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Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01

Overview of attention for article published in BMC Genomics, January 2016
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  • Above-average Attention Score compared to outputs of the same age and source (63rd percentile)

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Title
Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01
Published in
BMC Genomics, January 2016
DOI 10.1186/s12864-015-2344-0
Pubmed ID
Authors

Qijian Song, Jerry Jenkins, Gaofeng Jia, David L. Hyten, Vince Pantalone, Scott A. Jackson, Jeremy Schmutz, Perry B. Cregan

Abstract

A landmark in soybean research, Glyma1.01, the first whole genome sequence of variety Williams 82 (Glycine max L. Merr.) was completed in 2010 and is widely used. However, because the assembly was primarily built based on the linkage maps constructed with a limited number of markers and recombinant inbred lines (RILs), the assembled sequence, especially in some genomic regions with sparse numbers of anchoring markers, needs to be improved. Molecular markers are being used by researchers in the soybean community, however, with the updating of the Glyma1.01 build based on the high-resolution linkage maps resulting from this research, the genome positions of these markers need to be mapped. Two high density genetic linkage maps were constructed based on 21,478 single nucleotide polymorphism loci mapped in the Williams 82 x G. soja (Sieb. & Zucc.) PI479752 population with 1083 RILs and 11,922 loci mapped in the Essex x Williams 82 population with 922 RILs. There were 37 regions or single markers where marker order in the two populations was in agreement but was not consistent with the physical position in the Glyma1.01 build. In addition, 28 previously unanchored scaffolds were positioned. Map data were used to identify false joins in the Glyma1.01 assembly and the corresponding scaffolds were broken and reassembled to the new assembly, Wm82.a2.v1. Based upon the plots of the genetic on physical distance of the loci, the euchromatic and heterochromatic regions along each chromosome in the new assembly were delimited. Genomic positions of the commonly used markers contained in BARCSOYSSR_1.0 database and the SoySNP50K BeadChip were updated based upon the Wm82.a2.v1 assembly. The information will facilitate the study of recombination hot spots in the soybean genome, identification of genes or quantitative trait loci controlling yield, seed quality and resistance to biotic or abiotic stresses as well as other genetic or genomic research.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 88 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 2 2%
Egypt 1 1%
Unknown 85 97%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 20 23%
Researcher 19 22%
Student > Master 14 16%
Student > Postgraduate 5 6%
Student > Bachelor 3 3%
Other 6 7%
Unknown 21 24%
Readers by discipline Count As %
Agricultural and Biological Sciences 48 55%
Biochemistry, Genetics and Molecular Biology 10 11%
Veterinary Science and Veterinary Medicine 2 2%
Medicine and Dentistry 2 2%
Computer Science 2 2%
Other 3 3%
Unknown 21 24%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 4. 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 08 January 2016.
All research outputs
#7,477,223
of 23,498,099 outputs
Outputs from BMC Genomics
#3,515
of 10,787 outputs
Outputs of similar age
#119,808
of 397,024 outputs
Outputs of similar age from BMC Genomics
#94
of 264 outputs
Altmetric has tracked 23,498,099 research outputs across all sources so far. This one has received more attention than most of these and is in the 67th percentile.
So far Altmetric has tracked 10,787 research outputs from this source. They receive a mean Attention Score of 4.7. This one has gotten more attention than average, scoring higher than 66% 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 397,024 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 68% of its contemporaries.
We're also able to compare this research output to 264 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 63% of its contemporaries.