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| Status |
Public on Mar 18, 2024 |
| Title |
Domestication has altered gene expression in pea seed coat |
| Organisms |
Pisum sativum; Pisum sativum subsp. elatius; Pisum abyssinicum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In angiosperms, the mature seed consists of an embryo (E), a seed coat (SC), and, in many cases, an endosperm. In contrast to knowledge about embryo and endosperm, we have relatively little knowledge of SC, especially at the genomics level. In this study, we analyzed the gene expression during seed development using the panel of cultivated and wild pea genotypes. We report the comprehensive gene expression changes related both to development as well as domestication status. Analysis of seed developmental stages revealed extensive modification of gene expression between wild pea progenitor and cultivated pea crop. A significant difference in gene expression dynamics appeared between early and late developmental stages D1, D2, and D3, D4, D5 in wild pea genotypes, where the expression was increased 3-5-fold and 5-10-fold, respectively. Our work extends knowledge about the role of the seed coat during pea seed development. We described gene expression dynamic resulting in specific metabolic profiles providing new insight into pea domestication.
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| Overall design |
To obtain spatial and temporal representation, we performed RNA sequencing analysis of isolated seed tissues (SC and E) at 5 developmental stages (D1-5). There were three genotypes representing wild (P. elatius, JI64, JI261, JI1794), two domesticated (P. sativum, JI92 landrace and cv. Cameor) and Ethiopian pea P. abyssinicum (PI358617). Reads from each sample were mapped to the pea reference genome (Cameor v1.0).
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| Contributor(s) |
Klčová B, Balarynová J, Trněný O, Smýkal P |
| Citation |
Article DOI: 10.1111/tpj.16734
Article: Domestication has altered gene expression and secondary metabolites in pea seed coat
Journal: The Plant Journal
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| Submission date |
Oct 10, 2023 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Oldrich Trneny |
| E-mail(s) |
trneny.oldrich@gmail.com
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| Organization name |
Agricultural research Ltd.
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| Street address |
Zahradni 1
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| City |
Troubsko |
| ZIP/Postal code |
66441 |
| Country |
Czech Republic |
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| Platforms (3) |
| GPL32857 |
Illumina NovaSeq 6000 (Pisum sativum) |
| GPL33829 |
Illumina NovaSeq 6000 (Pisum abyssinicum) |
| GPL33830 |
Illumina NovaSeq 6000 (Pisum sativum subsp. elatius) |
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| Samples (117)
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| GSM7832677 |
