Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato

Autor: Michael Alonge, Michael C. Schatz, Samuel F. Hutton, Zachary H. Lemmon, Fritz J. Sedlazeck, Zachary B. Lippman, José M. Jiménez-Gómez, Sebastian Soyk, Joyce Van Eck
Přispěvatelé: Cold Spring Harbor Laboratory (CSHL), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Baylor College of Medecine, University of Florida [Gainesville] (UF), Boyce Thompson Institute for Plant Research, Cornell University [New York], Johns Hopkins University (JHU), Department of Surgery [Johns Hopkins Medicine], The Johns Hopkins Hospital, European Molecular Biology Organization (EMBO) ALTF 1589-2014, National Science Foundation Postdoctoral Research Fellowship in Biology Grant IOS-1523423, National Institute of Health Research Project with Complex Structure Cooperative Agreement 3UM1HG008898-01S2, US-Israel Binational Science Foundation IS-4818-15, US-Israel Binational Science Foundation, Agriculture and Food Research Initiative competitive grant of the USDA National Institute of Food and Agriculture 2016-67013-24452, ational Science Foundation (NSF) NSF - Office of the Director (OD) IOS-1732253, ANR-17-CE20-0024,tomaTE,Contribution des éléments transposables (ET) à la domestication et à l'amélioration de la tomate(2017), Cold Spring Harbor, Cold Spring Harbor Laboratory, Human Genome Sequencing Center, Baylor College of Medicine (BCM), Baylor University-Baylor University, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Horticultural Sciences Department, Boyce Thompson Institute [Ithaca], Plant Breeding and Genetics Section, School of Integrative Plant Science, Johns Hopkins Medicine, Partenaires INRAE
Jazyk: angličtina
Rok vydání: 2019
Předmět:
0106 biological sciences
0301 basic medicine
MESH: Gene Editing
MESH: CRISPR-Cas Systems
MESH: Domestication
[SDV]Life Sciences [q-bio]
Locus (genetics)
Plant Science
Gene mutation
Biology
MESH: CRISPR-Associated Protein 9
MESH: Reproduction
01 natural sciences
03 medical and health sciences
Genome editing
MESH: Lycopersicon esculentum
Gene duplication
Genetic variation
[SDV.IDA]Life Sciences [q-bio]/Food engineering
MESH: Epistasis
Genetic
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology
[SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering
MESH: Genetic Variation
Domestication
2. Zero hunger
Genetics
MESH: Gene Duplication
MESH: Flowers
MESH: Quantitative Trait Loci
030104 developmental biology
MESH: Plant Breeding
MESH: Plants
Genetically Modified
Epistasis
Tandem exon duplication
010606 plant biology & botany
Zdroj: Nature Plants
Nature Plants, Nature Publishing Group, 2019, 5 (5), pp.471-479. ⟨10.1038/s41477-019-0422-z⟩
Nature Plants, Nature Publishing Group, 2019, 5, pp.471-479. ⟨10.1038/s41477-019-0422-z⟩
ISSN: 2055-026X
2055-0278
DOI: 10.1038/s41477-019-0422-z⟩
Popis: International audience; Genome editing technologies are being widely adopted in plant breeding1. However, a looming challenge of engineering desirable genetic variation in diverse genotypes is poor predictability of phenotypic outcomes due to unforeseen interactions with pre-existing cryptic mutations2-4. In tomato, breeding with a classical MADS-box gene mutation that improves harvesting by eliminating fruit stem abscission frequently results in excessive inflorescence branching, flowering and reduced fertility due to interaction with a cryptic variant that causes partial mis-splicing in a homologous gene5-8. Here, we show that a recently evolved tandem duplication carrying the second-site variant achieves a threshold of functional transcripts to suppress branching, enabling breeders to neutralize negative epistasis on yield. By dissecting the dosage mechanisms by which this structural variant restored normal flowering and fertility, we devised strategies that use CRISPR-Cas9 genome editing to predictably improve harvesting. Our findings highlight the under-appreciated impact of epistasis in targeted trait breeding and underscore the need for a deeper characterization of cryptic variation to enable the full potential of genome editing in agriculture.
Databáze: OpenAIRE
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