Genetic Segregation and Genomic Hybridization Patterns Support an Allotetraploid Structure and Disomic Inheritance for Salix Species

Barcaccia, Gianni; Meneghetti, Stefano; Lucchin, Margherita; Jong, Hans de

doi:10.3390/d6040633

Cited by 15 publications

(22 citation statements)

References 27 publications

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“…Although some studies are published about tetraploid species in subgenus Salix s.l. (Triest et al 2000; Triest 2001; Barcaccia et al 2014) no molecular studies existed so far on the origin of polyploid species of the Chamaetia/Vetrix clade. In this study we included seven polyploids from Europe with different ploidy levels to test the suitability of RAD sequencing data for polyploids and to study different scenarios of their evolutionary origin.…”

Section: Discussionmentioning

confidence: 99%

“…An analytical toolkit for the discrimination of polyploid willows has been established, based on the combination of SSR markers and flow cytometry, but was only used to detect the ploidy level for breeding purposes (Guo et al 2016). In subgenus Salix , the tetraploid S. alba – S. fragilis complex has been analyzed with AFLP markers and revealed an allotetraploid nature of the species (Barcaccia et al 2014), but in the Chamaetia/Vetrix clade the polyploid species have never been analyzed with molecular markers.…”

Section: Introductionmentioning

confidence: 99%

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Relationships and genome evolution of polyploid Salix species revealed by RAD sequencing data

Wagner

Hörandl

2019

Preprint

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14Despite the general progress in using next generation sequencing techniques for 15 evolutionary research questions, the analysis of polyploid species is still hampered by the lack 16 of suitable analytical tools and the statistical difficulties of dealing with more than two alleles 17 per locus. Polyploidization and especially allopolyploidy leads to new combinations of traits 18 by combining genomes of two or more parental species. This enhances the adaptive potential 19 and often results in speciation. However, multiple origins of polyploids, backcrossing to the 20 parental species and post-origin evolution can strongly influence the genome composition of 21 polyploid species. Here, we used RAD sequencing, which revealed 23,393 loci and 320,010 22 high quality SNPs, to analyze the relationships and origin of seven polyploid species of the 23 diverse genus Salix by utilizing a phylogenomic and a network approach, as well as analyzing 24 the genetic structure and composition of the polyploid genome in comparison to putative 25 parental species. We adapted the SNiPloid pipeline that was originally developed to analyse 26 SNP composition of recently established allotetraploid crop lineages to RAD sequencing data 27 by using concatenated RAD loci as reference. Our results revealed a well-resolved phylogeny 28 of 35 species of Eurasian shrub willows (Salix subg. Chamaetia/Vetrix), including 28 diploid 29 and 7 polyploid species. Polyploidization in willows appears to be predominantly connected 30 to hybridization, i.e. to an allopolyploid origin of species. More ancient allopolyploidization 31 events involving hybridization of more distantly related, ancestral lineages were observed for 32 two hexaploid and one octoploid species. Our data suggested a more recent allopolyploid 33 origin for the included tetraploids within the major subclades and identified putative parental 34 taxa that appear to be plausible in the context of geographical, morphological and ecological 35 patterns. SNiPloid and HyDe analyses disentangled the different genomic signatures resulting 36 from hybrid origin, backcrossing, and secondary post-origin evolution in the polyploid 37 species. All tetraploids showed a considerable post-origin, species-specific proportion of 38 Origin of polyploid Salix species 3 SNPs. The amount of extant hybridization appears to be related to the degree of geographical 39 and ecological isolation of species. Our data demonstrate that high-quality RAD sequencing 40 data are suitable and highly informative for the analysis of the origin and relationships of 41 polyploid species. The combination of the traditional tools RAxML, STRUCTURE, 42 SplitsTree and recently developed programs like SNAPP, HyDe and SNiPloid established a 43 bioinformatic pipeline for unraveling the complexity of polyploid genomes.44

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Relationships and genome evolution of polyploid Salix species revealed by RAD sequencing data

Wagner

Hörandl

2019

Preprint

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“…disomic inheritance; Barcaccia et al . ), tetraploid C. stoebe shows tetrasomic inheritance of microsatellite alleles (Rosche et al . ).…”

Section: Methodsmentioning

confidence: 99%

“…Although allopolyploidy may lead to the independent segregations of the two parental genomes (i.e. disomic inheritance; Barcaccia et al 2014), tetraploid C. stoebe shows tetrasomic inheritance of microsatellite alleles (Rosche et al 2016a).…”

