Segmental allotetraploidy generates extensive homoeologous expression rewiring and phenotypic diversity at the population level in rice.

Abstract:

:Allopolyploidization, that is, concomitant merging and doubling of two or more divergent genomes in a common nucleus/cytoplasm, is known to instantly alter genomewide transcriptome dynamics, a phenomenon referred to as "transcriptomic shock." However, the immediate effects of transcriptomic alteration in generating phenotypic diversity at the population level remain underinvestigated. Here, we employed the MassARRAY-based Sequenom platform to assess and compare orthologous, allelic and homoeologous gene expression status in two tissues (leaf and root) of a set of randomly chosen individuals from populations of parental rice subspecies (indica and japonica), in vitro "hybrids" (parental mixes), reciprocal F1 hybrids and reciprocal tetraploids at the 5th-selfed generation (S5). We show that hybridization and whole genome duplication (WGD) have opposing effects on allelic and homoeologous expression in the F1 hybrids and tetraploids, respectively. Whereas hybridization exerts strong attenuating effects on allelic expression differences in diploid hybrids, WGD augments the intrinsic parental differences and generates extensive and variable homoeolog content which triggers diversification in expression patterning among the tetraploid plants. Coupled with the vast phenotypic diversity observed among the tetraploid individuals, our results provide experimental evidence in support of the notion that allopolyploidy catalyses rapid phenotypic diversification in higher plants. Our data further suggest that largely stochastic homoeolog content reshuffling rather than alteration in total expression level may be an important feature of evolution in young segmental allopolyploids, which underlies rapid expression diversity at the population level.

journal_name

Mol Ecol

journal_title

Molecular ecology

authors

Sun Y,Wu Y,Yang C,Sun S,Lin X,Liu L,Xu C,Wendel JF,Gong L,Liu B

doi

10.1111/mec.14297

subject

Has Abstract

pub_date

2017-10-01 00:00:00

pages

5451-5466

issue

20

eissn

0962-1083

issn

1365-294X

journal_volume

26

pub_type

杂志文章
  • Multiple population structure of the giant mottled eel, Anguilla marmorata.

    abstract::The population structure of the giant mottled eel, Anguilla marmorata, was investigated with mitochondrial and microsatellite DNA analyses using 449 specimens from 13 localities throughout the species range. Control region F-statistics indicated the North Pacific (Japan, Taiwan, Philippines, Sulawesi), South Pacific (...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2008.03822.x

    authors: Minegishi Y,Aoyama J,Tsukamoto K

    更新日期:2008-07-01 00:00:00

  • Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex.

    abstract::Modern analytical methods for population genetics and phylogenetics are expected to provide more accurate results when data from multiple genome-wide loci are analysed. We present the results of an initial application of parallel tagged sequencing (PTS) on a next-generation platform to sequence thousands of barcoded P...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.12049

    authors: O'Neill EM,Schwartz R,Bullock CT,Williams JS,Shaffer HB,Aguilar-Miguel X,Parra-Olea G,Weisrock DW

    更新日期:2013-01-01 00:00:00

  • Soft selective sweep near a gene that increases plant height in wheat.

    abstract::Strong selection within a given population locally reduces genetic variability not only in the selected gene itself but also in neighbouring loci. This so-called hitch-hiking effect is related to the initial linkage disequilibrium between markers and the selected gene, and depends mainly on the number of copies of the...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2007.03620.x

    authors: Raquin AL,Brabant P,Rhoné B,Balfourier F,Leroy P,Goldringer I

    更新日期:2008-02-01 00:00:00

  • Biogeography, habitat transitions and hybridization in a radiation of South American silverside fishes revealed by mitochondrial and genomic RAD data.

    abstract::Rivers and lake systems in the southern cone of South America have been widely influenced by historical glaciations, carrying important implications for the evolution of aquatic organisms, including prompting transitions between marine and freshwater habitats and by triggering hybridization among incipient species via...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.15350

    authors: Hughes LC,Cardoso YP,Sommer JA,Cifuentes R,Cuello M,Somoza GM,González-Castro M,Malabarba LR,Cussac V,Habit EM,Betancur-R R,Ortí G

    更新日期:2020-02-01 00:00:00

  • Multiple ice-age refugia in Pacific cod, Gadus macrocephalus.

    abstract::Pleistocene ice-ages greatly influenced the historical abundances of Pacific cod, Gadus macrocephalus, in the North Pacific and its marginal seas. We surveyed genetic variation at 11 microsatellite loci and mitochondrial (mt) DNA in samples from twelve locations from the Sea of Japan to Washington State. Both microsat...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2010.04815.x

    authors: Canino MF,Spies IB,Cunningham KM,Hauser L,Grant WS

    更新日期:2010-10-01 00:00:00

  • Population genetic structure of Chilo suppressalis (Walker) (Lepidoptera: Crambidae): strong subdivision in China inferred from microsatellite markers and mtDNA gene sequences.

