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Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing

Overview of attention for article published in BMC Genomics, November 2016
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Title
Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing
Published in
BMC Genomics, November 2016
DOI 10.1186/s12864-016-3297-7
Pubmed ID
Authors

F. Taranto, N. D’Agostino, B. Greco, T. Cardi, P. Tripodi

Abstract

Knowledge on population structure and genetic diversity in vegetable crops is essential for association mapping studies and genomic selection. Genotyping by sequencing (GBS) represents an innovative method for large scale SNP detection and genotyping of genetic resources. Herein we used the GBS approach for the genome-wide identification of SNPs in a collection of Capsicum spp. accessions and for the assessment of the level of genetic diversity in a subset of 222 cultivated pepper (Capsicum annum) genotypes. GBS analysis generated a total of 7,568,894 master tags, of which 43.4% uniquely aligned to the reference genome CM334. A total of 108,591 SNP markers were identified, of which 105,184 were in C. annuum accessions. In order to explore the genetic diversity of C. annuum and to select a minimal core set representing most of the total genetic variation with minimum redundancy, a subset of 222 C. annuum accessions were analysed using 32,950 high quality SNPs. Based on Bayesian and Hierarchical clustering it was possible to divide the collection into three clusters. Cluster I had the majority of varieties and landraces mainly from Southern and Northern Italy, and from Eastern Europe, whereas clusters II and III comprised accessions of different geographical origins. Considering the genome-wide genetic variation among the accessions included in cluster I, a second round of Bayesian (K = 3) and Hierarchical (K = 2) clustering was performed. These analysis showed that genotypes were grouped not only based on geographical origin, but also on fruit-related features. GBS data has proven useful to assess the genetic diversity in a collection of C. annuum accessions. The high number of SNP markers, uniformly distributed on the 12 chromosomes, allowed the accessions to be distinguished according to geographical origin and fruit-related features. SNP markers and information on population structure developed in this study will undoubtedly support genome-wide association mapping studies and marker-assisted selection programs.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 152 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Israel 1 <1%
Italy 1 <1%
Norway 1 <1%
Unknown 149 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 27 18%
Researcher 23 15%
Student > Master 19 13%
Student > Bachelor 11 7%
Student > Doctoral Student 11 7%
Other 25 16%
Unknown 36 24%
Readers by discipline Count As %
Agricultural and Biological Sciences 86 57%
Biochemistry, Genetics and Molecular Biology 19 13%
Business, Management and Accounting 2 1%
Arts and Humanities 1 <1%
Environmental Science 1 <1%
Other 6 4%
Unknown 37 24%
Attention Score in Context

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 26 November 2016.
All research outputs
#15,693,982
of 24,862,067 outputs
Outputs from BMC Genomics
#6,014
of 11,092 outputs
Outputs of similar age
#236,514
of 426,087 outputs
Outputs of similar age from BMC Genomics
#123
of 241 outputs
Altmetric has tracked 24,862,067 research outputs across all sources so far. This one is in the 34th percentile – i.e., 34% of other outputs scored the same or lower than it.
So far Altmetric has tracked 11,092 research outputs from this source. They receive a mean Attention Score of 4.8. This one is in the 41st percentile – i.e., 41% of its peers scored the same or lower than it.
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 426,087 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 42nd percentile – i.e., 42% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 241 others from the same source and published within six weeks on either side of this one. This one is in the 46th percentile – i.e., 46% of its contemporaries scored the same or lower than it.