@article{d2aa82f770fd43c29102180656ddceaa,
title = "A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity",
abstract = "Wild relatives of tomato are a valuable source of natural variation in tomato breeding, as many can be hybridized to the cultivated species (Solanum lycopersicum). Several, including Solanum lycopersicoides, have been crossed to S. lycopersicum for the development of ordered introgression lines (ILs), facilitating breeding for desirable traits. Despite the utility of these wild relatives and their associated ILs, few finished genome sequences have been produced to aid genetic and genomic studies. Here we report a chromosome-scale genome assembly for S. lycopersicoides LA2951, which contains 37 938 predicted protein-coding genes. With the aid of this genome assembly, we have precisely delimited the boundaries of the S. lycopersicoides introgressions in a set of S. lycopersicum cv. VF36 × LA2951 ILs. We demonstrate the usefulness of the LA2951 genome by identifying several quantitative trait loci for phenolics and carotenoids, including underlying candidate genes, and by investigating the genome organization and immunity-associated function of the clustered Pto gene family. In addition, syntenic analysis of R2R3MYB genes sheds light on the identity of the Aubergine locus underlying anthocyanin production. The genome sequence and IL map provide valuable resources for studying fruit nutrient/quality traits, pathogen resistance, and environmental stress tolerance. We present a new genome resource for the wild species S. lycopersicoides, which we use to shed light on the Aubergine locus responsible for anthocyanin production. We also provide IL boundary mappings, which facilitated identifying novel carotenoid quantitative trait loci of which one was likely driven by an uncharacterized lycopene β-cyclase whose function we demonstrate.",
keywords = "Solanum lycopersicoides, anthocyanin, carotenoids, disease resistance, drought, genome",
author = "Powell, {Adrian F.} and Ari Feder and Jie Li and Schmidt, {Maximilian H.W.} and Lance Courtney and Saleh Alseekh and Jobson, {Emma M.} and Alexander Vogel and Yimin Xu and David Lyon and Kathryn Dumschott and Marcus McHale and Ronan Sulpice and Kan Bao and Rohit Lal and Asha Duhan and Asis Hallab and Denton, {Alisandra K.} and Bolger, {Marie E.} and Fernie, {Alisdair R.} and Hind, {Sarah R.} and Mueller, {Lukas A.} and Martin, {Gregory B.} and Zhangjun Fei and Cathie Martin and Giovannoni, {James J.} and Strickler, {Susan R.} and Bj{\"o}rn Usadel",
note = "This study was supported by the joint ERA CAPS Regulatome project: DFG US98/7-1 (BU); FE552/29-1 (ARF); BBSRC BB/N005023/1 (CRM); National Science Foundation IOS-1539831 (JJG and ZF); and grants from National Science Foundation IOS-1546625 (GBM, SRS, and ZF); National Science Foundation IOS-1855585 (JJG and ZF); and the BTI Triad Foundation (SRS, AF, SRH, LAM, JJG, and GBM). SA and ARF were additionally supported by funding from the Max-Planck-Society and the European Union project PlantaSyst (SGA-CSA no. 664621 and no. 739582 under FPA no. 664620). BU was supported by BMBF 031A536C. We thank Brian Bell and Steve McKay for plant care, Dr. Theodore Thannhauser, Dr. Yaakov Tadmor, Dr. Mwafaq Ibdah, and Ayala Meir for help with carotenoid experiments, Dr. Surya Saha and Dr. Naama Menda for help with data handling and loading to Solgenomics.net, Dr. Yanna Shi, Jonathan M Peralta and Jonata Freschi for help with field trials and molecular assistance, Dr. Roger Chetelat for helpful suggestions on the manuscript. Finally, we want to acknowledge the Tomato Genetics Resource Center and Dr. Chetelat for making the introgressions lines available and Rudolf Thomann for donating LA2951 to the Tomato Genetics Resource Center. Open Access funding enabled and organized by Projekt DEAL. This study was supported by the joint ERA CAPS Regulatome project: DFG US98/7‐1 (BU); FE552/29‐1 (ARF); BBSRC BB/N005023/1 (CRM); National Science Foundation IOS‐1539831 (JJG and ZF); and grants from National Science Foundation IOS‐1546625 (GBM, SRS, and ZF); National Science Foundation IOS‐1855585 (JJG and ZF); and the BTI Triad Foundation (SRS, AF, SRH, LAM, JJG, and GBM). SA and ARF were additionally supported by funding from the Max‐Planck‐Society and the European Union project PlantaSyst (SGA‐CSA no. 664621 and no. 739582 under FPA no. 664620). BU was supported by BMBF 031A536C. We thank Brian Bell and Steve McKay for plant care, Dr. Theodore Thannhauser, Dr. Yaakov Tadmor, Dr. Mwafaq Ibdah, and Ayala Meir for help with carotenoid experiments, Dr. Surya Saha and Dr. Naama Menda for help with data handling and loading to Solgenomics.net , Dr. Yanna Shi, Jonathan M Peralta and Jonata Freschi for help with field trials and molecular assistance, Dr. Roger Chetelat for helpful suggestions on the manuscript. Finally, we want to acknowledge the Tomato Genetics Resource Center and Dr. Chetelat for making the introgressions lines available and Rudolf Thomann for donating LA2951 to the Tomato Genetics Resource Center. Open Access funding enabled and organized by Projekt DEAL.",
year = "2022",
month = jun,
doi = "10.1111/tpj.15770",
language = "English (US)",
volume = "110",
pages = "1791--1810",
journal = "Plant Journal",
issn = "0960-7412",
publisher = "Wiley-Blackwell",
number = "6",
}