Plant breeding

  • 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
  • Article
    | Open Access

    Breeding has increased crop productivity, but whether it has also changed phenotypic plasticity is unclear. Here, the authors find maize genomic regions selected for high productivity show reduced contribution to genotype by environment variation and provide evidence for regulatory control of phenotypic stability.

    • Joseph L. Gage
    • , Diego Jarquin
    •  & Natalia de Leon
  • 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

    Targeted homologous recombination between parental chromosomes could facilitate precision breeding of crop plants. Here, Filler Hayutet al. show that CRISPR-Cas9 can be used to induce DNA double strand breaks in somatic tissue and achieve targeted recombination between homologs at an endogenous locus in tomato.

    • Shdema Filler Hayut
    • , Cathy Melamed Bessudo
    •  & Avraham A. Levy
  • 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

    Peach is both an economically important crop species and a model for Rosaceae fruit development research. Here, the authors perform genome-wide association analysis in peach and find candidate genes associated with variation in agronomically important fruit phenotypes.

    • Ke Cao
    • , Zhengkui Zhou
    •  & Lirong Wang