Plant biotechnology

  • Article
    | Open Access

    Saline-alkaline stress affects worldwide crops production, but the tolerance mechanisms have not been fully elucidated. Here, the authors show that EF-hand Ca2 + -binding-protein coding gene ZmNSA1 can regulate root H + efflux, Na + homeostasis, and saline-alkaline tolerance in maize.

    • Yibo Cao
    • , Ming Zhang
    • , Xiaoyan Liang
    • , Fenrong Li
    • , Yunlu Shi
    • , Xiaohong Yang
    •  & Caifu Jiang
  • Article
    | Open Access

    The South African quality protein maize (QPM) cultivars have the desired high lysine content and kernel hardness due to o2 mutation and the introgression of modifiers of o2 (Mo2) QTLs, respectively. Here, the authors assemble the genome of a QPM line and identify candidate genes underlying Mo2 QTLs.

    • Changsheng Li
    • , Xiaoli Xiang
    • , Yongcai Huang
    • , Yong Zhou
    • , Dong An
    • , Jiaqiang Dong
    • , Chenxi Zhao
    • , Hongjun Liu
    • , Yubin Li
    • , Qiong Wang
    • , Chunguang Du
    • , Joachim Messing
    • , Brian A. Larkins
    • , Yongrui Wu
    •  & Wenqin Wang
  • Article
    | Open Access

    Existing methods to detect ethylene in plant tissue typically require gas chromatography or use ethylene-dependent gene expression as a proxy. Here Vong et al. show that an artificial metalloenzyme-based ethylene probe can be used to detect ethylene in plants with improved spatiotemporal resolution.

    • Kenward Vong
    • , Shohei Eda
    • , Yasuhiro Kadota
    • , Igor Nasibullin
    • , Takanori Wakatake
    • , Satoshi Yokoshima
    • , Ken Shirasu
    •  & Katsunori Tanaka
  • 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
    • , Jian Wang
    • , Hangqin Liu
    • , Leina Zhou
    • , Shuyang Zhong
    • , Yan Li
    • , Can Zhu
    • , Jiacheng Liu
    •  & Zhongwei Lin
  • Article
    | Open Access

    Improving crop nitrogen use efficiency can facilitate sustainable production, however, the genetic mechanisms have not been fully revealed. Here, the authors discover the NAC42-NPF6.1 signaling cascade mainly derives from indica and wild rice and demonstrate the potential of using the allele for cultivar improvement.

    • Weijie Tang
    • , Jian Ye
    • , Xiangmei Yao
    • , Pingzhi Zhao
    • , Wei Xuan
    • , Yunlu Tian
    • , Yuanyan Zhang
    • , Shuang Xu
    • , Hongzhou An
    • , Gaoming Chen
    • , Jun Yu
    • , Wei Wu
    • , Yuwei Ge
    • , Xiaolan Liu
    • , Jin Li
    • , Hanzhi Zhang
    • , Yaqin Zhao
    • , Bing Yang
    • , Xingzhou Jiang
    • , Chao Peng
    • , Cong Zhou
    • , William Terzaghi
    • , Chunming Wang
    •  & Jianmin Wan
  • Article
    | Open Access

    Indica rice has higher nitrate assimilation and nitrogen use efficiency (NUE) than japonica rice, but the mechanism is unclear. Here, the authors reveal that the difference is partly due to allelic variation of a nitrate reductase encoding gene and this indica allele can increase yield potential and NUE.

    • Zhenyu Gao
    • , Yufeng Wang
    • , Guang Chen
    • , Anpeng Zhang
    • , Shenglong Yang
    • , Lianguang Shang
    • , Danying Wang
    • , Banpu Ruan
    • , Chaolei Liu
    • , Hongzhen Jiang
    • , Guojun Dong
    • , Li Zhu
    • , Jiang Hu
    • , Guangheng Zhang
    • , Dali Zeng
    • , Longbiao Guo
    • , Guohua Xu
    • , Sheng Teng
    • , Nicholas P. Harberd
    •  & Qian Qian
  • Article
    | Open Access

    Steroidal glycoalkaloids (SGAs) accumulate in Solanum, but their hydroxylating enzymes are unknown. Here, the authors report 2-OXOGLUTARATE DEPENDENT DIOXYGENASE enzymes that catalyze the committed hydroxylation steps in the biosynthesis of leptinine insecticidal compounds in wild potato or non-bitter SGAs in cultivated tomato.