    abstract::Chilo suppressalis (Walker) displays significant geographical differences in ecological preference that may be congruent with patterns of molecular variation. To test this, we collected and analysed 381 individuals of this species from cultivated rice at 18 localities in China during the rice-growing season of 2005-20...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2008.03792.x

    authors: Meng XF,Shi M,Chen XX

    更新日期:2008-06-01 00:00:00

  • Gene expression under thermal stress varies across a geographical range expansion front.

    abstract::Many ectothermic species are currently expanding their distributions polewards due to anthropogenic global warming. Molecular genetic mechanisms facilitating range expansion under these conditions are largely unknown, but understanding these could help mitigate expanding pests and disease vectors, or help explain why ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.13548

    authors: Lancaster LT,Dudaniec RY,Chauhan P,Wellenreuther M,Svensson EI,Hansson B

    更新日期:2016-03-01 00:00:00

  • Comparative phylogeography among hydrothermal vent species along the East Pacific Rise reveals vicariant processes and population expansion in the South.

    abstract::The use of sequence polymorphism from individual mitochondrial genes to infer past demography has recently proved controversial because of the recurrence of selective sweeps acting over genes and the need for unlinked multilocus data sets. However, comparative analyses using several species for one gene and/or multipl...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2009.04325.x

    authors: Plouviez S,Shank TM,Faure B,Daguin-Thiebaut C,Viard F,Lallier FH,Jollivet D

    更新日期:2009-09-01 00:00:00

  • Identification of random amplified polymorphic DNA (RAPD) markers highly linked to sex determination in the red alga Gracilaria gracilis.

    abstract::The random amplified polymorphic DNA (RAPD) technique was employed in the haplo-diploid dioecious species Gracilaria gracilis to identify sex-linked PCR markers. Sixty-nine decamer oligonucleotide primers were tested on two bulks of DNA, one from five haploid males and the other from five haploid females. One of these...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.1999.00721.x

    authors: Martinez EA,Destombe C,Quillet MC,Valero M

    更新日期:1999-09-01 00:00:00

  • Mating system of the Eurasian badger, Meles meles, in a high density population.

    abstract::Badgers are facultatively social, forming large groups at high density. Group-living appears to have high reproductive costs for females, and may lead to increased levels of inbreeding. The extent of female competition for reproduction has been estimated from field data, but knowledge of male reproductive success and ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2004.02401.x

    authors: Carpenter PJ,Pope LC,Greig C,Dawson DA,Rogers LM,Erven K,Wilson GJ,Delahay RJ,Cheeseman CL,Burke T

    更新日期:2005-01-01 00:00:00

  • Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus).

    abstract::All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Despite some empirical counter examples, theory suggests that nonrecombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole-genome scans...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.13126

    authors: Geraldes A,Hefer CA,Capron A,Kolosova N,Martinez-Nuñez F,Soolanayakanahally RY,Stanton B,Guy RD,Mansfield SD,Douglas CJ,Cronk QC

    更新日期:2015-07-01 00:00:00

  • Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange and distinct demographic histories.

    abstract::Widely distributed taxa provide an opportunity to compare biogeographic responses to climatic fluctuations on multiple continents and to investigate speciation. We conducted the most geographically and genomically comprehensive study to date of the red fox (Vulpes vulpes), the world's most widely distributed wild terr...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.12898

    authors: Statham MJ,Murdoch J,Janecka J,Aubry KB,Edwards CJ,Soulsbury CD,Berry O,Wang Z,Harrison D,Pearch M,Tomsett L,Chupasko J,Sacks BN

    更新日期:2014-10-01 00:00:00

  • Spatial genetic structure in a metapopulation of the land snail Cepaea nemoralis (Gastropoda: Helicidae).

    abstract::Habitat fragmentation is a major force affecting demography and genetic structure of wild populations, especially in agricultural landscapes. The land snail Cepaea nemoralis (L.) was selected to investigate the impact of habitat fragmentation on the spatial genetic structure of an organism with limited dispersal abili...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2004.02357.x

    authors: Schweiger O,Frenzel M,Durka W

    更新日期:2004-12-01 00:00:00

  • Parasite genetic distance and local adaptation in co-evolving bacteria-bacteriophage populations.

