PGR Forum, Workshop 4, April 21-24, 2004 Genetic monitoring methodologies

1. PGR Forum, Workshop 4, April 21-24, 2004 Genetic monitoring methodologies Helena Korpelainen and Maria Pohjamo Department of Applied Biology, University of Helsinki, Finland

2. The main goals of conservation genetics • To prevent theloss of genetic diversity so that the ability to evolve in response to environmental change remains (correlation between genetic diversity and population size) • To prevent the deleterious effects of inbreeding on reproduction and survival (inbreeding depression) (not a problem in regularly self-pollinating plants)

3. Additional goals of conservation genetics • To prevent fragmentation of populations and reduction in gene flow • To prevent genetic drift overriding natural selection as the main evolutionary process • To resolve taxonomic uncertainties • To prevent deleterious effects on fitness possibly occurring as a result of outcrossing (outbreeding depression)

4. What explains the level of genetic diversity? • Historical and current population sizes • Population bottlenecks • Breeding system • Natural selection • Different mutation rates • Immigration and emigration among populations

5. Threats to genetic diversity • Extinction of species, populations, subspecies • Extinction of alleles (due to drift or directional selection) • Inbreeding reducing heterozygosity (alleles maintained but allocated to homozygotes → possibly inbreeding depression due to the homozygosity of deleterious recessive alleles)

6. Analysis of genetic diversity • Morphological traits often used for basic characterization - allows the interpretation of relationships between the genotype and environmental conditions • Molecular marker techniques - allow direct investigations of variation at the DNA level, thereby excluding all environmental influences - can be employed at very early growth stages - have marginalized other methods in the analysis of genetic diversity

7. Measures of inbreeding • The inbreeding coefficient (F) of an individual refers to how closely related its parents are • In the case of selfing, F=0.5 in the offspring • Inbreeding accumulates in isolated populations, and complete inbreeding can eventually be reached with repeated inbred matings (an F=0.999 reached after 10 generations of self-fertilization) • The average inbreeding coefficient of all individuals in a population: Average F increases at a rate of 1/(2N) per generation in a randomly breeding diploid population of size N • Levels of inbreeding can be determined from pedigrees or inferred from heterozygosities for genetic markers

8. Is the taxon suffering from inbreeding depression? • Usually less of an issue in selfing species (about 40% of flowering plants can self and 20% may do so commonly) • Typically higher in gymnosperms than angiosperms (could be related to a higher level of polyploidy in angiosperms) • Direct evidence obtained (lowered fertility & viability?) • Inbreeding depression may be inferred from its correlation with reduction in genetic variation, assessed by genetic markers (e.g., microsatellites have the power to detect reductions in heterozygosity and allelic diversity) • Slow inbreeding generally causes less inbreeding depression than an equivalent amount of rapid inbreeding

9. Loss of genetic diversity and loss of self-incompatibility alleles • About half of all flowering plant species have self-incompatibility systems that reduce or prevent selfing • Self-incompatibility regulated by one or more loci, presumed to have evolved to avoid inbreeding depression • Small population → loss of diversity & self-incompatibility alleles → inbreeding → lowered fitness • A potential problem in threatened self-incompatible plants

10. Characterizing genetic diversity • Genotype frequencies, allele frequencies • Expected heterozygosity: a) single locus h = 1- (p12 + p22+ ... + pn2), b) mean across loci (H) • Hardy-Weinberg equilibrium:statistical testing to assess agreement between observed and expected numbers of genotypes; allows detection of inbreeding, population fragmentation, migration and selection • Linkage disequilibrium:non-random associations of alleles among loci • Diversity indices, e.g., expected heterozygosity, allelic diversity (A=the number of alleles averaged across loci), the proportion of polymorphic loci (P), nucleotide diversity

11. Characterizing genetic diversity • Genetic distances between populatons:based on allele or genotype frequencies, or DNA sequence differences • Analysis of molecular variance (AMOVA):the partitioning of genetic variation into within population and among populations components - in inbred populations often a greater differentiation among populations than in outcrossing populations -in fragmented populations often a greater differentiation among populations than in more continuous populations