    • Pablo D. Cárdenas
    • , Prashant D. Sonawane
    • , Uwe Heinig
    • , Adam Jozwiak
    • , Sayantan Panda
    • , Bekele Abebie
    • , Yana Kazachkova
    • , Margarita Pliner
    • , Tamar Unger
    • , Dalia Wolf
    • , Itai Ofner
    • , Ester Vilaprinyo
    • , Sagit Meir
    • , Olga Davydov
    • , Amit Gal-on
    • , Saul Burdman
    • , Ashok Giri
    • , Dani Zamir
    • , Tali Scherf
    • , Jedrzej Szymanski
    • , Ilana Rogachev
    •  & Asaph Aharoni
  • Article
    | Open Access

    Engineering Taxol pathway in microbes needs to overcome the difficulty of expressing plant P450 enzymes. Here, the authors use a compartmentalized metabolic engineering strategy to construct the taxanes production pathway in chloroplasts of Nicotiana benthamiana and realize the production of taxadience-5α-ol.

    • Jianhua Li
    • , Ishmael Mutanda
    • , Kaibo Wang
    • , Lei Yang
    • , Jiawei Wang
    •  & Yong Wang
  • Article
    | Open Access

    Black pepper (Piper nigrum) belongs to the long-isolated lineage of basal angiosperm and its fruit has been used for food spice and phytomedicines for thousands of years. Here, the authors assemble the reference genome of this species and analyze gene families associated with piperine biosynthesis.

    • Lisong Hu
    • , Zhongping Xu
    • , Maojun Wang
    • , Rui Fan
    • , Daojun Yuan
    • , Baoduo Wu
    • , Huasong Wu
    • , Xiaowei Qin
    • , Lin Yan
    • , Lehe Tan
    • , Soonliang Sim
    • , Wen Li
    • , Christopher A Saski
    • , Henry Daniell
    • , Jonathan F. Wendel
    • , Keith Lindsey
    • , Xianlong Zhang
    • , Chaoyun Hao
    •  & Shuangxia Jin
  • 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
    • , Jonathan M. Flowers
    • , Dario Copetti
    • , Alain Lemansour
    • , Marc Lebrun
    • , Khaled Masmoudi
    • , Sylvie Ferrand
    • , Michael I. Dhar
    • , Zoë A. Fresquez
    • , Ulises Rosas
    • , Jianwei Zhang
    • , Jayson Talag
    • , Seunghee Lee
    • , David Kudrna
    • , Robyn F. Powell
    • , Ilia J. Leitch
    • , Robert R. Krueger
    • , Rod A. Wing
    • , Khaled M. A. Amiri
    •  & Michael D. Purugganan
  • Article
    | Open Access

    Meiotic crossovers (COs) are essential for proper chromosome segregation and generating novel combinations of alleles. Here, the authors develop haplotype-specific oligos on maize chromosome 10 for fluorescence in situ hybridization and analyze CO patterns in an intermated recombinant population derived from B73 and Mo17.

    • Lívia do Vale Martins
    • , Fan Yu
    • , Hainan Zhao
    • , Tesia Dennison
    • , Nick Lauter
    • , Haiyan Wang
    • , Zuhu Deng
    • , Addie Thompson
    • , Kassandra Semrau
    • , Jean-Marie Rouillard
    • , James A. Birchler
    •  & Jiming Jiang
  • Article
    | Open Access

    Soybean mosaic virus (SMV) is a potyvirus that reduces soybean yield and seed quality worldwide. Here, the authors reveal that the resistance gene Rsv4 encodes an RNase H family protein with dsRNA-degrading activity, and it can enter the viral replication compartment and degrade viral dsRNA.

    • Kazuhiro Ishibashi
    • , Masayasu Saruta
    • , Takehiko Shimizu
    • , Miao Shu
    • , Toyoaki Anai
    • , Kunihiko Komatsu
    • , Naohiro Yamada
    • , Yuichi Katayose
    • , Masayuki Ishikawa
    • , Masao Ishimoto
    •  & Akito Kaga
  • Article
    | Open Access

    Meiotic crossovers (COs) generate genetic variation and ensure proper chromosome segregation. Here, the authors develop a method for identifying COs at kilobase resolution in pooled recombinants using linked-read sequencing data, and apply it to investigate genome-wide CO landscapes of Arabidopsis thaliana.

