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...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2011-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21853065/?tool=EBI |
| _version_ | 1818338155480219648 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-13T15:06:37Z |
| format | Article |
| id | doaj.art-3cc43c7c566246aeab67577c594dc961 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-13T15:06:37Z |
| publishDate | 2011-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-3cc43c7c566246aeab67577c594dc9612022-12-21T23:40:59ZengPublic Library of Science (PLoS)PLoS ONE1932-62032011-01-0168e2304110.1371/journal.pone.0023041Lack of low frequency variants masks patterns of non-neutral evolution following domestication.Céline H FrèrePeter J PrentisEdward K GildingAgnieszka M MudgeAlan CruickshankIan D GodwinDetecting 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.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21853065/?tool=EBI |
| spellingShingle | 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. PLoS ONE |
| title | 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_short | 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 |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21853065/?tool=EBI |
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