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Genomic tools for the analysis of genetic diversity

Published online by Cambridge University Press:  16 March 2011

J. Antoni Rafalski
J. Antoni Rafalski*
Affiliation:
DuPont Agricultural Biotechnology Group and Pioneer Hi-Bred International, Wilmington, DE 19880-0353, USA
*
*Corresponding author. E-mail: [email protected]
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Abstract

We now understand that many different types of DNA structural polymorphisms contribute to functional diversity of plant genomes, including single nucleotide polymorphisms, insertions of retrotransposons and DNA transposons, including Helitrons carrying pseudogenes, and other types of insertion–deletion polymorphisms, many of which may contribute to the phenotype by affecting gene expression through a variety of mechanisms including those involving non-coding RNAs. These polymorphisms can now be probed with tools such as array comparative genomic hybridization and, most comprehensively, genomic sequencing. Rapid developments in next generation sequencing will soon make genomic sequencing of germplasm collections a reality. This will help eliminate an important difficulty in the estimation of genetic relationships between accessions caused by ascertainment bias. Also, it has now become obvious that epigenetic differences, such as cytosine methylation, also contribute to the heritable phenotype, although detailed understanding of their transgenerational stability in crop species is lacking. The degree of linkage disequilibrium of epialleles with DNA sequence polymorphisms has important implications to the analysis of genetic diversity. Epigenetic marks in complete linkage disequilibrium (LD) with DNA polymorphisms do not add additional diversity information. However, epialleles in partial or low LD with DNA sequence alleles constitute another layer of genetic information that should not be neglected in germplasm analysis, especially if they exhibit transgenerational stability.

Keywords

comparative genomic hybridizationepigenetichaplotypenext generation sequencingsingle nucleotide polymorphism
Type
Research Article
Information
Plant Genetic Resources , Volume 9 , Issue 2 , July 2011 , pp. 159 - 162
Copyright
Copyright © NIAB 2011

