Plant genetics

  • Article
    | Open Access

    Crossover numbers and positions are tightly controlled but the mechanism involved is still obscure. Here, the authors, using quantitative super-resolution cytogenetics and mathematical modelling, show that diffusion mediated coarsening of HEI10, an E3-ligase domain containing protein, may explain meiotic crossover positioning in Arabidopsis.

    • Chris Morgan
    • , John A. Fozard
    •  & Martin Howard
  • Article
    | Open Access

    Diploid potatoes are typically self-incompatible, complicating efforts to breed diploid cultivars. Here the authors report map-based cloning of the S-locus inhibitor (Sli) gene in potato which encodes a non S-locus F-box protein that is expressed in pollen and can functions like a general S-RNase inhibitor to overcome self-incompatibility.

    • Ling Ma
    • , Chunzhi Zhang
    •  & Yi Shang
  • Article
    | Open Access

    The LEC1 transcription factor is expressed in both embryo and endosperm during seed development. Here the authors show that LEC1 expression in the endosperm is necessary and sufficient for embryo maturation and that LEC1 protein is trafficked to the embryo to activate seed maturation.

    • Jingpu Song
    • , Xin Xie
    •  & Yuhai Cui
  • Article
    | Open Access

    In contrast to common bean, tepary bean is highly adapted to heat and drought. Here, the authors assemble the genomes of tepary bean landrace and wild accession, discuss the possible mechanism for resilience to heat stress, and reveal a reduced disease resistance gene repertoire.

    • Samira Mafi Moghaddam
    • , Atena Oladzad
    •  & Phillip E. McClean
  • Article
    | Open Access

    T-DNA mutants have been widely used for Arabidopsis gene function characterization. Here, by characterizing a null mutant created by CRISPR, the authors show that previous reported function of H2A.W is confounded by a T-DNA insertion induced chromosomal rearrangement and reveal its role in regulating heterochromatin accessibility.

    • Pierre Bourguet
    • , Colette L. Picard
    •  & Olivier Mathieu
  • Article
    | Open Access

    Plant somatic embryogenesis (SE) can be triggered by hormone application or overexpression of certain transcription factors such as BBM. Here Karami et al. show that AHL15 is required for induction of downstream BBM targets and promotes heterochromatin decondensation and endomitosis during the induction of SE.

    • Omid Karami
    • , Arezoo Rahimi
    •  & Remko Offringa
  • Article
    | Open Access

    The genus Miscanthus has great potential for bio-energy production due to its high biomass yield and strong stress resistance. Here, the authors report the genome assembly of the diploid M. lutarioriparius, showing it has an allotetraploid origin and an expanded number of genes in families related to stress resistance.

    • Jiashun Miao
    • , Qi Feng
    •  & Bin Han
  • Article
    | Open Access

    The WUSCHEL transcription factor promotes plant stem cell proliferation. Here the authors show that the maize Bif3 mutant contains a duplication of the ZmWUS1 locus leading to cytokinin hypersensitivity and overproliferation at the shoot meristem demonstrating the role of WUSCHEL in maize and how structural variation can impact plant morphology.

    • Zongliang Chen
    • , Wei Li
    •  & Andrea Gallavotti
  • Article
    | Open Access

    The development of hybrid wheat cultivars is hampered by the lack of an effective way to control male fertility in breeding lines. Here, the authors report the identification of two restorer-of-fertility genes Rf1 and Rf3 that can restore fertility of wheat plants carrying Triticum timopheevii-type cytoplasmic male sterility.

    • Joanna Melonek
    • , Jorge Duarte
    •  & Ian Small
  • Article
    | Open Access

    Winter wheat cultivar Forno harbors a race-specific leaf rust resistance locus Lr14a, but the causative gene is unknown. Here, the authors show that Lr14a encodes a membrane-localized protein containing ankyrin repeats and Lr14a-containing segments have been introgressed into the bread wheat gene pool multiple times.

    • Markus C. Kolodziej
    • , Jyoti Singla
    •  & Beat Keller
  • Article
    | Open Access

    The nucleolus organizing region (NOR) consists of multiple, highly repetitive rDNA genes. Here Sims et al. use both long- and short-read sequencing to determine the organization and sequence of Arabidopsis NOR2 rDNA and show that different rRNA gene variants are integrated into translating ribosomes in a tissue-specific manner.

    • Jason Sims
    • , Giovanni Sestini
    •  & Peter Schlögelhofer
  • Article
    | Open Access

    Dioecy has evolved independently from hermaphroditic ancestors in different plant lineages. Here, the authors assemble Populus deltoides male and female genomes, and show the putative roles of a femaleness gene and a maleness gene in sex determination, which suggests independent evolution in different poplar species.

    • Liangjiao Xue
    • , Huaitong Wu
    •  & Tongming Yin
  • Article
    | Open Access

    The perennial grass Miscanthus is a promising biomass crop. Here, via genomics and transcriptomics, the authors reveal its allotetraploid origin, characterize gene expression associated with rhizome development and nutrient recycling, and describe the hybrid origin of the triploid M. x giganteus.

    • Therese Mitros
    • , Adam M. Session
    •  & Daniel S. Rokhsar
  • Article
    | Open Access

    How plant biosynthetic gene clusters (BGCs) form and evolve remains unclear. Here, via examining available genomes within and between Arabidopsis species, the authors show that the thalianol BGC has evolved recently and is still dynamically evolving through involvement of auxiliary genes and chromosomal inversions.

    • Zhenhua Liu
    • , Jitender Cheema
    •  & Anne Osbourn
  • Article
    | Open Access

    Genetic variations present in landraces are critical for crop genetic improvement. Here, the authors map haplotype-trait associations in ~1000 doubled haploid lines derived from three European maize landraces and identify beneficial haplotypes for quantitative traits that are not present in breeding lines.

    • Manfred Mayer
    • , Armin C. Hölker
    •  & Chris-Carolin Schön
  • Article
    | Open Access

    MAPK signaling suppresses autoimmunity mediated by the SUMM2 receptor in Arabidopsis. Here Huang et al. show that a trimeric complex consisting of the GPI anchored protein LLG1, and the two receptor-like proteins LET1 and LET2, promotes activation of SUMM2 according to MAPK signaling status.

    • Yanyan Huang
    • , Chuanchun Yin
    •  & Ping He
  • 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