Dataset Information

Polymorphism and Divergence in Two Willow Species, Salix viminalis L. and Salix schwerinii E. Wolf.

ABSTRACT: We investigated species divergence, present and past gene flow, levels of nucleotide polymorphism, and linkage disequilibrium in two willows from the plant genus Salix. Salix belongs together with Populus to the Salicaceae family; however, most population genetic studies of Salicaceae have been performed in Populus, the model genus in forest biology. Here we present a study on two closely related willow species Salix viminalis and S. schwerinii, in which we have resequenced 33 and 32 nuclear gene segments representing parts of 18 nuclear loci in 24 individuals for each species. We used coalescent simulations and estimated the split time to around 600,000 years ago and found that there is currently limited gene flow between the species. Mean intronic nucleotide diversity across gene segments was slightly higher in S. schwerinii (?(i) = 0.00849) than in S. viminalis (?(i) = 0.00655). Compared with other angiosperm trees, the two willows harbor intermediate levels of silent polymorphisms. The decay of linkage disequilibrium was slower in S. viminalis compared with S. schwerinii, and we speculate that this is due to different demographic histories as S. viminalis has been partly domesticated in Europe.

SUBMITTER: Berlin S

PROVIDER: S-EPMC3276148 | biostudies-literature | 2011 Oct

REPOSITORIES: biostudies-literature

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Polymorphism and Divergence in Two Willow Species, Salix viminalis L. and Salix schwerinii E. Wolf.

Berlin Sofia S Fogelqvist Johan J Lascoux Martin M Lagercrantz Ulf U Rönnberg-Wästljung Ann Christin AC

G3 (Bethesda, Md.) 20111001 5

We investigated species divergence, present and past gene flow, levels of nucleotide polymorphism, and linkage disequilibrium in two willows from the plant genus Salix. Salix belongs together with Populus to the Salicaceae family; however, most population genetic studies of Salicaceae have been performed in Populus, the model genus in forest biology. Here we present a study on two closely related willow species Salix viminalis and S. schwerinii, in which we have resequenced 33 and 32 nuclear gen ...[more]

PMID: 22384349

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Project description:BackgroundSex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear.ResultsHere, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes.ConclusionsOur data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.

Project description:The short rotation biomass crop willow (Salix genera) has been of interest for bioenergy but recently also for biofuel production. For a faster development of new varieties molecular markers could be used as selection tool in an early stage of the breeding cycle. To identify markers associated with growth traits, genome-wide association mapping was conducted using a population of 291 Salix viminalis accessions collected across Europe and Russia and a large set of genotyping-by-sequencing markers. The accessions were vegetatively propagated and planted in replicated field experiments, one in Southern Sweden and one in Central Sweden. Phenology data, including bud burst and leaf senescence, as well as different growth traits were collected and measured repeatedly between 2010 and 2017 at both field environments. A value of the plasticity for each accession was calculated for all traits that were measured the same year in both environments as the normalized accession value in one environment subtracted by the corresponding value in the other environment. Broad-sense accession heritabilities and narrow-sense chip heritabilities ranged from 0.68 to 0.95 and 0.45 to 0.99, respectively for phenology traits and from 0.56 to 0.85 and 0.24 to 0.97 for growth traits indicating a considerable genetic component for most traits. Population structure and kinship between accessions were taken into account in the association analyses. In total, 39 marker-trait associations were found where four were specifically connected to plasticity and interestingly one particular marker was associated to several different plasticity growth traits. Otherwise association consistency was poor, possibly due to accession by environment interactions which were demonstrated by the low structure adjusted accession correlations across environments (ranging from 0.40 to 0.58). However, one marker association with biomass fresh weight was repeatedly observed in the same environment over two harvest years. For some traits where several associations were found, the markers jointly explained over 20% of the accession variation. The result from this study using a population of unrelated accessions has given useful information about marker-trait associations especially highlighting marker-plasticity associations and genotype-by-environment interactions as important factors to take account of in future strategies of Salix breeding.

Project description:Willow (Salix viminalis L.) is a species well adapted to the environment conditions of central Europe. It is mainly cultivated for energy purposes as solid fuel. In this study, an evaluation of its suitability for other purposes was made using a 4-year old short rotation coppice (SRC) willow regrowth to produce chipped biomass which was composted. Four composting methods were used: without additives (WC), with the addition of nitrogen to narrow the C:N ratio (WN), with the addition of mycelium (WPG) and with the addition of mycelium and nitrogen (WPGN). A mixture of WC and WPGN composts was also prepared at 75:25% and 50:50% by volume. Composts, different proportion (25, 50 and 75%) of peat (SM) were evaluated for suitability as a substrate for tomato and cucumber transplant production. Tomato transplants produced in the medium were prepared from mixtures of willow composts (WPGN + WC(1) and WPGN + WC(2) and these mixtures with peat (WPGN + WC(1):SM and WPGN + WC(2):SM) were characterised as having the best parameters: plant height, lateral leaf span and number of leaves. Similarly, for cucumber transplants, better growth conditions than in peat substrate were obtained in the variant WPGN + WC(1) and WPGN + WC(1):SM. The addition of nitrogen to the composted biomass positively influenced the composting process. N concentration in the substrate was too high and toxic for the growth of tomato and cucumber transplants. At the end of the tomato and cucumber experiment, the nitrate content was 1510 and 2260 mg dm-3, respectively, in the WN substrate. Similarly, the high N-NO3- content in the composted willow substrate with the addition of nitrogen and mycelium did not promote the growth of tomato and cucumber. Based on this research at least 25% of the mass of the peat can be replaced by different willow composts without having an adverse impact on seedling growth and with some of the willow compost mixtures this could be as high as 50%.

Dataset Information

Polymorphism and Divergence in Two Willow Species, Salix viminalis L. and Salix schwerinii E. Wolf.

Publications

Polymorphism and Divergence in Two Willow Species, Salix viminalis L. and Salix schwerinii E. Wolf.

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