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Other Indigenous Breeds Non-Descript Sheep Breeds Drivers

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Other Indigenous Breeds Non-Descript Sheep Breeds Drivers 1/25/2019 Other Indigenous Breeds • Namaqua Afrikaner - hardy, indigenous fat-tailed breed used in smallholder farming systems The Genomic Architecture of South African Mutton, Pelt • Blackhead Persian - initially introduced as a hair breed and Dual-purpose Sheep Breeds Relative to Global that is able to tolerate heat better than wool breeds Populations The breed is raised primarily for meat in SA • Karakul - originated from Central Asia, a multi-purpose Farai C. Muchadeyi, Agricultural Research Council-Biotechnology Platform, breed Gauteng, Pretoria, South Africa Swakara sheep derived from Karakul are raised predominantly for pelt [email protected] Edgar F. Dzomba, University of KwaZulu-Natal, Pietermaritzburg, KwaZulu-Natal, • Dorper - composite breed developed from South Africa interbreeding the Dorset Horn and the Persian breeds [email protected] Sheep Production in SA Non-descript Sheep Breeds • Vibrant sheep industry contributes significantly to the total livestock gross domestic product • Kept by village and smallholder farmers in the • Industrial breeds are reared on commercial farms with marginal areas of South Africa. extensively raised breeds found mainly in the smallholder areas • Uncharacterised sheep often referred to as • Three main production systems: 1. mutton, 2. wool, 3. pelt ecotypes and named after the ethnic groups also dual meat/wool breeds under which they are raised: • Smallholder communal farmers keep non-descript Nguni uncharacterised breeds for multiple purposes Pedi etc • Over 20 sheep breeds Merino & Merino-derived Breeds Drivers of Sheep Diversity in SA • SAMM developed in SA from the German Merino as a dual- purpose breed. • Natural and artificial selection processes • Merino-derived breeds were developed using the Merinos and Farmer-driven initiatives to crossbreed as an effort to develop other indigenous breeds i.e Blackhead Persian, Namaqua breeds that were better suited to produce optimally under the Afrikaner, and Damara harsh production conditions of the country • Objective was to improve the breed’s robustness while • Gene flow into and out of SA maintaining good production performance i.e Whilst sheep genetic resources of South Africa have spread to other Afrino (25% Merino, 25% Ronderib Afrikaner and 50% SA Mutton Merino) and thrives in the harshest conditions of SA countries globally, there have also been movement of breeds into South Africa. Meatmaster (SAMM and Damara sheep) improving the meat characteristics of fat-tailed sheep breeds and hardiness and suitability for • Such processes, though to some extend poorly desert documented, have shaped the genomic architecture of The Dohne Merino (Peppin-style Merino ewes and German Mutton Merino rams for high fertility and fine Merino wool under commercial the current gene pool of South African sheep. rangeland conditions 1 1/25/2019 Global Populations Aim Breed Region Sample size African Dorper African 21 i. Investigate genetic diversity, population genetic African White Dorper African 6 structure and divergence between breeds in order Ethiopian Menz African 34 to gain an insight into breed history and genomic Namaqua Afrikaner African 12 architecture of the various populations Red Maasai African 45 Ronderib Afrikaner African 17 ii. Assess breed relations and influence of exotic Bangladesh Garole Asian 24 breeds on the South African gene pool and vice Karakas Asian 18 versa by combining data with global sheep Australian Poll Dorset European 108 populations accessed from the International Sheep Australian Industry Merino European 50 Australian Poll Merino European 98 Genome Consortium (ISGC) Chinesse Merino European 23 http://www.sheephapmap.org MacArthur Merino European 10 Dorset Horn European 21 Merino landschaf European 24 Black headed Muttom European 