    • Hequan Sun
    • , Beth A. Rowan
    • , Pádraic J. Flood
    • , Ronny Brandt
    • , Janina Fuss
    • , Angela M. Hancock
    • , Richard W. Michelmore
    • , Bruno Huettel
    •  & Korbinian Schneeberger
  • Article
    | Open Access

    Stripe rust is a serious threat to wheat production. Here, the authors reveal that the resistance gene, only present in the wheat progenitor Aegilops tauschii and its derived synthetic wheat, encodes a nucleotide oligomerization domain-like receptor and confers resistance in common wheat and barley.

    • Chaozhong Zhang
    • , Lin Huang
    • , Huifei Zhang
    • , Qunqun Hao
    • , Bo Lyu
    • , Meinan Wang
    • , Lynn Epstein
    • , Miao Liu
    • , Chunlan Kou
    • , Juan Qi
    • , Fengjuan Chen
    • , Mengkai Li
    • , Ge Gao
    • , Fei Ni
    • , Lianquan Zhang
    • , Ming Hao
    • , Jirui Wang
    • , Xianming Chen
    • , Ming-Cheng Luo
    • , Youliang Zheng
    • , Jiajie Wu
    • , Dengcai Liu
    •  & Daolin Fu
  • Article
    | Open Access

    How plants deal with iron toxicity is still unclear. Here, the authors reveal that S-nitrosoglutathione-reductase (GSNOR) provides tolerance to iron toxicity by preventing iron-dependent nitrosative and oxidative cytotoxicity in Arabidopsis, legumes, and rice.

    • Baohai Li
    • , Li Sun
    • , Jianyan Huang
    • , Christian Göschl
    • , Weiming Shi
    • , Joanne Chory
    •  & Wolfgang Busch
  • Article
    | Open Access

    Pre-harvest sprouting reduces the yield of agriculturally important crops such as rice. Here, the authors show that mutating specific members of the MIR156 gene family can suppress pre-harvest sprouting in rice without negative effects on plant architecture, suggesting a practical route to elite crop varieties.

    • Chunbo Miao
    • , Zhen Wang
    • , Lin Zhang
    • , Juanjuan Yao
    • , Kai Hua
    • , Xue Liu
    • , Huazhong Shi
    •  & Jian-Kang Zhu
  • Article
    | Open Access

    Three-dimensional genome organization and its effect on transcription remain elusive in rice. Here, the authors map promoter–promoter interactions and heterochromatin interactions using ChIA-PET and reveal spatial correlation between the genetic regulation of eQTLs and e-traits.

    • Lun Zhao
    • , Shuangqi Wang
    • , Zhilin Cao
    • , Weizhi Ouyang
    • , Qing Zhang
    • , Liang Xie
    • , Ruiqin Zheng
    • , Minrong Guo
    • , Meng Ma
    • , Zhe Hu
    • , Wing-Kin Sung
    • , Qifa Zhang
    • , Guoliang Li
    •  & Xingwang Li
  • Article
    | Open Access

    The root microbiota is critical for promoting crop yield. Here, the authors create a synthetic pathway for the production of the rhizopine scyllo-inosamine in Medicago truncatula and barley, and show its perception by rhizosphere bacteria for targeted regulation of bacterial gene expression.

    • Barney A. Geddes
    • , Ponraj Paramasivan
    • , Amelie Joffrin
    • , Amber L. Thompson
    • , Kirsten Christensen
    • , Beatriz Jorrin
    • , Paul Brett
    • , Stuart J. Conway
    • , Giles E. D. Oldroyd
    •  & Philip S. Poole
  • Article
    | Open Access

    Castor is an important industrial oil crop, but knowledge on its genetic diversity is limited. Here, Fan et al. show geographic pattern of Chinese castors that have developed during domestication by population genetic analyses, and reveal candidate genes associated with agronomically important traits.

    • Wei Fan
    • , Jianjun Lu
    • , Cheng Pan
    • , Meilian Tan
    • , Qiang Lin
    • , Wanfei Liu
    • , Donghai Li
    • , Lijun Wang
    • , Lianlian Hu
    • , Lei Wang
    • , Chen Chen
    • , Aimin Wu
    • , Xinxin Yu
    • , Jue Ruan
    • , Jun Yu
    • , Songnian Hu
    • , Xingchu Yan
    • , Shiyou Lü
    •  & Peng Cui
  • Article
    | Open Access

    While multiple cotton genomes are available, genome wide variation comparison between allotetraploid upland cotton cultivars remain unexplored. Here, the authors assemble two upland cotton cultivars and reveal large scale structural variations on chromosome A08.

