Whole genome sequencing (WGS) meets biogeography and shows that genomic selection in forest trees is feasible


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email christian.lexer@unifr.ch

Recently developed approaches to high throughout sequencing (HTS) and single nucleotide polymorphism (SNP) detection offer unprecedented power to uncover functionally important genetic variation at the level of whole genomes and entire metapopulations in wild species. In a landmark paper published in this issue of New Phytologist, Slavov et al. (pp. 713–725) put these novel approaches to work in Populus trichocarpa (black cottonwood), an ecologically and economically important forest tree with an assembled and annotated genome (Tuskan et al., 2006). This study is important because it takes whole genome sequencing (WGS) in wild species to a level that allows a range of topics in the modern life sciences to be addressed, from biogeography to molecular plant domestication and breeding, with a level of precision normally only seen in human medical genetics.

Slavov et al. have demonstrated that whole genome resequencing in wild, outcrossing forest trees is now ready to tackle major issues of general scientific and applied interest.’

Making use of Illumina-based WGS and Infineum SNP detection assays, Slavov et al. uncover significant geographic differentiation in Populus trichocarpa at multiple spatial scales across the species’ range in western North America. They go on to demonstrate significant covariation of genetic polymorphisms and geographic latitude. Interestingly, this covariation is stronger for nongenic SNPs at the range-wide scale and for genic SNPs in the core of the species’ range. This points to neutral, demographic processes (‘isolation by distance’) as drivers of differentiation over larger geographic areas and to locally varying selection as a potential driver of differentiation at a smaller spatial scale. Next, Slavov et al. examine patterns of recombination and linkage disequilibrium (LD) along the genome and across the species’ range. Patterns along chromosomes indicate the presence of LD in this outcrossing species over much larger physical distances than previously thought (3–6 kilo bases), and levels of recombination along chromosomes covaried with several DNA sequence and epigenetic features. LD across the species’ range, however, varied across populations, thus pointing to important variation in effective population sizes (Ne) and contributing to our understanding of the biogeographic history of this important forest tree.

Current HTS approaches suitable for population genetics have been around for several years now (Metzker, 2010), but surprisingly few studies have managed to go beyond mere bioinformatic problem-solving exercises and address major biological or applied issues in wild, undomesticated species (Hohenlohe et al., 2010; Gompert et al., 2012). Most current HTS studies of wild species make use of genotyping-by-resequencing approaches such as restriction site associated DNA sequencing (RAD-seq; Hohenlohe et al., 2010), which provide sufficient coverage depth at a manageable cost by sequencing low-complexity DNA libraries rather than whole genomes (but see Turner et al. (2010) and Rubin et al. (2010) for rare examples of WGS studies involving populations of wild species). The Slavov et al. study stands out, because they convincingly manage to interpret WGS data for a wild, largely undomesticated forest tree (Populus trichocarpa) in terms of biogeography, domestication and breeding.

With regard to biogeography, their genomic data allow the authors to revisit long-standing questions on the phylogeographic history of plants in western North America (Soltis et al., 1997). In particular, the lack of a north–south gradient in diversity (and thus, of a gradient in Ne) speaks against migration from a single southern source and is consistent with colonization from multiple refugia following the last ice age (Soltis et al., 1997). Based on high genomic diversity and Ne of populations in the center of the species’ range, Slavov et al. argue that these may represent genomic ‘melting pots’, sensu Petit et al. (2003) or de Carvalho et al. (2010). Recent admixture in such ‘melting pots’ is expected to leave specific signatures in admixed genomes, with large tracts of DNA originating from each participating source gene pool (Stölting et al., 2012). It will be interesting to follow up on the ‘melting pot’ hypothesis by tracking the likely origin and size of chromosomal blocks present in central populations.

With a view towards tree domestication, recent work in humans and forest trees indicates that functionally important, potentially adaptive traits often have a polygenic basis (Pritchard et al., 2010; Neale & Kremer, 2011). Hence, HTS and SNP genotyping in trees offers great potential in genomic selection programs, that is, assessing the sum of gene effects (breeding values) for important traits directly from high-density molecular genetic data. The finding that LD extends over relatively large chromosomal distances (Slavov et al.) is encouraging, as it implies that fewer markers than expected are required to tag LD blocks for this purpose. This may hold true for Populus trichocarpa and for many other tree species with similar sets of life history traits.

