Natural variation in plants articles within Nature Communications

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  • Article
    | Open Access

    Winged bean is a tropical legume that can produce similar level of seed protein to soybean. Here, the authors report the genome assembly, population genetics, QTL mapping of the plant architecture, protein content and phytonutrients for this species.

    • Wai Kuan Ho
    • , Alberto Stefano Tanzi
    •  & Sean Mayes

  • 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 tools for structural variations (SVs) calling and merging often lead to fragmented SVs and the potential of introducing unnecessary errors. Here, the authors report the PanPop pipeline to address these issues by implementing sequence-aware SV merging algorithm to efficiently merge SVs of various types.

    • Zeyu Zheng
    • , Mingjia Zhu
    •  & Yongzhi Yang

  • Article
    | Open Access

    Pinnate compound leaves sequentially produce their leaflets along the longitudinal axes. The study identifies the MPL1 gene as a key regulator in orchestrating an acropetal pattern of leaflet formation during the chickpea pinnate leaf development.

    • Ye Liu
    • , Yuanfan Yang
    •  & Liangliang He

  • Article
    | Open Access

    Single reference genomes and short-read sequencing data are not enough to harness the full genetic variation of a species. Here, the authors report pan-genome of Arabidopsis thaliana based on chromosomal-level genomes of 32 accessions and identify variations associated with local adaptation.

    • Minghui Kang
    • , Haolin Wu
    •  & Jianquan Liu

  • Article
    | Open Access

    Genetic bases of grain shape differentiation between the two subspecies of Asian cultivated rice have not been fully elucidated. Here, the authors report GSE9, a de novo gene evolved from a non-coding region of wild rice through acquisition of start codon, contributes to the grain shape difference between the two subspecies.

    • Rujia Chen
    • , Ning Xiao
    •  & Zefeng Yang

  • Article
    | Open Access

    Rph7 is a previously mapped barley leaf rust resistance locus, but the causal resistance gene remains unclear. Here, combining a fine mapping approach with RNA-Seq based analysis, the authors clone Rph7 and show it encodes putative NAC transcription factor containing a C-terminal BED domain.

    • Chunhong Chen
    • , Matthias Jost
    •  & Peter M. Dracatos

  • Article
    | Open Access

    The lack of large-scale QTL cloning method hampers systematic dissection of genetic base of quantitative traits. Here, the authors develop a multi-omics data-based technique for large-scale and rapid cloning of quantitative genes of tassel branch number and discovery of selection signatures in maize breeding.

    • Xi Wang
    • , Juan Li
    •  & Lin Li

  • Article
    | Open Access

    The trade-off between grain number and grain weight is a major obstacle for increasing rice yield. Here, the authors show that variation in 5’ UTR of OsMADS17 can simultaneously increase grain number and grain weight through decreasing mRNA translation efficiency.

    • Yuanjie Li
    • , Sheng Wu
    •  & Chuanqing Sun

  • Article
    | Open Access

    Researchers identify an E3 ligase SGD1 and its E2 partner responsible for grain yield control using foxtail millet, and reveal its conserved role in wheat, maize, and rice. Furthermore, SGD1 ubiquitinates the brassinosteroid receptor BRI1 thus stabilizing it and promoting grain yield in crops.

    • Sha Tang
    • , Zhiying Zhao
    •  & Xianmin Diao

  • Article
    | Open Access

    Ambrosia artemisiifolia is an invasive weed and primary cause of pollen-induced hayfever. Here, the authors report its chromosome-level phased genome assembly, examine genome-wide variation among modern and historic accessions, and identify large haploblocks underling rapid adaptation.

    • Paul Battlay
    • , Jonathan Wilson
    •  & Kathryn A. Hodgins

  • Article
    | Open Access

    Understanding origin and adaptation of weeds is important for their management. Here, via genome assembly, population genomics, and QTL mapping, the authors establish Cardamine occulta as a model to study weed ruderality and show FLC and CRY2 as genetic drivers for the establishment of short life cycle.

    • Ling-Zi Li
    • , Zhou-Geng Xu
    •  & Jia-Wei Wang

  • Article
    | Open Access

    The power of pangenomic graphs to improve genetic mapping is still unclear. Here, the authors demonstrate its value in identification of genetic variants associated with disease resistance traits in melon using PanPipes, a pangenome construction and low-coverage genotype-by-sequencing pipeline.

    • Justin N. Vaughn
    • , Sandra E. Branham
    •  & William P. Wechter

  • Article
    | Open Access

    Tree peony (Paeonia ostii) has the largest chromosome of any sequenced plants to date. Here, the authors assemble its genome and reveal the association of a list of candidate genes with fatty acid biosynthesis and the possible contribution of transposon and histone expansion to maintain the giga-chromosomes.

    • Junhui Yuan
    • , Sanjie Jiang
    •  & Yonghong Hu

  • Article
    | Open Access

    Shoot branching is critical in determining soybean yield. Here, the authors report natural variation of Dt2 in controlling soybean branching number and the interaction of Dt2 with GmAgl22 and GmSoc1a to activate transcription of GmAp1a and GmAp1d.

    • Qianjin Liang
    • , Liyu Chen
    •  & Zhixi Tian

  • Article
    | Open Access

    While auxin has been implicated in the development of tomato fruit with pointed tips, the mechanism are largely unknown. Here, the authors report variation of a C2H2-type zinc finger transcription factor affects transcription of FUL2, which consequently regulates auxin transport and distribution to determine tomato fruit shape.

