Focus 26 January 2021

Plants and agriculture

Plants include hundreds of thousands of species with diverse morphology and physiology. Plant biology encompasses fundamental and applied research that aims to understand how plants evolve, develop and interact with their environment with implications for ecosystem function and agriculture. This page highlights exciting plant research published in Nature Communications.

Featured articles

Wheat powdery mildew resistance gene Pm13 encodes a mixed lineage kinase domain-like protein

Wheat powdery mildew is one of the most destructive diseases threatening global wheat production. Here, the authors report the cloning of powdery mildew resistance gene Pm13 from the wild wheat species Aegilops longissima encoding a mixed lineage kinase domain-like (MLKL) protein.
- Huanhuan Li
- Wenqiang Men
- Wenxuan Liu
ArticleOpen Access19 Mar 2024 Nature Communications
A double-stranded RNA binding protein enhances drought resistance via protein phase separation in rice

Drought is one of the major abiotic stresses affecting rice growth and development. Here, the authors identify a dsRNA-binding protein positively regulates rice drought resistance through promoting stability of OsNCED4 mRNAs, transcript of a key gene for the biosynthesis of abscisic acid, via protein phase separation.
- Huaijun Wang
- Tiantian Ye
- Lizhong Xiong
ArticleOpen Access21 Mar 2024 Nature Communications
Dynamic root microbiome sustains soybean productivity under unbalanced fertilization

Root-associated microbiomes contribute to plant growth and health. Here, the authors unveil the quantitative development of the root microbiome under unbalanced fertilization and highlight a key microbial cluster for soybean productivity.
- Mingxing Wang
- An-Hui Ge
- Ertao Wang
ArticleOpen Access23 Feb 2024 Nature Communications
Natural variation in BnaA9.NF-YA7 contributes to drought tolerance in Brassica napus L

Rapeseed production is often threatened by drought stress. Here, the authors report transcription factor BnaA9.NFYA7 negatively regulates rapeseed drought tolerance through ABA signal transduction pathway via feedback inhibition of the expression of BnaABF3/4s-related genes.
- Jia Wang
- Lin Mao
- Liezhao Liu
ArticleOpen Access7 Mar 2024 Nature Communications
Natural variation of STKc_GSK3 kinase TaSG-D1 contributes to heat stress tolerance in Indian dwarf wheat

Indian dwarf wheat (Triticum sphaerococcum) is thermotolerant, but the underlying mechanism is unclear. Here, the authors report the cloning of the heat tolerance gene encoding a STKc_GSK3 kinase and its variation affects phosphorylation level of downstream TaPIF4 in determining thermotolerance.
- Jie Cao
- Zhen Qin
- Mingming Xin
ArticleOpen Access7 Mar 2024 Nature Communications
A transposon insertion in the promoter of OsUBC12 enhances cold tolerance during japonica rice germination

Japonica rice generally has greater capacity for low temperatures germination (LTG) than indica rice. Here, the authors report an E2 ubiquitin-conjugating enzyme-encoding gene OsUBC12 can increase LTG in japonica rice by negatively regulate ABA signaling via promoting the proteasomal degradation of OsSnRK1.1.
- Chuanzhong Zhang
- Hongru Wang
- Jun Fang
ArticleOpen Access13 Mar 2024 Nature Communications
Natural variation in OsMYB8 confers diurnal floret opening time divergence between indica and japonica subspecies

Florets of indica rice open earlier than japonica rice, hindering utilization of the cross subspecies heterosis. Here, the authors show that an OsMYB8-OsJAR1 module regulates diurnal floret opening time divergences between the two subspecies.
- Yajun Gou
- Yueqin Heng
- Rongxin Shen
ArticleOpen Access13 Mar 2024 Nature Communications
Biosynthesis of the highly oxygenated tetracyclic core skeleton of Taxol

Despite intensive investigation, stepwise reactions from diol to Taxol tetracyclic core skeleton remain unclear. Here, authors fill this gap by identifying two P450s and confirming the reaction order.
- Chengshuai Yang
- Yan Wang
- Zhihua Zhou
ArticleOpen Access15 Mar 2024 Nature Communications
Synthetic microbe-to-plant communication channels

