800x265
Professor

Department of Plant Biology, SLU

Box 7080, 75007 Uppsala

par.ingvarsson@slu.se
Pär K. Ingvarsson

Population, quantitative and comparative genomics of adaptation 
in plants

The genetic architecture of local adaptation

Most species are distributed across heterogeneous environments and local adaptation is well documented in many animals and plants. Studying the genetic basis of local adaptation greatly benefits from both forward and reverse genetics approaches, including methods that take advantage of genome-wide SNP variation and relate them to eg. phenotypes or environmental variables of interest (GWAS) or by identifying effects on phenotypes following the disruption of known. In addition, phenotypic plasticity represents an important transitory state that can buffer populations from maladaptation until genetic adaptation can occur (so called genetic assimilation). The retention of plastic responses across generations involves epigenetic changes and epigenetic variation provides a bridge for adaptation to rapidly changing environmental condition. In this project we are investigating the genetic basis of local adaptation in European aspen (Populus tremula) using a combination of forward and reverse genetic methods as well as the importance of phenotypic plasticity and epigenetic variation in mediating adaptation to both historical and current climate shifts.

 

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Associations between SNPs in phyB2 and days until bud set in P. tremula

 

 

 

Forces shaping genome-wide patterns of genetic variation

Linked selection, the interaction between positive or negative natural selection and recombination, plays an important role in shaping patterns of genome-wide variation in nucleotide diversity. Linked selection reduce the local effective population size in regions of low recombination and therefore reduce the efficacy of selection, resulting a reduced fixation of favorable mutations and an increased frequency of deleterious mutations in these regions. In this project we are investigating how the interaction between natural selection and recombination shape polymorphism and divergence variation within and among species of the genus Populus.

 

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Nucleotide polymorphism across chromosome 1 in three species of Populus

 

 

Genomics-based breeding

Modern DNA sequencing and genotyping methods have opened up possibilities to apply genomics in the context of traditional breeding. In particular the introduction of genomic prediction (GP) has the potential to revolutionise plant and animal breeding. The basic idea behind GP is to predict phenotypes from genome-wide variation at SNP markers. In practice it involves using a large training populations where individuals are both genotyped and phenotyped to build a regression model of marker genotypes on measured phenotypes and using this model to predict phenotypes in individual where only genotype information is available. We are currently involved in evaluating the utility and efficiency of genomic prediction for breeding in hybrid Eucalyptus and Populus.

 

Selected recent publications

Wang, J., Street, N.R.,  Scofield, D.G., Ingvarsson, P.K. (2016) Variation in linked selection and recombination drive genomic divergence during allopatric speciation of European and American aspens. Molecular Biology and Evolution, 33, 1754-1767.

Wang, J., Street, N.R.,  Scofield, D.G., Ingvarsson, P.K.  (2016) Natural selection and recombination rate variation shape nucleotide polymorphism across the genomes of three related Populus species. Genetics, 202, 1185-1200.

De La Torre, A.R., Lin, Y-C, Van de Peer, Y., Ingvarsson, P. K. (2015) Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in Picea gene families. Genome Biology and Evolution 7, 1002-1015.

Bernhardsson, C., Robinson, K. M., Abreu, I. N., Jansson, S., Albrectsen, B.R., Ingvarsson, P.K. (2013) Geographic structure in metabolome and herbivore community co-occurs with genetic structure in plant defense genes. Ecology Letters, 16, 791-789.

Nystedt, B., Street, N.R., Wetterbom, A., […] Nilsson, O., Ingvarsson, P.K., Lundeberg, J., Jansson, S. (2103) The 20 Gbp Norway spruce genome sheds light on conifer genome evolution. Nature 497, 579-584.