A forward looking protocol

A forward looking protocol

By Jim Ruddock, Managing Editor

Rapid identification of lettuce seed germination mutants by bulked segregant analysis and whole genome sequencing.

Huo H, Henry IM, Coppoolse ER, Verhoef- Post M, Schut JW, de Rooij H, Vogelaar A, Joosen RV, Woudenberg L, Comai L, Bradford KJ (2016)

The Plant Journal 88, 345–360
http://onlinelibrary.wiley.com/doi/10.1111/tpj.13267/abstract

Forward genetics has the potential to be highly useful for the identification of genes associated with specific phenotypes. Protocols can be devised to efficiently screen mutagenized populations for phenotypes of interest. However, subsequently identifying the specific gene(s) responsible for the selected phenotype(s) can be slow, laborious and expensive in crop plants with long generation times, large genomes and limited sequence data. Huo et al. describe a sophisticated genetic analysis in the identification of a gene for seed germination in an important crop (Lactuca sativa) using allelic mutants that show enhanced germination under high temperatures. The authors used bulk segregant analysis by whole genome sequencing (BSA sequencing) of progeny obtained from crosses made between two allelic mutants to identify mutations in the ABA1 gene for both mutants. They also used traditional mapping to map the alleles to the same genomic region, complementing the mutant phenotype with a wild type copy of the gene and measuring ABA levels in the mutants. This genetic analysis allowed the authors to demonstrate that they had identified the causal mutations. Using the process described, Huo et al. claim that the time required to identify a causal locus can be at least halved, and also that it considerably reduces the amount of genomic sequencing required. As such this protocol will considerably increase the efficiency, and reduce the time and cost involved, in applying forward genetics in the identification of important traits relevant for industry.