The soil microbiome communicates with plant roots using a chemical language. Here, using p-coumaroyl-homoserine lactone as the synthetic communication signal, the authors demonstrate programmable microbe-to-plant communication from the sender in the soil bacteria to a receiver in the plant.
- Alice Boo
- Tyler Toth
- Christopher A. Voigt
ArticleOpen Access28 Feb 2024 Nature Communications
Choreographing root architecture and rhizosphere interactions through synthetic biology

Engineering the form and function of root systems and their associated microbiota could provide a means to mitigate adverse climate-driven effects. Here, the authors review the recent developments in plant and rhizobacterial synthetic biology and highlight engineering targets for applications in root systems and rhizosphere.
- Carin J. Ragland
- Kevin Y. Shih
- José R. Dinneny
Review ArticleOpen Access14 Feb 2024 Nature Communications
Genetic control of thermomorphogenesis in tomato inflorescences

Mechanisms underlying changes in inflorescence development in response to high ambient temperature remain unclear. Here, the authors report the cloning of the MIB2, encoding a homology of SPATULA, and its activation of CONSTANS-Like1 for determining tomato inflorescence branching at high ambient temperature.
- Shuai Sun
- Zhiqiang Liu
- Xia Cui
ArticleOpen Access17 Feb 2024 Nature Communications
Microbially mediated mechanisms underlie soil carbon accrual by conservation agriculture under decade-long warming

Agricultural soil C dynamics under climate change are difficult to predict. Here, the authors report that experimental warming increases soil organic C stocks in conservation agriculture but not in conventional agriculture, which appears driven by soil microbial responses to no tillage and C inputs from the crops.
- Jing Tian
- Jennifer A. J. Dungait
- Jizhong Zhou
ArticleOpen Access8 Jan 2024 Nature Communications
Diurnal switches in diazotrophic lifestyle increase nitrogen contribution to cereals

Engineering ammonium excretion diazotrophs suffers from severe penalties to the bacteria. Here, the authors utilize a thermo-sensitive glutamine synthetase-based regulatory switch that permits diurnal changes in diazotrophic lifestyle, coincident with seasonal temperatures for cereal cultivation.
- Yuqian Tang
- Debin Qin
- Yi-Ping Wang
ArticleOpen Access18 Nov 2023 Nature Communications
Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits

A pan-genome can reduce bias in genetic diversity analysis inherent in using a single reference genome. Here, the authors assemble genomes of 10 diverse apple accessions, conduct pan-genome analysis together with three existing genomes, and reveal the role of mitogen-activated protein kinase homolog MMK2 in fruit coloration.
- Ting Wang
- Shiyao Duan
- Ting Wu
ArticleOpen Access15 Nov 2023 Nature Communications
Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat

The direct impacts of transposable element dynamics on polyploid regulation and developmental specificity remain unclear. Here, the authors show that a large proportion of enhancer-like elements (ELEs) are mainly originated from RLG_famc7.3 specifically expanded in subgenome A, producing active nascent transcripts and influencing wheat spike development.
- Yilin Xie
- Songbei Ying
- Yijing Zhang
ArticleOpen Access17 Nov 2023 Nature Communications
Fostering temporal crop diversification to reduce pesticide use

The potential of crop diversification to reduce pesticide use has not been quantified at large scales. Here, the authors use a national network of 1334 cropping system to identify the effect of increasing temporal crop diversity on pesticide use for 16 common crops.
- Maé Guinet
- Guillaume Adeux
- Nicolas Munier-Jolain
ArticleOpen Access16 Nov 2023 Nature Communications
Deposition and water repelling of temperature-responsive nanopesticides on leaves

Weak adhesion is a common hindrance to efficient utilization of pesticides in agricultural applications. Here, authors demonstrate leaf-adhesive tebuconazole nanopesticides which can be water-dispersed via flash nanoprecipitation using temperature-responsive copolymers PDMAEMA-b-PCL as the carrier.
- Jie Tang
- Xiaojing Tong
- Yisheng Xu
ArticleOpen Access12 Oct 2023 Nature Communications
The pan-genome and local adaptation of Arabidopsis thaliana

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
ArticleOpen Access6 Oct 2023 Nature Communications
Characterization of the horse chestnut genome reveals the evolution of aescin and aesculin biosynthesis

