Whole-Genome SNP Characterisation Provides Insight for Sustainable Use of Local South African Livestock Populations
Local cattle and sheep populations are important for animal production and food security in South Africa. These genetic resources are well adapted to the diverse climatic conditions and hold potential to be utilized in production systems subjected to climate change. The local beef breeds are well in...
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| Format: | Article |
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Frontiers Media S.A.
2021-10-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.714194/full |
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| author | Esté van Marle-Köster Simon Frederick Lashmar Anel Retief Carina Visser |
| author_facet | Esté van Marle-Köster Simon Frederick Lashmar Anel Retief Carina Visser |
| author_sort | Esté van Marle-Köster |
| collection | DOAJ |
| description | Local cattle and sheep populations are important for animal production and food security in South Africa. These genetic resources are well adapted to the diverse climatic conditions and hold potential to be utilized in production systems subjected to climate change. The local beef breeds are well integrated into commercial livestock production systems with access to performance recording and genetic evaluations, while local sheep breeds are mainly utilised in smallholder and communal systems. The GeneSeek® Genomic Profiler™ Bovine 150 K SNP genotyping array was used to evaluate the diversity and inbreeding status of four indigenous (Boran, Drakensberger, Nguni, Tuli), two composite (Bonsmara and Beefmaster) and two exotic (SA Hereford and Charolais) beef breeds. The Illumina® Ovine 50 K SNP BeadChip was used to investigate five indigenous (Black Head Persian, Damara, Fat tail, Namaqua Afrikaner, Pedi) and three commercial (Dorper, Dohne Merino and SA Merino) populations. Although ascertainment bias was indicated by the low MAF (the autosome-wide proportion of SNPs with MAF< 0.05 ranged from 6.18 to 9.97% for cattle, and 7.59–13.81% for sheep), moderate genomic diversity was observed (mean Ho ranged from 0.296 to 0.403 for cattle, and 0.327 to 0.367 for sheep). Slightly higher levels of ROH-based inbreeding were calculated for cattle (FROH range: 0.018–0.104), than for sheep populations (FROH range: 0.002–0.031). The abundance of short ROH fragments (mean proportion of <4 Mb fragments: 0.405 for cattle, and 0.794 for sheep) indicated ancient inbreeding in both species. The eight cattle populations were categorized into indicine, taurine or Sanga subspecies based on principal component, model-based clustering and phylogenetic analyses, with high levels of admixture observed within the Drakensberger, Nguni and Tuli breeds. Within the sheep populations, a clear distinction could be seen between the dual-purpose breeds, the meat breed and the indigenous breeds. Despite directional selection practiced in the cattle breeds, genomic diversity was moderate with low inbreeding. The non-commercialized, indigenous sheep populations are more vulnerable with small effective populations. These results emphasise the value of genomic information for effective management to exploit the potential contribution of local genetic cattle and sheep resources in a changing environment. |
| first_indexed | 2024-12-19T02:56:35Z |
| format | Article |
| id | doaj.art-3f3c186be72443e0b0c03f72610ff42a |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-19T02:56:35Z |
| publishDate | 2021-10-01 |
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| series | Frontiers in Genetics |
| spelling | doaj.art-3f3c186be72443e0b0c03f72610ff42a2022-12-21T20:38:19ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-10-011210.3389/fgene.2021.714194714194Whole-Genome SNP Characterisation Provides Insight for Sustainable Use of Local South African Livestock PopulationsEsté van Marle-KösterSimon Frederick LashmarAnel RetiefCarina VisserLocal cattle and sheep populations are important for animal production and food security in South Africa. These genetic resources are well adapted to the diverse climatic conditions and hold potential to be utilized in production systems subjected to climate change. The local beef breeds are well integrated into commercial livestock production systems with access to performance recording and genetic evaluations, while local sheep breeds are mainly utilised in smallholder and communal systems. The GeneSeek® Genomic Profiler™ Bovine 150 K SNP genotyping array was used to evaluate the diversity and inbreeding status of four indigenous (Boran, Drakensberger, Nguni, Tuli), two composite (Bonsmara and Beefmaster) and two exotic (SA Hereford and Charolais) beef breeds. The Illumina® Ovine 50 K SNP BeadChip was used to investigate five indigenous (Black Head Persian, Damara, Fat tail, Namaqua Afrikaner, Pedi) and three commercial (Dorper, Dohne Merino and SA Merino) populations. Although ascertainment bias was indicated by the low MAF (the autosome-wide proportion of SNPs with MAF< 0.05 ranged from 6.18 to 9.97% for cattle, and 7.59–13.81% for sheep), moderate genomic diversity was observed (mean Ho ranged from 0.296 to 0.403 for cattle, and 0.327 to 0.367 for sheep). Slightly higher levels of ROH-based inbreeding were calculated for cattle (FROH range: 0.018–0.104), than for sheep populations (FROH range: 0.002–0.031). The abundance of short ROH fragments (mean proportion of <4 Mb fragments: 0.405 for cattle, and 0.794 for sheep) indicated ancient inbreeding in both species. The eight cattle populations were categorized into indicine, taurine or Sanga subspecies based on principal component, model-based clustering and phylogenetic analyses, with high levels of admixture observed within the Drakensberger, Nguni and Tuli breeds. Within the sheep populations, a clear distinction could be seen between the dual-purpose breeds, the meat breed and the indigenous breeds. Despite directional selection practiced in the cattle breeds, genomic diversity was moderate with low inbreeding. The non-commercialized, indigenous sheep populations are more vulnerable with small effective populations. These results emphasise the value of genomic information for effective management to exploit the potential contribution of local genetic cattle and sheep resources in a changing environment.https://www.frontiersin.org/articles/10.3389/fgene.2021.714194/fullcattlegenetic diversityinbreedingindigenoussheep |
| spellingShingle | Esté van Marle-Köster Simon Frederick Lashmar Anel Retief Carina Visser Whole-Genome SNP Characterisation Provides Insight for Sustainable Use of Local South African Livestock Populations Frontiers in Genetics cattle genetic diversity inbreeding indigenous sheep |
| title | Whole-Genome SNP Characterisation Provides Insight for Sustainable Use of Local South African Livestock Populations |
| title_full | Whole-Genome SNP Characterisation Provides Insight for Sustainable Use of Local South African Livestock Populations |
| title_fullStr | Whole-Genome SNP Characterisation Provides Insight for Sustainable Use of Local South African Livestock Populations |
| title_full_unstemmed | Whole-Genome SNP Characterisation Provides Insight for Sustainable Use of Local South African Livestock Populations |
| title_short | Whole-Genome SNP Characterisation Provides Insight for Sustainable Use of Local South African Livestock Populations |
| title_sort | whole genome snp characterisation provides insight for sustainable use of local south african livestock populations |
| topic | cattle genetic diversity inbreeding indigenous sheep |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2021.714194/full |
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