    • Zhaoen Yang
    • , Xiaoyang Ge
    • , Zuoren Yang
    • , Wenqiang Qin
    • , Gaofei Sun
    • , Zhi Wang
    • , Zhi Li
    • , Ji Liu
    • , Jie Wu
    • , Ye Wang
    • , Lili Lu
    • , Peng Wang
    • , Huijuan Mo
    • , Xueyan Zhang
    •  & Fuguang Li
  • Article
    | Open Access

    Developing hybrid rice cultivars requires time consuming random crossing. Here, the authors develop a new next generation sequencing-based quantitative trait locus mapping method to dissect heterotic gene OsMADS1 and demonstrate the feasibility of pyramiding two genes to achieve large heterotic effect.

    • Changsheng Wang
    • , Shican Tang
    • , Qilin Zhan
    • , Qingqing Hou
    • , Yan Zhao
    • , Qiang Zhao
    • , Qi Feng
    • , Congcong Zhou
    • , Danfeng Lyu
    • , Lingling Cui
    • , Yan Li
    • , Jiashun Miao
    • , Chuanrang Zhu
    • , Yiqi Lu
    • , Yongchun Wang
    • , Ziqun Wang
    • , Jingjie Zhu
    • , Yingying Shangguan
    • , Junyi Gong
    • , Shihua Yang
    • , Wuqi Wang
    • , Jianfu Zhang
    • , Huaan Xie
    • , Xuehui Huang
    •  & Bin Han
  • Article
    | Open Access

    Despite the economic importance of the allotetraploid crop Brassica napus, our knowledge of its phylogenomic relationships, genetic structure, and diversification is limited. Here, the authors show its complex origin and diversification by analyzing transcriptome and organellar sequencing data.

    • Hong An
    • , Xinshuai Qi
    • , Michelle L. Gaynor
    • , Yue Hao
    • , Sarah C. Gebken
    • , Makenzie E. Mabry
    • , Alex C. McAlvay
    • , Graham R. Teakle
    • , Gavin C. Conant
    • , Michael S. Barker
    • , Tingdong Fu
    • , Bin Yi
    •  & J. Chris Pires
  • Article
    | Open Access

    Spatial organization of regulatory elements and its impact on gene expression in plants remain unclear. Here, the authors construct maize chromatin interaction maps using chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) and show their associations with gene expression and agronomic traits.

    • Yong Peng
    • , Dan Xiong
    • , Lun Zhao
    • , Weizhi Ouyang
    • , Shuangqi Wang
    • , Jun Sun
    • , Qing Zhang
    • , Pengpeng Guan
    • , Liang Xie
    • , Wenqiang Li
    • , Guoliang Li
    • , Jianbing Yan
    •  & Xingwang Li
  • Article
    | Open Access

    Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) can discover specific protein-centered chromatin interactions in high resolution. Here, the authors use ChIA-PET to reveal the complex and dynamic interactions between proximal and distal regulatory regions of genes in maize.

    • En Li
    • , Han Liu
    • , Liangliang Huang
    • , Xiangbo Zhang
    • , Xiaomei Dong
    • , Weibin Song
    • , Haiming Zhao
    •  & Jinsheng Lai
  • Article
    | Open Access

    Grain of indica rice accumulates more toxic cadmium (Cd) than japonica, but the underlying genetic basis is unclear. Here, the authors show that natural variation of OsCd1 contributes to divergence in grain Cd accumulation and transferring japonica allele to indica rice leads to reduced Cd accumulation.

    • Huili Yan
    • , Wenxiu Xu
    • , Jianyin Xie
    • , Yiwei Gao
    • , Lulu Wu
    • , Liang Sun
    • , Lu Feng
    • , Xu Chen
    • , Tian Zhang
    • , Changhua Dai
    • , Ting Li
    • , Xiuni Lin
    • , Zhanying Zhang
    • , Xueqiang Wang
    • , Fengmei Li
    • , Xiaoyang Zhu
    • , Jinjie Li
    • , Zichao Li
    • , Caiyan Chen
    • , Mi Ma
    • , Hongliang Zhang
    •  & Zhenyan He
  • Article
    | Open Access

    Our limited understanding of the hybrid sterility (HS) mechanism in Asian–African rice hybrids hampers utilization of the interspecific heterosis for rice production. Here, the authors identify S1-mediated HS-related tripartite gamete killer-protector system, and explore their evolutionary relationship.

