
--- /dev/null
+++ b/README.md
@@ -0,0 +1,23 @@
+# Exploring natural genetic variation in photosynthesis-related traits of barley in the field
+
+## Original Publication
+
+Yanrong Gao, Merle Stein, Lilian Oshana, Wenxia Zhao, Shizue Matsubara, Benjamin Stich, Exploring natural genetic variation in photosynthesis-related traits of barley in the field, Journal of Experimental Botany, Volume 75, Issue 16, 28 August 2024, Pages 4904–4925, https://doi.org/10.1093/jxb/erae198
+
+## Abstract
+
+Optimizing photosynthesis is considered an important strategy for improving crop yields to ensure food security. To evaluate the potential of using photosynthesis-related parameters in crop breeding programs, we measured chlorophyll fluorescence along with growth-related and morphological traits of 23 barley inbred lines across different developmental stages in field conditions. The photosynthesis-related parameters were highly variable, changing with light intensity and developmental progression of plants. Yet, the variation in photosystem II quantum yield observed among the inbred lines in the field largely reflected the variation in CO2 assimilation properties in controlled climate chamber conditions, confirming that the chlorophyll fluorescence-based technique can provide proxy parameters of photosynthesis to explore genetic variation under field conditions. Heritability (â *H²*) of the photosynthesis-related parameters in the field ranged from 0.16 for the quantum yield of non-photochemical quenching to 0.78 for the fraction of open photosystem II center. Two parameters, the maximum photosystem II efficiency in the light-adapted state (â *H²=0.58*) and the total non-photochemical quenching (â *H²=0.53*), showed significant positive and negative correlations, respectively, with yield-related traits (dry weight per plant and net straw weight) in the barley inbred lines. These results indicate the possibility of improving crop yield through optimizing photosynthetic light use efficiency by conventional breeding programs.
+
+<ideally shape into a graphical abstract by adding a nice selected image from the publication.
+This is oftentimes done at the journal website as well; so we'll just use the same image.
+Store the image in `_publication` and link it in README via markdown or html.
+>
+
+## License
+
+This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (https://creativecommons. org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.
+
+## Data availability
+
+Data are publicly available in the manuscript and in the supplementary data.
+
diff --git a/_publication/erae198_fig1.jpeg b/_publication/erae198_fig1.jpeg
new file mode 100644
index 0000000..e01b34a
--- /dev/null
+++ b/_publication/erae198_fig1.jpeg
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:493782188bb611d409e55d7bc4a43c4cdd7c047741a5e714b00b38061b9ae5eb
+size 1113545
--
GitLab
From 7980170b45d81cd48e1a51616e1f83f925574b10 Mon Sep 17 00:00:00 2001
From: Mekhrona Mirzoeva <memir101@hhu.de>
Date: Fri, 27 Sep 2024 13:12:12 +0200
Subject: [PATCH 2/7] README.md with picture
---
README.md | 5 +----
1 file changed, 1 insertion(+), 4 deletions(-)
diff --git a/README.md b/README.md
index d51593e..8b3a4dd 100644
--- a/README.md
+++ b/README.md
@@ -8,10 +8,7 @@ Yanrong Gao, Merle Stein, Lilian Oshana, Wenxia Zhao, Shizue Matsubara, Benjamin
Optimizing photosynthesis is considered an important strategy for improving crop yields to ensure food security. To evaluate the potential of using photosynthesis-related parameters in crop breeding programs, we measured chlorophyll fluorescence along with growth-related and morphological traits of 23 barley inbred lines across different developmental stages in field conditions. The photosynthesis-related parameters were highly variable, changing with light intensity and developmental progression of plants. Yet, the variation in photosystem II quantum yield observed among the inbred lines in the field largely reflected the variation in CO2 assimilation properties in controlled climate chamber conditions, confirming that the chlorophyll fluorescence-based technique can provide proxy parameters of photosynthesis to explore genetic variation under field conditions. Heritability (â *H²*) of the photosynthesis-related parameters in the field ranged from 0.16 for the quantum yield of non-photochemical quenching to 0.78 for the fraction of open photosystem II center. Two parameters, the maximum photosystem II efficiency in the light-adapted state (â *H²=0.58*) and the total non-photochemical quenching (â *H²=0.53*), showed significant positive and negative correlations, respectively, with yield-related traits (dry weight per plant and net straw weight) in the barley inbred lines. These results indicate the possibility of improving crop yield through optimizing photosynthetic light use efficiency by conventional breeding programs.
-<ideally shape into a graphical abstract by adding a nice selected image from the publication.
-This is oftentimes done at the journal website as well; so we'll just use the same image.
-Store the image in `_publication` and link it in README via markdown or html.