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References

Beló, A, Beatty, MK, Hondred, D, Fengler, KA, Li, B and Rafalski, A (2009) Allelic genome structural variations in maize detected by array comparative genome hybridization. Theoretical and Applied Genetics 120: 355–357.CrossRefGoogle ScholarPubMed
Botstein, D, White, RL, Skolnick, MH and Davis, RW (1980) Construction of a genetic map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32: 314–331.Google ScholarPubMed
Chandler, V and Alleman, M (2008) Paramutation: epigenetic instructions passed across generations. Genetics 178: 1839–1844.CrossRefGoogle Scholar
Chen, X (2009) Small RNAs and their roles in plant development. Annual Review of Cell and Development Biology 25: 21–44.CrossRefGoogle ScholarPubMed
Chin, DB, Arroyo-Garcia, R, Ochoa, OE, Kesseli, RV, Lavelle, DO and Michelmore, RW (2001) Recombination and spontaneous mutation at the major cluster of resistance genes in lettuce (Lactuca sativa). Genetucs 157: 831–849.CrossRefGoogle ScholarPubMed
Clark, AG, Hubisz, MJ, Bustamante, CD, Williamson, SH and Nielsen, R (2005) Ascertainment bias in studies of human genome-wide polymorphism. Genome Research 15: 1496–1502.CrossRefGoogle ScholarPubMed
Cubas, P, Vincent, C and Coen, E (1999) An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401: 157–161.CrossRefGoogle ScholarPubMed
Edwards, D and Batley, J (2009) Plant genome sequencing: applications for crop improvement. Plant Biotechnol Journal 8: 2–9.CrossRefGoogle ScholarPubMed
Flusberg, BA, Webster, DR, Lee, JH, Travers, KJ, Olivares, EC, Clark, TA, Korlach, J and Turner, SW (2010) Direct detection of DNA methylation during single-molecule, real-time sequencing. Nature Methods 7: 461–465.CrossRefGoogle ScholarPubMed
Fu, H and Dooner, HK (2002) Intraspecific violation of genetic colinearity and its implications in maize. Proceedings of the National Academy of Sciences USA 99: 9573–9578.CrossRefGoogle ScholarPubMed
Hauben, M, Haesendonckx, B, Standaert, E, Van Der Kelen, K, Azmi, A, Akpo, H, Van Breusegem, F, Guisez, Y, Bots, M, Lambert, B, Laga, B and De Block, M (2009) Energy use efficiency is characterized by an epigenetic component that can be directed through artificial selection to increase yield. Proceedings of the National Academy of Sciences USA 106: 20109–20114.CrossRefGoogle ScholarPubMed
Henderson, IR and Jacobsen, SE (2007) Epigenetic inheritance in plants. Nature 447: 418–424.CrossRefGoogle ScholarPubMed
Hodges, E, Smith, AD, Kendall, J, Xuan, Z, Ravi, K, Rooks, M, Zhang, MQ, Ye, K, Bhattacharjee, A, Brizuela, L, McCombie, WR, Wigler, M, Hannon, GJ and Hicks, JB (2009) High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Research 19: 1593–1605.CrossRefGoogle ScholarPubMed
Lister, R and Ecker, JR (2009) Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Research 19: 959–966.CrossRefGoogle ScholarPubMed
Lister, R, Pelizzola, M, Dowen, RH, Hawkins, RD, Hon, G, Tonti-Filippini, J, Nery, JR, Lee, L, Ye, Z, Ngo, Q-M, Edsall, L, Antosiewicz-Bourget, J, Stewart, R, Ruotti, V, Millar, AH, Thomson, JA, Ren, B and Ecker, JR (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315–322.CrossRefGoogle ScholarPubMed
Peaston, AE and Whitelaw, E (2006) Epigenetics and phenotypic variation in mammals. Mammalian Genome 17: 365–374.CrossRefGoogle ScholarPubMed
Peterson, DG, Wessler, SR and Paterson, AH (2002) Efficient capture of unique sequences from eukaryotic genomes. Trends in Genetics 18: 547–550.CrossRefGoogle ScholarPubMed
Springer, NM, Ying, K, Fu, Y, Ji, T, Yeh, C-T, Jia, Y, Wu, W, Richmond, T, Kitzman, J, Rosenbaum, H, Iniguez, AL, Barbazuk, WB, Jeddeloh, JA, Nettleton, D and Schnable, PS (2009) Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genetics 5, (11): e1000734. doi:10.1371/journal.pgen.1000734.CrossRefGoogle Scholar
Varshney, RK, Nayak, SN, May, GD and Jackson, SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends in Biotechnology 27: 522–530.CrossRefGoogle ScholarPubMed
Wang, Q and Dooner, HK (2006) Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus. Proceedings of the National Academy of Sciences USA 103: 17644–17649.CrossRefGoogle ScholarPubMed
Wang, X, Elling, AA, Li, X, Li, N, Peng, Z, He, G, Sun, H, Qi, Y, Liu, XS and Deng, XW (2009) Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 21: 1053–1069.CrossRefGoogle ScholarPubMed
Williams, JGK, Kubelik, AR, Livak, KJ, Rafalski, JA and Tingey, SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic-markers. Nucleic Acids Research 18: 6531–6535.CrossRefGoogle ScholarPubMed
Yahiaoui, N, Kaur, N and Keller, B (2009) Independent evolution of functional Pm3 resistance genes in wild tetraploid wheat and domesticated bread wheat. Plant Journal 57: 846–856.CrossRefGoogle ScholarPubMed
Yang, L and Bennetzen, JL (2009) Distribution, diversity, evolution, and survival of Helitrons in the maize genome. Proceedings of the National Academy of Sciences USA 106: 19922–19927.CrossRefGoogle ScholarPubMed
Yuan, Y, SanMiguel, PJ and Bennetzen, JL (2003) High-Cot sequence analysis of the maize genome. Plant Journal 34: 249–255.CrossRefGoogle ScholarPubMed
Zabeau, M and Voss, P (1993) Selective restriction fragment amplification: a general method for DNA fingerprinting. European Patent Application 92402629.7 (publication no. 0 534 858 A1).Google Scholar