    • Yongyao Xie
    • , Jintao Tang
    • , Xianrong Xie
    • , Xiaojuan Li
    • , Jianle Huang
    • , Yue Fei
    • , Jingluan Han
    • , Shuifu Chen
    • , Huiwu Tang
    • , Xiucai Zhao
    • , Dayun Tao
    • , Peng Xu
    • , Yao-Guang Liu
    •  & Letian Chen
  • 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
    • , Shengyuan Sun
    • , Yelu Zou
    • , Shuangyi Yin
    • , Yannan Liu
    • , Shuzhu Tang
    • , Minghong Gu
    • , Zefeng Yang
    •  & Changjie Yan
  • Article
    | Open Access

    Flavor is one of the most important traits for improving tomato sensory quality and consumer acceptability. Here, the authors report meta-analysis of genome-wide association studies of flavor related traits and show genetic insights into the influence of human selection during domestication and improvement.

    • Jiantao Zhao
    • , Christopher Sauvage
    • , Jinghua Zhao
    • , Frédérique Bitton
    • , Guillaume Bauchet
    • , Dan Liu
    • , Sanwen Huang
    • , Denise M. Tieman
    • , Harry J. Klee
    •  & Mathilde Causse
  • Article
    | Open Access

    Existing apple genome assemblies all derive from Golden Delicious. Here, the authors combine different sequencing technologies to assemble a high quality genome of an anther-derived homozygous genotype HFTH1 and find the association of a retrotransposon and red fruit colour.

    • Liyi Zhang
    • , Jiang Hu
    • , Xiaolei Han
    • , Jingjing Li
    • , Yuan Gao
    • , Christopher M. Richards
    • , Caixia Zhang
    • , Yi Tian
    • , Guiming Liu
    • , Hera Gul
    • , Dajiang Wang
    • , Yu Tian
    • , Chuanxin Yang
    • , Minghui Meng
    • , Gaopeng Yuan
    • , Guodong Kang
    • , Yonglong Wu
    • , Kun Wang
    • , Hengtao Zhang
    • , Depeng Wang
    •  & Peihua Cong
  • Article
    | Open Access

    Scarcity of water and nutrients limit crop yields. Here Swift et al. show that gene expression in rice responds differently to changes in the absolute amount of nitrogen available compared to nitrogen concentration and identify expression profiles associated with crop performance in arid, low-nutrient soils.

    • Joseph Swift
    • , Mark Adame
    • , Daniel Tranchina
    • , Amelia Henry
    •  & Gloria M. Coruzzi
  • 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
    • , Man-Wah Li
    • , Fuk-Ling Wong
    • , Xin Wang
    • , Ailin Liu
    • , Zhili Wang
    • , Alden King-Yung Leung
    • , Tin-Hang Wong
    • , Suk-Wah Tong
    • , Zhixia Xiao
    • , Kejing Fan
    • , Ming-Sin Ng
    • , Xinpeng Qi
    • , Linfeng Yang
    • , Tianquan Deng
    • , Lijuan He
    • , Lu Chen
    • , Aisi Fu
    • , Qiong Ding
    • , Junxian He
    • , Gyuhwa Chung
    • , Sachiko Isobe
    • , Takanari Tanabata
    • , Babu Valliyodan
    • , Henry T. Nguyen
    • , Steven B. Cannon
    • , Christine H. Foyer
    • , Ting-Fung Chan
    •  & Hon-Ming Lam
  • Article
    | Open Access

    Despite the importance of grapevine cultivation in human history and the economic values of cultivar improvement, large-scale genomic variation data are lacking. Here the authors resequence 472 Vitis accessions and use the identified genetic variations for domestication history, demography, and GWAS analyses.

    • Zhenchang Liang
    • , Shengchang Duan
    • , Jun Sheng
    • , Shusheng Zhu
    • , Xuemei Ni
    • , Jianhui Shao
    • , Chonghuai Liu
    • , Peter Nick
    • , Fei Du
    • , Peige Fan
    • , Ruzhi Mao
    • , Yifan Zhu
    • , Weiping Deng
    • , Min Yang
    • , Huichuan Huang
    • , Yixiang Liu
    • , Yiqing Ding
    • , Xianju Liu
    • , Jianfu Jiang
    • , Youyong Zhu
    • , Shaohua Li
    • , Xiahong He
    • , Wei Chen
    •  & Yang Dong
  • Article
    | Open Access

    Brassica napus is a globally important oil crop, but the origin of the allotetraploid genome and its improvement process are largely unknown. Here, the authors take a population genetic approach to resolve its origin and evolutionary history, and identify candidate genes related to important agricultural traits.

