Sex chromosome in the context of Genome sequencing

In genetics, dominance is the phenomenon of one variant (allele) of a gene on a chromosome masking or overriding the effect of a different variant of the same gene on the other copy of the chromosome. The first variant is termed dominant and the second is called recessive. This state of having two different variants of the same gene on each chromosome is originally caused by a mutation in one of the genes, either new (de novo) or inherited. The terms autosomal dominant or autosomal recessive are used to describe gene variants on non-sex chromosomes (autosomes) and their associated traits, while those on sex chromosomes (allosomes) are termed X-linked dominant, X-linked recessive or Y-linked; these have an inheritance and presentation pattern that depends on the sex of both the parent and the child (see Sex linkage). Since there is only one Y chromosome, Y-linked traits cannot be dominant or recessive. Additionally, there are other forms of dominance, such as incomplete dominance, in which a gene variant has a partial effect compared to when it is present on both chromosomes, and co-dominance, in which different variants on each chromosome both show their associated traits.

Dominance is a key concept in Mendelian inheritance and classical genetics. Letters and Punnett squares are used to demonstrate the principles of dominance in teaching, and the upper-case letters are used to denote dominant alleles and lower-case letters are used for recessive alleles. An often quoted example of dominance is the inheritance of seed shape in peas. Peas may be round, associated with allele R, or wrinkled, associated with allele r. In this case, three combinations of alleles (genotypes) are possible: RR, Rr, and rr. The RR (homozygous) individuals have round peas, and the rr (homozygous) individuals have wrinkled peas. In Rr (heterozygous) individuals, the R allele masks the presence of the r allele, so these individuals also have round peas. Thus, allele R is dominant over allele r, and allele r is recessive to allele R.

Sex differences in humans have been studied in a variety of fields. Sex determination generally occurs by the presence or absence of a Y chromosome in the 23rd pair of chromosomes in the human genome. Phenotypic sex refers to an individual's sex as determined by their internal and external genitalia and expression of secondary sex characteristics.

Sex differences generally refer to traits that are sexually dimorphic. A subset of such differences is hypothesized to be the product of the evolutionary process of sexual selection.

The Y chromosome is one of two sex chromosomes in therian mammals and other organisms. Along with the X chromosome, it is part of the XY sex-determination system, in which the Y is used for sex-determining as the presence of the Y chromosome typically causes offspring produced in sexual reproduction to develop phenotypically male. In mammals, the Y chromosome contains the SRY gene, which usually triggers the differentiation of male gonads. The Y chromosome is typically only passed from male parents to male offspring.

The X chromosome is one of the two sex chromosomes in many organisms, including mammals, and is found in both males and females. It is a part of the XY sex-determination system and XO sex-determination system. The X chromosome was named for its unique properties by early researchers, which resulted in the naming of its counterpart Y chromosome, for the next letter in the alphabet, following its subsequent discovery.

Environmental sex determination is the establishment of sex by a non-genetic cue, such as nutrient availability, experienced within a discrete period after fertilization. Environmental factors which often influence sex determination during development or sexual maturation include light intensity and photoperiod, temperature, nutrient availability, and pheromones emitted by surrounding plants or animals. This is in contrast to genotypic sex determination, which establishes sex at fertilization by genetic factors such as sex chromosomes. Under true environmental sex determination, once sex is determined, it is fixed and cannot be switched again. Environmental sex determination is different from some forms of sequential hermaphroditism in which the sex is determined flexibly after fertilization throughout the organism's life.

An autosome is any chromosome that is not a sex chromosome. The members of an autosome pair in a diploid cell have the same morphology, unlike those in allosomal (sex chromosome) pairs, which may have different structures. The DNA in autosomes is collectively known as atDNA or auDNA.

For example, humans have a diploid genome that usually contains 22 pairs of autosomes and one allosome pair (46 chromosomes total). The autosome pairs are labeled with numbers (1–22 in humans) roughly in order of their sizes in base pairs, while allosomes are labelled with their letters. By contrast, the allosome pair consists of two X chromosomes in females or one X and one Y chromosome in males. Unusual combinations XYY, XXY, XXX, XXXX, XXXXX or XXYY, among other irregular combinations, are known to occur and usually cause developmental abnormalities.