PI358617, Seed Coat, DevStage 1, replication 1 [SC_PA.1.1] |
| GSM7832678 |
PI358617, Embryo, DevStage 1, replication 2 [E_PA.1.2] |
| GSM7832679 |
PI358617, Embryo, DevStage 2, replication 1 [E_PA.2.1] |
| GSM7832680 |
PI358617, Embryo, DevStage 2, replication 2 [E_PA.2.2] |
| GSM7832681 |
PI358617, Embryo, DevStage 4, replication 1 [E_PA.4.1] |
| GSM7832682 |
PI358617, Embryo, DevStage 4, replication 2 [E_PA.4.2] |
| GSM7832683 |
PI358617, Embryo, DevStage 5, replication 1 [E_PA.5.1] |
| GSM7832684 |
PI358617, Embryo, DevStage 5, replication 2 [E_PA.5.2] |
| GSM7832685 |
PI358617, Seed Coat, DevStage 1, replication 2 [SC_PA.1.2] |
| GSM7832686 |
PI358617, Seed Coat, DevStage 2, replication 1 [SC_PA.2.1] |
| GSM7832687 |
PI358617, Seed Coat, DevStage 3, replication 1 [SC_PA.3.1] |
| GSM7832688 |
PI358617, Seed Coat, DevStage 2, replication 2 [SC_PA.2.2] |
| GSM7832689 |
PI358617, Seed Coat, DevStage 3, replication 2 [SC_PA.3.2] |
| GSM7832690 |
PI358617, Embryo, DevStage 3, replication 1 [E_PA.3.1] |
| GSM7832691 |
PI358617, Embryo, DevStage 3, replication 2 [E_PA.3.2] |
| GSM7832692 |
PI358617, Seed Coat, DevStage 4, replication 1 [SC_PA.4.1] |
| GSM7832693 |
PI358617, Seed Coat, DevStage 4, replication 2 [SC_PA.4.2] |
| GSM7832694 |
PI358617, Seed Coat, DevStage 5, replication 1 [SC_PA.5.1] |
| GSM7832695 |
PI358617, Seed Coat, DevStage 5, replication 2 [SC_PA.5.2] |
| GSM7832696 |
PI358617, Embryo, DevStage 1, replication 1 [E_PA.1.1] |
| GSM7832697 |
Cameor, Seed Coat, DevStage 1, replication 1 [SC_Ca.1.1] |
| GSM7832698 |
Cameor, Embryo, DevStage 1, replication 2 [E_Ca.1.2] |
| GSM7832699 |
Cameor, Embryo, DevStage 2, replication 1 [E_Ca.2.1] |
| GSM7832700 |
Cameor, Embryo, DevStage 2, replication 2 [E_Ca.2.2] |
| GSM7832701 |
Cameor, Embryo, DevStage 4, replication 1 [E_Ca.4.1] |
| GSM7832702 |
Cameor, Embryo, DevStage 4, replication 2 [E_Ca.4.2] |
| GSM7832703 |
Cameor, Embryo, DevStage 5, replication 1 [E_Ca.5.1] |
| GSM7832704 |
Cameor, Embryo, DevStage 5, replication 2 [E_Ca.5.2] |
| GSM7832705 |
JI92, Seed Coat, DevStage 1, replication 1 [SC_JI92.1.1] |
| GSM7832706 |
JI92, Seed Coat, DevStage 1, replication 2 [SC_JI92.1.2] |
| GSM7832707 |
JI92, Seed Coat, DevStage 2, replication 1 [SC_JI92.2.1] |
| GSM7832708 |
Cameor, Seed Coat, DevStage 1, replication 2 [SC_Ca.1.2] |
| GSM7832709 |
JI92, Seed Coat, DevStage 2, replication 2 [SC_JI92.2.2] |
| GSM7832710 |
JI92, Seed Coat, DevStage 4, replication 1 [SC_JI92.4.1] |
| GSM7832711 |
JI92, Seed Coat, DevStage 4, replication 2 [SC_JI92.4.2] |
| GSM7832712 |
JI92, Seed Coat, DevStage 5, [SC_JI92.5] |
| GSM7832713 |
JI92, Embryo, DevStage 2, replication 1 [E_JI92.2.1] |
| GSM7832714 |
JI92, Embryo, DevStage 2, replication 2 [E_JI92.2.2] |
| GSM7832715 |
JI92, Embryo, DevStage 4, replication 1 [E_JI92.4.1] |
| GSM7832716 |
JI92, Embryo, DevStage 4, replication 2 [E_JI92.4.2] |
| GSM7832717 |
JI92, Embryo, DevStage 5, replication 1 [E_JI92.5.1] |
| GSM7832718 |
Cameor, Seed Coat, DevStage 2, replication 1 [SC_Ca.2.1] |
| GSM7832719 |
