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UPDATE ON GENOMIC RESEARCH Research conducted by the WCDoA on SA sheep L. Sandenbergh 4 May 2016

Sheep genomics Why? Increases accuracy of BLUP breeding values Lowly heritable Sex-limited Hard-to-measure E.g. reproduction, parasite, meat, robustness Reproduction Heritability of ~0.05 Highly reproductive flock (151% lambs weaned/year) Flock with 88% lambs weaned/year 55% and 60% difference between top and bottom third 2

Genes involved with reproduction Elsenburg Merino lines Divergently selected for NLW since 1985 High line vs Low line 43+ genomic regions under selection Some genes/regions are associated with: Sperm morphology and fertilisation Stress response Energy metabolism, food intake, immune responses, blood pressure, anxiety, fertility, sexual libido, ability to learn Length of gestation, timing of parturition Cell division Cell death Inflammation Aseasonal reproduction, Milk traits, Testis weight, Body weight at 56 weeks, Bone weight in carcass, Carcass fat percentage, Parasite resistance, Selection in dairy sheep 4

Sheep genomics Why? Increases accuracy of BLUP breeding values Lowly heritable (heritability for reproduction ~0.05) Sex-limited Hard-to-measure E.g. reproduction, parasite, meat, robustness Animals selected at an earlier age Increases the rate of genetic gain Many genes influence production/complex traits Move away from finding genes Rather determine effect of markers (SNPs) on BV 5

How? SNP markers Genetic markers spaced throughout genome Tested using SNP chip 50K for sheep 6

Genomic selection Reference population Selection candidates DNA info, Records, Pedigrees Prediction equation DNA info Genomic Breeding Value Selected breeders Genomics in South African sheep 7

Rome wasn t built in a day Genetic parameters for traits of interest Heritability Correlations Population differentiation Number of distinct breeds and groups within breeds Genetic variation How many individuals needed as reference DNA sampling Tissue Effective sampling methods, transport Reference population ID influential animals Links Records (traits not routinely measured) 8

Progress: Sample material Blood cards Blood from jugular Tail docking Hair Hair follicle Above hoof Ear clips Marking Swabs Nasal 9

Progress: Biobank Records and DNA samples: Elsenburg Resource flocks Wool, reproduction, internal parasite, meat, health traits, production Dohne, Dorper, Merino, Namaqua Afrikaner, SA Mutton Merino >4 000 samples Industry Wool, reproduction, production Dohne, Dormer, Dorper, Meat master, Merino, Namaqua Afrikaner, SA Mutton Merino, White Dorper ~3 500 samples DNA samples: GADI Industry and resource flocks Afrino, Dohne, Merino, Namaqua Afrikaner, SA Mutton Merino >18 000 samples 10

Progress: Genotypes Breed Number Resource animals Breeders Dohne 48 9 (SU) 14 SAMM 57 2 (SU); 19 (N) 13 Merino 102 87 (C&G) 10 Dormer 40 10 (Els) 10 Dorper 59 20 (N) 9 White Dorper 27-6 Namaqua Afrikaner 20 20 (N) 1 TOTAL 353 SU: Stellenbosch University resource flocks; N: Nortier Resource flock (WCDoA); Els: Elsenburg Resource flock (WCDoA); C: Cradock flock (DAFF); G: Grootfontein flock (DAFF) 11

Progress: Breeds Breed Markers on SNP chip (%) Heterozygosity Inbreeding (%) Merino 91 0.35 8 Dohne 89 0.36 7 Dorper 87 0.33 16 Dormer 86 0.32 15 SAMM 85 0.33 14 White Dorper 84 0.32 16 NAM 73 0.28 27 13

Progress: Breeds 14

Pairwise F ST values 15

Progress: Genomic Breeding Values Ovine reference population 1000 s of animals Probably 5 000+ needed per breed With appropriate records Across-breed prediction not possible Use of Australian reference population? Multi-breed reference population, ~20 000 animals 50K data to 12K subset Impute (predict) 50K using AUS reference Compare imputed with real data 16

Progress: Genomic Breeding Values Literature Recent study on Merino/Merino-crossbreds Accurate imputation of PWW, PW-EMD, Y-GFW at correlation >0.88 Improving prediction Addition of SA samples (with genotype and records) to AUS reference population More research Standardise recording More genotypes Breed Correlation Merino 0.86 White Dorper 0.85 Dohne 0.84 SAMM 0.84 Dorper 0.80 Dormer 0.77 NAM 0.56 17

Future TIA application Collaboration with industry, service providers, research institutions, government International collaboration Data Genotyping (R1800/sample; USD$130) Recording important (global standard) Carcass, Parasite, Reproduction traits Genotypes Indigenous breeds Combine with international data 18

Acknowledgements 19

Thank you