Forward genetics refers to the process of identifying a phenotype and then char­acterizing the genes that are involved in the phenotype’s biological pathway or process through the screening of populations of a modified organism (Lawson and Wolfe 2011). Forward genetics was successfully used to determine genes involved in metabolic and regulatory pathways in Chlamydomonas. The availability of a Chlamydomonas linkage map and a protocol for genetic crossing, along with the complete genome sequence, has boosted the gene identification process (Gonzalez — Ballester et al. 2011). Modification of an organism for screening purposes can be achieved through random mutagenesis (UV irradiation or chemically induced) to generate mutant populations to be mapped. An alternative approach to obtain a mutant population in various microalgal species is insertional mutagenesis. Inser­tion of a DNA fragment into the coding region of a particular gene results in the disruption of a protein-coding sequence and the loss of function of that gene (Vuttipongchaikij 2012).

Reverse genetics involves starting with a known gene and then disrupting the function of that gene to produce a phenotype and gain insight into what that gene does. Besides disruption, overexpression of a gene is another option. The gene sequences within a given organism need to be known, and the goal here is to define the sequences’ functions. In reverse genetics, mutations are made in specific genes or gene products to determine their effect on the organism, and from that determine the gene’s function. The availability of complete genome sequences combined with reverse genetics can allow every gene to be mapped to a function (Ahringer 2006). Using available characterized or annotated genes, improved microalgal strains can be generated through reverse genetics by gene silencing or random mutagenesis or even through gene modification by homologous recombination (Vuttipongchaikij 2012). Gene silencing by RNAi has also been used successfully for reducing gene expression levels in microalgal systems and for controlling gene function (Rohr et al. 2004). RNAi is proving to be a very useful tool for reverse genetics. Still, the most dramatic way to reduce gene activity is to eliminate the gene entirely by deleting it from the genome. This can be achieved through homologous recombi­nation (see Sect. 3.3).