    abstract::Antagonistic co-evolution between hosts and parasites can lead to local adaptation (LA) such that parasite fitness is greatest in sympatric hosts (or vice versa). The magnitude of LA typically increases with geographical distance, which is assumed to be because genetic (and hence phenotypic) distance increases with ge...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.13897

    authors: Scanlan PD,Hall AR,Buckling A

    更新日期:2017-04-01 00:00:00

  • Amassing diversity in an ancient lake: evolution of a morphologically diverse parthenogenetic gastropod assemblage in Lake Malawi.

    abstract::Exceptional ecological niche diversity, clear waters and unique divergent selection pressures have often been invoked to explain high morphological and genetic diversity of taxa within ancient lakes. However, it is possible that in some ancient lake taxa high diversity has arisen because these historically stable envi...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2006.03171.x

    authors: Genner MJ,Todd JA,Michel E,Erpenbeck D,Jimoh A,Joyce DA,Piechocki A,Pointier JP

    更新日期:2007-02-01 00:00:00

  • Historical isolation facilitates species radiation by sexual selection: Insights from Chorthippus grasshoppers.

    abstract::Theoretical and empirical studies have shown that species radiations are facilitated when a trait under divergent natural selection is also involved in sexual selection. It is yet unclear how quick and effective radiations are where assortative mating is unrelated to the ecological environment and primarily results fr...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.15695

    authors: Nolen ZJ,Yildirim B,Irisarri I,Liu S,Groot Crego C,Amby DB,Mayer F,Gilbert MTP,Pereira RJ

    更新日期:2020-12-01 00:00:00

  • Fine-grained adaptive divergence in an amphibian: genetic basis of phenotypic divergence and the role of nonrandom gene flow in restricting effective migration among wetlands.

    abstract::Adaptive ecological differentiation among sympatric populations is promoted by environmental heterogeneity, strong local selection and restricted gene flow. High gene flow, on the other hand, is expected to homogenize genetic variation among populations and therefore prevent local adaptation. Understanding how local a...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.12181

    authors: Richter-Boix A,Quintela M,Kierczak M,Franch M,Laurila A

    更新日期:2013-03-01 00:00:00

  • New insights into the population genetics of partially clonal organisms: When seagrass data meet theoretical expectations.

    abstract::Seagrass meadows are among the most important coastal ecosystems in terms of both spatial extent and ecosystem services, but they are also declining worldwide. Understanding the drivers of seagrass meadow dynamics is essential for designing sound management, conservation and restoration strategies. However, poor knowl...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.15532

    authors: Arnaud-Haond S,Stoeckel S,Bailleul D

    更新日期:2020-09-01 00:00:00

  • Genetic diversity and differentiation in a wide ranging anadromous fish, American shad (Alosa sapidissima), is correlated with latitude.

    abstract::Studies that span entire species ranges can provide insight into the relative roles of historical contingency and contemporary factors that influence population structure and can reveal patterns of genetic variation that might otherwise go undetected. American shad is a wide ranging anadromous clupeid fish that exhibi...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.12197

    authors: Hasselman DJ,Ricard D,Bentzen P

    更新日期:2013-03-01 00:00:00

  • Low genetic differentiation among seasonal cohorts in Senecio vulgaris as revealed by amplified fragment length polymorphism analysis.

    abstract::Common groundsel, Senecio vulgaris (Asteraceae), is a highly selfing semelparous ephemeral weed that belongs to the few plant species in central Europe capable of growing, flowering and fruiting all year round. In temperate climates, flowering S. vulgaris cohorts were found to appear up to three times per year. Using ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.2003.01915.x

    authors: Haldimann P,Steinger T,Müller-Schärer H

    更新日期:2003-10-01 00:00:00

  • Complex patterns of colonization and refugia revealed for European grayling Thymallus thymallus, based on complete sequencing of the mitochondrial DNA control region.

    abstract::The complete mitochondrial DNA (mtDNA) control region (1043 base pairs) and 162-bp of flanking transfer RNA genes were sequenced in 316 European grayling, Thymallus thymallus, from 44 populations throughout the Western European range of the species. A total of 58 haplotypes were revealed with pairwise divergence rangi...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.2002.01544.x

    authors: Weiss S,Persat H,Eppe R,Schlötterer C,Uiblein F

    更新日期:2002-08-01 00:00:00

  • Why UV vision and red vision are important for damselfish (Pomacentridae): structural and expression variation in opsin genes.

    abstract::Coral reefs belong to the most diverse ecosystems on our planet. The diversity in coloration and lifestyles of coral reef fishes makes them a particularly promising system to study the role of visual communication and adaptation. Here, we investigated the evolution of visual pigment genes (opsins) in damselfish (Pomac...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.13968

    authors: Stieb SM,Cortesi F,Sueess L,Carleton KL,Salzburger W,Marshall NJ

    更新日期:2017-03-01 00:00:00

  • Population genetic structure of the cyclic snowshoe hare (Lepus americanus) in southwestern Yukon, Canada.

    abstract::Spatial population structure has important ecological and evolutionary consequences. Little is known about the population structure of snowshoe hares (Lepus americanus), despite their ecological importance in North American boreal forests. We used seven variable microsatellite DNA loci to determine the spatial genetic...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1046/j.1365-294x.2002.01566.x

    authors: Burton C,Krebs CJ,Taylor EB

    更新日期:2002-09-01 00:00:00

  • Gynodioecy in structured populations: understanding fine-scale sex ratio variation in Beta vulgaris ssp. maritima.

    abstract::Natural selection, random processes and gene flow are known to generate sex ratio variations among sexually polymorphic plant populations. In gynodioecious species, in which hermaphrodites and females coexist, the relative effect of these processes on the maintenance of sex polymorphism is still up for debate. The aim...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2011.05414.x

    authors: De Cauwer I,Dufay M,Hornoy B,Courseaux A,Arnaud JF

    更新日期:2012-02-01 00:00:00

  • Uptake of Bt endotoxins by nontarget herbivores and higher order arthropod predators: molecular evidence from a transgenic corn agroecosystem.

    abstract::The planting of transgenic crops expressing Bacillus thuringiensis endotoxins is widespread throughout the world; the prolific increase in their application exposes nontarget organisms to toxins designed to control pests. To date, studies have focused upon the effects of Bt endotoxins on specific herbivores and detrit...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2005.02611.x

    authors: Harwood JD,Wallin WG,Obrycki JJ

    更新日期:2005-08-01 00:00:00

  • Colony kin structure and host-parasite relatedness in the barnacle goose.

    abstract::Conspecific brood parasitism (CBP), females laying eggs in the nest of other 'host' females of the same species, is a common alternative reproductive tactic among birds. For hosts there are likely costs of incubating and rearing foreign offspring, but costs may be low in species with precocial chicks such as waterfowl...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2009.04397.x

    authors: Anderholm S,Waldeck P,VAN DER Jeugd HP,Marshall RC,Larsson K,Andersson M

    更新日期:2009-12-01 00:00:00

  • Spatial patterning of soil microbial communities created by fungus-farming termites.

    abstract::Spatially overdispersed mounds of fungus-farming termites (Macrotermitinae) are hotspots of nutrient availability and primary productivity in tropical savannas, creating spatial heterogeneity in communities and ecosystem functions. These termites influence the local availability of nutrients in part by redistributing ...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.15585

    authors: Baker CCM,Castillo Vardaro JA,Doak DF,Pansu J,Puissant J,Pringle RM,Tarnita CE

    更新日期:2020-11-01 00:00:00

  • Heterozygosity, inbreeding and neonatal traits in Soay sheep on St Kilda.

    abstract::We investigated whether birth weight and neonatal survival, a period within which 24% of all mortalities occur, were correlated with levels of inbreeding in St Kilda Soay sheep, using pedigree inbreeding coefficients and four marker-based estimators of inbreeding. None of the inbreeding estimators, either of the offsp...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2005.02682.x

    authors: Overall AD,Byrne KA,Pilkington JG,Pemberton JM

    更新日期:2005-10-01 00:00:00

  • Geographic and genetic boundaries of brown bear (Ursus arctos) population in the Caucasus.

    abstract::The taxonomic status of brown bears in the Caucasus remains unclear. Several morphs or subspecies have been identified from the morphological (craniological) data, but the status of each of these subspecies has never been verified by molecular genetic methods. We analysed mitochondrial DNA sequences (control region) t...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/j.1365-294X.2010.04610.x

    authors: Murtskhvaladze M,Gavashelishvili A,Tarkhnishvili D

    更新日期:2010-05-01 00:00:00

  • Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline.

    abstract::This study presents genetic evidence that whale sharks, Rhincodon typus, are comprised of at least two populations that rarely mix and is the first to document a population expansion. Relatively high genetic structure is found when comparing sharks from the Gulf of Mexico with sharks from the Indo-Pacific. If mixing o...

    journal_title:Molecular ecology

    pub_type: 杂志文章

    doi:10.1111/mec.12754

    authors: Vignaud TM,Maynard JA,Leblois R,Meekan MG,Vázquez-Juárez R,Ramírez-Macías D,Pierce SJ,Rowat D,Berumen ML,Beeravolu C,Baksay S,Planes S

    更新日期:2014-05-01 00:00:00