12. Linkage disequilibrium (D) • Measured as the deviation of haplotype frequencies from linkage equilibrium • Linkage disequilibrium is common in threatened species as their population sizes are small • Population bottlenecks may cause linkage disequilibrium • Functionally important gene clusters exhibiting linkage disequilibrium are important to the persistence of threatened species • The level of linkage disequilibrium can be used to detect admixture of differentiated populations

13. Measuring inbreeding depression • A general measure of inbreedind depression (σ) is the proportionate decline in the mean due to a given amount of inbreeding: σ = 1-(fitness of inbred offspring/fitness of outbred offspring) • The formula itself does not specify the level of inbreeding • Since many plants can be selfed, the usual estimate of inbreeding depression is obtained by comparing selfed and outcrossed progeny (this provides the impact of inbreeding due to an inbreeding coefficient of 50%

14. Recovering from inbreeding depression • Recovery by outcrossing the inbred population to another unrelated (outbred or inbred) population (through immigration) • Fitness may recover as a result natural selection removing deleterious alleles

15. Solving genetic problems • Increase inpopulation size (especially the effective population size Ne, averages ~10% of the census size) • Establishment of populations in several locations (to minimize the risk of catastrophes) • Maximize the reproductive rate by improving environment • Genetic management of inbred/small populations, introduction of migrants from - outbred populations - inbred but genetically unrelated populations - from inter-fertile taxa (requires careful consideration, a risk of outbreeding depression)

16. Genetic management for introduction • Captive populations may provide a source of individuals to reintroduce and supplement wild populations of threatened taxa • The success of reintroduction is jeopardized by genetic deterioration in captivity due to inbreeding depression, loss of genetic variation, and genetic adaptation to captivity (leading to reduced adaptation to the wild environment) • Individuals for reintroduction should have maximum genetic diversity and maximum reproduction fitness in the wild environment

17. Things to be considered in the genetic monitoring • Population sizes (small, decreasing?) • The level of genetic diversity (low, decreasing?) • The level and history of inbreeding, the amount of inbreeding depression • Population fragmentation (measured by AMOVA, partitioning of variation within and among populations) and its impact on genetic diversity and inbreeding

18. How large should a population be? • Population should be large enough - to avoid inbreeding depression - to retain the ability to evolve in response to changes in the environment • Estimated effective population sizes (Ne, census size usually 10x) needed - to retain reproductive fitness: Ne=501 - to retain evolutionary potential: Ne=500-50002 1Franklin 1980, Soulé 1980 2Franklin 1980, Lande& Baroowclough 1987, Lande 1995

19. Measuring genetic diversity • Continuously varying (quantitative) characters (genetic and environmental effects, e.g., seed set) • Morphology (qualitative or quantitative) • Chromosomes • Proteins • DNA (nuclear, chloroplast and mitochondrial)

20. Protein assays (enzyme electrophoresis) • Used to distinguish different forms of proteins and to measure the level of genetic variation for a particulat protein locus • Co-dominant inheritance • About 30% of DNA base changes result in charge changes → electrophoresis underestimates the extent of genetic diversity • Coding genomic areas examined, not as much variation as in noncoding areas

21. DNA assays • Suitable DNA methods based on PCR (polymerase chain reaction = in vitro amplification of DNA)

22. PCR-based methods • 1) Sequence-arbitrary methods - Random amplified polymorphic DNAs (RAPDs) - Inter simple sequence repeats (ISSR) - Amplified fragment length polymorphisms (AFLP) • 2) Methods requiring a priori sequence information - Simple sequence repeats (SSRs)/short tandem repeats (STRs)/microsatellites - Sequence characterized amplified regions (SCARs) - Single nucleotide polymorphisms (SNPs)

