Advertisement

Germplasm and Molecular Resources

  • Emma M. Knee
  • Luz Rivero
  • Deborah Crist
  • Erich Grotewold
  • Randy Scholl
Chapter
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 9)

Abstract

A wide range of genetic diversity exists in various members of the Brassicaceae, notably in the genera Arabidopsis and Brassica. Comprehensive seed collections include mutants, transgenic lines, chromosomal variants, mapping populations, Targeting Induced Local Lesions in Genomes (TILLING), and natural accessions, collected from the wild. Many molecular resources have been developed and are widely utilized in research. These include expressed sequence tags (ESTs); full length, sequence-validated cDNA clones of many genes; bacterial artificial chromosome (BAC) libraries; and vectors with multiple applications. Diverse resources are maintained by numerous institutions and specialized centers. Various public and private databases with comprehensive information about the collections are also available. This chapter focuses on the resources for the members of this family, with emphasis on collections that are publicly available.

Keywords

Accession Clone collection Diversity fixed foundation set Forward genetic resource Gene bank Genomic library Germplasm collection Mapping population Mutant collection Natural accession Recombinant inbred line Resource Center Reverse genetic resource Seed collection Stock Center Teaching tool 

Abbreviations

ABRC

Arabidopsis Biological Resource Center

AGI

Arabidopsis genome initiative

AGRIKOLA

Arabidopsis Genomic RNAi Knock-Out Line Analysis

amiRNA

artificial microRNA

ATIDB

Arabidopsis thaliana integrated database

BAC

Bacterial artificial chromosome

BBSRC

Biological Sciences Research Council

BCCM

Belgian coordinated collections of micro-organisms

BiBAC

Binary BAC

BRC

Bioresource Center

CATMA

Complete Arabidopsis transcriptome microarray

CEPH

Centre d’Etude du polymorphisme humain

CIC

CEPH INRA CNRS

CNRGV

Centre National de Resource Genomique Vegetables

CNRS

Centre National de Recherche Scientifique

CSHL

Cold Spring Harbor Laboratory

CUGI

Clemson University Genome Institute

DFFS

Diversity fixed foundation sets

DH

Double haploid

DNA

Deoxyribonucleic acid

ECPGR

European Cooperative Programme for Plant Genetic Resources

EMS

Ethylmethanesulfonate

EST

Expressed sequence tag

EU RESGEN

European Union genetic resources project

GetCID

Gene transfer, clone identification, and distribution service

GRIN

Germplasm resources information network

GST

Gene-specific tag

HRI

Horticultural Research International

INRA

Institut National de la Recherche Agronomique

JGI

Joint Genomes Institute

MATDB

Munich Information Center for Protein Sequences Arabidopsis thaliana Database

MBGP

Multinational Brassica genome project

MBrGSP

Multinational Brassica rapa genome sequencing project

MTA

Material transfer agreement

NASC

Nottingham Arabidopsis Resource Center

NCBI

National Center for Biotechnology Information

NIL

Near-Isogenic line

NPGS

National Plant Germplasm System

ORF

Open reading frame

PCR

Polymerase chain reaction

PGML

Plant Genome Mapping Laboratory

QTL

Quantitative trait loci

RI

Recombinant inbred

RIL

Recombinant inbred line

RNA

Ribonucleic acid

RNAi

RNA interference

SIGnAL

Salk Institute Genomic Analysis Laboratory

TILLING

Targeting Induced Local Lesions in Genomes

References

  1. 1.
    Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408(6814):796–815Google Scholar
  2. 2.
    Ayele M, Haas BJ, Kumar N et al (2005) Whole genome shotgun sequencing of Brassica olearacea and its application to gene discovery and annotation in Arabidopsis. Genome Res 15:487–495CrossRefPubMedGoogle Scholar
  3. 4.
    Boukema IW, van Hintum TJL, Astley D et al (1997) Creation and composition of the Brassica oleracea core collection. Plant Genet Resour Newsl 111:29–32Google Scholar
  4. 3.
    Boukema IW, van Hintum TJL (1999) Genetic Resources. In: Gomez-Campo C (ed) Developments in plant genetics and breeding 4. Biology of Brassica coenospecies. Elsevier, The NetherlandsGoogle Scholar
  5. 5.
    Castelli V, Aury JM, Jaillon O et al (2004) Whole sequence comparisons and “full-length” cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation. Genome Res 14:406–413CrossRefPubMedGoogle Scholar
  6. 6.
    Chang YL, Henriquez X, Preuss D et al (2003) A plant transformation-competent BIBAC library prepared from the Arabidopsis thaliana Landsberg ecotype for functional and comparative genomics. Theor Appl Genet 106:269–276PubMedGoogle Scholar
  7. 7.
    Choi S, Creelman RA, Mullet JE, Wing RA et al (1995) Construction and characterization of a bacterial artificial chromosome library for Arabidopsis thaliana. Weeds World 2:17–20Google Scholar
  8. 8.
