Molecular Life Sciences

Editors: Robert D. Wells, Judith S. Bond, Judith Klinman, Bettie Sue Siler Masters, Ellis Bell

Genomic Sequence and Structural Diversity in Plants

Living reference work entry
DOI: https://doi.org/10.1007/978-1-4614-6436-5_106-2

Synopsis

Plant genomes can tolerate a wide range of variation derived from accumulation of mutations, hybridization, polyploidization, and other mechanisms. It is this diversity that underlies the array of phenotypes observed not only across the Plantae kingdom but also within each species. Characterization of sequence level variation (single nucleotide polymorphisms, insertions/deletions, presence/absence variation, copy number variation, and inversions) allows for the association of specific sequence variants with resulting phenotypes, understanding of genetic pathways, rapid varietal improvement by plant breeders, and continuing insight into basic biological phenomenon. The following essay describes the sequence and structural diversity within plant genomes and the implications and applications of this diversity.

Introduction

The phenotypic diversity exhibited within plant species has been widely documented. It is this diversity that has allowed plants to be used for human and...

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References

  1. 1001 Genomes (2014) 1001 genomes, A catalog of Arabidopsis thaliana genetic variation. Available at http://1001genomes.org. Verified 12 March 2014
  2. Cao J, Schneeberger K, Ossowski S, Gunther T, Bender S, Fitz J, Koenig D, Lanz C, Stegle O, Lippert C, Wang X, Ott F, Muller J, Alonso-Blanco C, Borgwardt K, Schmid KJ, Weigel D (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 43:956–963PubMedCrossRefGoogle Scholar
  3. Goicoechea J, Ammiraju J, Marri P, Chen M, Jackson S, Yu Y, Rounsley S, Wing R (2010) The future of rice genomics: sequencing the collective Oryza genome. Rice 3:89–97CrossRefGoogle Scholar
  4. Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, Mcmullen MD, Grills GS, Ross-Ibarra J, Ware DH, Buckler ES (2009) A first-generation haplotype map of maize. Science 326:1115–1117PubMedCrossRefGoogle Scholar
  5. Hurwitz BL, Kudrna D, Yu Y, Sebastian A, Zuccolo A, Jackson SA, Ware D, Wing RA, Stein L (2010) Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. Plant J 63:990–1003PubMedCrossRefGoogle Scholar
  6. Jander G, Norris SR, Rounsley SD, Bush DF, Levin IM, Last RL (2002) Arabidopsis map-based cloning in the post-genome era. Plant Physiol 129:440–450PubMedCentralPubMedCrossRefGoogle Scholar
  7. Kim S, Plagnol V, Hu TT, Toomajian C, Clark RM, Ossowski S, Ecker JR, Weigel D, Nordborg M (2007) Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat Genet 39:1151–1155PubMedCrossRefGoogle Scholar
  8. Lai J, Li R, Xu X, Jin W, Xu M, Zhao H, Xiang Z, Song W, Ying K, Zhang M, Jiao Y, Ni P, Zhang J, Li D, Guo X, Ye K, Jian M, Wang B, Zheng H, Liang H, Zhang X, Wang S, Chen S, Li J, Fu Y, Springer NM, Yang H, Wang J, Dai J, Schnable PS (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42:1027–1030PubMedCrossRefGoogle Scholar
  9. Mcnally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE, Stokowski R, Ballinger DG, Frazer KA, Cox DR, Padhukasahasram B, Bustamante CD, Weigel D, Mackill DJ, Bruskiewich RM, Ratsch G, Buell CR, Leung H, Leach JE (2009) Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A 106:12273–12278PubMedCentralPubMedCrossRefGoogle Scholar
  10. Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, Weigel D (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res 18:2024–2033PubMedCentralPubMedCrossRefGoogle Scholar
  11. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, Mcmahan L, Van Buren P, Vaughn MW et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115PubMedCrossRefGoogle Scholar
  12. Swanson-Wagner RA, Eichten SR, Kumari S, Tiffin P, Stein JC, Ware D, Springer NM (2010) Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Res 20:1689–1699PubMedCentralPubMedCrossRefGoogle Scholar
  13. TAIR (2014) The Arabidopsis information resource. Available at http://www.arabidopsis.org/. Verified 12 March 2014
  14. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815CrossRefGoogle Scholar
  15. Weigel D, Mott R (2009) The 1001 genomes project for Arabidopsis thaliana. Genome Biol 10:107PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulUSA