Plant genetics articles within Nature Communications

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  • Article
    | Open Access

    Chinese chestnut is widely cultivated for nut production and harbors value as a genetic resource for restoration of American and European chestnut trees destroyed by chestnut blight. Here, the authors reveal the genomic basis of homoploid hybrid speciation within Castanea spp. and find the nonrandom distribution of reproductive barrier loci based on a high-quality reference genome.

    • Yongshuai Sun
    • , Zhiqiang Lu
    •  & Hui Ma

  • Article
    | Open Access

    Grapevine is one of a few ancestrally dioecious crops that are reverted to hermaphroditism during domestication. Here, the authors identify candidate genes related to male- and female-sterility in grapes and describe the genetic process that led to hermaphroditism during domestication.

    • Mélanie Massonnet
    • , Noé Cochetel
    •  & Dario Cantu

  • Article
    | Open Access

    B chromosomes are supernumerary chromosomes exhibiting dramatic differences between different organs in same species. Here, the authors show programmed B chromosome elimination in goatgrass starts at the onset of embryo differentiation by nondisjunction of chromatids, anaphase lagging, and ends with the degradation of micronucleated DNA.

    • Alevtina Ruban
    • , Thomas Schmutzer
    •  & Andreas Houben

  • Article
    | Open Access

    Comprehensive epigenomic maps of various rice varieties are still unavailable. Here, the authors report the development of eChIP as a fast and low-input upgrade of regular plant ChIP-seq protocol for epigenome analysis of 20 rice varieties and annotate over 80% of the genome with different epigenome properties for transcriptional regulation.

    • Lun Zhao
    • , Liang Xie
    •  & Xingwang Li

  • Article
    | Open Access

    TRANSPARENT TESTA19 (TT19) encodes a glutathione S-transferase which functions in anthocyanin stabilization and vacuolar transport. Here, by tt19 suppressor screening, the authors show that RDR6/SGS3/DCL4 siRNA pathway constituents synergistically interact with components of the flavonoid pathway to control carbon metabolism.

    • Nan Jiang
    • , Aimer Gutierrez-Diaz
    •  & Erich Grotewold

  • Article
    | Open Access

    Segregation of an MSH1 RNAi transgene produces non-genetic memory that displays transgenerational inheritance in Arabidopsis. Here, the authors compare memory and non-memory full-sib progenies to show the involvement of DNA methylation reprogramming, involving the RdDM pathway, in transition to a heritable memory state.

    • Xiaodong Yang
    • , Robersy Sanchez
    •  & Sally A. Mackenzie

  • Article
    | Open Access

    Plant evolution is intimately associated with fungal partners. Here the authors provide evidence that Physcomitrella patens MACRO2, a gene likely derived from early mycorrhizae-like fungi, was transferred to early land plants and plays an important role in regulating stem cell growth and gametophore development in moss.

    • Shuanghua Wang
    • , Yanlong Guan
    •  & Jinling Huang

  • Article
    | Open Access

    Litsea cubeba belongs to the Lauraceae family within the Magnoliids clade. Here, the authors assemble its genome and reveal divergence of inflorescence and sexual differentiation, the phylogenetic relationships across the Lauraceae and related species, and biosynthetic genes related to essential oil synthesis.

    • Yi-Cun Chen
    • , Zhen Li
    •  & Yang-Dong Wang

  • Article
    | Open Access

    Karrikins are germination stimulants perceived by KAI2 in Arabidopsis. Here the authors show that Brassica tournefortii, a close relative to Arabidopsis, has multiple copies of KAI2 with amino acid substitutions that confer responsiveness to the specific karrikin compounds found in wildfire smoke.

    • Yueming Kelly Sun
    • , Jiaren Yao
    •  & Mark T. Waters

  • Article
    | Open Access

    Stem rust is an important disease of wheat and resistance present in some cultivars can be suppressed by the SuSr-D1 locus. Here the authors show that SuSr-D1 encodes a subunit of the Mediator Complex and that nonsense mutations are sufficient to abolish suppression and confer stem rust resistance.

    • Colin W. Hiebert
    • , Matthew J. Moscou
    •  & Wolfgang Spielmeyer

  • Article
    | Open Access

    White lupin is a legume crop that develops cluster roots for efficient phosphate acquisition. Here, the authors assemble its triplicated genome, reveal gene expression difference among sub-genomes, and characterize possible pathways related to high phosphorus-use efficiency.

    • Weifeng Xu
    • , Qian Zhang
    •  & Feng Cheng

  • Article
    | Open Access

    White lupin is an annual crop cultivated for protein rich seeds and can produce cluster roots for efficient phosphate acquisition. Here, the authors generate high quality genome assemblies of a cultivated accession, a landrace, and a wild relative and provides insight into soil exploration and seed quality.

    • Bárbara Hufnagel
    • , André Marques
    •  & Benjamin Péret

  • Article
    | Open Access

    Local adaptation contributes to plant colonization across extreme environmental gradients. Here, the authors reconstruct the colonization history of Lotus japonicus in Japan and identify extreme genetic signatures of local adaptation to a cold climate using genome resequencing and common garden experiments.

    • Niraj Shah
    • , Tomomi Wakabayashi
    •  & Stig Uggerhøj Andersen

  • Article
    | Open Access

    Relatively little is known about the complexity of regulatory evolution accompanying polyploid crop domestication. Here, using reciprocal hybrids between wild and domesticated allotetraploid cotton lines, the authors catalog cis and trans regulatory variants and show their equivalent effects on cotton fiber domestication.

    • Ying Bao
    • , Guanjing Hu
    •  & Jonathan F. Wendel

  • Article
    | Open Access

    Whole genome duplication (WGD) presents new challenges to the establishment of optimal allelic combinations and to the meiotic machinery. Here, the authors show that adaptive gene flow from Arabidopsis arenosa could rescue the nascent A. lyrata from extinction following WGD.

    • Sarah Marburger
    • , Patrick Monnahan
    •  & Levi Yant

  • Article
    | Open Access

    In plants, 3′ Pol II pausing helps prevent transcriptional interference. Here the authors provide evidence that BORDER proteins are enriched in intergenic regions and inhibit transcriptional interference between closely spaced genes by preventing RNA polymerase from intruding into the promoters of nearby downstream genes.

    • Xuhong Yu
    • , Pascal G. P. Martin
    •  & Scott D. Michaels

  • Article
    | Open Access

    Developing hybrid rice cultivars requires time consuming random crossing. Here, the authors develop a new next generation sequencing-based quantitative trait locus mapping method to dissect heterotic gene OsMADS1 and demonstrate the feasibility of pyramiding two genes to achieve large heterotic effect.

    • Changsheng Wang
    • , Shican Tang
    •  & Bin Han

  • Article
    | Open Access

    Plant roots elongate under mild nitrogen deficiency as part of a foraging response that facilitates nutrient uptake. Here the authors show that natural variation in this response among Arabidopsis accessions depends on the brassinosteroid (BR) signaling kinase BSK3, which can enhance BR sensitivity and root growth.

    • Zhongtao Jia
    • , Ricardo F. H. Giehl
    •  & Nicolaus von Wirén

  • Article
    | Open Access

    Domesticated maize and some varieties of wild teosinte grow in close proximity in parts of Mexico but rarely cross-fertilize. Here the authors show that a pistil-expressed pectin methylesterase, encoded by a gene within the Teosinte crossing barrier1-s haplotype, prevents fertilization of these teosintes by incompatible pollen.

    • Yongxian Lu
    • , Samuel A. Hokin
    •  & Mathew M. S. Evans

  • Article
    | Open Access

    While the role of effective population size (Ne) in explaining variation in genetic diversity has received much attention, the role of spontaneous mutation rate is largely ignored. Here, Xu et al. show that giant duckweed has a high Ne yet low genetic diversity, likely due to its low mutation rate.

    • Shuqing Xu
    • , Jessica Stapley
    •  & Meret Huber

  • Article
    | Open Access

    The sour taste of citrus fruit results from the extremely low pH of juice vesicle cell vacuoles. Here the authors provide genetic evidence that a vacuolar P-type ATPase, that is known to determine flower color in petunia via vacuolar acidification, is also responsible for extreme acidification in citrus.

    • Pamela Strazzer
    • , Cornelis E. Spelt
    •  & Francesca M. Quattrocchio

  • Article
    | Open Access

    Few approaches for targeted manipulation of the epigenome are available in plants. Here, the authors adapt the dCas9-SunTag system to engineer targeted gene activation and site-specific manipulation of DNA methylation in Arabidopsis.

    • Ashot Papikian
    • , Wanlu Liu
    •  & Steven E. Jacobsen

  • Article
    | Open Access

    Viruses are potential vectors for horizontal gene transfer. Here, studying viral infection of sugar beet plants, the authors report the generation of virus-host circular DNA hybrids and provide a picture of the initial steps in virus-mediated horizontal transfer of chromosomal DNA between plant species.

    • Marco Catoni
    • , Emanuela Noris
    •  & Gian Paolo Accotto

  • Article
    | Open Access

    Assembly of large, repeat-rich eukaryotic genomes remains challenging. Here, the authors use BioNano Genomics DLS optical mapping and single-molecule nanopore sequencing to generate a chromosome-scale assembly of a new Sorghum bicolor accession and identify variation compared to the publicly available S. bicolor genome.

    • Stéphane Deschamps
    • , Yun Zhang
    •  & Haining Lin

  • Article
    | Open Access

    Whether plant epigenetic variation is subject to selection and contributes to adaptation is under debate. Here, the authors compare DNA methylation and phenotypes of Arabidopsis lines subject to simulated selection and their nearly isogenic ancestors and provide evidence that epigenetic variation contributes to adaptive responses.

    • Marc W. Schmid
    • , Christian Heichinger
    •  & Ueli Grossniklaus

  • Article
    | Open Access

    Characterizing plant membrane transporters via genetic methods is complicated by functional redundancy among multi-gene transporter families. Here Zhang et al. use an artificial microRNA-based screen to overcome this issue and show that ABCB6 and ABCB20 act redundantly to regulate auxin transport.

    • Yuqin Zhang
    • , Victoria Nasser
    •  & Eilon Shani

  • Article
    | Open Access

    Imputation can effectively augment marker density in existing genetic datasets and enable integration across germplasm resources. Here Wang et al. present a public imputation server for rice using a diverse reference panel to facilitate imputation in the rice genetics community.

    • Diane R. Wang
    • , Francisco J. Agosto-Pérez
    •  & Susan R. McCouch

  • Article
    | Open Access

    Sex-specific meiotic crossover (CO) landscapes have been identified in multiple species. Here, the authors show that male and female meioses in maize have similar CO landscapes, and differences between COs in the two sexes only exists in their location relative to transcription start sites and some chromatin marks.

    • Penny M. A. Kianian
    • , Minghui Wang
    •  & Wojciech P. Pawlowski

  • Article
    | Open Access

    Mei (Prunus mume) is a woody tree that produces ornamental blossoms which symbolize spring in East Asia. Here, Zhang et al. resequence wild and domesticated mei to reveal considerable admixture and introgression from other Prunus species and identify loci associated with floral traits.

    • Qixiang Zhang
    • , He Zhang
    •  & Tangren Cheng

  • Article
    | Open Access

    Domestication reduces genetic diversity and constrains crop improvement. Here the authors identify factors that shaped species diversity in the wild progenitors of chickpea, and produce wild introgression populations that increase diversity for breeding by ~100-fold, including traits of agronomic relevance.

    • Eric J.B. von Wettberg
    • , Peter L. Chang
    •  & Douglas R. Cook

  • Article
    | Open Access

    Crops that allocate heavy metals to leaves rather than grains could allow phytoremediation of polluted soil while producing food that is safe to eat. Here, the authors show that a defensin-like protein promotes cadmium secretion from rice cells and allocation to leaves without causing accumulation in grain.

    • Jin-Song Luo
    • , Jing Huang
    •  & Ji-Ming Gong

  • Article
    | Open Access

    The canonical histone variant H3.1 of vascular plants contains a conserved Phe residue at position 41 that is unique to the plant kingdom. Here, Lu et al. provide evidence that H3.1Phe41 acts collaboratively with the H3.1 core domain to restrict H3.1 deposition to silent regions of the genome.

    • Li Lu
    • , Xiangsong Chen
    •  & Xuehua Zhong

  • Article
    | Open Access

    The role of differential gene content in the evolution and function of eukaryotic genomes remains poorly explored. Here the authors assemble and annotate the Brachypodium distachyon pan-genome consisting of 54 diverse lines and reveal the differential present genes as a major driver of phenotypic variation.

    • Sean P. Gordon
    • , Bruno Contreras-Moreira
    •  & John P. Vogel

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