Plant breeding articles within Nature Communications

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  • Article
    | Open Access

    Leaf rust is an economically significant disease of barley. Here the authors describe cloning of the barley Rph3 leaf rust resistance gene and reveal it encodes a predicted transmembrane protein that is expressed upon infection by Rph3-avirulent Puccinia hordei isolates.

    • Hoan X. Dinh
    • , Davinder Singh
    •  & Mohammad Pourkheirandish

  • Article
    | Open Access

    While a large amount of genomic resources is available, the phylogeny of wild and cultivated beets remains unclear. Here, the authors use the k-mer-based Mash method to analyze resequenced genomes of 606 accessions of the genus Beta and reveal Greece as the domestication site of sugar beet.

    • Felix L. Sandell
    • , Nancy Stralis-Pavese
    •  & Juliane C. Dohm

  • Article
    | Open Access

    Thermosensitive genic male-sterile (TGMS) lines are widely used for two-line hybrid rice breeding, but the mechanism of TGMS has not been fully elucidated. Here, the authors show that natural allele of the OsMS1 gene, encoding a histone binding PHD finger protein, responds to temperature change and confers TGMS in rice.

    • Lunying Wu
    • , Xiaohui Jing
    •  & Yunhai Li

  • Article
    | Open Access

    Unilaterial cross-incompatibility (UCI) systems are regulated by a male-female gene pair that are genetically linked, but no pair of the male and female determinants has been isolated so far. Here, the authors report the cloning of a pair of pectin methylesterases encoding genes at the Ga2 locus confer UCI in maize.

    • Zhibin Chen
    • , Zhaogui Zhang
    •  & Huabang Chen

  • Comment
    | Open Access

    By the end of this century, a 50% increase in agricultural productivity is required to feed the world. Recent studies have demonstrated de novo domestication of wild plants as a new crop breeding strategy to meet future food challenges.

    • Hong Yu
    •  & Jiayang Li

  • 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

    The genes underlying stripe rust host specificity between wheat and barley remain unknown. Here, the authors report that Rps6, Rps7 and Rps8 determine host species specificity in barley at different stages of the pathogen lifecycle and the barley powdery mildew immune receptor Mla8 and Rps7 are the same gene.

    • Jan Bettgenhaeuser
    • , Inmaculada Hernández-Pinzón
    •  & Matthew J. Moscou

  • 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

    Diploid potatoes are typically self-incompatible, complicating efforts to breed diploid cultivars. Here the authors report map-based cloning of the S-locus inhibitor (Sli) gene in potato which encodes a non S-locus F-box protein that is expressed in pollen and can functions like a general S-RNase inhibitor to overcome self-incompatibility.

    • Ling Ma
    • , Chunzhi Zhang
    •  & Yi Shang

  • Article
    | Open Access

    The long-term effectiveness of assisted gene flow of trees could be jeopardised by rapid climate change. Here the authors analyse a large dataset of relocated black spruce populations in Canada, finding that local adaptation to climate of origin improved NPP responses, but only for up to ~15 years after planting.

    • Martin P. Girardin
    • , Nathalie Isabel
    •  & Patrick Lenz

  • Article
    | Open Access

    Studies of fruit quality traits in pears are lagging behind the other major fruit trees. Here, the authors conduct GWAS of fruit quality and phenological traits in a panel of 312 sand pear accessions using SNPs called from resequencing data, and reveal the involvement of a lignin formation-related protein in regulating stone cell development.

    • Ming-Yue Zhang
    • , Cheng Xue
    •  & Jun Wu

  • Article
    | Open Access

    The development of hybrid wheat cultivars is hampered by the lack of an effective way to control male fertility in breeding lines. Here, the authors report the identification of two restorer-of-fertility genes Rf1 and Rf3 that can restore fertility of wheat plants carrying Triticum timopheevii-type cytoplasmic male sterility.

    • Joanna Melonek
    • , Jorge Duarte
    •  & Ian Small

  • Article
    | Open Access

    Septoria tritici blotch (STB) is a devastating foliar disease affecting worldwide wheat production. Here, the authors report a cysteine-rich receptor-like kinase that can confer resistance to Zymoseptoria tritici, the pathogen that causes STB, and slow penetration and intercellular growth of the pathogen.

