The genetic conservation of pig breeds, with special reference to the Oxford Sandy and Black

Dr Rex Walters F.L.S. (Source: M. Groenen)

Domestication

• 2 independent areas: – Anatolia (Turkey) – Central China • Exact dates unclear. • Some evidence of cross breeding with wild boar over many centuries.

(Source: K. Brook)

Pigs are number one!

• Global consumption of pigmeat is greater than for any other species. • The meat comes from many different breeds. • Growing awareness that their successful genetic conservation is of major importance. There is some evidence that locally adapted breeds show resistance for important diseases (good reason for the conservation of traditional breeds!). UK Traditional Breeds

Berkshire British Saddleback Gloucestershire Old Spots Large Black Middle White Oxford Sandy and Black Tamworth The Oxford Sandy and Black (OSB)

• ‘Plum pudding’ pig. • Exact origin unknown. • Developed in Oxfordshire some 200 years ago. • Numbers dwindled dramatically after the war and it nearly became extinct.

The Oxford Sandy and Black (OSB)

• Largely due to the efforts of Andrew Sheppy, F.L.S., the breed was saved. • He set up the Herdbook and Breed Society in 1985. • Gone from ‘strength to strength’! • Now one of the most popular breeds. • Good butchers’ carcase, good meat quality, docile and easy to manage.

(Source: K. Brook)

Warriss et al. The quality of pork from traditional pig breeds. Meat Focus 5: 179 -182 (P Fat) ₂ Warriss et al. The quality of pork from traditional pig breeds. Meat Focus 5: 179 -182 (P Fat)

Large Black₂ 23.0 Berkshire 18.7

Tamworth 18.6 Saddleback 17.3

Hampshire 16.9

GOS 16.8

Duroc 14.7

OSB 12.3 Warriss et al. The quality of pork from traditional pig breeds. Meat Focus 5: 179 -182 (Fat firmness, fat quality, water content)

OSB 1

Large White 2

Landrace 3

Pietrain 4 Where now with native breeds?

• British Pig Association. • Genetic analyses (Geneped). • Future conservation plans. Geneped analyses

• Breed structure. – Geographical spread. – Breeder numbers. – Herd inventories. • Effective population size. • Inbreeding. • ‘Bloodlines’. • Breeding strategies. OSB distribution Geneped analyses

• Breed structure. – Geographical spread. – Breeder numbers. – Herd inventories. • Effective population size. • Inbreeding. • ‘Bloodlines’. • Breeding strategies. Effective population size (Ne) • Ne is a key measure of the loss of genetic diversity and reflects the level of inbreeding. • Related to the number of breeding boars and breeding females (measures animals that contribute to the next generation). • The larger the Ne, the higher the genetic ‘health’ of the breed and the less chance of becoming endangered in the future.

Effective population size (Ne) • Standard equations are used in the estimation of Ne which assume random selection of parents and random matings. • However, practical pig breeding involves the selection of specific animals for particular planned matings – as a result, Ne tends to be over-estimated. • Thus Geneped estimates are higher than the likely actual figure.

Geneped analyses

• Breed structure. – Geographical spread. – Breeder numbers. – Herd inventories. • Effective population size. • Inbreeding. • Breeding strategies. Inbreeding

• Inbreeding increases likelihood of homozygosity for deleterious genes. • As a result, levels of fertility will fall and there will be an increase in genetic/congenital defects.

Geneped analyses

• Breed structure. – Geographical spread. – Breeder numbers. – Herd inventories. • Effective population size. • Inbreeding. • ‘Bloodlines’. • Breeding strategies. ‘Bloodlines’ (1)

• Inherent problem with ‘bloodline’ naming system (naming of female after the dam’s name and naming of male progeny after the sire’s name). • The progeny of a particular mating will have one of two ‘family’ names according only to the sex of a particular individual. ‘Bloodlines’ (2)

• System can result in high inbreeding as most breeders believe that the family names of animals truly represent different discrete genetic lines. • Accordingly, they assume that the amount of variation in their herd is directly related to the number of different male and female lines. ‘Bloodlines’ (3)

• The goal of the BPA is to educate breeders to look further than the ‘bloodline’ names of potential mates and to investigate the pedigrees for several generations to ensure that inbreeding is minimised. Geneped analyses

• Breed structure. – Geographical spread. – Breeder numbers. – Herd inventories. • Effective population size. • Inbreeding. • ‘Bloodlines’. • Breeding strategies. Breeding Strategies

