Patterns of genetic diversity and differentiation in resistance gene clusters of two hybridizing European Populus species

Caseys, Céline; Stölting, Kai N.; Barbará, Thelma; González‐Martínez, Santiago C.; Lexer, Christian

doi:10.1007/s11295-015-0904-8

Cited by 6 publications

(5 citation statements)

References 60 publications

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“…In the case of plant R-genesand immune system genes more generallynegative frequency dependence leading to balancing selection can maintain alleles in gene pools for a range of different timescales (Bakker et al 2006;Charlesworth 2006;Bomblies & Weigel 2007), likely including trans-species polymorphisms. We note that most of the NBS-LRRs under long-term positive selection in our study exhibited significantly increased nucleotide diversity compared with genomewide expectations (Table S8, Supporting Information) and that balancing selection has previously been detected for markers tagging NBS-LRR genes in these species (Caseys et al 2015b Speciation with recurrent gene flow: an intrinsic consequence of adaptive divergence?…”

Section: Genomic Footprints Of Selectionsupporting

confidence: 54%

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Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow

et al. 2016

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Speciation often involves repeated episodes of genetic contact between divergent populations before reproductive isolation (RI) is complete. Whole-genome sequencing (WGS) holds great promise for unravelling the genomic bases of speciation. We have studied two ecologically divergent, hybridizing species of the 'model tree' genus Populus (poplars, aspens, cottonwoods), Populus alba and P. tremula, using >8.6 million single nucleotide polymorphisms (SNPs) from WGS of population pools. We used the genomic data to (i) scan these species' genomes for regions of elevated and reduced divergence, (ii) assess key aspects of their joint demographic history based on genomewide site frequency spectra (SFS) and (iii) infer the potential roles of adaptive and deleterious coding mutations in shaping the genomic landscape of divergence. We identified numerous small, unevenly distributed genome regions without fixed polymorphisms despite high overall genomic differentiation. The joint SFS was best explained by ancient and repeated gene flow and allowed pinpointing candidate interspecific migrant tracts. The direction of selection (DoS) differed between genes in putative migrant tracts and the remainder of the genome, thus indicating the potential roles of adaptive divergence and segregating deleterious mutations on the evolution and breakdown of RI. Genes affected by positive selection during divergence were enriched for several functionally interesting groups, including well-known candidate 'speciation genes' involved in plant innate immunity. Our results suggest that adaptive divergence affects RI in these hybridizing species mainly through intrinsic and demographic processes. Integrating genomic with molecular data holds great promise for revealing the effects of particular genetic pathways on speciation.

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Section: Genomic Footprints Of Selectionsupporting

confidence: 54%

“…We note that most of the NBS‐LRRs under long‐term positive selection in our study exhibited significantly increased nucleotide diversity compared with genomewide expectations (Table S8, Supporting Information) and that balancing selection has previously been detected for markers tagging NBS‐LRR genes in these species (Caseys et al . ).…”

Section: Discussionmentioning

confidence: 97%

Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow

et al. 2016

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“…In the wpa-19 region, a cluster of 14 genes coding for TIR-NB-LRR disease resistance proteins genes was identified. Several works revealed the presence on chromosome 19 of disease resistance genes and resistant phenotypes because many of the poplar NB-LRR genes (more than 70,) are gathered into a supercluster localized on that chromosome [ 54 ]. The largest NB–LRR gene supercluster on Populus chromosome 19 co-localized with the resistance loci MER, R1, and RUS,.…”

Section: Discussionmentioning

confidence: 99%

QTLs for Woolly Poplar Aphid (Phloeomyzus passerinii L.) Resistance Detected in an Inter-Specific Populus deltoides x P. nigra Mapping Population

