News

DNA sequence data of 445 SSD lines of lettuce available

Published on
November 9, 2020

In a cooperation with the Beijing Genomics Institute, CGN’s Lactuca collection is being sequenced. Sequence data of 445 single seed descent (SSD) lines are now publicly available through the database of the China National Gene Bank and more data are underway.

Since 2018, CGN is involved in a cooperation with the Beijing Genomics Institute (Shenzhen, China) to sequence CGN’s entire lettuce collection. Recently, sequence data of the first batch of 445 SSD lines have become available. These lines constitute a core set of the CGN lettuce collection and can be assumed to represent the range of diversity present in this collection. Sequence data of another 1000 samples from CGN’s Lettuce collection are underway, while the last batch of 1109 samples is being prepared for analysis.

The sequence data

The sequence data are freely accessible in 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).

Access to the data is facilitated via CGN’s website: Special collection of 470 SSD lines of Lactuca spp. Here you can also find more information on the lines, such as passport data, photo’s and phenotypic data.

Wide range of applications

The large-scale DNA sequence data will allow more in-depth studies on a wide variety of research topics, including lettuce domestication, comparative genomics within the genus Lactuca, the distribution of genetic diversity in lettuce and its wild relatives and the genetic basis of phenotypic variation. Moreover, the data are expected to facilitate a better use of genetic diversity in the breeding of new lettuce varieties and to improve the management of genetic resources by gene banks. Application of the data is planned within the NWO-TTW research program "LettuceKnow, Science-Based Improvement of Salad", which started in 2019, and in the EU-funded Horizon 2020 project “Activated GEnebank NeTwork” (AGENT), which started in 2020.