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Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding
- Source :
- Nature Communications, Vol 11, Iss 1, Pp 1-11 (2020), Nature Communications
- Publication Year :
- 2020
- Publisher :
- Nature Publishing Group, 2020.
-
Abstract
- Solanum pimpinellifolium (SP) is the wild progenitor of cultivated tomato. Because of its remarkable stress tolerance and intense flavor, SP has been used as an important germplasm donor in modern tomato breeding. Here, we present a high-quality chromosome-scale genome sequence of SP LA2093. Genome comparison identifies more than 92,000 structural variants (SVs) between LA2093 and the modern cultivar, Heinz 1706. Genotyping these SVs in ~600 representative tomato accessions identifies alleles under selection during tomato domestication, improvement and modern breeding, and discovers numerous SVs overlapping genes known to regulate important breeding traits such as fruit weight and lycopene content. Expression quantitative trait locus (eQTL) analysis detects hotspots harboring master regulators controlling important fruit quality traits, including cuticular wax accumulation and flavonoid biosynthesis, and SVs contributing to these complex regulatory networks. The LA2093 genome sequence and the identified SVs provide rich resources for future research and biodiversity-based breeding.<br />Solanum pimpinellifolium (SP) is the progenitor of cultivated tomato and an important germplasm. Here, the authors assemble SP genome, identify structural variants (SVs) by comparing with modern cultivar, reveal SVs associated with important breeding traits, and detect SVs harboring master regulators of fruit quality traits.
- Subjects :
- 0106 biological sciences
0301 basic medicine
Germplasm
Genotype
Plant domestication
Science
Quantitative Trait Loci
General Physics and Astronomy
Solanum
01 natural sciences
Genome
Article
General Biochemistry, Genetics and Molecular Biology
Domestication
Structural variation
03 medical and health sciences
Lycopene
Solanum lycopersicum
Gene Expression Regulation, Plant
Selection, Genetic
lcsh:Science
Gene
Comparative genomics
Genetics
Whole genome sequencing
Multidisciplinary
biology
fungi
food and beverages
Sequence Analysis, DNA
General Chemistry
biology.organism_classification
Solanum pimpinellifolium
Plant Breeding
Natural variation in plants
030104 developmental biology
lcsh:Q
Genome, Plant
010606 plant biology & botany
Subjects
Details
- Language :
- English
- ISSN :
- 20411723
- Volume :
- 11
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- Nature Communications
- Accession number :
- edsair.doi.dedup.....9ae5282ca7dd23e62f1f133c82d44301