Plant domestication articles within Nature Communications

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  • Article
    | Open Access

    Seed dormancy is the preferred trait in rice production as it can prevent preharvest sprouting. Here, the authors report that MODD (mediator of OsbZIP46 deactivation and degradation) negatively regulates seed dormancy by inhibiting the transcriptional activity of ABSCISIC ACID INSENSITIVES (ABIs).

    • Naihui Guo
    • , Shengjia Tang
    •  & Peisong Hu

  • Article
    | Open Access

    Existing genetics and genomics studies of peppers mainly focus on single species. Here, the authors report a pepper graph pan-genome and a genome variation map of 500 accessions from five domesticated species and close wild relatives to reveal their domestication, introgression and population differentiation.

    • Feng Liu
    • , Jiantao Zhao
    •  & Xuexiao Zou

  • Article
    | Open Access

    Understanding the genetic basis of rubber tree domestication is critical for improving natural rubber production. Here, the authors assemble the genome of the rubber tree clone CATAS8-79 and conduct population and genetic association analyses to reveal the function of phytosulfokine in regulating number of laticifer rings.

    • Jinquan Chao
    • , Shaohua Wu
    •  & Wei-Min Tian

  • Article
    | Open Access

    During tomato fruit ripening, bitter and toxic steroidal glycoalkaloids (SGAs) are converted to nonbitter and less toxic forms, but proposed acylating enzyme in pathway remain unknown. Here, authors report BAHD-type acyltransferase that catalyze acylation step in biosynthesis of non-bitter SGAs in tomato.

    • Prashant D. Sonawane
    • , Sachin A. Gharat
    •  & Asaph Aharoni

  • Article
    | Open Access

    Despite archaeobotanical evidence for domesticated cereals, organic residue evidence is scarce. Here, the authors identify cereal-specific markers in pottery from Scottish ‘crannogs’, revealing the presence of cereals in Neolithic pottery which might have been mixed with dairy products as a milk-based gruel.

    • Simon Hammann
    • , Rosie R. Bishop
    •  & Lucy J. E. Cramp

  • Article
    | Open Access

    A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere. Here, the authors report QTLs and the associated candidate genes underlying rhizosphere microbiome composition in barley.

    • Carmen Escudero-Martinez
    • , Max Coulter
    •  & Davide Bulgarelli

  • Article
    | Open Access

    In soybean production, level of seed protein frequently shows a negative correlation with seed oil content and yield. Here, the authors report a CCT gene pleiotropically regulates these traits and the selection of larger seeds determining allele leads to higher oil content but lower protein content in soybean cultivars.

    • Wolfgang Goettel
    • , Hengyou Zhang
    •  & Yong-qiang Charles An

  • Article
    | Open Access

    While a large amount of genomic resources is available, the phylogeny of wild and cultivated beets remains unclear. Here, the authors use the k-mer-based Mash method to analyze resequenced genomes of 606 accessions of the genus Beta and reveal Greece as the domestication site of sugar beet.

    • Felix L. Sandell
    • , Nancy Stralis-Pavese
    •  & Juliane C. Dohm

  • Comment
    | Open Access

    By the end of this century, a 50% increase in agricultural productivity is required to feed the world. Recent studies have demonstrated de novo domestication of wild plants as a new crop breeding strategy to meet future food challenges.

    • Hong Yu
    •  & Jiayang Li

  • Article
    | Open Access

    Reports on the origin of European wine grapes are controversial. Here, the authors perform population genetics analyses on a large set of representative wine-making varieties and reveal a single domestication event at the origin of the entire germplasm followed by repeated introgression from wild populations.

    • Gabriele Magris
    • , Irena Jurman
    •  & Michele Morgante

  • Article
    | Open Access

    How soybean, a temperate origin crop, adapted to a tropical environment remains unclear. Here, the authors report Tof16, an ortholog of LHY, and the previously identified J locus, control soybean yield under short-day condition and loss of function of these two genes contributes to the adaptation to tropics.

