Plant genetics articles within Nature Communications

Featured

  • 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

  • Article
    | Open Access

    Maize was domesticated from wild lowland progenitors that co-existed with upland subspecies in Southwestern Mexico. Here Yang et al. use a meta-assembly approach to assemble an upland mexicana genome and find evidence of introgression suggesting it contributed to modern maize adaptation

    • Ning Yang
    • , Xi-Wen Xu
    •  & Jianbing Yan

  • Article
    | Open Access

    Breeding has increased crop productivity, but whether it has also changed phenotypic plasticity is unclear. Here, the authors find maize genomic regions selected for high productivity show reduced contribution to genotype by environment variation and provide evidence for regulatory control of phenotypic stability.

    • Joseph L. Gage
    • , Diego Jarquin
    •  & Natalia de Leon

  • Article
    | Open Access

    Several models have been proposed to explain the emergence of sex chromosomes. Here, through comparative genomics and mutant analysis, Harkess et al. show that linked but separate genes on the Y chromosome are responsible for sex determination in Asparagus, supporting a two-gene model for sex chromosome evolution.

    • Alex Harkess
    • , Jinsong Zhou
    •  & Guangyu Chen

  • Article
    | Open Access

    The VRS genes of barley control the fertility of the lateral spikelets on the barley inflorescence. Here, Bull et al. show that VRS3 encodes a putative Jumonji C-type histone demethylase that regulates expression of other VRS genes, and genes involved in stress, hormone and sugar metabolism.

    • Hazel Bull
    • , M. Cristina Casao
    •  & Robbie Waugh

  • Article
    | Open Access

    Variation among wild relatives of crop plants can be used to identify genes underlying traits of agronomic importance. Here, the authors show that a modified mapping-by-sequencing approach can rapidly identify the genetic basis for viral resistance in sugar beet using wild beet populations in their natural habitat.

    • Gina G. Capistrano-Gossmann
    • , D. Ries
    •  & F. J. Kopisch-Obuch

  • Article
    | Open Access

    Iron is an essential micronutrient for plants and a lack of iron availability limits crop yield in many parts of the world. Here the authors show that natural variation in root growth ofArabidopsis plants under iron deficiency can be caused by allelic variation at the FRO2locus.

    • Santosh B. Satbhai
    • , Claudia Setzer
    •  & Wolfgang Busch

  • Article
    | Open Access

    Spinach is an economically important vegetable crop but previous genomic resources were of limited use for comparative and functional analyses. Here, Xuet al. present a high quality draft spinach genome and transcriptome data for multiple Spinaciaaccessions providing insight into Caryophyllales genome evolution.

    • Chenxi Xu
    • , Chen Jiao
    •  & Quanhua Wang

  • Article
    | Open Access

    The male-sterilems2 mutant has facilitated commercial production of wheat for over 40 years. Here, Xia et al. map Ms2and describe how a retrotransposon insertion event in the regulatory element of an orphan gene is associated with expression in anthers and development of male sterility.

    • Chuan Xia
    • , Lichao Zhang
    •  & Xiuying Kong

  • Article
    | Open Access

    High-quality reference genomes facilitate analysis of genome structure and variation. Here Duet al. create a near-complete assembly of the indicarice genome by combining single molecule sequencing with mapping data and fosmid sequences and identify genetic variants by comparison with other rice genomes.

    • Huilong Du
    • , Ying Yu
    •  & Chengzhi Liang

  • Article
    | Open Access

    Host genomes have evolved multiple silencing mechanisms to repress transposable element activity. Here Ikedaet al. show that the Arabidopsis MAIL1 and MAINgenes encode a retrotransposon-related plant mobile domain and define an alternative silencing pathway largely independent of DNA methylation and siRNAs.

    • Yoko Ikeda
    • , Thierry Pélissier
    •  & Olivier Mathieu

  • Article
    | Open Access

    The dominant male-sterile geneMs2 has facilitated the release of hundreds of wheat-breeding lines and cultivars in China. Here Ni et al. describe the cloning of the Ms2 gene, which appears as an orphan gene in the Triticinae, and show that Ms2 can be used to confer male sterility in wheat, barley and Brachypodium.

    • Fei Ni
    • , Juan Qi
    •  & Daolin Fu

  • Article
    | Open Access

    Genome assembly for many plant species can be challenging due to large size and high repeat content. Here, the authors usein vitroproximity ligation to assemble the genome of lettuce, revealing a family-specific triplication event and providing a comprehensive reference genome for a member of the Compositae.

    • Sebastian Reyes-Chin-Wo
    • , Zhiwen Wang
    •  & Richard W. Michelmore

  • Article
    | Open Access

    Peking-type and PI 88788-type soybeans are both used as sources of resistance against soybean cyst nematode. Here the authors show that in contrast to PI 88788-type resistance, whereGmSNAP18 acts in combination with two neighbouring genes, in Peking-type resistance GmSNAP18 acts with GmSHMT08to confer resistance.