• Practical rules. • Kinship analyses. • Mate selection. • Gene bank. Boar contribution ‘rules’ (1) – Use as many boars as possible (whilst maintaining breed standards for conformation, type and performance). – Do not keep too many offspring from any one male - only one boar per litter for future breeding. – Never allow one male to sire more 5% of future generation. This is particularly important when using AI from limited numbers of sires. Boar contribution ‘rules’ (2)

– Minimize inbreeding through controlled mating plans. – Use family line names very carefully – remember the name only gives an indication of one ‘side’ of the pedigree. Boar representation

• Ideally identify ‘over-represented’ and ‘under-represented’ sires in future mating plans. For genetic conservation it would be helpful to increase the representation of the ‘least popular’ boars. • But, practical knowledge is needed to decide ‘policy’ as they be under- represented for a good reason!

Breeding Strategies

• Practical rules. • Kinship analyses. • Mate selection. • Gene bank. Kinship analyses

• The identification of the relationship (kinship) of each living animals with all other animals in the breed. • The number of registered progeny per mating candidate.

Kinship analyses

• Consider using boars with a low kinship to the population and with a low number of registered offspring. • Alternatively, boars which have a larger number of offspring or a higher kinship to the male population may be ‘switched’ to non-pedigree matings.

Mating plan – Traffic lights

Registration Name Birth date Mean Kinship Breeder Owner Offspring

R000216MW Tollbar Rajah 32 07/04/2004 0.0257 PSP ZZZ11 4

R001144MW Greenan Captain 15/09/2008 0.0308 EXE SZG 20

R001504MW Redbrook Revival 484 15/11/2008 0.0311 ACJ ACJ 4

R000382MW Templeson Revival 402 12/08/2005 0.0327 LEE ZZZ11 2

R000932MW Smallicombe Revival 6 02/07/2007 0.0328 TMM 88031 3

R001124MW Loughans Mischief 4 08/10/2008 0.0467 MZL CSC 1

R000649MW Fairoaks Revival 2 05/11/2005 0.0492 CIM CCC 28

R000702MW Westham Mischief 567 20/08/2006 0.0598 CVM CSC 47

R001572MW Dappleheath Sovereign 12 05/09/2009 0.063 HJH XDJ 2

R001333MW Chalkhill Mischief 9 15/10/2008 0.0655 NCN ZZZ11 1

R001589MW Mabon Rajah 5 20/01/2010 0.0692 IPB XNF 1

R001293MW Aggett Rajah 4 20/01/2009 0.0718 RCN SXK 20

R000241MW Ferrylane Rajah 2 28/08/2004 0.0811 TWA BTS 46

R001011MW Gracebank Rajah 10 19/07/2007 0.0832 BTS IPB 37

R000465MW Gracebank Rajah 2 23/07/2005 0.0855 BTS PMC 51 Breeding Strategies

• Practical rules. • Kinship analyses. • Mate selection. • Gene bank. Mate selection

• The identification of ‘unrelated’ boars matched to females prior to breeding. • Estimation of inbreeding coefficients for potential matings (‘what if’ inbreeding levels). • As a ‘rule of thumb’ planned matings should aim to have an inbreeding coefficient of 2% or less. Mate selection - example

• Selected 3 boars and 5 gilts:

Registration Sex D.o.B R002623 M 25/04/2016 R002463 M 01/05/2016 R002404 M 15/08/2016 Mate selection - example

• Selected 3 boars and 5 gilts:

Registration Sex D.o.B R002623 M 25/04/2016 R002463 M 01/05/2016 R002404 M 15/08/2016 R002873 F 05/08/2016 R002795 F 10/08/2016 R002796 F 10/08/2016 R002868 F 22/08/2016 R002865 F 29/08/2016 Mate selection - example

Inbreeding from each prospect mating:

Boar candidate Female Litter ΔF R002404 R002795 0.0063 R002404 R002796 0.0063 R002623 R002873 0.0085 R002463 R002865 0.0087 R002463 R002873 0.0069 R002404 R002868 0.0132 R002404 R002880 0.0167 R002623 R002795 0.0219 R002623 R002796 0.0219 R002623 R002865 0.0232 R002404 R002865 0.0263 R002463 R002868 0.0278 R002623 R002868 0.0333 R002404 R002873 0.0409 R002463 R002795 0.0418 R002463 R002796 0.0418 Mate selection - example

