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A maternal effect is a situation where the phenotype of an organism is determined not only by the environment it experiences and its genotype, but also by the environment and phenotype of its mother. In genetics, maternal effects occur when a mutant organism shows not the mutant phenotype, but rather the phenotype expected from the genotype of the mother, often due the mother supplying mRNA or proteins to the egg. Maternal effects can also be caused by the maternal environment independent of genotype, sometimes controlling the size, sex, or behaviour of the offspring. It has been proposed that maternal effects are important for the evolution of adaptive responses to environmental heterogeneity.

Example: maternal effect genes in Drosophila embyrogenesis
The formation of the anterior-posterior axis in Drosophila is created by the regional synthesis of transcription factors encoded by the hunchback & caudal genes. These genes are transcribed among nurse cells of the maternal germ line that support the growth and development of an oocyte. Maternal transcripts of the hunchback and caudal genes are transported into the oocyte to become uniformly distributed in the cytoplasm.

Although hunchback and caudal genes are evenly transcribed, their translation is regulated so that the hunchback protein is more concentrated at the anterior determination of the oocyte while the caudal protein is accumulated more in the posterior. The "bicoid" and "nanos" proteins described below are the translational regulators. Hunchback and caudal proteins act as transcription factors of many genes involved in the differentiation of an embryo along the anterior-posterior axis.

Bicoid and nanos RNAs are synthesized in the nurse cells of the maternal germ line and are transported into the oocyte.

Paternal effect genes
In contrast, a paternal effect is when a phenotype results from the genotype of the father, rather than the genotype of the individual. The genes responsible for these effects are components of sperm that are involved in fertilization and early development. An example of a paternal-effect gene is the ms(3)sneaky in Drosophila, males with a mutant allele of this gene produce sperm that are able to fertilize an egg, but the snky-inseminated eggs do not develop normally. However, females with this mutation produce eggs that undergo normal development when fertilized.