    • Kun Lu
    • , Lijuan Wei
    • , Xiaolong Li
    • , Yuntong Wang
    • , Jian Wu
    • , Miao Liu
    • , Chao Zhang
    • , Zhiyou Chen
    • , Zhongchun Xiao
    • , Hongju Jian
    • , Feng Cheng
    • , Kai Zhang
    • , Hai Du
    • , Xinchao Cheng
    • , Cunming Qu
    • , Wei Qian
    • , Liezhao Liu
    • , Rui Wang
    • , Qingyuan Zou
    • , Jiamin Ying
    • , Xingfu Xu
    • , Jiaqing Mei
    • , Ying Liang
    • , You-Rong Chai
    • , Zhanglin Tang
    • , Huafang Wan
    • , Yu Ni
    • , Yajun He
    • , Na Lin
    • , Yonghai Fan
    • , Wei Sun
    • , Nan-Nan Li
    • , Gang Zhou
    • , Hongkun Zheng
    • , Xiaowu Wang
    • , Andrew H. Paterson
    •  & Jiana Li
  • Article
    | Open Access

    Cytosolic lipid droplets are ER-derived organelles that accumulate in seeds to fuel germination. Here, Sadre et al. show that by boosting lipid production and anchoring key terpenoid biosynthetic enzymes to the droplet surface, an efficient terpenoid production platform can be established in leaves.

    • Radin Sadre
    • , Peiyen Kuo
    • , Jiaxing Chen
    • , Yang Yang
    • , Aparajita Banerjee
    • , Christoph Benning
    •  & Bjoern Hamberger
  • Article
    | Open Access

    Few approaches for targeted manipulation of the epigenome are available in plants. Here, the authors adapt the dCas9-SunTag system to engineer targeted gene activation and site-specific manipulation of DNA methylation in Arabidopsis.

    • Ashot Papikian
    • , Wanlu Liu
    • , Javier Gallego-Bartolomé
    •  & Steven E. Jacobsen
  • Article
    | Open Access

    Broomcorn millet is one of the earliest domesticated plants and has the highest water use efficiency among cereals. Here, the authors report its genome assembly and annotation, which provides a valuable resource for breeders and paves the way for studying plant drought tolerance and C4 photosynthesis.

    • Changsong Zou
    • , Leiting Li
    • , Daisuke Miki
    • , Delin Li
    • , Qiming Tang
    • , Lihong Xiao
    • , Santosh Rajput
    • , Ping Deng
    • , Li Peng
    • , Wei Jia
    • , Ru Huang
    • , Meiling Zhang
    • , Yidan Sun
    • , Jiamin Hu
    • , Xing Fu
    • , Patrick S. Schnable
    • , Yuxiao Chang
    • , Feng Li
    • , Hui Zhang
    • , Baili Feng
    • , Xinguang Zhu
    • , Renyi Liu
    • , James C. Schnable
    • , Jian-Kang Zhu
    •  & Heng Zhang
  • Article
    | Open Access

    Broomcorn millet is one of the oldest crops cultivated by human that has strong abiotic stress tolerance. To facilitate genome assisted breeding of this and related species, the authors report its genome assembly and conduct comparative genome structure and evolution analyses with foxtail millet.

    • Junpeng Shi
    • , Xuxu Ma
    • , Jihong Zhang
    • , Yingsi Zhou
    • , Minxuan Liu
    • , Liangliang Huang
    • , Silong Sun
    • , Xiangbo Zhang
    • , Xiang Gao
    • , Wei Zhan
    • , Pinghua Li
    • , Lun Wang
    • , Ping Lu
    • , Haiming Zhao
    • , Weibin Song
    •  & Jinsheng Lai
  • Article
    | Open Access

    The origin of Tibetan barley (qingke) has been a controversial issue for many years. Here, the authors conduct population genomics study to support that qingke is derived from eastern domesticated barley instead of Tibetan wild barley and suggest southern Tibetan Plateau as its introduction route.