The pseudoautosomal regions or PARs are homologous sequences of nucleotides found within the sex chromosomes of species with an XY or ZW mechanism of sex determination.

The pseudoautosomal regions get their name because any genes within them (so far at least 29 have been found for humans) are inherited just like any autosomal genes. In humans, these regions are referred to as PAR1 and PAR2. PAR1 comprises 2.6 Mbp of the short-arm tips of both X and Y chromosomes in humans and great apes (X and Y are 154 Mbp and 62 Mbp in total). PAR2 is at the tips of the long arms, spanning 320 kbp. The monotremes, including the platypus and echidna, have a multiple sex chromosome system, and consequently have 8 pseudoautosomal regions.

Sex-determining region Y protein (SRY), or testis-determining factor (TDF), is a DNA-binding protein (also known as gene-regulatory protein/transcription factor) encoded by the SRY gene that is responsible for the initiation of male sex determination in therian mammals (placentals and marsupials). SRY is an intronless sex-determining gene on the Y chromosome. Mutations in this gene lead to a range of disorders of sex development with varying effects on an individual's phenotype and genotype.

SRY is a member of the SOX (SRY-like box) gene family of DNA-binding proteins. When complexed with the steroidogenic factor 1 (SF-1) protein, SRY acts as a transcription factor that causes upregulation of other transcription factors, most importantly SOX9. Its expression causes the development of primary sex cords, which later develop into seminiferous tubules. These cords form in the central part of the yet-undifferentiated gonad, turning it into a testis. The now-induced Leydig cells of the testis then start secreting testosterone, while the Sertoli cells produce anti-Müllerian hormone. Effects of the SRY gene, which normally take place 6–8 weeks after fetus formation, inhibit the growth of female anatomical structure in males. The gene also contributes towards developing the secondary sexual characteristics of males.

Sex differences in human physiology are distinctions of physiological characteristics associated with either male or female humans. These differences are caused by the effects of the different sex chromosome complement in males and females, and differential exposure to gonadal sex hormones during development. Sexual dimorphism is a term for the phenotypic difference between males and females of the same species.

The process of meiosis and fertilization (with rare exceptions) results in a zygote with either two X chromosomes (an XX female) or one X and one Y chromosome (an XY male) which then develops the typical female or male phenotype. Physiological sex differences include discrete features such as the respective male and female reproductive systems, as well as average differences between males and females including size and strength, bodily proportions, hair distribution, breast differentiation, voice pitch, and brain size and structure.

Whole genome sequencing (WGS), also known as full genome sequencing or just genome sequencing, is the process of determining the entirety of the DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast.

Whole genome sequencing has largely been used as a research tool, but was being introduced to clinics in 2014. In the future of personalized medicine, whole genome sequence data may be an important tool to guide therapeutic intervention. The tool of gene sequencing at SNP level is also used to pinpoint functional variants from association studies and improve the knowledge available to researchers interested in evolutionary biology, and hence may lay the foundation for predicting disease susceptibility and drug response.

Sex linkage describes the sex-specific patterns of inheritance and expression when a gene is present on a sex chromosome (allosome) rather than a non-sex chromosome (autosome). Genes situated on the X-chromosome are thus termed X-linked, and are transmitted by both males and females, while genes situated on the Y-chromosome are termed Y-linked, and are transmitted by males only. As human females possess two X-chromosomes and human males possess one X-chromosome and one Y-chromosome, the phenotype of a sex-linked trait can differ between males and females due to the differential number of alleles (polymorphisms) possessed for a given gene. In humans, sex-linked patterns of inheritance are termed X-linked recessive, X-linked dominant and Y-linked. The inheritance and presentation of all three differ depending on the sex of both the parent and the child. This makes sex-linked patterns of inheritance characteristically different from autosomal dominance and recessiveness. This article will discuss each of these patterns of inheritance, as well as diseases that commonly arise through these sex-linked patterns of inheritance. Variation in these inheritance patterns arising from aneuploidy of sex chromosomes, sex-linkage in non-human animals, and the history of the discovery of sex-linked inheritance are briefly introduced.