Horse chestnut (Aesculus chinensis) is a tree species that can produce medicinal compounds such as aescin and aesculin. Here, the authors assemble its genome, identify key genes involved in the biosynthesis of these two group of compounds, and achieve the de novo synthesis of aesculin in E. coli.
- Wei Sun
- Qinggang Yin
- Shilin Chen
ArticleOpen Access13 Oct 2023 Nature Communications
Global mean nitrogen recovery efficiency in croplands can be enhanced by optimal nutrient, crop and soil management practices

Enhancing nitrogen use efficiency can improve global food production while minimizing environmental damage. Here, the authors combine 29 meta-analyses revealing that tailored practices based on local conditions can boost NUEr by 30% with variation between high- and middle-income regions.
- Luncheng You
- Gerard H. Ros
- Wim de Vries
ArticleOpen Access16 Sep 2023 Nature Communications
A de novo evolved gene contributes to rice grain shape difference between indica and japonica

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
ArticleOpen Access22 Sep 2023 Nature Communications
Cloning of the wheat leaf rust resistance gene Lr47 introgressed from Aegilops speltoides

Leaf rust is one of the most severe foliar diseases of wheat. Here, the authors report the cloning of Lr47, a broadly effective leaf rust resistance gene introgressed into wheat from Aegilops speltoides, and show it encodes a coiled-coil nucleotide-binding leucine-rich repeat protein.
- Hongna Li
- Lei Hua
- Shisheng Chen
ArticleOpen Access28 Sep 2023 Nature Communications
Efficient plant genome engineering using a probiotic sourced CRISPR-Cas9 system

In the field of plant genome engineering, new nucleases with improved editing efficiency and alterative PAM requirements are needed. Here, the authors report a probiotic sourced CRISPR-LrCas9 system with similar PAM requirement to Cas12a and show its high efficiencies in various genome editing applications.
- Zhaohui Zhong
- Guanqing Liu
- Yong Zhang
ArticleOpen Access29 Sep 2023 Nature Communications
Arabidopsis TCP4 transcription factor inhibits high temperature-induced homeotic conversion of ovules

Global warming threatens food security and plant survival. This paper demonstrates that Class II TCP transcription factors are critical for specifying ovule identity and inhibiting the conversion of ovules into carpelloids under high temperature.
- Jingqiu Lan
- Ning Wang
- Genji Qin
ArticleOpen Access13 Sep 2023 Nature Communications
A pathogen-induced putative NAC transcription factor mediates leaf rust resistance in barley

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
ArticleOpen Access6 Sep 2023 Nature Communications
Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation

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
ArticleOpen Access7 Sep 2023 Nature Communications
High-efficiency green management of potato late blight by a self-assembled multicomponent nano-bioprotectant

Unlike the other plant pathogens, Phytophtora infestans, the causative pathogen of potato late blight, can hardly take up dsRNA, which is a key obstacle in using dsRNA for disease control. Here, the authors design a self-assembled multicomponent nano-bioprotectant for potato late blight management.
- Yuxi Wang
- Mingshan Li
- Xiaodan Wang
ArticleOpen Access12 Sep 2023 Nature Communications
Two complementary genes in a presence-absence variation contribute to indica-japonica reproductive isolation in rice

The mechanisms of the partial reproductive isolation between the two subspecies of rice remains obscure. Here, the authors show that the two adjacent genes form a killer-protector system to induce hybrid male sterility and reproductive isolation between indica and japonica.
- Daiqi Wang
- Hongru Wang
- Ziqiang Liu
ArticleOpen Access28 Jul 2023 Nature Communications
Genomic insight into domestication of rubber tree

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
ArticleOpen Access2 Aug 2023 Nature Communications
Subtelomeric 5-enolpyruvylshikimate-3-phosphate synthase copy number variation confers glyphosate resistance in Eleusine indica

Resistance to herbicide glyphosate can be evolved trough copy number variation (CNV) of its target gene EPSPS in goosegrass. Here, the authors assemble the genomes of glyphosate susceptible and resistance lines and provide evidence of sub-telomeric-repeat driven CNV of EPSPS could lead to glyphosate resistance.
- Chun Zhang
- Nicholas A. Johnson
- Eric L. Patterson
ArticleOpen Access11 Aug 2023 Nature Communications
The MOM1 complex recruits the RdDM machinery via MORC6 to establish de novo DNA methylation

