Natural variation in plants articles within Nature Communications

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  • Article
    | Open Access

    Floral phenotypes impact interactions between plants and pollinators. Here, the authors show that Moricandia arvensis displays discrete seasonal plasticity in floral phenotype, with large, lilac flowers attracting long-tongued bees in spring and small, rounded, white flowers attracting generalist pollinators in summer.

    • José M. Gómez
    • , Francisco Perfectti
    •  & Rubén Torices

  • Article
    | Open Access

    Wild teas are considered as valuable resource for studying domestication and breeding. Here, Zhang et al. report genome of wild tea DASZ and transcriptome of 217 accessions, which clarify pedigree of Chinese tea cultivars and show tea may not have undergone long-term artificial directional selection on flavor-related metabolites.

    • Weiyi Zhang
    • , Youjun Zhang
    •  & Weiwei Wen

  • 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

    Callus browning heavily affects indica rice transformation regeneration. Here, the authors show transposon insertion in the promoter of BOC1 gene, encoding a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE protein, can upregulate its expression and decrease callus browning in cultivated rice by releasing oxidative stress.

    • Kun Zhang
    • , Jingjing Su
    •  & Yongcai Fu

  • Article
    | Open Access

    Developmental plasticity of plant root systems has been intensively studied, but the mechanisms underpinning robustness remain unclear. Here, the authors show that DNA-methylation-mediated transcriptional repression serves as a backup system to control lateral root development when auxin signalling is perturbed.

    • Zaigham Shahzad
    • , Ross Eaglesfield
    •  & Anna Amtmann

  • 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

    Major effect loci controlling natural, heritable variation in telomere length are not known. Here, the authors use QTL mapping and transgenic manipulations in Arabidopsis to implicate the rRNA-processing genes NOP2A and RPL5 in telomere length set point regulation in this model species.

    • Liliia R. Abdulkina
    • , Callie Kobayashi
    •  & Eugene V. Shakirov

  • Article
    | Open Access

    Cucurbits fruits have diverse shapes and sizes, but their genomes evolution and genetic basis of diversity are unclear. Here, the authors show that the wax gourd genome has the most ancestral karyotype among cucurbits and identify candidate genes which contribute to large fruit size by comparative and population genomics analyses.

    • Dasen Xie
    • , Yuanchao Xu
    •  & Zhonghua Zhang

  • Article
    | Open Access

    Date palm is an important fruit crop in the Middle East and North Africa. Here, the authors report an improved genome assembly of this species and perform GWAS mapping of sex determining region and 21 fruit traits using high density SNP data generated from re-sequencing of the mapping population.

    • Khaled M. Hazzouri
    • , Muriel Gros-Balthazard
    •  & Michael D. Purugganan

  • Article
    | Open Access

    Grain protein content determines rice nutrition quality. Here, the authors show that a single nucleotide polymorphism in the promoter region of OsGluA2, encoding a glutelin type-A2 precursor, is responsible for glutelin content difference between the indica and japonica rice subspecies.

    • Yihao Yang
    • , Min Guo
    •  & Changjie Yan

  • Article
    | Open Access

    Wild relatives of crop plants are invaluable germplasm for genetic improvement. Here, Xie et al. report a reference-grade wild soybean genome and show that it can be used to identify structural variation and refine quantitative trait loci.

    • Min Xie
    • , Claire Yik-Lok Chung
    •  & Hon-Ming Lam

  • Article
    | Open Access

    Transposable elements (TE) are the dominant constituent of plant genomes. Here the authors develop a tool to analyze TE insertion sites in 3000 rice genomes and provide evidence for recent TE activity during cultivation and that external, rather than genetic, stimuli trigger most activations.

    • Marie-Christine Carpentier
    • , Ernandes Manfroi
    •  & Olivier Panaud

  • 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

    Rice grain shape or size is an important trait associated with both yield and appearance quality. Here, the authors identify GS9 as a negative transcription regulator of slender grain and show it can improve grain shape and appearance independently from other previously identified grain size genes.

