Global gene profilings in embryo and seed coat of lentil during embryogenesis
Ontology highlight
ABSTRACT:
ORGANISM(S): Lens culinaris
PROVIDER: GSE216220 | GEO | 2023/09/20
REPOSITORIES: GEO
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Project description:Global gene profilings in embryo and seed coat of lentil during embryogenesis
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Project description:Soybean cultivars, OX951 & OX736, comparison of seed coat at 3 growth stages, early, mid & late Keywords: time course
2007-01-01 | GSE4276 | GEO
Project description: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.
2024-03-18 | GSE244961 | GEO
Project description:Cultivation of canola at temperatures above the optimum growth temperature of 21°C for prolonged periods, especially during the flowering stage, resulted in several adverse effects, including rapid vegetative growth, reduced viability of female gametophytes, increased seed abortion rate, accelerated embryo development, and a reduction in seed oil composition (Young et al., 2004; Mácová et al., 2022; Secchi et al., 2023). One of the distinctive phenotypes observed during the seed development of certain canola cultivars subjected to prolonged heat stress affecting the seed yield is the occurrence of the pre-harvest sprouting phenotype (PHS) (Mácová et al., 2022). Misregulation of seed dormancy by abscisic acid and dormancy-related genes is thought to be the primary cause of PHS in many cereal crops (Benech-Arnold & Rodríguez, 2018; Tai et al., 2021). This phenotype is associated with seed coat rupture (SCR), observed in seeds during the early stages of maturation. In this study, we employed a multi-methodological approach to investigate the occurrence of SCR phenotype in seeds of Brassica napus cv. Topas. The results demonstrate that SCR occurs in seeds around 20 days after pollination (20DAP) when the plants are cultivated in elevated temperatures over an extended period. The unrestricted embryonic growth exerts pressure on the seed coat, as evidenced by a reduction in the thickness of the seed coat cell layers. This results in an early alteration to the cell wall composition, with an increased proportion of demethylesterified pectin, which is likely to stiffen the seed coat, thereby rendering it more susceptible to rupture. The precise mechanism by which accelerated embryo development influences heat stress-mediated seed development in canola plants has yet to be elucidated.
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Project description:Seed coat colour is determined by the type of pigment deposited in the seed coat cells. It is related to important agronomic traits of seeds, such as seed dormancy, longevity, oil content, protein content and fibre content. In Brassica napus, inheritance of seed coat colour is related to maternal effects and pollen effects (xenia effects). In this research, we isolated a mutation of yellow seeded B. napus controlled by a single Mendelian locus with pollen effect. Microcopy of transverse sections of the mature seed shows pigment is deposited only in the epidermal cells, the first cell layer of seed coat. By Illumina Hiseq 2000 sequencing technology, a total of 12 G clean data, 116x coverage of coding sequences of B. napus, was achieved from 26-day old brown and yellow seeds. It was assembled into 172,238 independent transcripts and 55,637 unigenes by Trinity. A total of 150 orthologous genes of Arabidopsis transparent testa (TT) genes were mapped in silico to 19 chromosomes of B. napus. Only 49 of the TT orthologous genes are transcripted in seeds. However transcription of all the orthologs was independent of the embryonal control of seed coat colour. Of all the Trinity-assembled unigenes, only 55 genes were found to be differentially expressed between the brown seeds and yellow mutant. Among them 50 were up-regulated and 5 were down-regulated in the yellow seeds as compared to the brown counterpart. By KEGG classification, 14 metabolic pathways were enriched significantly. Of these, 5 pathways: phenylpropanoid biosynthesis, cyanoamino acid metabolism, plant hormone signal transduction, metabolic pathways and biosynthesis of secondary metabolites, were related with seed coat pigmentation. Free amino acid quantification showed that Ala and Phe were produced at higher levels in the embryo of yellow seeds as compared to brown seeds. This increase was not observed in the seed coat. Moreover, the excess amount of free Ala was exactly twice that of Phe in the 26-day embryo of yellow seeds. Pigment indispensable substrate chalcone is synthesized from two molecules of Ala and one molecule of Phe. The correlation between accumulation of Ala and Phe and disappearance of pigment in the yellow seeded mutant indicate that embryonal control of seed coat colour is related with Phe and Ala metabolism in the embryo of B. napus.
2018-05-19 | GSE69137 | GEO
Project description:Plant-specific DOF-type transcription factors regulate various biological processes. Here, we characterized a silique-abundant gene AtDOF4.2 for its functions in Arabidopsis. AtDOF4.2 is localized in the nuclear region and has transcriptional activation activity in both yeast and plant protoplast assays. The Thr-Met-Asp motif in AtDOF4.2 is essential for its activation. AtDOF4.2-overexpressing plants exhibit an increased branching phenotype, and the mutation of Thr-Met-Asp motif in AtDOF4.2 significantly reduces the branching in transgenic plants. AtDOF4.2 may achieve this function through the upregulation of three branching-related genes, AtSTM, AtTFL1 and AtCYP83B1. The seeds of an AtDOF4.2-overexpressing plant show collapse-like morphology in epidermal cells of the seed coat. Mucilage contents and the concentration and composition of mucilage monosaccharides are significantly changed in the seed coat of transgenic plants. AtDOF4.2 may exert its effects on the seed epidermis through the direct binding and activation of the cell wall loosening-related gene AtEXPA9. The dof4.2 mutant did not exhibit changes in branching or its seed coat; however, the silique length and seed yield were increased. AtDOF4.4, which is a close homolog of AtDOF4.2, also promotes shoot branching and affects silique size and seed yield. Manipulation of these genes should have a practical use in the improvement of agronomic traits in important crops.
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Project description:We present an atlas of global gene expression covering embryo and seed coat development in B. rapa, B. nigra, B. oleracea, B. juncea, B. napus and B. carinata, providing insights into the evolution of gene expression in embryogenesis and seed development of brassica species.
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