It has generally been considered that MOM1, a transcriptional silencing factor in plants, mediated silencing is independent or downstream of DNA methylation. Here, the authors show that MOM1 complex recruits the RdDM machinery through MORC6 to establish de novo DNA methylation in Arabidopsis.
- Zheng Li
- Ming Wang
- Steven E. Jacobsen
ArticleOpen Access12 Jul 2023 Nature Communications
Manipulating microRNA miR408 enhances both biomass yield and saccharification efficiency in poplar

Modifying plant lignin pathway to enhance saccharification efficiency is often associated with growth penalty. Here, the authors show that overexpression of Pag-miR408 in poplar leads to enhanced saccharification efficiency and growth in both laboratory and field conditions, and laccase genes are the targets of Pag-miR408.
- Yayu Guo
- Shufang Wang
- Jinxing Lin
ArticleOpen Access18 Jul 2023 Nature Communications
Comparative genomics reveals a unique nitrogen-carbon balance system in Asteraceae

Asteraceae is the largest family of flowering plants. Here, the authors assemble the genomes of stem lettuce (within Asteraceae) and beach cabbage (within Goodeniaceae) for evolutionary genomics analyses and reveal the absence of the core regulatory gene of nitrogen and carbon assimilation in Asteraceae.
- Fei Shen
- Yajuan Qin
- Xiaozeng Yang
ArticleOpen Access20 Jul 2023 Nature Communications
Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet

Finger millet is an orphan crop key to food security of people living in eastern Africa, India and Nepal. Here, the authors assemble its genome, conduct population genetics analyses to infer the diversification history, and reveal a candidate gene for purple coloration of anthers and stigma.
- Katrien M. Devos
- Peng Qi
- Damaris A. Odeny
ArticleOpen Access21 Jun 2023 Nature Communications
Genome-wide association studies identify OsWRKY53 as a key regulator of salt tolerance in rice

Only a few genetic variants have been identified to mediate salt tolerance in major crops and their molecular mechanisms are largely unknown. Here, the authors identify WRKY53 as a negative regulator of salt tolerance in rice, and show that it directly trans-regulates expression of MKK10.2 and HKT1;5 to meditate salt tolerance.
- Jun Yu
- Chengsong Zhu
- Jianmin Wan
ArticleOpen Access15 Jun 2023 Nature Communications
Transposon signatures of allopolyploid genome evolution

Assigning assembled chromosomes to subgenome in allopolypoid genome analysis is challenging. Here, the authors report a statistical formwork for identifying evolutionarily coherent subgneomes relying on transposable elements to group chromosomes into sets with shared ancestry and apply it in cyprinids, false flax and strawberry.
- Adam M. Session
- Daniel S. Rokhsar
ArticleOpen Access1 Jun 2023 Nature Communications
An E2-E3 pair contributes to seed size control in grain crops

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
ArticleOpen Access29 May 2023 Nature Communications
The COG1-OsSERL2 complex senses cold to trigger signaling network for chilling tolerance in japonica rice

Improvement of chilling tolerance is a key strategy in rice production. Here the authors report that the QTL gene COG1 confers chilling tolerance in japonica rice. COG1 interacts and activates OsSERL2 to transmit the cold signal for chilling defense.
- Changxuan Xia
- Guohua Liang
- Yunyuan Xu
ArticleOpen Access29 May 2023 Nature Communications
OsMADS17 simultaneously increases grain number and grain weight in rice

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
ArticleOpen Access29 May 2023 Nature Communications
Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding

Lablab is a legume native to Africa and cultivated throughout the tropics for food and forage; however, as an orphan crop, limited genomic resources hampers its genetic improvement. Here, an African-led South-North plant genome collaboration produces an improved genome assembly and population genomic resource to accelerate its breeding.
- Isaac Njaci
- Bernice Waweru
- Chris S. Jones
ArticleOpen Access17 Apr 2023 Nature Communications
Engineering α-carboxysomes into plant chloroplasts to support autotrophic photosynthesis