23. Problems with sequence-arbitrary amplification methods • Less robust than sequence-dependent methods because - multiple amplicons are present competing for available enzyme and substrate - low-stringency thermal-cycling permits mismatch annealing between primer and template • To overcome potential problems it is important to create optimal and consistent amplification conditions

24. Random amplified polymorphic DNAs (RAPDs) • DNA fragments amplified from genomic DNA using only single, sequence-arbitrary primers (10mer typical) • When the same primer is used with DNA template from different individuals of the same species, fragment patterns are nearly similar (some amplified fragments present in one individual and absent in another) • Typically dominant markers; less informative than co-dominant markers, especially when examining mating systems • A more serious drawback are concerns with fragment allelism and fragment pattern reproducibility RAPD profiles of grape DNA generated with two arbitrary primers (Ye et al. 1996)

25. Inter simple sequence repeats (ISSR) • Exploits the highly polymorphic nature of simple sequence repeats (SSRs) • Highly informative fingerprints using anchored SSR primers, e.g., [GA]8C • Quite complex fragment patterns • Dominant inheritance • A good choice for a sequence-arbitrary method ISSR profiles of moss DNA generated with one primer(Pohjamo & Korpelainen)

26. Amplified fragment length polymorphisms (AFLP) • Genomic DNA first digested with one or more restriction enzymes • An adapter of known sequence ligated to the digested genomic DNA • Amplification using primers with sequence specificity for the adapter • Amplification products observed by labelling and using acrylamide gels or specialized detection equipment • Usually fairly complex fragment patterns • Dominant inheritance • Allelism and reproducibility question; the use of long primers which are perfect matches to adapter-genomic DNA templates → reliability AFLP analysis of Solanum commersonii(+) S. tuberosum somatic hybrids(Baronet et al. 2002)

27. Sequence-dependent, PCR-based methods • Nowadays commonly used despite considerable development cost • Attractive features: allelism, codominance, assay robustness, information of the highly variable areas of the genome

28. Simple sequence repeats (SSRs) = short tandem repeats (STRs) = microsatellites • Tandemly repeated DNA motifs composed of di-, tri-, tetra- and sometimes greater repeated nucleotide sequences, e.g., [AT]n • Different alleles vary in the number of units of the repeat motifs • Co-dominant inheritance • Even in self-pollinated species in which the polymorphism detected by other methods may be low, considerable levels of polymorphism are detected with SSRs • Detection using genotyping equipment or high-resolution gel systems, radio- or fluorescent labelling Giancola et al. 2002)

29. SSRs • Developed markers species-specific (perhaps usable within genus) • Procedures very robust • Good primer design essential • Disadvantage: small amount of information generated from each amplification reaction • Through careful experimentation, sets of primer pairs can be found which exhibit consistent co-amplification

30. Sequence characterized amplified regions (SCARs) • Sequence-dependent markers derived from sequence-arbitrary marker loci • Sequence-dependent primers designed after sequencing RAPD (or other) amplification products • Dominant inheritance • Disadvantage: a small amount of information generated from each amplification reaction

31. Single nucleotide polymorphisms (SNPs) • Sequencing of segments distributed throughout the genome → SNP discovery • Several methods to detect SNPs a) Sequencing b) RFLP (involves cutting a fragment of amplified DNA; if the recognition site for the restriction enzyme is altered, the enzyme will not cut the DNA) c) SSCP (single-strand conformation polymorphism; a SNP may effect the conformation of an amplified DNA strand) d) DNA chips (large-scale genotyping, high costs, allele-specific hybridization with amplified DNA from each polymorphic region)

32. Markers for ecologically important traits • Many studies concerning diversity and plant genetic resources have been based on neutral molecular markers • However, studies of genetic diversity could benefit from targeting variation in such genes that exhibit ecologically relevant variation • Procedure: to assess which traits matter, identify the genes that potentially affect such traits, and develop markers within, or flanking these genes → gene-targeted, multilocus profiles for the management of genetic resources