    • Cyrille Saintenac
    • , Florence Cambon
    •  & Thierry Langin

  • Article
    | Open Access

    Fruit firmness is an important target for breeders and a key determinant of shelf life for many fruits. Here the authors show that mutating tomato FIS1, a GA2-oxidase, increases the concentration of bioactive gibberellins, enhances cutin and wax biosynthesis and increases fruit firmness.

    • Ren Li
    • , Shuai Sun
    •  & Xia Cui

  • 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

    Azaleas are one of the most diverse ornamental plants and have cultural and economic importance. Here, the authors report a chromosome-scale genome assembly for the primary ancestor of the azalea cultivar Rhododendro simsi and identify transcription factors that may function in flower coloration at different stages.

    • Fu-Sheng Yang
    • , Shuai Nie
    •  & Jian-Feng Mao

  • 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

    Fonio millet is a fast growing orphan cereal crop with a great potential for dryland agriculture. Here, the authors report chromosome-scale reference genome assembly and population genomic resources to shed light on genetic diversity, population structure and domestication of fonio millet.

    • Michael Abrouk
    • , Hanin Ibrahim Ahmed
    •  & Simon G. Krattinger

  • Article
    | Open Access

    Increasing grain yield needs to be put in the context of environmental stress. Here, the authors reveal that a UDP-glucosyltransferase is associated with regulation of rice grain size, abiotic stress tolerance, flavonoid-mediated auxin signaling, and redirection of carbon flux to flavonoid glycosides synthesis.

    • Nai-Qian Dong
    • , Yuwei Sun
    •  & Hong-Xuan Lin

  • Article
    | Open Access

    Existing examples of targeted gene insertion in plants either rely on a selectable marker gene or result in short DNA inserts. Here, the authors use an optimized CRISPR-Cas9 method to insert a 5.2 kb carotenoid biosynthesis cassette into genomic safe harbors in rice, and obtain marker-free lines with high carotenoid content.

    • Oliver Xiaoou Dong
    • , Shu Yu
    •  & Pamela C. Ronald

  • Article
    | Open Access

    A transposon insertion in the regulatory region of maize Tb1 gene leads to increased apical dominance and a reduction of tillering. Here, the authors showed that a duplicated rice Tb1 orthologue, OsTb2, has gained a regulatory effect on tillering opposite that of OsTb1 during artificial selection only in upland japonica rice.

    • Jun Lyu
    • , Liyu Huang
    •  & Fengyi Hu

  • 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
    •  & Jianmin Wan

  • 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
    •  & Bin Han

  • 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

    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

    The sour taste of citrus fruit results from the extremely low pH of juice vesicle cell vacuoles. Here the authors provide genetic evidence that a vacuolar P-type ATPase, that is known to determine flower color in petunia via vacuolar acidification, is also responsible for extreme acidification in citrus.

    • Pamela Strazzer
    • , Cornelis E. Spelt
    •  & Francesca M. Quattrocchio

  • Article
    | Open Access

    Meiotic crossover (CO) landscape differs inter- and intra-species, as well as between sexes. Here, the authors show that male meiosis produces more COs than female in maize and detect CO maturation inefficiency in some genetic backgrounds, which may help to improve breeding efficiency.

    • Cheng Luo
    • , Xiang Li
    •  & Jianbing Yan

  • 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

    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

    Domestication reduces genetic diversity and constrains crop improvement. Here the authors identify factors that shaped species diversity in the wild progenitors of chickpea, and produce wild introgression populations that increase diversity for breeding by ~100-fold, including traits of agronomic relevance.

    • Eric J.B. von Wettberg
    • , Peter L. Chang
    •  & Douglas R. Cook

  • Article
    | Open Access

    In flowering plants, the pollen coat surrounds the male germ cells and protects against dehydration, damage and pathogen attack. Here, the authors show that a deficiency in terpenoid synthesis results in rice pollen over-dehydration and leads to a humidity-sensitive conditional male sterile phenotype.

    • Zheyong Xue
    • , Xia Xu
    •  & Xiaoquan Qi

  • 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

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