Section: T H E S T U D Y S Y S T E M C E N T a U R E A S T O E B E S Lmentioning

confidence: 99%

Invasion success in polyploids: the role of inbreeding in the contrasting colonization abilities of diploid versus tetraploid populations of Centaurea stoebe s.l.

et al. 2016

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Summary As a consequence of founder effects, inbreeding can hamper colonization success: First, in species with self‐incompatibility controlled by an S‐locus, inbreeding may decrease cross‐compatibility, mainly due to the sharing of identical S‐alleles between closely related mating partners. Secondly, inbreeding can reduce fitness of inbred relative to outbred offspring (i.e. inbreeding depression). Polyploids often show reduced inbreeding depression compared to diploids, which may contribute to the overrepresentation of polyploids among invasive species. This is the first study that tests how the effects of inbreeding differ between geocytotypes (i.e. ploidy levels within a given range). Our model organism, Centaurea stoebe, is strictly self‐incompatible and comprises three geocytotypes: diploids are more frequent than tetraploids in the native range, while only tetraploids occur in the invasive range. We conducted a breeding experiment (sib‐mating vs. outcrossing) with 14 native diploid, 13 native tetraploid and 15 invasive tetraploid populations. We recorded cross‐compatibility and estimated a cumulative index for offspring fitness. Since frequent inbreeding can result in purging of genetic load responsible for inbreeding depression, our analyses included a metric for within‐population relatedness, based on eight microsatellite markers, to assess the effect of purging. Inbreeding was found to reduce cross‐compatibility, which was similarly pronounced in diploids and tetraploids. It also caused inbreeding depression in cumulative fitness, which was significant in diploids but not in tetraploids. No evidence of purging was observed as inbred fitness was not affected by within‐population relatedness. Synthesis. Our results provide new insights into the contrasting invasion success of the cytotypes of C. stoebe. As the effects of cross‐compatibility and purging were comparable between cytotypes, both processes can be ruled out to affect the colonization success of diploids versus tetraploids. Our findings are consistent with the hypothesis that polyploidy increases the masking of recessive mutations, which maintains high fitness in inbred tetraploids and may thus facilitate colonization of new ranges. We highlight that reduced inbreeding depression may add to previously acknowledged advantages of polyploids in range expansions, a mechanism that may hitherto have been underestimated due to a lack of data on variation in inbreeding depression across geocytotypes.

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“…It has been suggested that this might be a consequence of the allotetraploid nature of the genomes of S. alba and S. fragilis, with the two species sharing one common or two highly related diploid ancestor species, but differentiated from each other by the genomic contributions of divergent second diploid ancestor species (Barcaccia et al 2014). The allotetraploid iForest 10: 422-429 426 Rungis genomes of both species, may suggest disomic segregation of genetic loci.…”

Section: Discussionmentioning

confidence: 99%

Genetic analysis of Latvian Salix alba L. and hybrid populations using nuclear and chloroplast DNA markers

Ruņģis¹,

Laiviņš²,

Gailīte³

et al. 2017

iForest

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Latvia is at the northern border of the species range of S. alba L. in Europe, and there has been some debate whether the Latvian populations of S. alba are autochthonous, as this species has long been planted in Latvia as an ornamental tree in gardens, parks and roadsides. In addition, there is increasing interest in the use of several Salix species (including S. alba) as bioenergy crops. Natural S. alba stands throughout Latvia, as well as stands of possibly hybrid origin were analysed using nuclear and chloroplast markers. Our results showed that S. alba populations are probably natural, and that the rate of vegetative reproduction is low, supporting the evidence that Latvia is within the natural range of S. alba. These results provide the basis for the identification of possibly introduced or artificially regenerated stands of S.alba in Latvia. In addition, our results confirm that S. alba hybridises with S. fragilis, and that natural stands including hybrid individuals can be established. The analysis of chloroplast markers indicated that the predominant hybridisation occurs by fertilisation of S. fragilis by S. alba pollen; however, the extent of haplotype sharing between these two species should be further investigated.

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Genetic Segregation and Genomic Hybridization Patterns Support an Allotetraploid Structure and Disomic Inheritance for Salix Species

Cited by 15 publications

References 27 publications

Relationships and genome evolution of polyploid Salix species revealed by RAD sequencing data

Relationships and genome evolution of polyploid Salix species revealed by RAD sequencing data

Invasion success in polyploids: the role of inbreeding in the contrasting colonization abilities of diploid versus tetraploid populations of Centaurea stoebe s.l.

Genetic analysis of Latvian Salix alba L. and hybrid populations using nuclear and chloroplast DNA markers

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