Clinal Variation in Flowering Time and Vernalisation Requirement across a 3000-M Altitudinal Range in Perennial Arabidopsis kamchatica Ssp.Kamchatica and Annual Lowland Subspecies Kawasakiana

Kenta, Tanaka; Yamada, Ayumu; Onda, Yoshihiko

doi:10.4172/2157-7625.s6-001

Cited by 15 publications

(18 citation statements)

References 43 publications

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“…; Kenta et al . ). The suggestion of higher rates of colonization of novel environments after genome duplications is still a controversial topic (Brochmann et al .…”

Section: Discussionmentioning

confidence: 97%

Northern glacial refugia and altitudinal niche divergence shape genome‐wide differentiation in the emerging plant model Arabidopsis arenosa

et al. 2016

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Quaternary climatic oscillations profoundly impacted temperate biodiversity. For many diverse yet undersampled areas, however, the consequences of this impact are still poorly known. In Europe, particular uncertainty surrounds the role of Balkans, a major hotspot of European diversity, in postglacial recolonization of more northerly areas, and the Carpathians, a debatable candidate for a northern 'cryptic' glacial refugium. Using genome-wide SNPs and microsatellites, we examined how the interplay of historical processes and niche shifts structured genetic diversity of diploid Arabidopsis arenosa, a little-known member of the plant model genus that occupies a wide niche range from sea level to alpine peaks across eastern temperate Europe. While the northern Balkans hosted one isolated endemic lineage, most of the genetic diversity was concentrated further north in the Pannonian Basin and the Carpathians, where it likely survived the last glaciation in northern refugia. Finally, a distinct postglacial environment in northern Europe was colonized by populations of admixed origin from the two Carpathian lineages. Niche differentiation along altitude-related bioclimatic gradients was the main trend in the phylogeny of A. arenosa. The most prominent niche shifts, however, characterized genetically only slightly divergent populations that expanded into narrowly defined alpine and northern coastal postglacial environments. Our study highlights the role of eastern central European mountains not only as refugia for unique temperate diversity but also sources for postglacial expansion into novel high-altitude and high-latitude niches. Knowledge of distinct genetic substructure of diploid A. arenosa also opens new opportunities for follow-up studies of this emerging model of evolutionary biology.

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“…; Kenta et al . ). The suggestion of higher rates of colonization of novel environments after genome duplications is still a controversial topic (Brochmann et al .…”

Section: Discussionmentioning

confidence: 97%

Northern glacial refugia and altitudinal niche divergence shape genome‐wide differentiation in the emerging plant model Arabidopsis arenosa

et al. 2016

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“…; Kenta et al . ) and inherited its gene expression patterns of cold responses from one of the parents, Arabidopsis lyrata . The expression levels of many genes were intermediate between the two parents, A. lyrata and Arabidopsis halleri (Akama et al .…”

Section: Discussionmentioning

confidence: 99%

Plant adaptive radiation mediated by polyploid plasticity in transcriptomes

et al. 2016

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The habitats of polyploid species are generally distinct from their parental species. Stebbins described polyploids as 'general purpose genotypes', which can tolerate a wide range of environmental conditions. However, little is known about its molecular basis because of the complexity of polyploid genomes. We hypothesized that allopolyploid species might utilize the expression patterns of both parents depending on environments (polyploid plasticity hypothesis). We focused on hydrological niche segregation along fine-scale soil moisture and waterlogging gradients. Two diploid species, Cardamine amara and Cardamine hirsuta, grew best in submerged and unsubmerged conditions, respectively, consistent with their natural habitats. Interestingly, the allotetraploid Cardamine flexuosa derived from them grew similarly in fluctuating as well as submerged and unsubmerged conditions, consistent with its wide environmental tolerance. A similar pattern was found in another species trio: allotetraploid Cardamine scutata and its parents. Using the close relatedness of Cardamine and Arabidopsis, we quantified genomewide expression patterns following dry and wet treatments using an Arabidopsis microarray. Hierarchical clustering analysis revealed that the expression pattern of C. flexuosa clustered with C. hirsuta in the dry condition and with C. amara in the wet condition, supporting our hypothesis. Furthermore, the induction levels of most genes in the allopolyploid were lower than in a specialist diploid species. This reflects a disadvantage of being allopolyploid arising from fixed heterozygosity. We propose that recurrent allopolyploid speciation along soil moisture and waterlogging gradients confers niche differentiation and reproductive isolation simultaneously and serves as a model for studying the molecular basis of ecological speciation and adaptive radiation.

