Lack of low frequency variants masks patterns of non-neutral evolution following domestication.

Detecting artificial selection in the genome of domesticated species can not only shed light on human history but can also be beneficial to future breeding strategies. Evidence for selection has been documented in domesticated species including maize and rice, but few studies have to date detected s...

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Autores principales:	Céline H Frère, Peter J Prentis, Edward K Gilding, Agnieszka M Mudge, Alan Cruickshank, Ian D Godwin
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3cc43c7c566246aeab67577c594dc961
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spelling	oai:doaj.org-article:3cc43c7c566246aeab67577c594dc9612021-11-18T06:48:21ZLack of low frequency variants masks patterns of non-neutral evolution following domestication.1932-620310.1371/journal.pone.0023041https://doaj.org/article/3cc43c7c566246aeab67577c594dc9612011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21853065/?tool=EBIhttps://doaj.org/toc/1932-6203Detecting artificial selection in the genome of domesticated species can not only shed light on human history but can also be beneficial to future breeding strategies. Evidence for selection has been documented in domesticated species including maize and rice, but few studies have to date detected signals of artificial selection in the Sorghum bicolor genome. Based on evidence that domesticated S. bicolor and its wild relatives show significant differences in endosperm structure and quality, we sequenced three candidate seed storage protein (kafirin) loci and three candidate starch biosynthesis loci to test whether these genes show non-neutral evolution resulting from the domestication process. We found strong evidence of non-neutral selection at the starch synthase IIa gene, while both starch branching enzyme I and the beta kafirin gene showed weaker evidence of non-neutral selection. We argue that the power to detect consistent signals of non-neutral selection in our dataset is confounded by the absence of low frequency variants at four of the six candidate genes. A future challenge in the detection of positive selection associated with domestication in sorghum is to develop models that can accommodate for skewed frequency spectrums.Céline H FrèrePeter J PrentisEdward K GildingAgnieszka M MudgeAlan CruickshankIan D GodwinPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 8, p e23041 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Céline H Frère Peter J Prentis Edward K Gilding Agnieszka M Mudge Alan Cruickshank Ian D Godwin Lack of low frequency variants masks patterns of non-neutral evolution following domestication.
description	Detecting artificial selection in the genome of domesticated species can not only shed light on human history but can also be beneficial to future breeding strategies. Evidence for selection has been documented in domesticated species including maize and rice, but few studies have to date detected signals of artificial selection in the Sorghum bicolor genome. Based on evidence that domesticated S. bicolor and its wild relatives show significant differences in endosperm structure and quality, we sequenced three candidate seed storage protein (kafirin) loci and three candidate starch biosynthesis loci to test whether these genes show non-neutral evolution resulting from the domestication process. We found strong evidence of non-neutral selection at the starch synthase IIa gene, while both starch branching enzyme I and the beta kafirin gene showed weaker evidence of non-neutral selection. We argue that the power to detect consistent signals of non-neutral selection in our dataset is confounded by the absence of low frequency variants at four of the six candidate genes. A future challenge in the detection of positive selection associated with domestication in sorghum is to develop models that can accommodate for skewed frequency spectrums.
format	article
author	Céline H Frère Peter J Prentis Edward K Gilding Agnieszka M Mudge Alan Cruickshank Ian D Godwin
author_facet	Céline H Frère Peter J Prentis Edward K Gilding Agnieszka M Mudge Alan Cruickshank Ian D Godwin
author_sort	Céline H Frère
title	Lack of low frequency variants masks patterns of non-neutral evolution following domestication.
title_short	Lack of low frequency variants masks patterns of non-neutral evolution following domestication.
title_full	Lack of low frequency variants masks patterns of non-neutral evolution following domestication.
title_fullStr	Lack of low frequency variants masks patterns of non-neutral evolution following domestication.
title_full_unstemmed	Lack of low frequency variants masks patterns of non-neutral evolution following domestication.
title_sort	lack of low frequency variants masks patterns of non-neutral evolution following domestication.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/3cc43c7c566246aeab67577c594dc961
work_keys_str_mv	AT celinehfrere lackoflowfrequencyvariantsmaskspatternsofnonneutralevolutionfollowingdomestication AT peterjprentis lackoflowfrequencyvariantsmaskspatternsofnonneutralevolutionfollowingdomestication AT edwardkgilding lackoflowfrequencyvariantsmaskspatternsofnonneutralevolutionfollowingdomestication AT agnieszkammudge lackoflowfrequencyvariantsmaskspatternsofnonneutralevolutionfollowingdomestication AT alancruickshank lackoflowfrequencyvariantsmaskspatternsofnonneutralevolutionfollowingdomestication AT iandgodwin lackoflowfrequencyvariantsmaskspatternsofnonneutralevolutionfollowingdomestication
_version_	1718424345835995136

Lack of low frequency variants masks patterns of non-neutral evolution following domestication.

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