Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding

Nature Communications
Xin WangZhangjun Fei

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.

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Citations

Dec 22, 2020·The Plant Journal : for Cell and Molecular Biology·Xiaofei ZhangWencai Yang
Jan 22, 2021·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Hitomi TakeiTohru Ariizumi
Jun 5, 2021·Communications Biology·You-Long CaoZhong-Jian Liu
May 26, 2021·Proceedings of the National Academy of Sciences of the United States of America·Susanne S RennerGuillaume Chomicki
Jun 9, 2021·Plant Biotechnology Journal·Yuxuan YuanDavid Edwards
Apr 22, 2021·Molecular Plant-microbe Interactions : MPMI·Ankita PandeyKee Hoon Sohn
Oct 2, 2021·Molecular Biology and Evolution·Roven Rommel FuentesSander A Peters

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Datasets Mentioned

BETA
PRJNA396272

Methods Mentioned

BETA
Hi-C
RNA-Seq
genotyping
Ligation Sequencing

Software Mentioned

Blast2GO suite
Trimmomatic
Maker pipeline
hot
SMRT
BWA
StringTie
PopLDdecay
_ scan
MUMmer4

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