Abstract
The giant embryo of the scarlet runner bean (Phaseolus coccineus) has been used historically to investigate the molecular and developmental processes that control the early events of plant embryo development. In more recent years, our laboratory has been using scarlet runner bean embryos to uncover the genes and regulatory events that control embryo proper and suspensor region differentiation shortly after fertilization. In this chapter we describe methods that we have developed to isolate scarlet runner bean embryos at the globular stage of development, and capture embryo proper and suspensor regions by either hand dissection or laser capture microdissection (LCM) for use in downstream genomic analysis. These methods are also applicable for use in investigating the early events of common bean (Phaseolus vulgaris) embryo development, a close relative of scarlet runner bean, which also has a giant embryo in addition to a sequenced genome.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Kerk NM et al (2003) Laser capture microdissection of cells from plant tissues. Plant Physiol 132(1):27–35
Deal RB, Henikoff S (2010) A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev Cell 18(6):1030–1040
Amatori S et al (2014) PAT-ChIP coupled with laser microdissection allows the study of chromatin in selected cell populations from paraffin-embedded patient samples. Epigenetics Chromatin 7:18
Belmonte MF et al (2013) Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed. Proc Natl Acad Sci U S A 110(5):E435–E444
Palovaara J et al (2017) Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo. Nat Plants 3(11):894–904
Slane D et al (2014) Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo. Development 141(24):4831–4840
Brady T (1973) Feulgen cytophotometric setermination of the DNA content of the embryo proper and suspensor cells of Phaseolus coccineus. Cell Differ 2(2):65–75
Clutter M et al (1974) Macromolecular synthesis during plant embryogeny. Cellular rates of RNA synthesis in diploid and polytene cells in bean embryos. J Cell Biol 63(3):1097–1102
Henry KF, Goldberg RB (2015) Using giant scarlet runner bean embryos to uncover regulatory networks controlling suspensor gene activity. Front Plant Sci 6:44
Kawashima T, Goldberg RB (2010) The suspensor: not just suspending the embryo. Trends Plant Sci 15(1):23–30
Le BH et al (2007) Using genomics to study legume seed development. Plant Physiol 144(2):562–574
Sussex I et al (1973) Biosynthetic activity of the suspensor of Phaseolus coccineus. Caryologia 25:261–272
Yeung EC, Sussex I (1979) Embryogeny of Phaseolus coccineus: the suspensor and the growth of the embryo-proper in vitro. Z. Pflanzenphysiol 91(5):423–433
Walbot V et al (1972) Macromolecular synthesis during plant embryogeny: rates of RNA synthesis in Phaseolus coccineus embryos and suspensors. Dev Biol 29(1):104–111
Walbot V, Clutter M, Sussex I (1972) Reproductive development and embryogeny in Phaseolus. Phytomorphology 22:59–78
Lorenzi R et al (1978) Embryo-suspensor relations in Phaseolus coccineus: Cytokinins during seed development. Planta 143:59–62
Zhan J et al (2015) RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation. Plant Cell 27(3):513–531
Weterings K et al (2001) Regional localization of suspensor mRNAs during early embryo development. Plant Cell 13(11):2409–2425
Henry KF et al (2018) A shared cis-regulatory module activates transcription in the suspensor of plant embryos. Proc Natl Acad Sci U S A 115(25):E5824–E5833
Henry KF, Kawashima T, Goldberg RB (2015) A cis-regulatory module activating transcription in the suspensor contains five cis-regulatory elements. Plant Mol Biol 88(3):207–217
Kawashima T et al (2009) Identification of cis-regulatory sequences that activate transcription in the suspensor of plant embryos. Proc Natl Acad Sci U S A 106(9):3627–3632
Cox KH, Goldberg RB (1988) In: Shaw CH (ed) Analysis of plant gene expression. Plant molecular biology: a practical approach. IRL Press, Oxford, United Kingdom
Sanders PM (2005) Differentiation and degeneration of cells that play a major role in tobacco anther dehiscence. Sex Plant Reprod 17:219–241
Lin JY et al (2017) Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development. Proc Natl Acad Sci U S A 114(45):E9730–E9739
Blackwall RLC (1971) A study of the plant/insect relationships and pod-setting in the runner bean (Phaseolus multiflorus). J Hort Sci 46:365–379
Quagliotti L, Marletto F (1987) Research on the pollination of runner bean (Phaseolus coccineus) for dry grain production. Adv Hortic Sci 1(1):43–49
Singh SP, Gepts P, Debouck DG (1991) Races of common bean (Phaseolus vulgaris, Fabaceae). Econ Bot 45(3):379–396
Schmutz J et al (2014) A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 46(7):707–713
Inada N, Wildermuth MC (2005) Novel tissue preparation method and cell-specific marker for laser microdissection of Arabidopsis mature leaf. Planta 221(1):9–16
Acknowledgments
Our work with scarlet runner bean embryos was supported by grants from the US Department of Agriculture, Ceres, Inc., and the National Science Foundation.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Chen, M., Bui, A.Q., Goldberg, R.B. (2020). Using Giant Scarlet Runner Bean (Phaseolus coccineus) Embryos to Dissect the Early Events in Plant Embryogenesis. In: Bayer, M. (eds) Plant Embryogenesis. Methods in Molecular Biology, vol 2122. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0342-0_15
Download citation
DOI: https://doi.org/10.1007/978-1-0716-0342-0_15
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-0341-3
Online ISBN: 978-1-0716-0342-0
eBook Packages: Springer Protocols