    • Xingquan Zeng
    • , Yu Guo
    • , Qijun Xu
    • , Martin Mascher
    • , Ganggang Guo
    • , Shuaicheng Li
    • , Likai Mao
    • , Qingfeng Liu
    • , Zhanfeng Xia
    • , Juhong Zhou
    • , Hongjun Yuan
    • , Shuaishuai Tai
    • , Yulin Wang
    • , Zexiu Wei
    • , Li Song
    • , Sang Zha
    • , Shiming Li
    • , Yawei Tang
    • , Lijun Bai
    • , Zhenhua Zhuang
    • , Weiming He
    • , Shancen Zhao
    • , Xiaodong Fang
    • , Qiang Gao
    • , Ye Yin
    • , Jian Wang
    • , Huanming Yang
    • , Jing Zhang
    • , Robert J. Henry
    • , Nils Stein
    •  & Nyima Tashi
  • Article
    | Open Access

    Assembly of large, repeat-rich eukaryotic genomes remains challenging. Here, the authors use BioNano Genomics DLS optical mapping and single-molecule nanopore sequencing to generate a chromosome-scale assembly of a new Sorghum bicolor accession and identify variation compared to the publicly available S. bicolor genome.

    • Stéphane Deschamps
    • , Yun Zhang
    • , Victor Llaca
    • , Liang Ye
    • , Abhijit Sanyal
    • , Matthew King
    • , Gregory May
    •  & Haining Lin
  • Article
    | Open Access

    Remarkable organ shape morphological diversity exists in fruits, vegetables and seeds. Here, the authors establish a link between OVATE Family Proteins and TONNEAU1 Recruiting Motif family proteins in the development pathway that governs fruit shape of tomato, melon, and cucumber as well as potato tuber shape.

    • Shan Wu
    • , Biyao Zhang
    • , Neda Keyhaninejad
    • , Gustavo R. Rodríguez
    • , Hyun Jung Kim
    • , Manohar Chakrabarti
    • , Eudald Illa-Berenguer
    • , Nathan K. Taitano
    • , M. J Gonzalo
    • , Aurora Díaz
    • , Yupeng Pan
    • , Courtney P. Leisner
    • , Dennis Halterman
    • , C. Robin Buell
    • , Yiqun Weng
    • , Shelley H. Jansky
    • , Herman van Eck
    • , Johan Willemsen
    • , Antonio J. Monforte
    • , Tea Meulia
    •  & Esther van der Knaap
  • Article
    | Open Access

    Drought resistant plants typically have reduced growth. Here the authors show that overexpression of the BRL3 brassinosteroid receptor confers drought tolerance and accumulation of osmoprotectant metabolites without penalizing growth, demonstrating that drought response and growth can be uncoupled.

    • Norma Fàbregas
    • , Fidel Lozano-Elena
    • , David Blasco-Escámez
    • , Takayuki Tohge
    • , Cristina Martínez-Andújar
    • , Alfonso Albacete
    • , Sonia Osorio
    • , Mariana Bustamante
    • , José Luis Riechmann
    • , Takahito Nomura
    • , Takao Yokota
    • , Ana Conesa
    • , Francisco Pérez Alfocea
    • , Alisdair R. Fernie
    •  & Ana I. Caño-Delgado
  • Article
    | Open Access

    Plant architecture transition is one of the great consequences during rice domestication. Here, the authors find that chromosomal deletions linked to the previously known PROG1 gene also participate in plant architecture domestication in both Asian and African cultivated rice.

    • Yongzhen Wu
    • , Shuangshuang Zhao
    • , Xianran Li
    • , Bosen Zhang
    • , Liyun Jiang
    • , Yanyan Tang
    • , Jie Zhao
    • , Xin Ma
    • , Hongwei Cai
    • , Chuanqing Sun
    •  & Lubin Tan
  • Article
    | Open Access

    Unilateral cross-incompatibility between certain varieties of maize prevents cross-fertilization and can facilitate hybrid breeding. Here the authors show that a PECTIN METHYLESTERASE gene is able to overcome this reproductive barrier and confer fertility when expressed in pollen of the male parent.

    • Zhaogui Zhang
    • , Baocai Zhang
    • , Zhibin Chen
    • , Dongmei Zhang
    • , Huairen Zhang
    • , Hang Wang
    • , Yu’e Zhang
    • , Darun Cai
    • , Juan Liu
    • , Senlin Xiao
    • , Yanqing Huo
    • , Jie Liu
    • , Lanjun Zhang
    • , Mingming Wang
    • , Xu Liu
    • , Yongbiao Xue
    • , Li Zhao
    • , Yihua Zhou
    •  & Huabang Chen
  • Article
    | Open Access

    Previous efforts to assemble Rubisco within a cyanobacterial carboxysome-derived protein shell in plant chloroplasts to concentrate CO2 have been unsuccessful. Here, Long et al. produce carboxysomes in tobacco chloroplasts that encapsulate the introduced Rubisco and enable autotrophic growth at elevated CO2.