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“…We applied a candidate gene approach to Pool-Seq by preparing Next Genera- Eight genes associated with flowering pathways or herbivore defense traits (DFL2, GI, GL1, HEN2, MAM1, TTG1, CRY1 and PHYB) were selected to be screened for nucleotide polymorphisms because these genes are considered to be single-copy genes, and putative divergent selective pressure associated with these traits in the target populations [16] could have resulted in nucleotide polymorphisms in the target genes. We used Primer3 [24] and conserved genome sequences between the A. halleri subsp.…”

Section: Methodsmentioning

confidence: 99%

“…The second site was in the PHYB-H-homeolog and had 15-bp insertiondeletion polymorphism (indel). We genotyped the GL1-H-homeolog SNP for 20 individuals from each of four populations (Populations 12, 13 and 29 in Kenta et al [16] and Syomyodaki described above) using SNP-SCALE [25] [38]. We genotyped the PHYB-H-homeolog indel for 20 individuals from each of five populations (Populations 12, 13, 16 and 20 in Kenta et al [16] and Syomyodaki) using fragment analyses.…”

Section: Validation Of Pool-seqmentioning

confidence: 99%

“…Arabidopsis kamchatica-a wild relative of the model plant A. thaliana-is an allotetraploid (2n = 4x = 32) species with a broad habitat range, wide altitudinal distribution [16], lowland seaside and lakeside sites [17]. This perennial species has a self-compatibility mating system [18] and originated from a hybridization event between two diploid species: A. lyrata and A. halleri [19] [20].…”

Section: Introductionmentioning

confidence: 99%

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Cost-Effective Discovery of Nucleotide Polymorphisms in Populations of an Allopolyploid Species Using Pool-Seq

Hirao¹,

Onda²,

Shimizu‐Inatsugi³

et al. 2017

AJMB

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Population genetics studies of allopolyploid species lag behind those of diploid species because of practical difficulties in analysis of homeologs-duplicated gene copies originating from hybridized parental species. Pool-Seq, i.e. massive parallel sequencing of pooled individuals, has high potential for detecting nucleotide polymorphisms within and among multiple populations; however, its use has been limited to diploid species. We applied Pool-Seq to an allopolyploid species by developing a bioinformatic pipeline that assigns reads to each homeolog as well as to each polymorphic allele within each homeolog. We simultaneously sequenced eight genes from twenty individuals from each of 24 populations, and found over 100 polymorphic sites in each homeolog. For two sites, we estimated allele frequencies using the number of reads and then validated these estimations by making individual-based estimations. Pool-Seq using our bioinformatic pipeline allows efficient evaluation of nucleotide polymorphisms in a large number of individuals, even in allopolyploid species.

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Clinal Variation in Flowering Time and Vernalisation Requirement across a 3000-M Altitudinal Range in Perennial Arabidopsis kamchatica Ssp.Kamchatica and Annual Lowland Subspecies Kawasakiana

Cited by 15 publications

References 43 publications

Northern glacial refugia and altitudinal niche divergence shape genome‐wide differentiation in the emerging plant model Arabidopsis arenosa

Northern glacial refugia and altitudinal niche divergence shape genome‐wide differentiation in the emerging plant model Arabidopsis arenosa

Plant adaptive radiation mediated by polyploid plasticity in transcriptomes

Cost-Effective Discovery of Nucleotide Polymorphisms in Populations of an Allopolyploid Species Using Pool-Seq

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