    • Jianwen Song
    • , Lele Shang
    •  & Junhong Zhang

  • Article
    | Open Access

    Genetic basis of the drought tolerance of upland rice is unclear. Here, the authors report the cloning of a COBRA-like protein encoding gene DROT1 and reveal that it is repressed by ERF3 and activated by ERF71 to help control the balance between growth and drought tolerance in upland rice.

    • Xingming Sun
    • , Haiyan Xiong
    •  & Zichao Li

  • Article
    | Open Access

    Improving phosphorus (P) acquisition efficiency is important for sustainable agriculture. Here, the authors report a natural variation in an upstream open reading frame of a SEC12-like gene GmPHF1 is crucial for protein abundance and spatial distribution of GmPHF1, which contribute to P acquisition diversity in soybean.

    • Zilong Guo
    • , Hongrui Cao
    •  & Hong Liao

  • Article
    | Open Access

    Phenomic and genomic approaches are required to evaluate the progress of breeding strategies. Here, the authors analyse 65 years of genetic progress in maize, showing that breeders have selected traits with stable effects on yield whereas not for adaptive traits key for climate change adaptation.

    • Claude Welcker
    • , Nadir Abusamra Spencer
    •  & François Tardieu

  • 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

    Most crops are farmed under high transpiring environments, but our understanding of transpiration-dependent salt tolerance (TDST) remains limited. Here, the authors report a dirigent family protein is responsible for TDST by affecting lignin deposition at Casparian strip barrier and transportation of Na+ across the endodermis.

    • Yanyan Wang
    • , Yibo Cao
    •  & Caifu Jiang

  • Article
    | Open Access

    Detailing how populations adapted to environmental change is needed to predict future responses, but identifying adaptive variants and detailing their fitness effects is rare. Here, the authors show that parallel loss of FRI and FLC function reduces time to flowering and drives adaptation in a drought prone environment.

    • Andrea Fulgione
    • , Célia Neto
    •  & Angela M. Hancock

  • Article
    | Open Access

    Low glume coverage is the preferred for easy threshing in grain production, but the genetic basis remains unclear. Here, the authors report the gene GC1, which encodes an atypical G protein γ subunit, negatively regulates sorghum glume coverage and the naturally truncated alleles can be useful in the naked grain breeding.

    • Peng Xie
    • , Sanyuan Tang
    •  & Qi Xie

  • Article
    | Open Access

    While multiple resistance-to-Phytophthora sojae loci/alleles have been mapped in soybean, many of them have become ineffective to newly evolved isolates. Here, the authors show that a 27.7-kb nucleotide-binding site-leucine-rich repeat gene confers broad-spectrum resistance to P. sojae in soybean.

    • Weidong Wang
    • , Liyang Chen
    •  & Jianxin Ma

  • Article
    | Open Access

    The genetic basis of low-temperature tolerance in maize is unclear. Here, the authors show that the type-A Response Regulator 1 (ZmRR1) and mitogen-activated protein kinase (MPK8) are positive and negative regulators of maize chilling tolerance, and ZmRR1 is phosphorylated by ZmMPK8 during cold treatment.

    • Rong Zeng
    • , Zhuoyang Li
    •  & Shuhua Yang

  • Article
    | Open Access

    The role of non-structural carbohydrates (NSC) in mediating the impacts of drought in tropical trees is unclear. Here, the authors analyse leaf and branch NSC in 82 Amazon tree species across a Basin-wide precipitation gradient, finding that allocation of leaf NSC to soluble sugars is higher in drier sites and is coupled to tree hydraulic status.

    • Caroline Signori-Müller
    • , Rafael S. Oliveira
    •  & David Galbraith

  • 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

    The molecular basis for the unique taste and aroma of tea cultivars is largely unknown, but is critical for breeding new cultivars. Here the authors use transcriptomics and metabolomics to study the relationship among phylogenetic groups and specialized metabolites from 136 tea accessions in China.

    • Xiaomin Yu
    • , Jiajing Xiao
    •  & Renyi Liu

  • Article
    | Open Access

    Very little is known about how vitreous endosperm in the mature maize kernel is created. Here, via map-based cloning, the authors find that mutation of a β-carotene hydroxylase 3 encoding gene Ven1 affects carotenoids and lipids composition, which consequently influences amyloplast envelope integrity.

    • Haihai Wang
    • , Yongcai Huang
    •  & Yongrui Wu

  • Article
    | Open Access

    The molecular connection between nitrogen utilization efficiency (NUE) and biomass production is unclear. Here, the authors show that differences in NUE and cellulose biogenesis between rice indica and japonica subspecies can be explained by variation at the MYB61 locus, which is regulated by the NUE regulator GRF4.

    • Yihong Gao
    • , Zuopeng Xu
    •  & Yihua Zhou

  • 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

    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

    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

    Transposable element insertion polymorphisms (TIPs) are a potential source of large effect alleles. Here, the authors use genome resequencing data for 602 tomato accessions together with transcriptomic and extensive phenotypic information to investigate the contribution of TIPs to tomato diversity.

    • Marisol Domínguez
    • , Elise Dugas
    •  & Leandro Quadrana

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