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Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data |
Mingyue Hu1,a 
, Lulu Shi1,a
, Wenfeng Yi1
, Feng Li2,*
, Shouqing Yan1,*
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1Department of Animal Science, Jilin University, Changchun 130062, China
2Shandong Binzhou Animal Science & Veterinary Medicine Academy, Binzhou, 256600, China |
Correspondence:
Feng Li, Tel: +86-543-3414357, Email: fenglibz_198@163.com
Shouqing Yan, Tel: +86-431-87836177, Email: yansq@jlu.edu.cn
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Received: 15 August 2023 • Revised: 13 October 2023 • Accepted: 28 November 2023
aThese authors contributed equally to this work. |
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| Abstract |
Objective
The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures of Luxi cattle to reveal its genomic characteristics in terms of meat and carcass traits, skeletal muscle development, body size, and other traits.
Methods
To further analyze the genomic characteristics of Luxi cattle, this study sequenced the whole-genome of 16 individuals from the core conservation farm in Shandong region, and collected 174 published genomes of cattle for conjoint analysis. Furthermore, three different statistics (pi, Fst, and XP-EHH) were used to detect potential positive selection signatures related to selection in Luxi cattle. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed to reveal the potential biological function of candidate genes harbored in selected regions.
Results
The results showed that Luxi cattle had high genomic diversity and low inbreeding levels. Using three complementary methods (pi, Fst, and XP-EHH) to detect the signatures of selection in the Luxi cattle genome, there were 2,941, 2,221 and 1,304 potentially selected genes identified, respectively. Furthermore, there were 45 genes annotated in common overlapping genomic regions covered 0.723 Mb, including PLAG1 zinc finger (PLAG1), dedicator of cytokinesis 3 (DOCK3), ephrin A2 (EFNA2), DAZ associated protein 1 (DAZAP1), Ral GTPase activating protein catalytic subunit alpha 1 (RALGAPA1), mediator complex subunit 13 (MED13), and decaprenyl diphosphate synthase subunit 2 (PDSS2), most of which were enriched in pathways related to muscle growth and differentiation and immunity.
Conclusion
In this study, we provided a series of genes associated with important economic traits were found in positive selection regions, and a scientific basis for the scientific conservation and genetic improvement of Luxi cattle. |
| Keywords:
Luxi Cattle; Genetic Diversity; Selection Signature; Whole-genome Sequencing |
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