    • Shiming Liu
    • , Pramod K. Kandoth
    •  & Khalid Meksem

  • Article
    | Open Access

    Low temperature is a major factor limiting productivity in rice. Here the authors show that theCTB4a gene confers cold tolerance to japonicavarieties adapted to cold habitats at the booting stage of development, and propose that CTB4a acts via an interaction with the beta subunit of ATP synthase.

    • Zhanying Zhang
    • , Jinjie Li
    •  & Zichao Li

  • Article
    | Open Access

    Miniature inverted-repeat transposable elements (MITEs) are common components of eukaryotic genomes. Here the authors show that a stowaway-like MITE in the 3′-untranslated region of the riceGhd2gene can suppress translation in a DCL3a-dependent manner representing a novel role for transposons in translation.

    • Jianqiang Shen
    • , Juhong Liu
    •  & Lizhong Xiong

  • Article
    | Open Access

    As sessile organisms, plants are exposed to recurrent solar UV-B radiation that can induce DNA damage. Here, the authors characterize mutations that occur in Arabidopsisunder light regimes simulating natural UV-B exposure and find that the UVR2 photolyase is the major component required to maintain genome stability.

    • Eva-Maria Willing
    • , Thomas Piofczyk
    •  & Ales Pecinka

  • Article
    | Open Access

    Image-based plant phenotyping can be used to collect data with high temporal and spatial resolution. Here, the authors develop a computationally efficient method using smoothing splines and a new marker-by-trait association model to identify loci in a diverse rice population associated with early response to salinity.

    • Nadia Al-Tamimi
    • , Chris Brien
    •  & Sónia Negrão

  • Article
    | Open Access

    Brassica oleracea is a single species that includes diverse crops such as cabbage, broccoli and Brussels sprouts. Here, the authors identify genes not captured in existing B. oleraceareference genomes by the assembly of a pangenome and show variations in gene content that may be related to important agronomic traits

    • Agnieszka A. Golicz
    • , Philipp E. Bayer
    •  & David Edwards

  • Article
    | Open Access

    Japanese morning glory (Ipomoea nil) has diverse flowering traits. Here, the authors describe the reference genome sequence of I. nil, annotations of genes and transposons, and compare evolution of the I. nilgenome to other Convolvulaceae and Solanales genomes.

    • Atsushi Hoshino
    • , Vasanthan Jayakumar
    •  & Yasubumi Sakakibara

  • Article
    | Open Access

    Peach is both an economically important crop species and a model for Rosaceae fruit development research. Here, the authors perform genome-wide association analysis in peach and find candidate genes associated with variation in agronomically important fruit phenotypes.

    • Ke Cao
    • , Zhengkui Zhou
    •  & Lirong Wang

  • Article
    | Open Access

    Plant genome editing typically relies upon transgenic intermediates, which is a concern given the current regulatory requirements concerning GMOs. Here, Zhang et al. describe a method to edit wheat genomes by transiently expressing CRISPR/Cas9 DNA or RNA, and are able to generate mutant plants with no detectable transgenes.

    • Yi Zhang
    • , Zhen Liang
    •  & Caixia Gao

  • Article
    | Open Access

    Protection from UV-B is critical for land plant survival. Here Tohge et al. show that saiginols, a novel class of flavonols that efficiently absorb UV-B, accumulate in Arabidopsisaccessions collected from high irradiance regions and identify a flavonol phenylacyltransferase gene required for saiginol production.

    • Takayuki Tohge
    • , Regina Wendenburg
    •  & Alisdair R. Fernie

  • Article
    | Open Access

    Plant-feeding insects of the Lygus genus have emerged as a major pest effecting cotton crops in the USA. Here the authors optimize the insecticidal activity of a Bacillus thuringiensis crystal protein and produce transgenic plants that are resistant to feeding damage by Lygusspecies.

    • Anilkumar Gowda
    • , Timothy J. Rydel
    •  & James A. Baum

  • Article
    | Open Access

    Laboratory-based studies of the effect of plant genotype on plant microbiome composition often do not consider the influence of environmental heterogeneity. Here, Wagner et al. use a large-scale field experiment to assess the extent of host genetic and environmental factors on the microbiome of Boechera stricta.

    • Maggie R. Wagner
    • , Derek S Lundberg
    •  & Thomas Mitchell-Olds

  • Article
    | Open Access

    Seed dormancy allows wild barley grains to survive dry summers in the Near East but has been selected against for industrial applications such as beer and whisky production that require quicker germination. Here Sato et al. show that Qsd1is a major seed dormancy gene in barley and encodes an alanine aminotransferase.

