Selection Signatures in South African Nguni and Bonsmara Cattle Populations Reveal Genes Relating to Environmental Adaptation
Climate change is a major influencing factor in beef production. The greenhouse gases produced from livestock production systems contribute to the overall greenhouse gas emissions. The aim of this study was to identify selection signatures within and between Nguni and Bonsmara cattle in relation to...
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Frontiers Media S.A.
2022-06-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.909012/full |
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| author | Bhaveni B. Kooverjee Bhaveni B. Kooverjee Pranisha Soma Magrieta A. Van Der Nest Michiel M. Scholtz Michiel M. Scholtz Frederick W. C. Neser |
| author_facet | Bhaveni B. Kooverjee Bhaveni B. Kooverjee Pranisha Soma Magrieta A. Van Der Nest Michiel M. Scholtz Michiel M. Scholtz Frederick W. C. Neser |
| author_sort | Bhaveni B. Kooverjee |
| collection | DOAJ |
| description | Climate change is a major influencing factor in beef production. The greenhouse gases produced from livestock production systems contribute to the overall greenhouse gas emissions. The aim of this study was to identify selection signatures within and between Nguni and Bonsmara cattle in relation to production and adaptation. For this purpose, genomic 150 K single nucleotide polymorphism data from Nguni (n = 231) and Bonsmara (n = 252) cattle in South Africa were used. Extended haplotype homozygosity (EHH) based analysis was executed within each population using integrated haplotype score (iHS). The R package rehh was used for detecting selection signatures across the two populations with cross population EHH (XP-EHH). Total of 121 regions of selection signatures were detected (p < 0.0001) in the Bonsmara and Nguni populations. Several genes relating to DNA methylation, heat stress, feed efficiency and nitrogen metabolism were detected within and between each population. These regions also included QTLs associated with residual feed intake, residual gain, carcass weight, stature and body weight in the Bonsmara, while QTLs associated with conception rate, shear force, tenderness score, juiciness, temperament, heat tolerance, feed efficiency and age at puberty were identified in Nguni. Based on the results of the study it is recommended that the Nguni and Bonsmara be utilized in crossbreeding programs as they have beneficial traits that may allow them to perform better in the presence of climate change. Results of this study coincide with Nguni and Bonsmara breed characteristics and performance, and furthermore support informative crossbreeding programs to enhance livestock productivity in South Africa. |
| first_indexed | 2024-04-13T17:54:56Z |
| format | Article |
| id | doaj.art-2c2a6c4a947a42bbb98b87f05cbf1e58 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-13T17:54:56Z |
| publishDate | 2022-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-2c2a6c4a947a42bbb98b87f05cbf1e582022-12-22T02:36:33ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-06-011310.3389/fgene.2022.909012909012Selection Signatures in South African Nguni and Bonsmara Cattle Populations Reveal Genes Relating to Environmental AdaptationBhaveni B. Kooverjee0Bhaveni B. Kooverjee1Pranisha Soma2Magrieta A. Van Der Nest3Michiel M. Scholtz4Michiel M. Scholtz5Frederick W. C. Neser6Department of Animal Breeding and Genetics, Animal Production, Agricultural Research Council, Pretoria, South AfricaDepartment of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South AfricaDepartment of Animal Breeding and Genetics, Animal Production, Agricultural Research Council, Pretoria, South AfricaBiotechnology Platform, Agricultural Research Council, Pretoria, South AfricaDepartment of Animal Breeding and Genetics, Animal Production, Agricultural Research Council, Pretoria, South AfricaDepartment of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South AfricaDepartment of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South AfricaClimate change is a major influencing factor in beef production. The greenhouse gases produced from livestock production systems contribute to the overall greenhouse gas emissions. The aim of this study was to identify selection signatures within and between Nguni and Bonsmara cattle in relation to production and adaptation. For this purpose, genomic 150 K single nucleotide polymorphism data from Nguni (n = 231) and Bonsmara (n = 252) cattle in South Africa were used. Extended haplotype homozygosity (EHH) based analysis was executed within each population using integrated haplotype score (iHS). The R package rehh was used for detecting selection signatures across the two populations with cross population EHH (XP-EHH). Total of 121 regions of selection signatures were detected (p < 0.0001) in the Bonsmara and Nguni populations. Several genes relating to DNA methylation, heat stress, feed efficiency and nitrogen metabolism were detected within and between each population. These regions also included QTLs associated with residual feed intake, residual gain, carcass weight, stature and body weight in the Bonsmara, while QTLs associated with conception rate, shear force, tenderness score, juiciness, temperament, heat tolerance, feed efficiency and age at puberty were identified in Nguni. Based on the results of the study it is recommended that the Nguni and Bonsmara be utilized in crossbreeding programs as they have beneficial traits that may allow them to perform better in the presence of climate change. Results of this study coincide with Nguni and Bonsmara breed characteristics and performance, and furthermore support informative crossbreeding programs to enhance livestock productivity in South Africa.https://www.frontiersin.org/articles/10.3389/fgene.2022.909012/fullclimate changecompositeDNA methylationgenomic selectiongenomic structureindigenous |
| spellingShingle | Bhaveni B. Kooverjee Bhaveni B. Kooverjee Pranisha Soma Magrieta A. Van Der Nest Michiel M. Scholtz Michiel M. Scholtz Frederick W. C. Neser Selection Signatures in South African Nguni and Bonsmara Cattle Populations Reveal Genes Relating to Environmental Adaptation Frontiers in Genetics climate change composite DNA methylation genomic selection genomic structure indigenous |
| title | Selection Signatures in South African Nguni and Bonsmara Cattle Populations Reveal Genes Relating to Environmental Adaptation |
| title_full | Selection Signatures in South African Nguni and Bonsmara Cattle Populations Reveal Genes Relating to Environmental Adaptation |
| title_fullStr | Selection Signatures in South African Nguni and Bonsmara Cattle Populations Reveal Genes Relating to Environmental Adaptation |
| title_full_unstemmed | Selection Signatures in South African Nguni and Bonsmara Cattle Populations Reveal Genes Relating to Environmental Adaptation |
| title_short | Selection Signatures in South African Nguni and Bonsmara Cattle Populations Reveal Genes Relating to Environmental Adaptation |
| title_sort | selection signatures in south african nguni and bonsmara cattle populations reveal genes relating to environmental adaptation |
| topic | climate change composite DNA methylation genomic selection genomic structure indigenous |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.909012/full |
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