Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding.
Nat Commun, 2020/11/16;11(1):5817.
Wang X[1], Gao L[1, 2], Jiao C[1], Stravoravdis S[1], Hosmani PS[1], Saha S[1], Zhang J[1], Mainiero S[1], Strickler SR[1], Catala C[1], Martin GB[1, 3], Mueller LA[1], Vrebalov J[1], Giovannoni JJ[1, 4], Wu S[5], Fei Z[6, 7]
Affiliations
PMID: 33199703DOI: 10.1038/s41467-020-19682-0
Impact factor: 17.694
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.
MeSH terms
Domestication; Gene Expression Regulation, Plant; Genome, Plant; Genotype; Lycopene; Lycopersicon esculentum; Plant Breeding; Quantitative Trait Loci; Selection, Genetic; Sequence Analysis, DNA; Solanum
More resources
Full text:
Europe PubMed Central; PubMed Central
EndNote: Download