    • Kazuhiro Sato
    • , Miki Yamane
    •  & Takao Komatsuda

  • Article
    | Open Access

    Species-specific gamete recognition is needed to maintain species boundaries. Here, Müller et al. show that ARTUMES regulates pollen tube recognition between different Arabidopsisspecies, representing the first gene known to exclusively influence inter- but not intraspecific gamete interaction in plants.

    • Lena M. Müller
    • , Heike Lindner
    •  & Ueli Grossniklaus

  • Article
    | Open Access

    Panicle architecture is an important determinant of crop yield and a target of selection by plant breeders. Here, Crowell et al.combine image-based phenotyping with high-density array-based genotyping to perform a genome-wide association study revealing a number of candidate genes linked to panicle variation in rice.

    • Samuel Crowell
    • , Pavel Korniliev
    •  & Susan McCouch

  • Article
    | Open Access

    Understanding the link between genotype and phenotype can facilitate efforts by breeders to utilize natural variation and develop new crop varieties. Here the authors present a diverse germplasm collection, a high-density genotyping array and a set of bioinformatic tools to enable association mapping in rice.

    • Susan R. McCouch
    • , Mark H. Wright
    •  & Jason Mezey

  • Article
    | Open Access

    Cotton plants are characterized by the presence of darkly pigmented glands that accumulate metabolites that contribute to plant defence but limit the use of cottonseed as food. Here, Ma et al. provide evidence that GoPGF, a bHLH transcription factor, is responsible for gland formation.

    • Dan Ma
    • , Yan Hu
    •  & Tianzhen Zhang

  • Article
    | Open Access

    In plants, the shoot apical meristem generates all of the above ground organs and meristem morphology may predict important agricultural traits. Here Leiboff et al. use high throughput phenotyping and a genome-wide association study to uncover genes associated with variation in maize meristem size.

    • Samuel Leiboff
    • , Xianran Li
    •  & Michael J. Scanlon

  • Article
    | Open Access

    Date palm is a perennial fruit tree crop that thrives in arid environments of North Africa and the Middle East. Here Hazzouriet al. analyze the date palm germplasm by re-sequencing 62 different varieties and uncover selection signatures and candidate genes associated with important agronomic traits.

    • Khaled M. Hazzouri
    • , Jonathan M. Flowers
    •  & Michael D. Purugganan

  • Article
    | Open Access

    Sesame is a valuable oilseed crop with a small diploid genome and high seed-oil content making it an attractive model for genetic studies. Here, Wei et al.sequence more than 705 sesame varieties and perform a genome-wide association study to identify genes associated with important agronomic traits.

    • Xin Wei
    • , Kunyan Liu
    •  & Xiurong Zhang

  • Article |

    Protein phosphatases are central regulators of abscisic acid (ABA) signalling and stress responses in plants. Here, Wang et al. show that different splice variants of the phosphatase HAB1 antagonistically influence ABA sensitivity in Arabidopsisand propose that alternative splicing fine tunes ABA signalling.

    • Zhijuan Wang
    • , Hongtao Ji
    •  & Xia Li

  • Article
    | Open Access

    Drought is a major cause of yield loss in maize and understanding the genetic determinants of natural variation in drought tolerance may aid breeding programs produce more tolerant varieties. Here, Mao et al.identify a MITE transposon insertion in a NAC transcription factor, which is associated with natural variation in drought tolerance.

    • Hude Mao
    • , Hongwei Wang
    •  & Feng Qin

  • Article
    | Open Access

    A hybrid incompatibility between Capsellaplant species is due to an interaction between two immune regulators. Here, the authors show that highly divergent haplotypes result from balancing selection in the ancestral lineage and their sorting into derived lineages facilitated the evolution of the incompatibility.

    • Adrien Sicard
    • , Christian Kappel
    •  & Michael Lenhard

  • Article
    | Open Access

    Phytochromes are red-light photoreceptors in plants that regulate key life cycle processes, yet their evolutionary origins are not well understood. Using transcriptomic and genomic data, Li et al.find that canonical plant phytochromes originated in a common ancestor of land plants and charophyte algae.

    • Fay-Wei Li
    • , Michael Melkonian
    •  & Sarah Mathews

  • Article
    | Open Access

    Kelps are ecologically and economically important seaweeds. Here the authors sequence the genome of Saccharina japonicato gain insights into the evolutionary adaptation of polysaccharide biosynthesis, iodine concentration and antioxidation mechanisms and the population genetics of kelp domestication.

    • Naihao Ye
    • , Xiaowen Zhang
    •  & Fangqing Zhao

Browse broader subjects

Browse narrower subjects

Browse Plant genetics across other nature.com journals