We anticipate that the impact of the Slavov et al. study – and potential future studies arising from their data – will extend far beyond Populus trichocarpa to other species of Populus (poplars, aspens, cottonwoods) and to other groups of taxa not yet perceived as model species. This potential is most easily illustrated by a comparison to our own HTS data in two hybridizing Eurasian species of Populus, P. alba (white poplar) and P. tremula (European aspen) (Stölting et al., 2012). The genomic ‘coldspots’ of recombination identified in P. trichocarpa by Slavov et al. have a remarkable tendency to coincide with genomic ‘hotspots’ of differentiation between P. alba and P. tremula in our study (Stölting et al., 2012). The low-recombination region at 8 Mio base pairs on Populus chromosome VII (fig. 7 in Slavov et al.), for example, coincides exactly with a region of increased interspecific differentiation (e.g. FST) and reduced diversity (SNP density) in P. alba and P. tremula (Stölting et al., 2012). Similar parallels can be found on several other chromosomes (e.g. VIII, X, XIV, XV, see the Supporting materials of both studies). For convenience, we have magnified and redrawn our interspecific genome scan results (Stölting et al., 2012) for chromosome VII in Fig. 1 of this Commentary. Viewed in combination, the HTS data of Slavov et al. and Stölting et al. (2012) are suggestive of stronger selection and/or drift in genomic regions with low recombination, effectively reducing diversity and contributing to the maintenance of genomic differentiation between species in the face of gene flow (Smadja & Butlin, 2011). Of course, a caveat is in line here: Slavov et al. used a WGS approach whereas our study is based on c. 38 000 SNPs from RAD-seq (Stölting et al., 2012), and recombination rates were not addressed directly in our study. Still, our comparison indicates a great potential for comparative genomics to ‘tie together’ and synthesize ecological and evolutionary genomic data between highly syntenic species of Populus; WGS-based genome scans of populations from both Eurasian species (P. alba and P. tremula) are currently underway in our laboratory.

Figure 1.

Genomic differentiation between two Eurasian species of Populus, P. alba and P. tremula, along linkage group VII, based on single nucleotide polymorphisms (SNPs) detected by restriction site associated DNA (RAD) sequencing. Results are redrawn from Stölting et al. (2012), where the data are fully documented. Windowed analyses (window size 1 Mio base pairs, step size 200 kilo bases) of two measures of differentiation are indicated along the x-axis (window midpoints as physical distances in Mio base pairs): the proportion of SNPs fixed between species (fix ratio; red solid line) and FST (red hatched line). The blue curve indicates SNP density per window (number of SNPs per Mio base pairs). A region of particularly low recombination identified by Slavov et al. (this issue of New Phytologist, pp. 713–725; fig. 7) is highlighted in gray.

Short-read HTS studies such as those by Slavov et al. or ourselves (Stölting et al., 2012) are by no means limited to taxa with completely sequenced reference genomes (recall that standard HTS approaches in population genetics normally rely on annotated and assembled reference genomes for mapping sequence reads and detecting SNPs). Fig. 2 shows a re-analysis of our Populus alba and P. tremula HTS data (fully documented in Stölting et al., 2012) with and without the use of the P. trichocarpa genome sequence for reference mapping. Polymorphism detection without the reference genome was achieved by de novo clustering of sequence reads, using sequence alignment criteria as in Stölting et al. (2012) and widely used software (see the legend of Fig. 2). After de novo sequence clustering and SNP calling, the P. trichocarpa genome was used to visualize and plot the results from both approaches (Fig. 2), again using chromosome VII as a convenient example. The results should encourage students with an interest in applying HTS to populations of nonmodel species. Although fewer SNPs are detected by de novo clustering compared with reference mapping (Fig. 2, red and blue curves), SNP densities exhibit highly similar patterns along chromosomes with both approaches (Pearson's correlation = 0.827 for chromosome VII). In effect, our visualization and direct comparison of both strategies using the P. trichocarpa genome sequence confirms the validity and usefulness of de novo clustering of HTS reads, corroborating recent findings by Catchen et al. (2011).

Figure 2.

Direct comparison of genomic reference mapping vs reference-free de novo clustering of high throughout sequencing (HTS) sequence reads, exemplified by restriction site associated DNA sequencing (RAD-seq) data for Populus alba and P. tremula (Stölting et al., 2012). Single nucleotide polymorphism (SNP) densities (y-axis, number of SNPs per Mio base pairs) from both approaches are shown along Populus chromosome VII (x-axis, physical distance in Mio base pairs). SNP calling by genomic reference mapping (blue curve) was carried out with open source software following Stölting et al. (2012), using P. trichocarpa genome assembly v2 and a minimum threshold of eight reads per SNP, not permitting missing data in the final SNP table. Reference-free SNP calling (red curve) was achieved by de novo clustering of HTS reads with the Uclust v3.0 software (http://drive5.com/usearch/usearch3.0.html) using the same statistical criteria. Window sizes are as in Fig. 1, total sample size was = 14 haploid genomes per species, and all analyses were restricted to biallelic SNPs. A region of particularly low recombination identified by Slavov et al. (this issue of New Phytologist, pp. 713–725; fig. 7) is highlighted in gray.

In conclusion, Slavov et al. have demonstrated that whole genome resequencing in wild, outcrossing forest trees is now ready to tackle major issues of general scientific and applied interest. We anticipate that future work in Populus spp. will reveal: how strongly the genomic landscape of recombination (and thus the size of DNA blocks of relevance to selection programs) varies across individuals, populations, and species; how exactly drift and selection interact to shape the response of genomes to environmental shifts (e.g. climate change); how drift and selection interact to drive the build-up and maintenance of genomic ‘islands’ or ‘continents’ of differentiation between species, thus preventing or facilitating the breakdown of reproductive barriers. Populus offers the great advantage of multiple ecologically and economically important species with highly syntenic genomes. Rapidly evolving bioinformatic approaches to HTS-based genotyping are starting to enable studies of genomic diversity in many other species that have not been ‘on the radar’ of molecular biology and genomics so far. Clearly, HTS (formerly known as ‘next generation sequencing’) is starting to change how we approach key issues in the fundamental and applied life sciences.