->
+<img src="./_publication/erae198_fig1.jpeg" style="width:100%;display: block;margin: auto; padding: 30px 0px;">
## License
--
GitLab
From 56df18cab0b312203ffeb257d99635d72aeccf1e Mon Sep 17 00:00:00 2001
From: Mekhrona Mirzoeva <memir101@hhu.de>
Date: Fri, 27 Sep 2024 11:23:59 +0000
Subject: [PATCH 3/7] Added LICENSE
---
LICENSE | 402 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 402 insertions(+)
create mode 100644 LICENSE
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..236ac28
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,402 @@
+Attribution-NonCommercial-NoDerivatives 4.0 International
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\ No newline at end of file
--
GitLab
From 49e557e14590d9f7ee352d23bc13011412cae8a4 Mon Sep 17 00:00:00 2001
From: Mekhrona Mirzoeva <memir101@hhu.de>
Date: Fri, 27 Sep 2024 13:36:45 +0200
Subject: [PATCH 4/7] Added publication files (issue 3) + README.md
---
.gitattributes | 2 ++
...tural genetic variation in photosynthe.pdf | 3 +++
_publication/README.md | 5 +++++
...e198_suppl_supplementary_figures_s1-s7.pdf | 3 +++
...e198_suppl_supplementary_tables_s1-s3.xlsx | Bin 0 -> 32181 bytes
isa.investigation.xlsx | Bin 2445 -> 7378 bytes
6 files changed, 13 insertions(+)
create mode 100644 _publication/Gao et al._2024 - Exploring natural genetic variation in photosynthe.pdf
create mode 100644 _publication/README.md
create mode 100644 _publication/erae198_suppl_supplementary_figures_s1-s7.pdf
create mode 100644 _publication/erae198_suppl_supplementary_tables_s1-s3.xlsx
diff --git a/.gitattributes b/.gitattributes
index 951e266..56ee1a3 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,3 +1,5 @@
**/dataset/** filter=lfs diff=lfs merge=lfs -text
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_publication/erae198_fig1.jpeg filter=lfs diff=lfs merge=lfs -text
+_publication/Gao[[:space:]]et[[:space:]]al._2024[[:space:]]-[[:space:]]Exploring[[:space:]]natural[[:space:]]genetic[[:space:]]variation[[:space:]]in[[:space:]]photosynthe.pdf filter=lfs diff=lfs merge=lfs -text
+_publication/erae198_suppl_supplementary_figures_s1-s7.pdf filter=lfs diff=lfs merge=lfs -text
diff --git a/_publication/Gao et al._2024 - Exploring natural genetic variation in photosynthe.pdf b/_publication/Gao et al._2024 - Exploring natural genetic variation in photosynthe.pdf
new file mode 100644
index 0000000..3abffcd
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@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:00bda17a4613c6cbf3bf81e71b7ba4dc95e3abb49caea4aa5c8b2d82be66993a
+size 4065201
diff --git a/_publication/README.md b/_publication/README.md
new file mode 100644
index 0000000..1cebc75
--- /dev/null
+++ b/_publication/README.md
@@ -0,0 +1,5 @@
+# Supplementary data files
+
+erae198_suppl_Supplementary_Figures_S1-S7 - pdf file
+erae198_suppl_Supplementary_Tables_S1-S3 - xlsx file
+https://academic.oup.com/jxb/article/75/16/4904/7663878#supplementary-data
\ No newline at end of file
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GitLab
From f0c00fff9c3f496db246a9f818986febbe5ccd3b Mon Sep 17 00:00:00 2001
From: Mekhrona Mirzoeva <memir101@hhu.de>
Date: Fri, 27 Sep 2024 13:42:59 +0200
Subject: [PATCH 5/7] deleting accepted manuscript replacing with paper from
journal
---
...24 - Exploring natural genetic variation in photosynthe.pdf | 3 ---
1 file changed, 3 deletions(-)
delete mode 100644 _publication/Gao et al. - 2024 - Exploring natural genetic variation in photosynthe.pdf
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index d4240bc..0000000
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--
GitLab
From ad5c6a83c5046f97f0fb2fb33a5d7787247b86ba Mon Sep 17 00:00:00 2001
From: Mekhrona Mirzoeva <memir101@hhu.de>
Date: Fri, 27 Sep 2024 14:07:19 +0200
Subject: [PATCH 6/7] Added metadata
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--
GitLab
From d98d78f003950ba9fe6c1e582bedb446f2cfff4c Mon Sep 17 00:00:00 2001
From: Mekhrona Mirzoeva <memir101@hhu.de>
Date: Fri, 27 Sep 2024 14:21:21 +0200
Subject: [PATCH 7/7] added publication dates once again
---
isa.investigation.xlsx | Bin 8577 -> 8577 bytes
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diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx
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