Agricultural genetics articles within Nature Communications

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  • 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
    •  & 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
    •  & Jinsheng Lai

  • 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
    •  & 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
    •  & 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
    •  & Mathilde Causse

  • 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
    •  & 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
    •  & 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
    •  & Yang Dong

  • 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
    •  & 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
    •  & 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
    •  & 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.

    • StĂ©phane Deschamps
    • , Yun Zhang
    •  & 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
    •  & Esther van der Knaap

  • 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
    •  & 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
    •  & Chengcai Chu

  • 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 GÎł 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

    Inflorescence architecture affects crop grain yield. Here, the authors deploy whole-genome sequencing-based bulk segregant analysis to identify the causal gene of a sorghum multi-seeded (msd) mutant and suggest MSD1 regulating the fertility of the pedicellate spikelets through jasmonic acid pathway.

    • Yinping Jiao
    • , Young Koung Lee
    •  & Zhanguo Xin

  • 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

    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

    The newly recognized Fusarium wilt pathogen tropical race 4 is threatening worldwide banana production. Here, the authors transform Cavendish bananas with a resistance gene, RGA2, from diploid banana or a nematode-derived gene, Ced9, and confer resistance to natural infection under field conditions.

    • James Dale
    • , Anthony James
    •  & Robert Harding

  • Article
    | Open Access

    A reproductive barrier between japonica and indica rice subspecies hinders hybrid breeding. Here, the authors reveal that structural and copy number variations of a pollen-essential gene, which encodes a DUF1618-domain protein, result in allelic suppression and subsequently cause hybrid male sterility.

    • Rongxin Shen
    • , Lan Wang
    •  & Yao-Guang Liu

  • Article
    | Open Access

    The VRS genes of barley control the fertility of the lateral spikelets on the barley inflorescence. Here, Bull et al. show that VRS3 encodes a putative Jumonji C-type histone demethylase that regulates expression of other VRS genes, and genes involved in stress, hormone and sugar metabolism.

    • Hazel Bull
    • , M. Cristina Casao
    •  & Robbie Waugh

  • Article
    | Open Access

    Variation among wild relatives of crop plants can be used to identify genes underlying traits of agronomic importance. Here, the authors show that a modified mapping-by-sequencing approach can rapidly identify the genetic basis for viral resistance in sugar beet using wild beet populations in their natural habitat.

    • Gina G. Capistrano-Gossmann
    • , D. Ries
    •  & F. J. Kopisch-Obuch

  • Article
    | Open Access

    The male-sterilems2 mutant has facilitated commercial production of wheat for over 40 years. Here, Xia et al. map Ms2and describe how a retrotransposon insertion event in the regulatory element of an orphan gene is associated with expression in anthers and development of male sterility.

    • Chuan Xia
    • , Lichao Zhang
    •  & Xiuying Kong

  • Article
    | Open Access

    The dominant male-sterile geneMs2 has facilitated the release of hundreds of wheat-breeding lines and cultivars in China. Here Ni et al. describe the cloning of the Ms2 gene, which appears as an orphan gene in the Triticinae, and show that Ms2 can be used to confer male sterility in wheat, barley and Brachypodium.

    • Fei Ni
    • , Juan Qi
    •  & Daolin Fu

  • Article
    | Open Access

    Peking-type and PI 88788-type soybeans are both used as sources of resistance against soybean cyst nematode. Here the authors show that in contrast to PI 88788-type resistance, whereGmSNAP18 acts in combination with two neighbouring genes, in Peking-type resistance GmSNAP18 acts with GmSHMT08to confer resistance.

    • Shiming Liu
    • , Pramod K. Kandoth
    •  & Khalid Meksem

  • Article
    | Open Access

    Low temperature is a major factor limiting productivity in rice. Here the authors show that theCTB4a gene confers cold tolerance to japonicavarieties adapted to cold habitats at the booting stage of development, and propose that CTB4a acts via an interaction with the beta subunit of ATP synthase.

    • Zhanying Zhang
    • , Jinjie Li
    •  & Zichao Li

  • Article
    | Open Access

    Cpf1 is a type V CRISPR effector protein that has different target and guide RNA requirements compared to Cas9, thus offering an addition tool for precision genome editing. Here Kimet al. show that Cpf1 ribonucleoprotein can be introduced into protoplasts and used for transgene-free gene editing in plants.

    • Hyeran Kim
    • , Sang-Tae Kim
    •  & Sang-Gyu Kim

  • Article
    | Open Access

    Brassica oleracea is a single species that includes diverse crops such as cabbage, broccoli and Brussels sprouts. Here, the authors identify genes not captured in existing B. oleraceareference genomes by the assembly of a pangenome and show variations in gene content that may be related to important agronomic traits

    • Agnieszka A. Golicz
    • , Philipp E. Bayer
    •  & David Edwards

  • Article
    | Open Access

    Plant-feeding insects of the Lygus genus have emerged as a major pest effecting cotton crops in the USA. Here the authors optimize the insecticidal activity of a Bacillus thuringiensis crystal protein and produce transgenic plants that are resistant to feeding damage by Lygusspecies.

    • Anilkumar Gowda
    • , Timothy J. Rydel
    •  & James A. Baum

  • Article
    | Open Access

    Cassava is a major source of food in tropical and subtropical regions. Here the authors sequence the genomes of wild and domesticated cassava varieties and identify genes that have been selected for and against during the evolution and domestication of this economically important crop.

    • Wenquan Wang
    • , Binxiao Feng
    •  & Ming Peng

  • 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 |

    Sorghum is an important crop species for the African continent but the grain is difficult to digest. The authors of this study examine a previously identified sorghum mutant known for improved digestion and find that the mutant is the result of a point mutation in the seed-processing protein kafirin.

    • Yongrui Wu
    • , Lingling Yuan
    •  & Joachim Messing

  • Article
    | Open Access

    Barley is an important food crop that has been adapted to grow on acidic soils that often contain toxic soluble aluminium. In this study, an insertion in the upstream region of a citrate transporter is shown to confer resistance of barley to aluminium toxicity and is found in aluminium-tolerant barley accessions.

    • Miho Fujii
    • , Kengo Yokosho
    •  & Jian Feng Ma

  • Article
    | Open Access

    Much effort has been devoted to the generation of rice plants with short stature to improve grain yield and increased resistance to lodging. Through quantitative trait analysis, these authors identify a gene—STRONG CULM2—that confers increased grain yield, culm strength and spikelet number in rice.

    • Taiichiro Ookawa
    • , Tokunori Hobo
    •  & Makoto Matsuoka

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