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Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing

Overview of attention for article published in BMC Genomics, February 2016
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (90th percentile)
  • High Attention Score compared to outputs of the same age and source (93rd percentile)

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Title
Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing
Published in
BMC Genomics, February 2016
DOI 10.1186/s12864-016-2431-x
Pubmed ID
Authors

João Vitor Maldonado dos Santos, Babu Valliyodan, Trupti Joshi, Saad M. Khan, Yang Liu, Juexin Wang, Tri D. Vuong, Marcelo Fernandes de Oliveira, Francismar Corrêa Marcelino-Guimarães, Dong Xu, Henry T. Nguyen, Ricardo Vilela Abdelnoor

Abstract

Soybean [Glycine max (L.) Merrill] is one of the most important legumes cultivated worldwide, and Brazil is one of the main producers of this crop. Since the sequencing of its reference genome, interest in structural and allelic variations of cultivated and wild soybean germplasm has grown. To investigate the genetics of the Brazilian soybean germplasm, we selected soybean cultivars based on the year of commercialization, geographical region and maturity group and resequenced their genomes. We resequenced the genomes of 28 Brazilian soybean cultivars with an average genome coverage of 14.8X. A total of 5,835,185 single nucleotide polymorphisms (SNPs) and 1,329,844 InDels were identified across the 20 soybean chromosomes, with 541,762 SNPs, 98,922 InDels and 1,093 CNVs that were exclusive to the 28 Brazilian cultivars. In addition, 668 allelic variations of 327 genes were shared among all of the Brazilian cultivars, including genes related to DNA-dependent transcription-elongation, photosynthesis, ATP synthesis-coupled electron transport, cellular respiration, and precursors of metabolite generation and energy. A very homogeneous structure was also observed for the Brazilian soybean germplasm, and we observed 41 regions putatively influenced by positive selection. Finally, we detected 3,880 regions with copy-number variations (CNVs) that could help to explain the divergence among the accessions evaluated. The large number of allelic and structural variations identified in this study can be used in marker-assisted selection programs to detect unique SNPs for cultivar fingerprinting. The results presented here suggest that despite the diversification of modern Brazilian cultivars, the soybean germplasm remains very narrow because of the large number of genome regions that exhibit low diversity. These results emphasize the need to introduce new alleles to increase the genetic diversity of the Brazilian germplasm.

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Mendeley readers

Mendeley readers

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Geographical breakdown

Country Count As %
United States 1 1%
Unknown 90 99%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 20 22%
Student > Master 16 18%
Researcher 15 16%
Student > Bachelor 6 7%
Professor 5 5%
Other 13 14%
Unknown 16 18%
Readers by discipline Count As %
Agricultural and Biological Sciences 40 44%
Biochemistry, Genetics and Molecular Biology 16 18%
Computer Science 4 4%
Environmental Science 3 3%
Engineering 2 2%
Other 5 5%
Unknown 21 23%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 15. 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 31 May 2023.
All research outputs
#2,181,669
of 23,901,621 outputs
Outputs from BMC Genomics
#591
of 10,826 outputs
Outputs of similar age
#40,295
of 406,625 outputs
Outputs of similar age from BMC Genomics
#16
of 245 outputs
Altmetric has tracked 23,901,621 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 90th percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 10,826 research outputs from this source. They receive a mean Attention Score of 4.8. This one has done particularly well, scoring higher than 94% 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 406,625 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 90% of its contemporaries.
We're also able to compare this research output to 245 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 93% of its contemporaries.