24 SA-Sheep Breeds PCA-based Clustering - SA Breeds Breed Production system Number of samples South African Merino Dual- Purpose 56 Mutton Merino Mutton 10 Dohne Merino Dual-purpose 50 Meat Master Mutton 48 Blackhead Persian Mutton 14 Namaqua Afrikaner Mutton 12 Grey vital Swakara Pelt 22 Black vital Swakara Pelt 16 White vital Swakara Pelt 41 White subvital Swakwara Pelt 17 Karakul Pelt 10 Dorper Dual-purpose 23 Afrino Dual Purpose 51 Nguni Non-descript (unimproved) 30 PCA-based Clustering – SA with Global Genotyping & Data QC Population Breeds • Illumina OvineSNP50 BeadChip using the infinium assay platform at the Afrino South African Merino Australian Poll Merino Agricultural Research Council-Biotechnology Platform in South Africa Karakas Merinolandschaf Karakul Chinese Merino Swakara Australian Industry Merino South African mu on Merino • SNP genotypes called using genotyping module integrated in GenomeStudio™ V2010.1 (Illumina Inc.) Ethiopian Menz Red Massai Black Headed Mountain • The SNPs pruned for: Ronderib Afrikaner Namaqua Afrikaner missing genotypes (GENO) > 0.95, African Dorper African White Dorper Dorper genotype calling (MIND) > 0.95, Nguni Black Head Persian Meat Master minor allele frequency (MAF) > 0.01; and deviation from Hardy Weinberg Equilibrium (HWE > 0.0001) Dorset Horn Australian Poll Dorset 2 1/25/2019 Runs of homozygosity and fROH Per Population Pairwise FST iHS between Merino/Dorper, BHP/Dorper, Nguni/Dorper Swakara Pelt-producing Sheep • Swakara - fat-tailed sheep breed, important for pelt production for fashion industry • The white lambs of Swakara sheep experience a recessive sub-vital factor that hampers development at post weaning stage as lambs fail to digest feed (Schoeman et al., 1998) Sub-vital factor affects homozygous white lambs by hampering development resulting in death of lambs. • The sub-vital factor probably affected by genetic variants associated with colour & metabolic pathways Swakara sheep breed has undergone intensive selection during and following domestication. • OvineSNP50 to investigate genomic difference between colour subpopulations and its implications on sub-vital performance Breed-differentiating Genes & Gene Study Population & Genomic Scans Functions 1. Sample collection • Hair and blood samples were collected from 96 Swakara lambs of: Breed comparisons CHR SNPs Genes Functions (i) Black (16) (ii) White (58) (iii) Grey (22) BHP/Dorper; 3 S34488.1 QTLs ADG; Growth traits; Nguni/Dorper and OAR3_843 MF; SL & Muscle growth Merino/Dorper 301 MDLUMB3 and thickness Nguni/SAMM; 6 OAR6_648 EYS; Immune Nguni/DSH and 32803.1 GCNT1P4 response; • Animals were sampled from Namibia, Northern Cape (SA), & NQA/SAMM; OAR6_649 PHF3 Metabolic Halle, Germany from which the Swakara Sheep are thought to NQA/DSH 21019.1 pathways; have originated & genotyped on the Ovine SNP50K Growth traits 3 1/25/2019 Distribution of ROH Acknowledgements Genes Within ROH Summary 1. Sample collection • Diversity1. Sample observedcollection within and between SA sheep breeds • .GenomicHair and signaturesblood samples of ancestralwere collected populationsfrom 96 Swakaradefined lamband sustainedof: in crossbreds. Hair and andblood compositesamples were breedscollected i.e merinofrom 96 derivedSwakara breeds,lamb theof: BHP and (i) Black (16) (ii) White (58) (iii) Grey (22) NQA(i) Black effects(16 etc) (ii) White (58) (iii) Grey (22) • Genomics could provide the tools required for tackling some of the production challenges i.e : Swakara pelt producing sheep and subvital performance. Genomics and transcriptomics to investigate resistance to Haemonchus contortus in Dohne Merino Sheep (PE0226) • Ongoing analysis on breed specific parameters . Animal were sampled from Namibia, Northern Cape, & Halle, Germany from which the . Animal were sampled from Namibia, Northern Cape, & Halle, Germany from which the Swakara Sheep are thought to have originated. Swakara Sheep are thought to have originated. 4.
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