Structure, evolution and biodiversity of crop plant genomes

Research

The genetic variation of a species - its biodiversity - is encoded by the different DNA sequences in all the individuals of that species. This biodiversity has built up during millions of years of naturally arising mutation and natural selection. Biodiversity thus represents the ‘genetic wealth’ of the species, allowing adaptation to new environmental stimuli such as habitat change or disease (Figure 1).  A major goal for the future is the harnessing of this wealth for improvement of plant crops by breeding

One of the big problems facing biodiversity research is the measurement of genetic variation across thousands or millions of organisms. We are using single nucleotide polymorphisms (SNPs), gene sequences (11) and transposon insertions (1, 4-5, 7-9, 12) as molecular markers to assess biodiversity of a variety of crop plant species and their wild relatives, including pea and barley (Figure 1).

One of our strongest interests is the characterisation of barley genetic diversity. We coordinate the EXBARDIV project (url below), which involves 7 European partners and is developing a novel incremental association genetics approach for the exploitation of natural barley diversity for breeding. It is based upon high throughput SNP genotyping of barley germplasm using the Illumina genotyping platform (http://www.illumina.com), combined with phenotypic analysis.

  Transposons are segments of DNA that move to new chromosome positions and the genomes of most plants contain huge numbers of them, which can add up to more than half the entire DNA content of the organism (10). We are particularly interested in one transposon group called LTR retrotransposons, which make up more than half the DNA of many crop plants (1-5, 7, 9, 10).

 We use versatile, rapid and powerful methods for biodiversity assessment using molecular markers based on transposons and SNPs (1, 4-5, 7-9, 12-14). One technique that we developed (8) uses microarray technology to visualise the presence or absence of retrotransposon insertions in thousands of organisms in parallel (Figure 2).

Such high-throughput approaches require new computational tools to organise the huge amount of biodiversity data and make it useful for the breeder, the conservationist and the geneticist. We have therefore developed a new bioinformatic tool, the Germinate database for, analysing and visualising biodiversity (3).

Useful Links to websites for projects we are involved in:
EXBARDIV Project - http://pgrc.ipk-gatersleben.de/barleynet/ (follow ‘Projects link)
http://www.biocenter.helsinki.fi/bi/tegerm/ http://www.eugrainlegumes.org/
http://germinate.scri.sari.ac.uk/cgi-bin/germinate/germinate.cgi
http://www.plant.wageningen-ur.nl/projects/angel/
http://www.bioexploit.net

Publications

1. Syed N., Sundar S., Wilkinson M., Bhau B. Cavalcanti J. and Flavell A. J. (2005) Ty1-copia retrotransposon-based SSAP marker development in Cashew (Anacardium occidentale L.). Theor. Appl. Genet. 110: 1195-1202.

2. Hill P, Burford D, Martin DMA and Flavell AJ (2005) Retrotransposons and Genome Size Variation in the Vicia genus. Mol. Genet. Genomics 273: 371-381

3. Lee, JM, Davenport, GF, Marshall, D, Ellis, THN, Ambrose, MJ, Dicks, J, van Hintum, TJL and Flavell, AJ (2005) GERMINATE - A Generic Database for Plant Genetic Resources Plant Physiology 139: 619-631.

4. Jing, R., Knox, MR, Lee, JM, Vershinin, AV, Ambrose, MJ, Ellis, THN and Flavell, AJ (2005) Insertional polymorphism and antiquity of PDR1 retrotransposon insertions in Pisum species. Genetics 171: 741-752.

5. Syed N, Sørensen, AP, Antonise, R, van de Wiel. C, van der Linden, CG, van ’t Westende, W, Hooftman, DAP, den Nijs, HCM and Flavell AJ (2006) A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers. Theor. Appl. Genet. 112: 517-527

6. Muehlbauer GJ, Bhau BS, Syed NH, Heinen S, Cho S Marshall D, Pateyron S, Buisine N, Chalhoub B and Flavell AJ (2006) A hAT superfamily transposase domesticated by the cereal grass genome Mol. Genet. Genomics 275: 553-563

7. Syed NH and Flavell AJ (2007) Sequence specific amplification polymorphisms (SSAP) - a multi-locus approach for analysing transposon insertions. Nature Protocols 1: 2746-2752

8. Jing R, Bolshakov VI and Flavell AJ (2007). The Tagged Microarray Marker (TAM) method for high throughput detection of single nucleotide and indel polymorphisms. Nature Protocols 2: 168-177

9. Sanz AM, Gonzalez SG, Syed NH, Suso MJ, Saldaña CC and Flavell AJ (2007) Genetic diversity analysis in Vicia species using retrotransposon-based SSAP markers. Mol Genet Genomics 278: 433-441

10. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P and Schulman AH (2007) A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics 8: 973-982

11. Jing R, Johnson R, Seres A, Kiss G, Ambrose MJ, Knox MR, Ellis THN, and Flavell AJ (2007) Gene-based sequence diversity analysis of field pea (Pisum). Genetics 177: 2263-2275

12. Smýkal P, Hýbl M, Corander J, Jarkovský J, Flavell AJ and Griga M (2008) Genetic diversity and population structure of pea (Pisum sativum L.) varieties derived from combined retrotransposon, microsatellite and morphological marker analysis. Theoretical and Applied Genetics online DOI 10.1007/s00122-008-0785-4

13. Lyons M, Milne L, Rostoks N, Waugh R and Flavell AJ (2008) Isolation and analysis of novel miniature inverted repeat transposable elements from the barley genome. Molecular genetics Genomics 280: 275-285

14. Kiær LP, Felber F, Flavell AJ, Guadagnuolo R, Hauser TP, Olivieri AM, Scotti I, Syed NH, Vischi M, van de Wiel C and Jørgensen RB (2008) Gene flow and genetic variation in wild and cultivated chicory Genetic Resources and Crop Evolution DOI 10.1007/s10722-008-9375-1