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Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

Overview of attention for article published in BMC Genomic Data, May 2018
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Title
Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle
Published in
BMC Genomic Data, May 2018
DOI 10.1186/s12863-018-0622-y
Pubmed ID
Authors

Minhui Chen, Jiying Wang, Yanping Wang, Ying Wu, Jinluan Fu, Jian-feng Liu

Abstract

Currently, genome-wide scans for positive selection signatures in commercial breed have been investigated. However, few studies have focused on selection footprints of indigenous breeds. Laiwu pig is an invaluable Chinese indigenous pig breed with extremely high proportion of intramuscular fat (IMF), and an excellent model to detect footprint as the result of natural and artificial selection for fat deposition in muscle. In this study, based on GeneSeek Genomic profiler Porcine HD data, three complementary methods, FST, iHS (integrated haplotype homozygosity score) and CLR (composite likelihood ratio), were implemented to detect selection signatures in the whole genome of Laiwu pigs. Totally, 175 candidate selected regions were obtained by at least two of the three methods, which covered 43.75 Mb genomic regions and corresponded to 1.79% of the genome sequence. Gene annotation of the selected regions revealed a list of functionally important genes for feed intake and fat deposition, reproduction, and immune response. Especially, in accordance to the phenotypic features of Laiwu pigs, among the candidate genes, we identified several genes, NPY1R, NPY5R, PIK3R1 and JAKMIP1, involved in the actions of two sets of neurons, which are central regulators in maintaining the balance between food intake and energy expenditure. Our results identified a number of regions showing signatures of selection, as well as a list of functionally candidate genes with potential effect on phenotypic traits, especially fat deposition in muscle. Our findings provide insights into the mechanisms of artificial selection of fat deposition and further facilitate follow-up functional studies.

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Geographical breakdown

Country Count As %
Unknown 21 100%

Demographic breakdown

Readers by professional status Count As %
Other 2 10%
Student > Master 2 10%
Student > Doctoral Student 1 5%
Student > Bachelor 1 5%
Student > Ph. D. Student 1 5%
Other 3 14%
Unknown 11 52%
Readers by discipline Count As %
Agricultural and Biological Sciences 5 24%
Biochemistry, Genetics and Molecular Biology 2 10%
Nursing and Health Professions 1 5%
Unknown 13 62%
Attention Score in Context

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 20 May 2018.
All research outputs
#22,767,715
of 25,382,440 outputs
Outputs from BMC Genomic Data
#1,008
of 1,204 outputs
Outputs of similar age
#301,911
of 343,554 outputs
Outputs of similar age from BMC Genomic Data
#11
of 13 outputs
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