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In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping

Overview of attention for article published in BMC Genomics, May 2017
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Title
In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping
Published in
BMC Genomics, May 2017
DOI 10.1186/s12864-017-3805-4
Pubmed ID
Authors

Paula A. M. R. Valdisser, Wendell J. Pereira, Jâneo E. Almeida Filho, Bárbara S. F. Müller, Gesimária R. C. Coelho, Ivandilson P. P. de Menezes, João P. G. Vianna, Maria I. Zucchi, Anna C. Lanna, Alexandre S. G. Coelho, Jaison P. de Oliveira, Alessandra da Cunha Moraes, Claudio Brondani, Rosana P. Vianello

Abstract

Common bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs. Using this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56.7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average H E of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (F ST  = 0.747 between gene pools), 0.440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (F ST  = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r(2)SV) was ~ 88 kbp, while for the Andean gene pool was ~ 395 kbp, and for the Mesoamerican was ~ 130 kbp. For common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 83 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Chile 1 1%
Netherlands 1 1%
Unknown 81 98%

Demographic breakdown

Readers by professional status Count As %
Student > Master 17 20%
Student > Ph. D. Student 17 20%
Researcher 12 14%
Student > Doctoral Student 10 12%
Student > Postgraduate 5 6%
Other 11 13%
Unknown 11 13%
Readers by discipline Count As %
Agricultural and Biological Sciences 53 64%
Biochemistry, Genetics and Molecular Biology 9 11%
Environmental Science 1 1%
Business, Management and Accounting 1 1%
Unspecified 1 1%
Other 4 5%
Unknown 14 17%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. 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 09 January 2018.
All research outputs
#10,966,813
of 12,342,061 outputs
Outputs from BMC Genomics
#6,379
of 7,271 outputs
Outputs of similar age
#227,278
of 269,553 outputs
Outputs of similar age from BMC Genomics
#5
of 7 outputs
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