Understanding the genetic architecture of a quantitative trait in gymnosperms by genotyping haploid megagametophytes

The gymnosperms are a group of plants characterized by a haploid female gametophyte (megagametophyte). With the function of bearing the female gametes and nourishing the developing embryo, the megagametophyte has provided a simple way to understand the genetics of gymnosperm species using biochemical or genetic markers. In this paper, a quantitative genetic approach is proposed to study the genetic architecture of a quantitative trait in gymnosperms by taking advantage of the megagametophyte and the concept of average effect of a gene. Average effect describes the value associated with an allele carried by an individual and transmitted to its offspring. Through the genetic dissection of the average effect and genetic variance associated with a gamete carrying candidate genes, this approach can provide estimates of basic population genetic parameters, such as additive, dominant and epistatic effects, allelic frequencies and linkage disequilibrium. The candidate genes, known through their major mutant phenotype, have been reported in gymnosperms. An example for a candidate gene affecting lignin biosynthesis was applied to demonstrate the statistical procedures of the approach and its advantage. The conditions upon which the approach can be effectively used are discussed.