    • Dong-Sheng Zhao
    • , Qian-Feng Li
    •  & Qiao-Quan Liu

  • Article
    | Open Access

    Grain size is a major determinant of cereal yield. Here the authors characterize five subunits of the rice heterotrimeric G proteins and find that manipulating the three Gγ proteins can achieve designed grain size, which provides a predictable approach to improving grain yield and quality.

    • Shengyuan Sun
    • , Lei Wang
    •  & Qifa Zhang

  • Article
    | Open Access

    Understanding the regulatory mechanisms of nitrogen assimilation is crucial for developing crop cultivars with improved nitrogen utilization efficiency (NUE). Here the authors identify a new negative regulator of NUE and mutation of this gene increases 10–20% rice grain yield under nitrogen-limiting field conditions.

    • Qing Wang
    • , Jinqiang Nian
    •  & Jianru Zuo

  • 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

    Long-read sequencing technologies facilitate efficient and high quality genome assembly. Here Michael et al. achieve a fast reference assembly for Arabidopsis thaliana KBS-Mac-74 accession using the handheld Oxford Nanopore MinION sequencer and consumer computing hardware, and demonstrate its usefulness in resolving complex structural variation.

    • Todd P. Michael
    • , Florian Jupe
    •  & Joseph R. Ecker

  • Article
    | Open Access

    Rice grain yield is a quantitative trait determined by multiple genes. Here, the authors find NOG1, which encodes an enoyl-CoA hydratase/isomerase in fatty acid β-oxidation pathway, can increase grain yield by enhancing grain number per panicle without affecting the other yield component traits.

    • Xing Huo
    • , Shuang Wu
    •  & Chuanqing Sun

  • Article
    | Open Access

    Natural genetic variation of photosynthesis is an underexplored resource for plant genetic improvement. Here, the authors find allelic variations of YS1 affect Arabidopsis photosynthesis acclimation using genome-wide association study, reverse genetics, and quantitative complementation approaches.

    • Roxanne van Rooijen
    • , Willem Kruijer
    •  & Mark G. M. Aarts

  • 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

    Population structure of the model plantArabidopsis thaliana is shaped by glacial refugia and recent admixture. Here the authors show that genetically distinct groups of A. thalianahave spread east-west across Europe since the most recent ice age, likely as a result of human activity.

    • Cheng-Ruei Lee
    • , Hannes Svardal
    •  & Magnus Nordborg

  • Article
    | Open Access

    Exposure of plants to heat can promote increased tolerance to subsequent heat stress. Here, the authors show that prolonged expression of Arabidopsissmall heat shock protein HSP21 promotes this thermomemory effect and that HSP21 levels are regulated by the plastid metalloprotease FtsH6 during the memory period.

    • Mastoureh Sedaghatmehr
    • , Bernd Mueller-Roeber
    •  & Salma Balazadeh

  • Article
    | Open Access

    Copper (Cu) is an essential mineral nutrient but high concentrations in rice grain can cause toxicity. Here the authors provide evidence that natural variation in rice grain Cu concentration is caused by altered sequestration of Cu into root vacuoles due to a single amino acid substitution in the OsHMA4 transporter.

    • Xin-Yuan Huang
    • , Fenglin Deng
    •  & Jian Feng Ma

  • 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

    Next-generation sequencing technology has made the generation of huge amounts of genetic data possible, but phenotype characterization remains slow and difficult. Here the authors develop a high-throughput phenotyping facility for rice that is able to accurately identify and characterize traits related to morphology, biomass and yield.

    • Wanneng Yang
    • , Zilong Guo
    •  & Lizhong Xiong

  • Article
    | Open Access

    Gene expression at FLOWERING LOCUS T controls floral transition in many plants and is regulated by both environmental signals and internal cues. Liu et al. show that the distance between two regulatory sequences in the FT promoter varies with geographical location and determines responsiveness to photoperiod.

    • Liangyu Liu
    • , Jessika Adrian
    •  & Franziska Turck

  • Article
    | Open Access

    Understanding the genetics and physiology of domesticated species is important for crop improvement. By studying natural variation and the phenotypic traits of 413 diverse accessions of rice, Zhao et al. identify many common genetic variants that influence quantitative traits such as seed size and flowering time.

    • Keyan Zhao
    • , Chih-Wei Tung
    •  & Susan R. McCouch

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