Using Genomics to Study Legume Seed Development

Le, Brandon H.; Wagmaister, Javier A.; Kawashima, Tomokazu; Bui, Anhthu Q.; Harada, John J.; Goldberg, Robert B.

doi:10.1104/pp.107.100362

Cited by 148 publications

(164 citation statements)

References 125 publications

(148 reference statements)

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“…This, and work by Casson et al (2005), Day et al (2007b), Le et al (2007), and Spencer et al (2007), demonstrates the power of laser-assisted microdissection for studying tissuespecific expression during early seed development, even in Arabidopsis, which has relatively small seeds. The proliferative stage of endosperm development is unusual in that rapid nuclear division occurs in the absence of cell division.…”

Section: Resultsmentioning

confidence: 99%

Transcriptome Analysis of Proliferating Arabidopsis Endosperm Reveals Biological Implications for the Control of Syncytial Division, Cytokinin Signaling, and Gene Expression Regulation

et al. 2008

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During the early stages of seed development, Arabidopsis (Arabidopsis thaliana) endosperm is syncytial and proliferates rapidly through repeated rounds of mitosis without cytokinesis. This stage of endosperm development is important in determining final seed size and is a model for studying aspects of cellular and molecular biology, such as the cell cycle and genomic imprinting. However, the small size of the Arabidopsis seed makes high-throughput molecular analysis of the early endosperm technically difficult. Laser capture microdissection enabled high-resolution transcript analysis of the syncytial stage of Arabidopsis endosperm development at 4 d after pollination. Analysis of Gene Ontology representation revealed a developmental program dominated by the expression of genes associated with cell cycle, DNA processing, chromatin assembly, protein synthesis, cytoskeleton-and microtubule-related processes, and cell/organelle biogenesis and organization. Analysis of core cell cycle genes implicates particular gene family members as playing important roles in controlling syncytial cell division. Hormone marker analysis indicates predominance for cytokinin signaling during early endosperm development. Comparisons with publicly available microarray data revealed that approximately 800 putative early seed-specific genes were preferentially expressed in the endosperm. Early seed expression was confirmed for 71 genes using quantitative reverse transcription-polymerase chain reaction, with 27 transcription factors being confirmed as early seed specific. Promoter-reporter lines confirmed endosperm-preferred expression at 4 d after pollination for five transcription factors, which validates the approach and suggests important roles for these genes during early endosperm development. In summary, the data generated provide a useful resource providing novel insight into early seed development and identify new target genes for further characterization.

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Section: Resultsmentioning

confidence: 99%

Transcriptome Analysis of Proliferating Arabidopsis Endosperm Reveals Biological Implications for the Control of Syncytial Division, Cytokinin Signaling, and Gene Expression Regulation

et al. 2008

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“…Thus, to make use of the massive amount of functional data as it pertains to soybean, it would be important to have a useful annotation of the soybean expressed sequence tag (EST) annotation. This information has recently been provided for the EST collection (Le et al 2007) and an annotated reference genome (http://www.phytozome.net/soybean) (Schmutz et al 2010). Through cross comparative analyses, genes that are conserved in primary DNA or protein structure can be identified.…”

Section: Pathway Analysesmentioning

confidence: 99%

Cell-Specific Studies of Soybean Resistance to Its Major Pathogen, the Soybean Cyst Nematode as Revealed by Laser Capture Microdissection, Gene Pathway Analyses and Functional Studies

Klink¹,

Matsye²,

Lawrence³

2011

Soybean - Molecular Aspects of Breeding

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“…Thus, a variety of cellular, molecular, and physiological processes contribute to seeds' ability to withstand desiccation and to resume germination under favorable conditions. describe the progress in the field of research (for detail see Bove et al, 2001;Chaudhury et al, 2001;Weber et al, 2005;Le et al, 2007;Linkies et al, 2010;Nonogaki et al, 2010;Rajjou et al, 2012;Ventura et al, 2012;Sreenivasulu and Wobus, 2013).…”

Section: Associated Changes Effects Referencesmentioning

confidence: 99%

“…In genomic DNA, methylation of fifth carbon of cytosine (5-methylcytosine) is frequently linked with heterochromatic loci comprising centromeres and telomeres and is also concurrent with various silent loci, especially transposable elements and repetitive sequences (Lu et al, 2006;Le et al, 2007;Bauer and Fisher, 2011). The involvement of DNA methylation in the seed germination process was c o n f i r m e d t h r o u g h m e t h y l a t i o n -s e n s i t i v e amplification polymorphisms (Portis et al, 2004;Meng et al, 2012).…”

Section: Dna Methylationmentioning

confidence: 99%

Genomics: A Hallmark to Monitor Molecular and Biochemical Processes Leading Toward a Better Perceptive of Seed Aging and ex-situ Conservation

Ahmad¹,

Shah²,

Rehman³

et al. 2017

Current Issues in Molecular Biology

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Abbreviations:AFLP, amplified fragment length polymorphism AGO, argonaute miRNA, micro RNA NGS, next generation sequencing PCD, programmed cell death PIMT, protein L-isoaspartyl methyltransferase PRC2, Polycomb repressive complex 2 RAPD, random amplification of polymorphic DNA ROS, reactive oxygen species SSR, simple sequence repeat TUNEL, terminal deoxynucleotide transferasemediated dUTP nick-end labeling qRT-PCR, quantitative reverse transcriptional polymerase chain reaction Abstract For human food security, the preservation of 7.4 million ex-situ germplasm is a global priority. However, ex situ-conserved seeds are subject to aging, which reduces their viability and ultimately results in the loss of valuable genetic material over long periods. Recent progress in seed biology and genomics has revealed new opportunities to improve the long-term storage of ex-situ seed germplasm. This review summarizes the recent improvements in seed physiology and genomics, with the intention of developing genomic tools for evaluating seed aging. Several lines of seed biology research have shown promise in retrieving viability signal from various stages of seed germination. We conclude that seed aging is associated with mitochondrial alteration and programmed cell death, DNA and enzyme repair, anti-oxidative genes, telomere length, and epigenetic regulation. Clearly, opportunities exist for observing seed aging for developing genomic tools to increment the traditional germination test for effective conservation of ex-situ germplasm.

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Using Genomics to Study Legume Seed Development

Cited by 148 publications

References 125 publications

Transcriptome Analysis of Proliferating Arabidopsis Endosperm Reveals Biological Implications for the Control of Syncytial Division, Cytokinin Signaling, and Gene Expression Regulation

Transcriptome Analysis of Proliferating Arabidopsis Endosperm Reveals Biological Implications for the Control of Syncytial Division, Cytokinin Signaling, and Gene Expression Regulation

Cell-Specific Studies of Soybean Resistance to Its Major Pathogen, the Soybean Cyst Nematode as Revealed by Laser Capture Microdissection, Gene Pathway Analyses and Functional Studies

Genomics: A Hallmark to Monitor Molecular and Biochemical Processes Leading Toward a Better Perceptive of Seed Aging and ex-situ Conservation

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