Tortoiseshell and calico coats result from an interaction between genetic and developmental factors. The primary gene for coat color (C) is located on the X Chromosome and has two co-dominant alleles, Orange (XO) and Black (XB), that produce orange phaeomelanin and black eumelanin pigments, respectively. The cells of female cats, which like other mammalian females have two X Chromosome (XX), undergo the phenomenon of X-inactivation, in which one or the other of the X-chromosomes is turned off at random in each cell in very early development. The inactivated X becomes a Barr body. Cells in which the chromosome carrying the Orange (XO) allele is inactivated express the alternative Black (XB) allele. Cells in which the Black (XB) allele is inactivated express the Orange (XO) allele. Pigment genes are expressed in melanocytes that migrate to the skin surface later in development. In bi-colored tortoiseshell cats, the melanocytes arrive relatively early, and the two cell types become intermingled, producing the characteristic brindled appearance consisting of an intimate mixture of orange and black cells, with occasional small diffuse spots of orange and black.
Male cats, like other mammalian males, have only a single X chromosome (XY) that does not undergo X-inactivation: coat color is determined by which allele is present on the X, and they will be either entirely black or orange. Very rarely (approximately 1 in 3,000) a male tortoiseshell or calico is born. These animals typically have an extra X chromosome (XXY), a condition known in humans as Klinefelter syndrome, and undergo an inactivation process like that in females. As in humans, these cats are almost always sterile because of the imbalance in sex chromosomes. Some male calico or tortoiseshell cats may be chimeras, which result from the fusion in early development of two embryos with different color genotypes. Others are mosaics, in which the XXY condition arises after conception and the cat is a mixture of cells with different numbers of X chromosomes.