JI92, Embryo, DevStage 5, replication 2 [E_JI92.5.2] |
| GSM7832720 |
JI64, Seed Coat, DevStage 1, replication 1 [SC_JI64.1.1] |
| GSM7832721 |
JI64, Seed Coat, DevStage 1, replication 2 [SC_JI64.1.2] |
| GSM7832722 |
JI64, Seed Coat, DevStage 2, replication 1 [SC_JI64.2.1] |
| GSM7832723 |
JI64, Seed Coat, DevStage 2, replication 2 [SC_JI64.2.2] |
| GSM7832724 |
JI64, Seed Coat, DevStage 4, replication 1 [SC_JI64.4.1] |
| GSM7832725 |
JI64, Seed Coat, DevStage 4, replication 2 [SC_JI64.4.2] |
| GSM7832726 |
JI64, Seed Coat, DevStage 5, replication 1 [SC_JI64.5.1] |
| GSM7832727 |
JI64, Seed Coat, DevStage 5, replication 2 [SC_JI64.5.2] |
| GSM7832728 |
JI64, Embryo, DevStage 1, replication 1 [E_JI64.1.1] |
| GSM7832729 |
Cameor, Seed Coat, DevStage 2, replication 2 [SC_Ca.2.2] |
| GSM7832730 |
JI64, Embryo, DevStage 1, replication 2 [E_JI64.1.2] |
| GSM7832731 |
JI64, Embryo, DevStage 2, replication 1 [E_JI64.2.1] |
| GSM7832732 |
JI64, Embryo, DevStage 2, replication 2 [E_JI64.2.2] |
| GSM7832733 |
JI64, Embryo, DevStage 4, replication 1 [E_JI64.4.1] |
| GSM7832734 |
JI64, Embryo, DevStage 4, replication 2 [E_JI64.4.2] |
| GSM7832735 |
JI1794, Seed Coat, DevStage 1, replication 1 [SC_JI1794.1.1] |
| GSM7832736 |
JI1794, Seed Coat, DevStage 1, replication 2 [SC_JI1794.1.2] |
| GSM7832737 |
JI1794, Seed Coat, DevStage 2, replication 1 [SC_JI1794.2.1] |
| GSM7832738 |
JI1794, Seed Coat, DevStage 2, replication 2 [SC_JI1794.2.2] |
| GSM7832739 |
JI1794, Seed Coat, DevStage 4, replication 1 [SC_JI1794.4.1] |
| GSM7832740 |
Cameor, Seed Coat, DevStage 4, replication 1 [SC_Ca.4.1] |
| GSM7832741 |
JI1794, Seed Coat, DevStage 4, replication 2 [SC_JI1794.4.2] |
| GSM7832742 |
JI1794, Seed Coat, DevStage 5, replication 1 [SC_JI1794.5.1] |
| GSM7832743 |
JI1794, Seed Coat, DevStage 5, replication 2 [SC_JI1794.5.2] |
| GSM7832744 |
JI1794, Embryo, DevStage 2, replication 1 [E_JI1794.2.1] |
| GSM7832745 |
JI1794, Embryo, DevStage 2, replication 2 [E_JI1794.2.2] |
| GSM7832746 |
JI1794, Embryo, DevStage 4, replication 1 [E_JI1794.4.1] |
| GSM7832747 |
JI1794, Embryo, DevStage 4, replication 2 [E_JI1794.4.2] |
| GSM7832748 |
JI1794, Embryo, DevStage 5, replication 1 [E_JI1794.5.1] |
| GSM7832749 |
JI1794, Embryo, DevStage 5, replication 2 [E_JI1794.5.2] |
| GSM7832750 |
JI92_17, Seed Coat, DevStage 1, replication 1, year 2017 [SC_JI92_17.1.1] |
| GSM7832751 |
Cameor, Seed Coat, DevStage 4, replication 2 [SC_Ca.4.2] |
| GSM7832752 |
JI92_17, Seed Coat, DevStage 1, replication 2, year 2017 [SC_JI92_17.1.2] |
| GSM7832753 |
JI92_17, Seed Coat, DevStage 2, replication 1, year 2017 [SC_JI92_17.2.1] |
| GSM7832754 |
JI92_17, Seed Coat, DevStage 2, replication 2, year 2017 [SC_JI92_17.2.2] |
| GSM7832755 |
JI92_17, Seed Coat, DevStage 4, replication 1, year 2017 [SC_JI92_17.4.1] |
| GSM7832756 |
JI92_17, Seed Coat, DevStage 4, replication 2, year 2017 [SC_JI92_17.4.2] |
| GSM7832757 |
JI64_17, Seed Coat, DevStage 1, replication 1, year 2017 [SC_JI64_17.1.1] |
| GSM7832758 |
