Editing Domestication (section)

=== Changes to plant genome ===

[[File:Polyploid wheat origins.svg|thumb|upright=2|Domesticated [[wheat]] evolved by repeated [[Hybrid (biology)|hybridization]] and [[polyploidy]] from multiple wild ancestors, increasing the size and evolvability of the genome.<ref name="Golovnina Glushkov Blinov Mayorov 2007"/> ]]

During domestication, crop species undergo intense artificial selection that alters their genomes, establishing core traits that define them as domesticated, such as increased grain size.<ref name="Purugganan Fuller 2009"/><ref name="Gepts 2004">{{cite journal |last=Gepts |first=Paul |title=Crop Domestication as a long-term selection experiment |journal=Plant Breeding Reviews |date=2004 |volume=24 |series=2 |url=http://www.plantsciences.ucdavis.edu/gepts/LTS.pdf}}</ref> Comparison of the [[coding DNA]] of [[chromosome]] 8 in rice between fragrant and non-fragrant varieties showed that aromatic and fragrant rice, including [[basmati]] and [[Jasmine rice|jasmine]], is derived from an ancestral rice domesticate that suffered a deletion in [[exon]] 7 which altered the coding for betaine aldehyde dehydrogenase (BADH2).<ref>{{cite journal |last1=Shao |first1=G. |first2=A. |last2=Tang |first3=S. Q. |last3=Tang |first4=J. |last4=Luo |first5=G. A. |last5=Jiao |first6=J. L. |last6=Wu |first7=P. S. |last7=Hu |title=A new deletion mutation of the fragrant gene and the development of three molecular markers for fragrance in rice |journal=Plant Breeding |date=April 2011 |volume=130 |issue=2 |series=2 |doi=10.1111/j.1439-0523.2009.01764.x |pages=172–176|bibcode=2011PBree.130..172S }}</ref> Comparison of the potato genome with that of other plants located genes for resistance to potato blight caused by ''[[Phytophthora infestans]]''.<ref>{{cite journal |last=The Potato Genome Sequencing Consortium|title=Genome sequence and analysis of the tuber crop potato |journal=Nature |date=July 2011 |volume=475 |doi=10.1038/nature10158 |issue=7355 |pmid=21743474 |pages=189–195 |doi-access=free}}</ref>

In [[coconut]], genomic analysis of 10 [[Microsatellite (genetics)|microsatellite loci]] (of [[noncoding DNA]]) found two episodes of domestication based on differences between individuals in the [[Indian Ocean]] and those in the [[Pacific Ocean]].<ref name="coco">{{cite journal |last1=Gunn |first1=Bee |first2=Luc |last2=Baudouin |first3=Kenneth M. |last3=Olsen |title=Independent Origins of Cultivated Coconut (Cocos nucifera L.) in the Old World Tropics |journal=PLOS ONE |date=2011 |volume=6 |issue=6 |doi=10.1371/journal.pone.0021143 |pmid=21731660 |pmc=3120816 |page=e21143 |bibcode=2011PLoSO...621143G |doi-access=free}}</ref><ref name="zeder">{{cite journal |last1=Zeder |first1=Melinda |first2=Eve |last2=Emshwiller |first3=Bruce D. |last3=Smith |first4=Daniel G. |last4=Bradley |title=Documenting domestication: the intersection of genetics and archaeology |journal=Trends in Genetics |date=March 2006 |volume=22 |issue=3 |doi=10.1016/j.tig.2006.01.007 |url=http://www.cell.com/trends/genetics/abstract/S0168-9525(06)00026-6 |accessdate=28 November 2011 |pmid=16458995 |pages=139–55}}</ref>
The coconut experienced a [[founder effect]], where a small number of individuals with low diversity founded the modern population, permanently losing much of the genetic variation of the wild population.<ref name="coco" /> [[Population bottleneck]]s which reduced variation throughout the genome at some later date after domestication are evident in crops such as [[pearl millet]], [[cotton]], [[common bean]] and [[lima bean]].<ref name="zeder" />

In wheat, domestication involved repeated [[Hybrid (biology)|hybridization]] and [[polyploidy]]. These steps are large and essentially instantaneous changes to the genome and the [[epigenome]], enabling a rapid evolutionary response to artificial selection. Polyploidy increases the number of chromosomes, bringing new combinations of genes and alleles, which in turn [[evolvability|enable further changes]] such as by [[chromosomal crossover]].<ref name="Golovnina Glushkov Blinov Mayorov 2007">{{cite journal |last1=Golovnina |first1=K. A. |last2=Glushkov |first2=S. A. |last3=Blinov |first3=A. G. |last4=Mayorov |first4=V. I. |last5=Adkison |first5=L. R. |last6=Goncharov |first6=N. P. |title=Molecular phylogeny of the genus Triticum L |journal=Plant Systematics and Evolution |publisher=Springer |volume=264 |issue=3–4 |date=2007-02-12 |doi=10.1007/s00606-006-0478-x |pages=195–216 <!--|url=http://ressources.semencespaysannes.org/docs/triticum.pdf-->|bibcode=2007PSyEv.264..195G |s2cid=39102602 }}</ref>