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

00

2001

2002

2003

2004

2005

2006

2007

2008

2009

2010

2011

2012

0

5000

10000

15000

20000

25000

30000

35000

Dorper

Year

Num

ber

Resources: commercial records20

00

2001

2002

2003

2004

2005

2006

2007

2008

2009

2010

2011

2012

0

5000

10000

15000

20000

25000

30000

35000

DorperSAMM

Year

Num

ber

Resources: commercial records20

00

2001

2002

2003

2004

2005

2006

2007

2008

2009

2010

2011

2012

0

5000

10000

15000

20000

25000

30000

35000

DorperSAMMDohne

Year

Num

ber

Resources: commercial records20

00

2001

2002

2003

2004

2005

2006

2007

2008

2009

2010

2011

2012

0

5000

10000

15000

20000

25000

30000

35000

DorperSAMMDohneMerino

Year

Num

ber

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