Special collection of 470 SSD lines of Lactuca spp.
Collection of 470 Lactuca single seed descent (SSD) lines, mainly derived from CGN’s regular collection.
The collection was largely developed within the framework of the TKI project, entitled ‘International Lactuca Genomics Consortium’ (ILGC). For this project a cross section of the lettuce gene pool, comprising nearly 500 accessions, was selected for DNA resequencing purposes. Resequencing of the lines was initiated in 2017 within the framework of the ILGC and continued in 2018 in a cooperation between CGN and the Beijing Genomics Institute (BGI, Shenzhen, China). Access to the DNA sequencing data generated for 445 lines by BGI is provided on this webpage, and this resequencing study is described in the journal Nature Genetics (2021). Large-scale metabolomics data were generated for part of the collection and are also made available on this webpage. Results of this research are described in the journal Metabolomics (2018). The collection is currently being used for transcriptomics research and phenotypic analyses in the NWO-TTW research program "LettuceKnow, Science-Based Improvement of Salad", which started in 2019.
Documentation of the collection
Information about the collection can be found in the following spreadsheets:
- The sheet ‘Line data’ contains information that is specific for the lines. Links are provided to pictures of the lines, while it is also indicated which lines have been used for DNA resequencing and metabolomics research.
- The sheet ‘Accession data’ contains information about the accessions from which the lines were derived. Basic passport data are included, and links are provided to access more detailed information about the accessions. The sheet also includes morphological data recorded during field trials and accession regeneration, and trait data obtained in collaboration with the user community.
- The sheet ‘Variety registration data’ includes morphological and trait data from published variety descriptions for part of the cultivated lettuces.
Data_DNA sequencing BGI
- Resequencing data generated by BGI for 445 SSD lines. Data are available from the CNGB Nucleotide Sequence Archive (CNSA), the database of the China National Gene Bank (CNGB). The data include the original sequence reads (FASTQ format), the mapping of the sequence reads (BAM format) against the L. sativa cv. Salinas (v8.0) reference genome and the identified sequence variation (indels, SNPs and structural variants in VCF format).
- Data of individual samples can be downloaded via the sheet ‘Table’. This sheet includes links to the CNSA entries, the sequence reads and mapping data. The sheet also includes links to the corresponding SSD lines and to the accessions from which the lines were derived.
- Five lines are represented by two samples from different plants (sample codes with suffix ‘d’) as these were used in a pilot run. The identity of s084d appeared uncertain.
- Data can also be downloaded in bulk using the CNSA File Transfer Protocol (FTP). This bulk download contains the sequence reads, the mapping data and the sequence variants. In addition, assemblies of 12 lines are provided. Instructions on downloading procedures from FTP under Windows 10 can be found here. For bulk downloads ftp://ftp.cngb.org/pub/CNSA/data2/CNP0000335/ should be used as internet or network address.
- The raw sequencing data are also available from the Sequence Read Archive under BioProject accession PRJNA693894 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA693894/).
- Data on the relative abundance of 2026 phytochemicals revealed by untargeted metabolic profiling of part of the collection, with annotations provided as far as possible.
In 2016, a single individual per selected accession was raised in the greenhouse facilities at Wageningen Plant Research. These individuals were used for tissue sampling, and plants from autogamous species were maintained for seed production by selfing. Due to the absence of flowering in 2016 seed production for some lines took place in 2017. Second generation SSD lines were produced in 2018 in case of low seed yield. Plants with virus symptoms were tested for LMV, but test results were negative. Prior to seed set, all plants belonging to wild Lactuca species were covered in perforated plastic bags to protect the lines from contamination. Seed samples were cleaned, and dried at 15 °C and 15% RH to reach a seed moisture content of 3-7%. All lines were checked for sample purity. Some off-types, most probably resulting from contamination during post-harvesting procedures were detected and subsequently removed from the sample. It cannot be ruled out that some lines may contain off types that could not be identified based on seed characteristics, but obviously this probability is low. Neither can we rule out the possibility of genetic impurities due to heterozygous loci in maternal plants. No germination tests were performed on the samples. Germination rates of newly regenerated Lactuca samples are typically high. Since dormancy is not uncommon for wild Lactuca species, it is recommended to apply dormancy-breaking procedures, such as cold-treatment, when using wild material. Seed samples are stored in vacuum-sealed bags and maintained at -20 °C in the genebank facilities of CGN.
Distribution bags contain 20 seeds per line. Seeds are distributed as Plant Genetic Resources for Food and Agriculture (PGRFA) under development using a Standard Material Transfer Agreement (SMTA) and an accompanying contract governing the transfer of seed samples of the special collection. Contract issues and payment conditions are to be arranged with the responsible curator Rob van Treuren (contact details presented below).
CGN does not accept any liability for the incorrect identity of the material, insufficient germination or the presence of diseases.
Contact for further information and ordering of seed samples
Rob van Treuren, curator leafy vegetables
Centre for Genetic Resources, the Netherlands (CGN), Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen
- Telephone: +31(0)317480916