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A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes

Overview of attention for article published in Genome Biology (Online Edition), February 2015
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About this Attention Score

  • In the top 5% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (96th percentile)
  • Good Attention Score compared to outputs of the same age and source (71st percentile)

Mentioned by

news
1 news outlet
blogs
3 blogs
twitter
40 tweeters
weibo
1 weibo user
facebook
1 Facebook page

Citations

dimensions_citation
128 Dimensions

Readers on

mendeley
183 Mendeley
citeulike
2 CiteULike
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Title
A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes
Published in
Genome Biology (Online Edition), February 2015
DOI 10.1186/s13059-015-0606-4
Pubmed ID
Authors

Katherine W Jordan, Shichen Wang, Yanni Lun, Laura-Jayne Gardiner, Ron MacLachlan, Pierre Hucl, Krysta Wiebe, Debbie Wong, Kerrie L Forrest, Andrew G Sharpe, Christine HD Sidebottom, Neil Hall, Christopher Toomajian, Timothy Close, Jorge Dubcovsky, Alina Akhunova, Luther Talbert, Urmil K Bansal, Harbans S Bariana, Matthew J Hayden, Curtis Pozniak, Jeffrey A Jeddeloh, Anthony Hall, Eduard Akhunov

Abstract

Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines. A sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies. Evidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets.

Twitter Demographics

The data shown below were collected from the profiles of 40 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 183 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 6 3%
Australia 4 2%
Japan 2 1%
France 2 1%
United Kingdom 2 1%
Sweden 1 <1%
Canada 1 <1%
Italy 1 <1%
Germany 1 <1%
Other 0 0%
Unknown 163 89%

Demographic breakdown

Readers by professional status Count As %
Researcher 62 34%
Student > Ph. D. Student 50 27%
Student > Doctoral Student 12 7%
Student > Master 12 7%
Other 10 5%
Other 26 14%
Unknown 11 6%
Readers by discipline Count As %
Agricultural and Biological Sciences 137 75%
Biochemistry, Genetics and Molecular Biology 21 11%
Business, Management and Accounting 1 <1%
Pharmacology, Toxicology and Pharmaceutical Science 1 <1%
Unspecified 1 <1%
Other 2 1%
Unknown 20 11%

Attention Score in Context

This research output has an Altmetric Attention Score of 54. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 04 December 2016.
All research outputs
#369,809
of 14,642,680 outputs
Outputs from Genome Biology (Online Edition)
#330
of 3,225 outputs
Outputs of similar age
#7,287
of 214,594 outputs
Outputs of similar age from Genome Biology (Online Edition)
#2
of 7 outputs
Altmetric has tracked 14,642,680 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 97th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 3,225 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 24.7. This one has done well, scoring higher than 89% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 214,594 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 96% of its contemporaries.
We're also able to compare this research output to 7 others from the same source and published within six weeks on either side of this one. This one has scored higher than 5 of them.