    • Benedict M. Long
    • , Wei Yih Hee
    • , Robert E. Sharwood
    • , Benjamin D. Rae
    • , Sarah Kaines
    • , Yi-Leen Lim
    • , Nghiem D. Nguyen
    • , Baxter Massey
    • , Soumi Bala
    • , Susanne von Caemmerer
    • , Murray R. Badger
    •  & G. Dean Price
  • Article
    | Open Access

    The effect of long noncoding RNAs (lncRNAs) on crop yield is unknown. Here, the authors show overexpression of a lncRNA, transcribed from the antisense strand of the previously discovered gene cluster LRK, can upregulate LRK genes’ expression, change histone modification status of LRK1, and increase rice grain yield.

    • Ying Wang
    • , Xiaojin Luo
    • , Fan Sun
    • , Jianhua Hu
    • , Xiaojun Zha
    • , Wei Su
    •  & Jinshui Yang
  • Article
    | Open Access

    Japonica rice can grow further north than wild or indica rice and is more tolerant of cold climates. Here, the authors show that bZIP73 likely underwent selection in the early phase of rice domestication to facilitate cold tolerance in japonica by modulating ABA and ROS homeostasis.

    • Citao Liu
    • , Shujun Ou
    • , Bigang Mao
    • , Jiuyou Tang
    • , Wei Wang
    • , Hongru Wang
    • , Shouyun Cao
    • , Michael R. Schläppi
    • , Bingran Zhao
    • , Guoying Xiao
    • , Xiping Wang
    •  & Chengcai Chu
  • Article
    | Open Access

    Asparaginyl endopeptidases (AEPs) are plant proteases that can also function as ligases, catalyzing the production of cyclic plant peptides. Here, the authors identify structural features that govern AEP ligase activity, providing insights to aid the discovery and engineering of ligase-type AEPs.

    • M. A. Jackson
    • , E. K. Gilding
    • , T. Shafee
    • , K. S. Harris
    • , Q. Kaas
    • , S. Poon
    • , K. Yap
    • , H. Jia
    • , R. Guarino
    • , L. Y. Chan
    • , T. Durek
    • , M. A. Anderson
    •  & D. J. Craik
  • Article
    | Open Access

    There are various indigenous cattle breeds in East Asia which have a complex history. Here, the authors analyse the genomes of 49 modern breeds and eight ancient samples and identify three distinct ancestries and multiple adaptive introgressions from other bovine species.

    • Ningbo Chen
    • , Yudong Cai
    • , Qiuming Chen
    • , Ran Li
    • , Kun Wang
    • , Yongzhen Huang
    • , Songmei Hu
    • , Shisheng Huang
    • , Hucai Zhang
    • , Zhuqing Zheng
    • , Weining Song
    • , Zhijie Ma
    • , Yun Ma
    • , Ruihua Dang
    • , Zijing Zhang
    • , Lei Xu
    • , Yutang Jia
    • , Shanzhai Liu
    • , Xiangpeng Yue
    • , Weidong Deng
    • , Xiaoming Zhang
    • , Zhouyong Sun
    • , Xianyong Lan
    • , Jianlin Han
    • , Hong Chen
    • , Daniel G Bradley
    • , Yu Jiang
    •  & Chuzhao Lei
  • Article
    | Open Access

    Genes that confer resistance to plant pathogens such as rice blast disease typically encode NLR-type receptor proteins. Here, Zhao et al. describe a new resistance locus that encodes a non-NLR Armadillo repeat protein required for broad-spectrum resistance in rice.

    • Haijun Zhao
    • , Xueyan Wang
    • , Yulin Jia
    • , Bastian Minkenberg
    • , Matthew Wheatley
    • , Jiangbo Fan
    • , Melissa H. Jia
    • , Adam Famoso
    • , Jeremy D. Edwards
    • , Yeshi Wamishe
    • , Barbara Valent
    • , Guo-Liang Wang
    •  & Yinong Yang
  • Article
    | Open Access

    Efficient gene targeting in higher plants remains challenging. Here, the authors develop a sequential transformation method for CRISPR/Cas9-mediated gene targeting in Arabidopsis and demonstrate its functionality at five genomic sites in two endogenous loci.

    • Daisuke Miki
    • , Wenxin Zhang
    • , Wenjie Zeng
    • , Zhengyan Feng
    •  & Jian-Kang Zhu