Figuring out what causes genetic mutations in agricultural plants

Arabidopsis thaliana, a member of the mustard plant family, is considered a model plant by the scientific community. There are many reasons for this. The plant's genome only has five chromosomes, and has been fully mapped out by scientists. This plant is also suitable to do testing on, owning to the short period that a generation can be grown. In addition, the plant's genome shares many common traits with other organisms, allowing breakthroughs to be applied to other organisms when discovered.

Within the plants genome, there are many classes of genes which serve different purposes in the genome. One class is the extensins, a group of flexuous, rodlike, hydroxyproline-rich glycoproteins (HRGPs) 1, integral to the structural integrity of the plant's cell wall 2 3. One extensin whose silencing is particularly interesting is EXTENSIN3 (EXT3)2. This gene mutation results in a mutant genotype called root, -shoot, -hypocotyl-defective (rsh). Wild type plants have two functional copies of the gene, usually denoted as RSH RSH (note the capitalization). Through random mutation, a plant can become heterozygous, denoted as RSH rsh. The rsh mutation is recessive. This heterozygous genotype will grow up normally, look normal, and bear fruit. Crossing two heterozygous plants, however, results in 25% of the progeny of the cross coming out wild type, 50% results in heterozygous, and 25% are homozygous. The homozygous progeny has both copies of EXT3 knocked out, with a rsh rsh genotype.

Knocking out both copies of the EXT3 gene has now been proven to result in two distinct phenotypes. One phenotype is a small, shriveled version of the A. thaliana plant, with pathetic roots, and resembling a miniature bush than a stalky plant. The other phenotype is called the Apparently Normal Phenotype (ANP). It is so called because despite exhibiting the knocked out EXT3 gene, the plant grows up and appears every bit as vital as the wild type. It is thought that one or more other extension genes are upregulating to "make up for" the EXT3 getting knocked out.

Agricultural plants also commonly have the same gene knocked out, similarly resulting in a feeble and unproductive phenotype. When it does happen, it often results in farmers having a failed harvest, causing them to lose money and impacting the global agriculture as a whole. This research seeks to examine why the ANP plant manages to grow up normally despite both copies of the EXT3 gene getting knocked out, in hopes that the findings can be applied to agricultural plants.