    Cooke R, Raynal M, Laudié M et al (1996) Further progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTs. Plant J 9(1):101–124CrossRefPubMedGoogle Scholar
  9. 9.
    Creusot F, Fouilloux E, Dron M et al (1995) The CIC library: a large insert YAC library for genome mapping in Arabidopsis thaliana. Plant J 8(5):763–770CrossRefPubMedGoogle Scholar
  10. 10.
    Gong Z, Dong CH, Lee H et al (2004) Genome wide ORFeome cloning and analysis of transcription factor genes. Plant Physiol 135(2):773–782CrossRefPubMedGoogle Scholar
  11. 11.
    Hilson P, Allemeersch J, Altmann T et al (2004) Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res 14:2176–2189CrossRefPubMedGoogle Scholar
  12. 12.
    Katari MS, Balija V, Wilson RK et al (2005) Comparing low coverage random shotgun sequence data from Brassica oleracea and rice genome sequence for their ability to add to the annotation of Arabidopsis thaliana. Genome Res 15:487–495CrossRefGoogle Scholar
  13. 14.
    Liu Y-G, Mitsukawa N, Vazquez-Tello A, Whittier RF et al (1995) Generation of a high-quality P1 Library of Arabidopsis suitable for chromosome walking. Plant J 7(2):351–358CrossRefGoogle Scholar
  14. 15.
    Liu Q, Li MZ, Leibham D et al (1998) The univector plasmid fusion system, a method for rapid construction of recombinant DNA without restriction enzymes. Curr Biol 8:1300–1309CrossRefPubMedGoogle Scholar
  15. 16.
    Liu YG, Shirano Y, Fukaki H et al (1999) Complementation of plant mutants with large genomic DNA fragments by a transformation competent artificial chromosome vector accelerates positional cloning. Proc Natl Acad Sci 96:6535–3540Google Scholar
  16. 17.
    Love C, Logan E, Erwin T et al (2006) Analysis of the Brassica A and C genomes and comparison with the genome of Arabidopsis thaliana. Acta Horticulturae (ISHS) 706:99–104Google Scholar
  17. 18.
    Lysak MA, Lexer C et al (2006) Towards the era of comparative evolutionary genomics in Brassicaceae. Plant Syst Evol 259:175–198CrossRefGoogle Scholar
  18. 19.
    Mozo T, Fischer S, Shizuya H, Altmann T et al (1998) Construction and characterization of the IGF Arabidopsis BAC library. Mol Gen Genet 258(5):562–570CrossRefPubMedGoogle Scholar
  19. 20.
    Mun JH, Kwon SJ, Yang TJ et al (2008) The first generation of a BAC-based physical map of Brassica rapa. BMC Genomics 9:280–291CrossRefPubMedGoogle Scholar
  20. 21.
    Newman T, deBruijn FJ, Green P et al (1994) Genes galore: a summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones. Plant Physiol 106(4):1241–1255CrossRefPubMedGoogle Scholar
  21. 22.
    Pink D, Bailey L, McClement S et al (2008) Double haploids, markers and QTL analysis in vegetable Brassicas. Euphytica 164:509–514CrossRefGoogle Scholar
  22. 23.
    Rivero-Lepinckas L, Christ D, Scholl R (2006) Growth of plants and preservation of seeds. In Salinas J, Sanchez-Serrano J (eds) Methods in molecular biology. Arabidopsis protocols. Humana Press, Totowa, NJGoogle Scholar
  23. 24.
    Schranz ME, Song BH, Windsor AJ, Mitchell-Olds T (2007a) Comparative genomics in the Brassicaceae: a family-wide perspective. Curr Opin Plant Biol 10(2):168–175CrossRefPubMedGoogle Scholar
  24. 25.
    Schranz ME, Windsor AJ, Song BH et al (2007b) Comparative genetic mapping in Boechera stricta, a close relative of Arabidopsis. Plant Physiol 144(1):286–298CrossRefPubMedGoogle Scholar
  25. 26.
    Schulz B, Bennett MJ, Dilkes P, Feldmann KA et al (1998) T-DNA tagging in Arabidopsis thaliana: cloning by gene disruption. In Gelvin S, Schilperoort R (eds) Plant molecular biology manual K3. Kluwer Academic Publishers, BelgiumGoogle Scholar
  26. 27.
    Schwab R, Ossowski S, Riester M et al (2006) Highly specific gene silencing by artificial MicroRNAs in Arabidopsis. Plant Cell May 18(5):1121–1133CrossRefGoogle Scholar
  27. 28.
    Stone SL, Hauksdóttir H, Troy A et al (2005) Functional analysis of the RING-type ubiquitin ligase family of Arabidopsis. Plant Physiol 137(1):13–30CrossRefPubMedGoogle Scholar
  28. 29.
    Wang N, Wang Y, Tian F et al (2008) A functional genomics resource for Brassica napus: development of an EMS mutagenized population and discovery of FAE1 point mutations by TILLING. New Phytol 180(4):751–765CrossRefPubMedGoogle Scholar
  29. 30.
    White JA, Tood J, Newman T et al (2000) A new set of Arabidopsis expressed sequence tags from developing seeds. The metabolic pathway from carbohydrates to seed oil. Plant Physiol 124(4):1582–1594CrossRefPubMedGoogle Scholar
  30. 13.
    Yamada K, Lim J, Dale JM et al (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302:842–846CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Emma M. Knee
    • 1
  • Luz Rivero
    • 1
  • Deborah Crist
    • 1
  • Erich Grotewold
    • 1
  • Randy Scholl
    • 1
  1. 1.Department of Plant Cellular and Molecular BiologyArabidopsis Biological Resource Center, The Plant Biotechnology Center, The Ohio State UniversityColumbusUSA

Personalised recommendations