Carletti¹,

Carrà²,

Allegro³

et al. 2016

PLoS ONE

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The genus Populus represents one of the most economically important groups of forest trees. It is composed by approximately 30 species used for wood and non-wood products, phytoremediation and biomass. Poplar is subjected to several biological and environmental threats although, compared to annual crops, we know far less about the genetic bases of biotic stress resistance. Woolly poplar aphid (Phloeomyzus passerinii) is considered a main pest of cultivated poplars in European and American countries. In this work we present two high density linkage maps in poplar obtained by a genotyping by sequencing (GBS) approach and the identification of QTLs involved in Ph. passerinii resistance. A total of 5,667 polymorphic markers (5,606 SNPs and 61 SSRs) identified on expressed sequences have been used to genotype 131 plants of an F1 population P ×canadensis obtained by an interspecific mate between Populus deltoides (resistant to woolly poplar aphid) and Populus nigra (susceptible to woolly poplar aphid). The two linkage maps, obtained following the two-way pseudo-testcross mapping strategy, have been used to investigate the genetic bases of woolly poplar aphid resistance. One major QTL and two QTLs with minor effects (mapped on LGV, LGXVI and LG XIX) explaining the 65.8% of the genetic variance observed in the progeny in response to Ph. passerinii attack were found. The high density coverage of functional markers allowed the identification of three genes belonging to disease resistance pathway as putative candidates for P. deltoides resistance to woolly poplar aphid. This work is the first report on genetic of woolly poplar aphid genetic resistance and the resistant loci associated markers identified represent a valuable tool in resistance poplar breeding programs.

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“…We used analyses of genomic clines implemented in bgc (Gompert & Buerkle, 2012) to study patterns of introgression in hybrids and identify genomic regions that resist introgression due to selection. This genomic cline approach has been used in several recent studies to explore patterns of introgression in hybrids (e.g., Caseys, Stölting, Barbará, González-Martínez, & Lexer, 2015;Gompert et al, 2012a;Janousek et al, 2012;Nosil et al, 2012;Parchman et al, 2013;Trier, Hermansen, Saetre, & Bailey, 2014), and simulations have demonstrated that it is robust to the detection of loci with clines that deviate from the genomewide expectation (Gompert & Buerkle, 2011). Finally, to explore potential selective pressures driving patterns of divergence and introgression, we test the hypothesis that a priori sets of candidate genes are enriched for outlier loci ( Figure 1b).…”

Section: Introductionmentioning

confidence: 99%

Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes

Schield

Adams

Card

et al. 2017

Ecology and Evolution

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Investigating secondary contact of historically isolated lineages can provide insight into how selection and drift influence genomic divergence and admixture. Here, we studied the genomic landscape of divergence and introgression following secondary contact between lineages of the Western Diamondback Rattlesnake (Crotalus atrox) to determine whether genomic regions under selection in allopatry also contribute to reproductive isolation during introgression. We used thousands of nuclear loci to study genomic differentiation between two lineages that have experienced recent secondary contact following isolation, and incorporated sampling from a zone of secondary contact to identify loci that are resistant to gene flow in hybrids. Comparisons of patterns of divergence and introgression revealed a positive relationship between allelic differentiation and resistance to introgression across the genome, and greater‐than‐expected overlap between genes linked to lineage‐specific divergence and loci that resist introgression. Genes linked to putatively selected markers were related to prominent aspects of rattlesnake biology that differ between populations of Western Diamondback rattlesnakes (i.e., venom and reproductive phenotypes). We also found evidence for selection against introgression of genes that may contribute to cytonuclear incompatibility, consistent with previously observed biased patterns of nuclear and mitochondrial alleles suggestive of partial reproductive isolation due to cytonuclear incompatibilities. Our results provide a genome‐scale perspective on the relationships between divergence and introgression in secondary contact that is relevant for understanding the roles of selection in maintaining partial isolation of lineages, causing admixing lineages to not completely homogenize.

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Patterns of genetic diversity and differentiation in resistance gene clusters of two hybridizing European Populus species

Cited by 6 publications

References 60 publications

Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow

Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow

QTLs for Woolly Poplar Aphid (Phloeomyzus passerinii L.) Resistance Detected in an Inter-Specific Populus deltoides x P. nigra Mapping Population

Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes

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