Salient Biological Features, Systematics, and Genetic Variation of Populus

Slavov, Gancho; Zhelev, P.

doi:10.1007/978-1-4419-1541-2_2

Cited by 65 publications

(55 citation statements)

References 125 publications

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“…Compared with its congeners (reviewed by Slavov and Zhelev, 2010), genetic structure across the range of P. angustifolia is much stronger than expected. P. angustifolia is dioecious with putatively long-distance dispersal of pollen and seed, traits that are expected to minimize population structure (Hamrick and Godt, 1996), as has been shown in other species (for example, Namroud et al, 2008).…”

Section: Population Structurementioning

confidence: 88%

Geographical barriers and climate influence demographic history in narrowleaf cottonwoods

et al. 2015

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Studies of genetic variation can clarify the role of geography and spatio-temporal variation of climate in shaping demography, particularly in temperate zone tree species with large latitudinal ranges. Here, we examined genetic variation in narrowleaf cottonwood, Populus angustifolia, a dominant riparian tree. Using multi-locus surveys of polymorphism in 363 individuals across the species' 1800 km latitudinal range, we found that, first, P. angustifolia has stronger neutral genetic structure than many forest trees (simple sequence repeat (SSR) F ST = 0.21), with major genetic groups corresponding to large apparent geographical barriers to gene flow. Second, using SSRs and putatively neutral sequenced loci, coalescent simulations indicated that populations diverged before the last glacial maximum (LGM), suggesting the presence of population structure before the LGM. Third, the LGM and subsequent warming appear to have had different influences on each of these distinct populations, with effective population size reduction in the southern extent of the range but major expansion in the north. These results are consistent with the hypothesis that climate and geographic barriers have jointly affected the demographic history of P. angustifolia, and point the importance of both factors as being instrumental in shaping genetic variation and structure in widespread forest trees.

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Section: Population Structurementioning

confidence: 88%

Geographical barriers and climate influence demographic history in narrowleaf cottonwoods

et al. 2015

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“…Most Populus species are dioecious, although reports of hermaphroditism have been published (reviewed in Slavov and Zhelev, 2010). Due to its small genome size, rapid growth, easy vegetative propagation, huge genomic resources and easy biotechnological handling ability, this genus has become a model species for forest tree genomics (Wullschleger et al, 2002), resulting in the publication of the full nuclear genome sequence of western black cottonwood, P. trichocarpa (section Tacamahaca; Tuskan et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Whole-genome draft assembly of Populus tremula x P. alba clone INRA 717-1B4

Mäder¹,

Paslier

Bounon

et al. 2016

Silvae Genetica

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Populus trichocarpa and P. deltoides are the only Populus species known to date to have a publicly available nuclear genome sequence that has been assembled to chromosomes and annotated (https://phytozome.jgi.doe.gov/). Here we focus on the clone INRA 717-1B4, a female P. tremula x P. alba (P. x canescens) interspecific hybrid that is universally used by scientists worldwide as a tree model in transgenic experiments. The already available INRA 717-1B4 nuclear genomic resource (v1.1 of sPta717 at http://aspendb.uga.edu/index.php/databases/ spta-717-genome) presents only INRA 717-1B4 genomic regions with high similarity to the P. trichocarpa genomic reference sequences. We assembled draft genomic scaffolds by a combination of de novo assembly with reference-based assembly using 30x resequencing NGS data (Illumina MiSeq® and Ion Torrent Ion PGM™) of INRA 717-1B4. In total, 419,969 scaffolds of length larger than 500 bp were generated. The mean length of the scaffolds is 2,166 bp and the size of the largest scaffold 84,573 bp. The N50 contig length is 3,850 bp when considering contigs larger than 1,000 bp. Probably due to the high level of heterozygosity of this interspecific hybrid, the accumulated scaffold length is with 0.9 GB about twice the expected size of the haploid nuclear genome. DNA sequences of the genomic scaffolds of INRA 717-1B4 are publicly available for Blast analyses and download via the new INRA web portal at https://urgi. versailles.inra.fr/Species/Forest-trees/Populus/Clone-INRA-717-1B4/. This new genomic sequence resource will complement the already available INRA 717-1B4 resources and will facilitate the future optimization of genetic transformation experiments to discover gene function.

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“…All poplars, aspens, and cottonwoods (genus Populus) play important roles in natural ecosystems as pioneer species ( [25,26]) and are economically important for various industrial products with an increasing role as bioenergy crops ( [27,28,29,30]). Populus species are still largely undomesticated with very low population differentiation indicative of extensive long-distance intraspecific gene flow [31]. In western North America, P. trichocarpa has an extensive cordilleran range (31-62°N), yet with no clear north-south differentiation in genetic diversity (and no decreasing genetic diversity with latitude), consistent with the species' colonization history from multiple potential glacial refugia [32].…”

Section: Introductionmentioning

confidence: 78%

Evolutionary quantitative genomics ofPopulus trichocarpa

Porth

Klápště

McKown

et al. 2015

Preprint

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Forest trees generally show high levels of local adaptation and efforts focusing on understanding adaptation to climate will be crucial for species survival and management. Here, we address fundamental questions regarding the molecular basis of adaptation in undomesticated forest tree populations to past climatic environments by employing an integrative quantitative genetics and landscape genomics approach. Using this comprehensive approach, we studied the molecular basis of climate adaptation in 433 Populus trichocarpa (black cottonwood) genotypes originating across western North America. Variation in 74 field-assessed traits (growth, ecophysiology, phenology, leaf stomata, wood, and disease resistance) was investigated for signatures of selection (comparing Q ST -F ST ) using clustering of individuals by climate of origin (temperature and precipitation). 29,354 SNPs were investigated employing three different outlier detection methods and marker-inferred relatedness was estimated to obtain the narrow-sense estimate of population differentiation in wild populations. In addition, we compared our results with previously assessed selection of candidate SNPs using the 25 topographical units (drainages) across the P. trichocarpa sampling range as population groupings. Narrow-sense Q ST for 53% of distinct field traits was significantly divergent from expectations of neutrality (indicating adaptive trait variation); 2,855 SNPs showed signals of diversifying selection and of these, 118 SNPs (within 81 genes) were associated with adaptive traits (based on significant Q ST ). Many SNPs were putatively pleiotropic for functionally uncorrelated adaptive traits, such as autumn phenology, height, and disease resistance. Evolutionary quantitative genomics in P. trichocarpa provides an enhanced understanding regarding the molecular basis of climate-driven selection in forest trees and we highlight that important loci underlying adaptive trait variation also show relationship to climate of origin. We consider our approach the most comprehensive, PLOS ONE |

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Salient Biological Features, Systematics, and Genetic Variation of Populus

Cited by 65 publications

References 125 publications

Geographical barriers and climate influence demographic history in narrowleaf cottonwoods

Geographical barriers and climate influence demographic history in narrowleaf cottonwoods

Whole-genome draft assembly of Populus tremula x P. alba clone INRA 717-1B4

Evolutionary quantitative genomics ofPopulus trichocarpa

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