Germplasm Management in the Post-genomics Era-a case study with lettuce

High-throughput genotyping platforms and next-generation sequencing technologies revolutionized our ways in germplasm characterization. In collaboration with UC Davis Genome Center, we completed a project of genotyping the entire cultivated lettuce (Lactuca sativa L.) collection of 1,066 accessions with 384 EST (expressed sequence tag)-derived SNP (single nucleotide polymorphism) markers, deploying Illumina's GoldenGate assay. The results not only considerably enhanced our knowledge in the genetic diversity and population structure in our lettuce germplasm collection, but also revealed a problem, a high level of intra-accession heterozygosity in a large number of accessions.  The intra-accession heterozygosity could be the result of mixing difference genotypes when they were collected by the collector, or when they went through periodic regeneration processes by human error, and occasional cross pollination by insect or wind when they were grown side by side. This presents a serious problem for germplasm utilization. As technology advances and the cost drops, the research community will be able to genotype an entire collection with large number of markers or even sequence it at whole genome level in the foreseeable future. This new use demands pure-line accessions for effective genome-wide gene-trait association studies to identify genes useful for genetic improving crop productivity. In response, we plan to maintain our original collection "as is" in order to preserve the diversity captured in the collection with limited resources; we are also developing a subset of pure-line accessions from the collection through the fingerprinting process for distribution to meet the need of the user community.