Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data
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 fu...
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| Format: | Article |
| Language: | English |
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Asian-Australasian Association of Animal Production Societies
2024-03-01
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| Series: | Animal Bioscience |
| Subjects: | |
| Online Access: | http://www.animbiosci.org/upload/pdf/ab-23-0304.pdf |
| _version_ | 1797272552459993088 |
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| author | Mingyue Hu Lulu Shi Wenfeng Yi Feng Li Shouqing Yan |
| author_facet | Mingyue Hu Lulu Shi Wenfeng Yi Feng Li Shouqing Yan |
| author_sort | Mingyue Hu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-07T14:31:02Z |
| format | Article |
| id | doaj.art-64d134052ab34744ab1bf2b162c99464 |
| institution | Directory Open Access Journal |
| issn | 2765-0189 2765-0235 |
| language | English |
| last_indexed | 2024-03-07T14:31:02Z |
| publishDate | 2024-03-01 |
| publisher | Asian-Australasian Association of Animal Production Societies |
| record_format | Article |
| series | Animal Bioscience |
| spelling | doaj.art-64d134052ab34744ab1bf2b162c994642024-03-06T05:12:44ZengAsian-Australasian Association of Animal Production SocietiesAnimal Bioscience2765-01892765-02352024-03-0137346147010.5713/ab.23.030425181Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing dataMingyue Hu0Lulu Shi1Wenfeng Yi2Feng Li3Shouqing Yan4 Department of Animal Science, Jilin University, Changchun 130062, China Department of Animal Science, Jilin University, Changchun 130062, China Department of Animal Science, Jilin University, Changchun 130062, China Shandong Binzhou Animal Science & Veterinary Medicine Academy, Binzhou, 256600, China Department of Animal Science, Jilin University, Changchun 130062, ChinaObjective 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.http://www.animbiosci.org/upload/pdf/ab-23-0304.pdfluxi cattlegenetic diversityselection signaturewhole-genome sequencing |
| spellingShingle | Mingyue Hu Lulu Shi Wenfeng Yi Feng Li Shouqing Yan Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data Animal Bioscience luxi cattle genetic diversity selection signature whole-genome sequencing |
| title | Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data |
| title_full | Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data |
| title_fullStr | Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data |
| title_full_unstemmed | Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data |
| title_short | Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data |
| title_sort | identification of genomic diversity and selection signatures in luxi cattle using whole genome sequencing data |
| topic | luxi cattle genetic diversity selection signature whole-genome sequencing |
| url | http://www.animbiosci.org/upload/pdf/ab-23-0304.pdf |
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