    • Lidong Dong
    • , Chao Fang
    •  & Baohui Liu

  • Article
    | Open Access

    To explore the nature of wild and cultivated mandarins, the authors carry out genomic analysis of diverse east Asian citrus. The discovery of a wild species Citrus ryukyuensis native to the Ryukyu islands and a new population of wild mainland Asian mandarin explains the origin and diversity of mandarins and their ability to reproduce apomictically.

    • Guohong Albert Wu
    • , Chikatoshi Sugimoto
    •  & Daniel S. Rokhsar

  • Article
    | Open Access

    Solanum pimpinellifolium (SP) is the progenitor of cultivated tomato and an important germplasm. Here, the authors assemble SP genome, identify structural variants (SVs) by comparing with modern cultivar, reveal SVs associated with important breeding traits, and detect SVs harboring master regulators of fruit quality traits.

    • Xin Wang
    • , Lei Gao
    •  & Zhangjun Fei

  • Article
    | Open Access

    Mechanism of high altitude adaptation of wheat remains unknown. Here, the authors assemble the draft genome of a Tibetan semi-wild wheat accession and resequence 245 wheat accessions to reveal that Tibetan semi-wild wheat has been de-domesticated from local landraces to adapt to high altitude.

    • Weilong Guo
    • , Mingming Xin
    •  & Qixin Sun

  • Article
    | Open Access

    Fonio millet is a fast growing orphan cereal crop with a great potential for dryland agriculture. Here, the authors report chromosome-scale reference genome assembly and population genomic resources to shed light on genetic diversity, population structure and domestication of fonio millet.

    • Michael Abrouk
    • , Hanin Ibrahim Ahmed
    •  & Simon G. Krattinger

  • Article
    | Open Access

    Tea is an important beverage crop with a large and heterozygous genome. Here, the authors assemble the genome of the cultivar Longjing 43 and conduct a population genetics study to reveal divergent selection for disease resistance and flavor between the two variety groups.

    • Xinchao Wang
    • , Hu Feng
    •  & Yajun Yang

  • Article
    | Open Access

    Little is known about the diets of early modern humans as they dispersed into Australia. Here, Florin et al. study charred plant remains from Madjedbebe rockshelter, which show that 65–53 thousand years ago, early modern humans in northern Australia already had a broad diet of plants.

    • S. Anna Florin
    • , Andrew S. Fairbairn
    •  & Chris Clarkson

  • 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

    Maize rough dwarf disease threatens its production. Here, the authors show that a helitron transposon insertion in the Rab GDP dissociation inhibitor alpha leads to recessive viral resistance by affecting its interaction with viral P7-1 protein and that all naturally occurring alleles come from a single mutation event after domestication.

    • Qingcai Liu
    • , Suining Deng
    •  & Mingliang Xu

  • Article
    | Open Access

    Unlike the other domesticated maize, sweet maize and popcorn retain tillering growth habit, but the underlying mechanism is unknown. Here, the authors identify a transcription factor tin1 that maintains outgrowth of tiller independent of tb1 and show its conservation in foxtail millet and rice.

    • Xuan Zhang
    • , Zhelong Lin
    •  & Zhongwei Lin

  • Article
    | Open Access

    Long mesocotyl is a critical trait for the application of rice deep direct seeding or mechanized dry seeding cultivation method. Here, Sun et al. find OsGSK2 is selected for mesocotyl length variation during domestication and it coordinates strigolactone and brassinosteroid signaling to determine mesocotyl elongation.

    • Shiyong Sun
    • , Tao Wang
    •  & Xuelu Wang

  • 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

    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

    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

    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

    Transition from a spread panicle typical of ancestral wild rice to the compact panicle of present cultivars was a crucial event in rice domestication. Here the authors show that this panicle architecture is controlled by the transcription factor OsLG1 and that a mutation in its regulatory region led to the compact panicle phenotype.

    • Zuofeng Zhu
    • , Lubin Tan
    •  & Chuanqing Sun

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