JI64_17, Seed Coat, DevStage 2, replication 1, year 2017 [SC_JI64_17.2.1] |
| GSM7832759 |
JI64_17, Seed Coat, DevStage 2, replication 2, year 2017 [SC_JI64_17.2.2] |
| GSM7832760 |
JI64_17, Seed Coat, DevStage 4, replication 1, year 2017 [SC_JI64_17.4.1] |
| GSM7832761 |
Cameor, Seed Coat, DevStage 5, [SC_Ca.5] |
| GSM7832762 |
JI64_17, Seed Coat, DevStage 4, replication 2, year 2017 [SC_JI64_17.4.2] |
| GSM7832763 |
Cameor, Embryo, DevStage 1, replication 1 [E_Ca.1.1] |
| GSM7832764 |
JI261, Seed Coat, DevStage 1, replication 1 [SC_JI261.1.1] |
| GSM7832765 |
JI261, Seed Coat, DevStage 1, replication 2 [SC_JI261.1.2] |
| GSM7832766 |
JI261, Seed Coat, DevStage 3, replication 1 [SC_JI261.3.1] |
| GSM7832767 |
JI261, Seed Coat, DevStage 3, replication 2 [SC_JI261.3.2] |
| GSM7832768 |
JI261, Seed Coat, DevStage 4, replication 1 [SC_JI261.4.1] |
| GSM7832769 |
JI261, Seed Coat, DevStage 4, replication 2 [SC_JI261.4.2] |
| GSM7832770 |
JI261, Seed Coat, DevStage 5, replication 1 [SC_JI261.5.1] |
| GSM7832771 |
JI261, Seed Coat, DevStage 5, replication 2 [SC_JI261.5.2] |
| GSM7832772 |
JI261, Embryo, DevStage 3, replication 1 [E_JI261.3.1] |
| GSM7832773 |
JI261, Embryo, DevStage 3, replication 2 [E_JI261.3.2] |
| GSM7832774 |
JI261, Embryo, DevStage 4, replication 1 [E_JI261.4.1] |
| GSM7832775 |
JI261, Embryo, DevStage 4, replication 2 [E_JI261.4.2] |
| GSM7832776 |
JI261, Embryo, DevStage 5, replication 1 [E_JI261.5.1] |
| GSM7832777 |
JI261, Embryo, DevStage 5, replication 2 [E_JI261.5.2] |
| GSM7832778 |
Cameor, Seed Coat, DevStage 3, replication 1 [SC_Ca.3.1] |
| GSM7832779 |
Cameor, Seed Coat, DevStage 3, replication 2 [SC_Ca.3.2] |
| GSM7832780 |
Cameor, Embryo, DevStage 3, replication 1 [E_Ca.3.1] |
| GSM7832781 |
Cameor, Embryo, DevStage 3, replication 2 [E_Ca.3.2] |
| GSM7832782 |
JI92, Seed Coat, DevStage 3, replication 1 [SC_JI92.3.1] |
| GSM7832783 |
JI92, Seed Coat, DevStage 3, replication 2 [SC_JI92.3.2] |
| GSM7832784 |
JI92, Embryo, DevStage 3, replication 1 [E_JI92.3.1] |
| GSM7832785 |
JI92, Embryo, DevStage 3, replication 2 [E_JI92.3.2] |
| GSM7832786 |
JI64, Seed Coat, DevStage 3, replication 1 [SC_JI64.3.1] |
| GSM7832787 |
JI64, Seed Coat, DevStage 3, replication 2 [SC_JI64.3.2] |
| GSM7832788 |
JI64, Embryo, DevStage 3, replication 1 [E_JI64.3.1] |
| GSM7832789 |
JI64, Embryo, DevStage 3, replication 2 [E_JI64.3.2] |
| GSM7832790 |
JI1794, Seed Coat, DevStage 3, replication 1 [SC_JI1794.3.1] |
| GSM7832791 |
JI1794, Seed Coat, DevStage 3, replication 2 [SC_JI1794.3.2] |
| GSM7832792 |
JI1794, Embryo, DevStage 3, replication 1 [E_JI1794.3.1] |
| GSM7832793 |
JI1794, Embryo, DevStage 3, replication 2 [E_JI1794.3.2] |
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| Relations |
| BioProject |
PRJNA1026526 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE244961_fpkm_pea_dormancy.csv.gz |
15.9 Mb |
(ftp)(http) |
CSV |
| GSE244961_gene_count_pea_dormancy.csv.gz |
5.8 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
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