Editing Haplotype (section)

{{Short description|Group of genes from one parent}}
{{technical|date=February 2021}}
[[File:dna-SNP.svg|thumb|363px|DNA molecule 1 differs from DNA molecule 2 at a single base-pair location (a C/A polymorphism).]]
A '''haplotype''' ([[haploid]] [[genotype]]) is a group of [[allele]]s in an [[organism]] that are inherited together from a single parent.<ref name=cox2016/><ref name=editorial2012/>

Many organisms contain genetic material ([[DNA]]) which is inherited from two parents. Normally these organisms have their DNA organized in two sets of pairwise similar [[chromosome]]s. The offspring gets one chromosome in each pair from each parent. A set of pairs of chromosomes is called [[diploid]] and a set of only one half of each pair is called haploid. The haploid genotype (haplotype) is a genotype that considers the singular chromosomes rather than the pairs of chromosomes. It can be all the chromosomes from one of the parents or a minor part of a chromosome, for example a sequence of 9000 [[base pair]]s or a small set of alleles.

Specific contiguous parts of the chromosome are likely to be inherited together and not be split by [[chromosomal crossover]], a phenomenon called [[genetic linkage]].<ref>[http://users.rcn.com/jkimball.ma.ultranet/ BiologyPages/H/Haplotypes.html Kimball's Biology Pages] (Creative Commons Attribution 3.0)</ref><ref>{{Cite web|url=http://www.nature.com/scitable/definition/haplotype-haplotypes-142|title=haplotype / haplotypes &#124; Learn Science at Scitable|website=www.nature.com}}</ref> As a result, identifying these statistical associations and a few alleles of a specific haplotype sequence can facilitate identifying ''all other such'' polymorphic sites that are nearby on the chromosome ([[Imputation (genetics)|imputation]]).<ref>{{cite journal |last1=Yoosefzadeh-Najafabadi|first1=Mohsen |last2=Rajcan|first2=Istvan|last3=Eskandari|first3=Milad|title=Optimizing genomic selection in soybean: An important improvement in agricultural genomics |journal=Heliyon |volume=8 |year=2022 |issue=11 |pages=e11873|doi=10.1016/j.heliyon.2022.e11873 |pmid=36468106 |pmc=9713349 |bibcode=2022Heliy...811873Y |doi-access=free }}</ref> Such information is critical for investigating the genetics of common [[diseases]]; which have been investigated in humans by the [[International HapMap Project]].<ref>{{cite journal|author=The International HapMap Consortium|title=The International HapMap Project|journal=Nature|year=2003|volume=426|pages=789–796|doi=10.1038/nature02168|pmid=14685227|issue=6968|bibcode=2003Natur.426..789G|hdl=2027.42/62838|s2cid=4387110|url=https://deepblue.lib.umich.edu/bitstream/2027.42/62838/1/nature02168.pdf|hdl-access=free}}</ref><ref>{{cite journal|author=The International HapMap Consortium|title=A haplotype map of the human genome|journal=Nature|year=2005|volume=437|pages=1299–1320|doi=10.1038/nature04226|pmid=16255080|issue=7063|pmc=1880871|bibcode=2005Natur.437.1299T}} &ndash; This article speaks of a ''haplotype length'', which is the length of a contiguous run of the chromosome inherited from a single parent.</ref>

Other parts of the genome are almost always haploid and do not undergo crossover: for example, human [[mitochondrial DNA]] is passed down through the maternal line and the [[Y chromosome]] is passed down the paternal line. In these cases, the entire sequence can be grouped into a simple evolutionary tree, with each branch founded by a [[unique-event polymorphism]] mutation (often, but not always, a [[single-nucleotide polymorphism]] (SNP)). Each [[clade]] under a branch, containing haplotypes with a single shared ancestor, is called a [[haplogroup]].<ref name=arora2015/><ref name=ISGS2015/><ref>{{Cite web|url=http://www.familytreedna.com/facts_genes.aspx|archive-url=https://web.archive.org/web/20080509091745/http://www.familytreedna.com/facts_genes.aspx|url-status=dead|title=Facts & Genes. Volume 7, Issue 3|archive-date=May 9, 2008}}</ref>