Towards genomic breeding values for sheep in South Africa
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Transcript of Towards genomic breeding values for sheep in South Africa
Towards genomic breeding values for sheep in South Africa
Geoff Kingwill
Outline
• Background• Why Genomic breeding values?• Need for a reference population• Resources• Implementation• Progress thus far• Budget
Background
• Large parts of SA arid and not suitable for cropping - only fit for the extensive production of meat and fibre
• Stock farming dominant enterprise among small-scale and emerging farmers
• Small stock is predominant in the central and western regions
Background
• Small stock relatively small at ~8% of animal GDP
• Mostly sheep (~21 M) and goats (~3 M)• Of major regional importance despite modest
monetary output • Shown to be sustainable under adverse
conditions• Concentrate on the sheep industry
Background: Sheep numbers and products
Background: A wool example
• Wool competes with other fibres (cotton, synthetics)
• Synthetics produced in factory environment – great potential for productivity improvements
• Cotton yields increased by 66% over the past 15 years
• Similar progress is needed for wool to remain competitive
• Harnessing genomic information is essential
Why Genomic breeding values?• Genomic revolution
• To harness this technology certain things need to be put in place
• Genomic Estimated Breeding value• Reproduction hugely important. Currently we are limited
because it is sex specific and due to short herd life.• Increased accuracy of selection• Selection at earlier age
• Opportunity for sheep industry in RSA• Increases in economic output & lower greenhouse gasses / kg of
product• Increase reproduction among small scale farmers in what is
often a harsh environment
TOTAL Weight weaned135 ewes with 4 lambing chances
7 8
15
25
2124
19
75 4
0
5
10
15
20
25
Num
ber
<12
12--
17
18-2
2
23-2
7
28-3
2
33-3
7
38-4
2
43-4
7
48-5
2
>53
Kg weaned/ewe/annum
Potential Gains• This variation is in all flocks• Best 15 ewes - 48 kg of lambs per year
(weaned 1.75 lambs)• Worst 15 ewes - 11 kg of lambs per year (weaned 0.5 lambs)• Difference = 37 kg of lamb per ewe per
year – 148 kg per ewe over 4 years
Genomic Breeding ValuePrediction equation
Reference populationSelection candidates
Selected animals
GenotypePhenotype
Genotype
Need for a reference population
• Quantify the relationship between variation trait and SNP alleles in the South African sheep
• Genotyping –R1500/animal• Phenotyping (trait recording)• >5000 animals representative of selection group
– Capture all genetic and phenotypic variation– Least related– Heritability of traits– Constant maintenance
Resources: Institutional resource flocks
• Resource flocks (Schoeman et al., 2010)• Include different breeds• Mostly under institutional control• Could fulfill a similar role to the
Information Nucleus Flock in Australia• Traits no recorded by commercial flocks
are recorded in these resource flocks
Resources: Commercial flocks
• Flocks with data and pedigrees recorded• Roughly 92.6 thousand weaning weights
recorded in 2012• Phenotyped for standard production
traits• Influential sires and dams can be
identified for genotyping
Resources: commercial records20
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Dorper
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DorperSAMM
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DorperSAMMDohne
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DorperSAMMDohneMerino
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Resources
• All breeds at once?• Across breed GEBV’s not very accurate• Cost prevents reference population for all
breeds• Which breed to consider?
– Presently Merino• Well-phenotyped resource flocks• Relatively stable commercial flock
Implementation
• Genotyping of a representative sample from resource flocks – Genetic composition of the available resource – Calculate population parameters– Determine necessary composition of reference population
• Identification of samples representative of the national flock – Create genetic links between resource flocks, industry flocks and the larger
national flock – Influential sires
• Genotyping at GeneSeek Inc (USA) and/or ARC Biotech Platform• BLUP EBV + genomic information →GBLUP→GEBV
– Assess accuracy of GEBV in validation flock– National GEBV for producers to use in selection
Implementation
• Sample processing:– Labs at Elsenburg and GADI– Sample storage in -80 °C freezers at Elsenburg and GADI– Genotyping at GeneSeek Inc (USA) and/or ARC Biotech
Platform
• Data: – Storage on allocated harddrives and analyses on CAF
HPC
Implementation - people• WCDA - Prof SWP Cloete and Dr JJ Olivier• GADI - Dr Gretha Snyman, Dr Willem Olivier• UP - Prof Este Van Marle-Köster• US - Prof Kennedy Dzama and Ms Lise Sandenbergh• UFS - Prof Japie van Wyk• Industry Partners - Cape Wools SA, WCART, GADI,
THRIP and RMRDT ? as co-funders• Commercial farmers - access to phenotypic records
and commercial flocks• International groups already involved in ovine GBLUP
Progress thus far• Illumina SNP50K beadchip evaluated in several
resource flocks– Namaqua Afrikaner – 34448 informative SNP’s– Dorper – 41352 informative SNP’s– SAMM – 41948 informative SNP’s– Grootfontein Merino – 44595 informative SNP’s– Cradock Merino – 44936 informative SNP’s
• Consistent with results during international evaluation of chip
• Appropriate genotyping tool in all breeds
Progress thus far
• Blood sampling for 2014 completed in 3 identified commercial Merino flocks
• A fourth flock scheduled to be sampled in May-June 2014
• Samples stored in duplicate at -80C at Elsenburg and GADI
• Genotyped when needed
Progress thus far• Phenotype of two divergently selected
Elsenburg lines differ significantly• Factorial component analysis confirmed
presence of two genetically distinct lines• Several loci under selection on all 27
chromosomes– 48 SNP markers identified under directional
selection by both Bayesian and Frequentist methods– Therefore several loci affecting reproduction
Current Funding: 2014
Item WCDA WCART Cape Wools SA THRIP Total
Personnel 320 000 90 000 410 000
Operating cost 60 000 130 000 130 000 250 000 570 000
Total 380 000 220 000 130 000 250 000 980 000
Item WCDA GADI WCART Cape Wools THRIP PRODUCER
FLOCKS Total
Personnel 320 000 320 000 90 000 730 000
Operating cost 60 000 80 000 200 000 200 000 400 000 120 000 1060 000
Total 380 000 400 000 290 000 200 000 400 000 120 000 1 790 000
7 year Budget for 4 sheep breeds
2014 2015 2016 2017 2018 2019 2020R 0
R 1,000,000
R 2,000,000
R 3,000,000
R 4,000,000
R 5,000,000
R 6,000,000
R 7,000,000
R 8,000,000
R 9,000,000
Personel & Operational Costs Current Genotyping FundsGenotyping request from TIA