Boyce Thompson Institute, Ithaca, NY, 14853, USA.
CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
Nat Commun. 2020 Nov 16;11(1):5817. doi: 10.1038/s41467-020-19682-0.
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.
刺茄（Solanum pimpinellifolium，SP）是栽培番茄的野生祖种。由于其具有显著的抗逆性和浓郁的风味，SP 已被用作现代番茄育种的重要种质资源。本文介绍了刺茄 LA2093 的高质量染色体级别的基因组序列。基因组比较鉴定出 LA2093 与现代栽培品种海因茨 1706 之间超过 92000 个结构变异（SV）。在约 600 个代表性番茄品种中对这些 SV 进行基因分型，鉴定出番茄驯化、改良和现代育种过程中选择的等位基因，并发现了许多与调控重要农艺性状（如果实重量和番茄红素含量）相关基因重叠的 SV。表达数量性状基因座（eQTL）分析检测到控制重要果实品质性状的主调控因子的热点区域，包括角质层蜡质积累和类黄酮生物合成，以及对这些复杂调控网络有贡献的 SV。LA2093 基因组序列和鉴定的 SV 为未来的研究和基于生物多样性的育种提供了丰富的资源。
