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2022-10-18Subject
630 Agriculture 590 Animals; zoology Mangalica-SchweinSchweinezuchtHomozygotieGenetische VariabilitätMetadata
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Aufsatz
An insight into the runs of homozygosity distribution and breed differentiation in Mangalitsa pigs
Abstract
Mangalitsa pigs exhibit three distinct coat color patterns based on which they are described as Red, Blond, and Swallow-bellied. The current study investigated genome-wide diversity and selection signatures in the three breeds using fixation index, runs of homozygosity and population structure analyses. The analyses were originally based on quality-controlled data on 77 Mangalitsa animals from Germany, including 23 Blond, 30 Swallow-bellied and 24 Red Mangalitsa genotyped with a customized version of the ProcineSNP60 v2 Genotyping Bead Chip. Also, 20 Hungarian Mangalitsa genotypes were included as outgroup data for comparison. Estimates of observed heterozygosity were 0.27, 0.28, and 0.29, and inbreeding coefficients estimated based on runs of homozygosity were 24.11%, 20.82%, and 16.34% for Blond, Swallow-bellied and Red Mangalitsa, respectively. ROH islands were detected in all breeds, however, none of these were shared amongst them. The KIF16B gene previously reported to play a role in synaptic signaling was found in a ROH island (SSC17: 16–26) in Swallow-bellied Mangalitsa. The same gene was found to harbor a significantly differentiated SNP (MARC0032380) while contrasting either Blond or Red to Swallow-belied Mangalitsa. In the Red Mangalitsa, some ROH islands were associated with genes that play a role in meat quality traits, i.e., ABCA12, VIL1, PLSCR5, and USP37. Our population structure analysis highlighted a separation of the three breeds, but also showed the closest relatedness between Red and Blond Mangalitsa pigs. Findings of this study improve our understanding of the diversity in the three breeds of Mangalitsa pigs.
Citation
In: Frontiers in Genetics Vol 13 (2022-10-18) eissn:1664-8021Sponsorship
Gefördert durch den Publikationsfonds der Universität KasselCitation
@article{doi:10.17170/kobra-202211077074,
author={Addo, Sowah and Jung, Lisa},
title={An insight into the runs of homozygosity distribution and breed differentiation in Mangalitsa pigs},
journal={Frontiers in Genetics},
year={2022}
}
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2022-11-07T13:55:31Z 2022-11-07T13:55:31Z 2022-10-18 doi:10.17170/kobra-202211077074 http://hdl.handle.net/123456789/14235 Gefördert durch den Publikationsfonds der Universität Kassel eng Namensnennung 4.0 International http://creativecommons.org/licenses/by/4.0/ Mangalitsa pig ROH islands genetic diversity selection signatures runs of homozygosity 630 590 An insight into the runs of homozygosity distribution and breed differentiation in Mangalitsa pigs Aufsatz Mangalitsa pigs exhibit three distinct coat color patterns based on which they are described as Red, Blond, and Swallow-bellied. The current study investigated genome-wide diversity and selection signatures in the three breeds using fixation index, runs of homozygosity and population structure analyses. The analyses were originally based on quality-controlled data on 77 Mangalitsa animals from Germany, including 23 Blond, 30 Swallow-bellied and 24 Red Mangalitsa genotyped with a customized version of the ProcineSNP60 v2 Genotyping Bead Chip. Also, 20 Hungarian Mangalitsa genotypes were included as outgroup data for comparison. Estimates of observed heterozygosity were 0.27, 0.28, and 0.29, and inbreeding coefficients estimated based on runs of homozygosity were 24.11%, 20.82%, and 16.34% for Blond, Swallow-bellied and Red Mangalitsa, respectively. ROH islands were detected in all breeds, however, none of these were shared amongst them. The KIF16B gene previously reported to play a role in synaptic signaling was found in a ROH island (SSC17: 16–26) in Swallow-bellied Mangalitsa. The same gene was found to harbor a significantly differentiated SNP (MARC0032380) while contrasting either Blond or Red to Swallow-belied Mangalitsa. In the Red Mangalitsa, some ROH islands were associated with genes that play a role in meat quality traits, i.e., ABCA12, VIL1, PLSCR5, and USP37. Our population structure analysis highlighted a separation of the three breeds, but also showed the closest relatedness between Red and Blond Mangalitsa pigs. Findings of this study improve our understanding of the diversity in the three breeds of Mangalitsa pigs. open access Addo, Sowah Jung, Lisa doi:10.3389/fgene.2022.909986 Mangalica-Schwein Schweinezucht Homozygotie Genetische Variabilität publishedVersion eissn:1664-8021 Frontiers in Genetics Vol 13 false 909986
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