Engineering carboxysomes into crop chloroplasts is a potential route to improve photosynthesis and crop yield. Here, the authors engineer functional CO₂-fixing modules into tobacco chloroplasts to improve their photosynthesis and productivity.
- Taiyu Chen
- Marta Hojka
- Lu-Ning Liu
ArticleOpen Access25 Apr 2023 Nature Communications
An integrase toolbox to record gene-expression during plant development

Synthetic circuits that can record in vivo signaling networks is critical in elucidating developmental process. Here, the authors describe the engineering and application of synthetic in vivo recorders with different promoters that can drive spatiotemporally-specific integrase switching during lateral root initiation.
- Sarah Guiziou
- Cassandra J. Maranas
- Jennifer L. Nemhauser
ArticleOpen Access3 Apr 2023 Nature Communications
Selection and adaptive introgression guided the complex evolutionary history of the European common bean

Common bean has two distinct domestication centers in Mesoamerica and in the Andes. The authors show that the Andean is the first gene pool successfully introduced in Europe and identify signature of pervasive introgression among gene pools and of selection for flowering underlying adaptation.
- Elisa Bellucci
- Andrea Benazzo
- Roberto Papa
ArticleOpen Access5 Apr 2023 Nature Communications
The methylation landscape of giga-genome and the epigenetic timer of age in Chinese pine

DNA methylation level declines during aging of mammals. Here, the authors report single-base resolution landscape of cytosine DNA methylation at different ages of Chinese pine and show that the global cytosine DNA methylation gradually increases as age progresses.
- Jiang Li
- Fangxu Han
- Shihui Niu
ArticleOpen Access7 Apr 2023 Nature Communications
Impact of small farmers' access to improved seeds and deforestation in DR Congo

Availability of modern seed varieties in developing countries has had positive effects on households’ well-being. Here, the authors show that without support to maintain soil fertility, access to modern seed varieties increases primary forest clearance in DR Congo.
- Tanguy Bernard
- Sylvie Lambert
- Margaux Vinez
ArticleOpen Access23 Mar 2023 Nature Communications
The Torreya grandis genome illuminates the origin and evolution of gymnosperm-specific sciadonic acid biosynthesis

Torreya grandis is a gymnosperm species that produces edible seeds with high level of sciadonic acid (SCA). Here, the authors assemble the genome of this species, preform methylone analysis of seeds at different developmental stages, and reveal two key genes involved in SCA biosynthesis.
- Heqiang Lou
- Lili Song
- Jiasheng Wu
ArticleOpen Access10 Mar 2023 Nature Communications
Revealing evolution of tropane alkaloid biosynthesis by analyzing two genomes in the Solanaceae family

Tropane alkaloids (TAs) are synthesized by some species in Solanaceae. Here, the authors assemble the genomes of two representative TAs producing species, show that gene loss shapes uneven distribution of TAs in Solanaceae, and identify a cytochrome P450 gene catalyzing N-demethylation of hyoscyamine to generate norhyoscyamine.
- Fangyuan Zhang
- Fei Qiu
- Zhihua Liao
ArticleOpen Access15 Mar 2023 Nature Communications
Allelic variation of TaWD40-4B.1 contributes to drought tolerance by modulating catalase activity in wheat

Drought stress limits wheat production around the world. Here, the authors report allelic variation of a WD40 encoding gene TaWD40-4B.1 contributes to wheat drought tolerance by interacting with canonical catalases as a chaperone to promote their activities to avoid ROS over accumulation.
- Geng Tian
- Shubin Wang
- Mengcheng Wang
ArticleOpen Access2 Mar 2023 Nature Communications
Histone H2A monoubiquitination marks are targeted to specific sites by cohesin subunits in Arabidopsis

How histone H2A monoubiquitination (H2Aub1) is established at specific genomic locations remains unclear. Here, the authors report that Arabidopsis cohesin subunits SCC3 and SYN4 are involved in H2Aub1 through their direct or indirect interaction with BMI1A/B/C subunits of PRC1, the E3 ligases in PRC1 for H2Aub1.
- Yu Zhang
- Min Ma
- Yuda Fang
ArticleOpen Access3 Mar 2023 Nature Communications

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