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Application of whole genome re-sequencing data in the development of diagnostic DNA markers tightly linked to a disease-resistance locus for marker-assisted selection in lupin (Lupinus angustifolius)

Overview of attention for article published in BMC Genomics, September 2015
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Title
Application of whole genome re-sequencing data in the development of diagnostic DNA markers tightly linked to a disease-resistance locus for marker-assisted selection in lupin (Lupinus angustifolius)
Published in
BMC Genomics, September 2015
DOI 10.1186/s12864-015-1878-5
Pubmed ID
Authors

Huaan Yang, Jianbo Jian, Xuan Li, Daniel Renshaw, Jonathan Clements, Mark W. Sweetingham, Cong Tan, Chengdao Li

Abstract

Molecular marker-assisted breeding provides an efficient tool to develop improved crop varieties. A major challenge for the broad application of markers in marker-assisted selection is that the marker phenotypes must match plant phenotypes in a wide range of breeding germplasm. In this study, we used the legume crop species Lupinus angustifolius (lupin) to demonstrate the utility of whole genome sequencing and re-sequencing on the development of diagnostic markers for molecular plant breeding. Nine lupin cultivars released in Australia from 1973 to 2007 were subjected to whole genome re-sequencing. The re-sequencing data together with the reference genome sequence data were used in marker development, which revealed 180,596 to 795,735 SNP markers from pairwise comparisons among the cultivars. A total of 207,887 markers were anchored on the lupin genetic linkage map. Marker mining obtained an average of 387 SNP markers and 87 InDel markers for each of the 24 genome sequence assembly scaffolds bearing markers linked to 11 genes of agronomic interest. Using the R gene PhtjR conferring resistance to phomopsis stem blight disease as a test case, we discovered 17 candidate diagnostic markers by genotyping and selecting markers on a genetic linkage map. A further 243 candidate diagnostic markers were discovered by marker mining on a scaffold bearing non-diagnostic markers linked to the PhtjR gene. Nine out from the ten tested candidate diagnostic markers were confirmed as truly diagnostic on a broad range of commercial cultivars. Markers developed using these strategies meet the requirements for broad application in molecular plant breeding. We demonstrated that low-cost genome sequencing and re-sequencing data were sufficient and very effective in the development of diagnostic markers for marker-assisted selection. The strategies used in this study may be applied to any trait or plant species. Whole genome sequencing and re-sequencing provides a powerful tool to overcome current limitations in molecular plant breeding, which will enable plant breeders to precisely pyramid favourable genes to develop super crop varieties to meet future food demands.

Twitter Demographics

The data shown below were collected from the profiles of 2 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 35 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Netherlands 1 3%
Unknown 34 97%

Demographic breakdown

Readers by professional status Count As %
Researcher 9 26%
Student > Ph. D. Student 6 17%
Student > Master 6 17%
Student > Doctoral Student 5 14%
Other 2 6%
Other 4 11%
Unknown 3 9%
Readers by discipline Count As %
Agricultural and Biological Sciences 25 71%
Biochemistry, Genetics and Molecular Biology 6 17%
Computer Science 1 3%
Environmental Science 1 3%
Unknown 2 6%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 24 May 2016.
All research outputs
#3,797,809
of 7,747,098 outputs
Outputs from BMC Genomics
#3,255
of 5,597 outputs
Outputs of similar age
#109,275
of 229,696 outputs
Outputs of similar age from BMC Genomics
#200
of 292 outputs
Altmetric has tracked 7,747,098 research outputs across all sources so far. This one is in the 48th percentile – i.e., 48% of other outputs scored the same or lower than it.
So far Altmetric has tracked 5,597 research outputs from this source. They receive a mean Attention Score of 4.1. This one is in the 36th percentile – i.e., 36% of its peers scored the same or lower than it.
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We're also able to compare this research output to 292 others from the same source and published within six weeks on either side of this one. This one is in the 23rd percentile – i.e., 23% of its contemporaries scored the same or lower than it.