Inbreeding from each prospect mating: Boar candidate Female Litter ΔF R002404 R002795 0.0063 R002404 R002796 0.0063 R002623 R002873 0.0085 R002463 R002865 0.0087 R002463 R002873 0.0069 R002404 R002868 0.0132 R002404 R002880 0.0167 R002623 R002795 0.0219 R002623 R002796 0.0219 R002623 R002865 0.0232 R002404 R002865 0.0263 R002463 R002868 0.0278 R002623 R002868 0.0333 R002404 R002873 0.0409 R002463 R002795 0.0418 R002463 R002796 0.0418 Breeding Strategies

• Practical rules. • Kinship analyses. • Mate selection. • Gene bank. Gene bank

• Boars selected for semen collection (and freezing). • Joint programme – BPA, RBST and Deerpark.

Finalé

Thank you for your work!

Thank you for your inspiration!

Thank you for your friendship! Finalé Finalé

Thank you for your work!

Thank you for your inspiration!

Thank you for your friendship!

Inter-national framework for the improved management and conservation of breed diversity.

At the national level, ‘governments shall assess the capability of existing institutions to manage breeding/conservation programmes, and adapt policies as necessary to increase their capacities’.

Breed numbers

B BSB GOS LB MW OSB TAM Breeders 234 238 240 163 133 260 153 Boars 218 321 270 127 120 268 183 Females 795 1267 1701 467 513 1022 721 Total animals 1013 1588 1971 594 633 1290 904 Boars/herd 0.93 1.35 1.12 0.78 0.90 1.03 1.20 Females/herd 3.40 6.67 8.21 2.87 3.86 4.96 5.91 Herd Inventories

Animals B BSB GOS LB MW OSB TAM >100 0 0 1 0 1 0 0

50-99 1 1 1 0 0 0 1

20-49 1 7 4 1 2 4 2

10-19 17 19 16 11 5 10 8

6-9 20 30 32 11 11 26 15

1-5 195 181 186 140 114 220 127

234 238 240 163 133 260 153 Small Herds!

% Herds with 5 or % Herds with 20 or % breed population less animals more animals in largest 2 herds

BERKS 83.3 0.9 10.0% BSB 76.1 3.4 6.8% GOS 77.5 2.5 41.4% LB 85.9 0.6 7.2% MW 85.7 2.2 25.3% OSB 84.6 1.5 3.3% TAM 83.0 2.0 10.7% Who is important?

• Note that several large herds do not sell breeding stock. • They are a genetic resource but are not actively involved in conservation breeding programmes. • Level of crossbreeding.

Take home messages:

All breeds had good geographical distribution, aiding effective mating strategies, avoiding isolation and acting as a ‘safety net’ in health emergencies.

Boar and sow numbers are relatively low, with a large number of small herds.

Take home messages:

Effective population sizes have been variable across breeds. As expected, GOS is largest and BSB second-largest. Other breeds are similar. Some breeds shown significant increase in the past decade. No major concerns.

Inbreeding

0.12 MW OSB 0.1 TAM

0.08

0.06

0.04

0.02

0

1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 Geneped analyses

• Breed structure. – Geographical spread. – Breeder numbers. – Herd inventories. • Effective population size. • Inbreeding. • ‘Founders’. • ‘Bloodlines’. • Breeding strategies. ‘Founders’

• For practical genetic conservation of a breed there is a need to maintain genetic diversity. • Some conservation geneticists maintain that it is desirable to have representation of ‘founder’ animals in the pedigrees of the latest generation. Problems with ‘Founders’

• Necessary to use an arbitrary selection date (we do not have the pedigree records when a breed ‘started’). • The result is that different start dates will identify different ‘founder’ animals. • The BPA is not recommending the use of ‘founders’. Boar numbers

B BSB GOS LB MW OSB TAM

Boars 218 321 270 127 120 268 183

Boars with 101 166 135 57 52 136 87 progeny Boars without 117 155 135 70 68 132 96 progeny

% young boars 54 48 50 55 57 49 52 Boar status

B BSB GOS LB MW OSB TAM

Boars with progeny 101 166 135 57 52 136 87

Active boars 95 116 97 50 49 118 71 Registered 8.2 8.5 9.1 10.6 10.9 10.2 8.7 progeny/active boar Kinship % of boars 3.41 2.06 2.90 4.32 5.31 6.06 3.99 with progeny Take home messages:

All breeds have a satisfactory number of living boars with registered progeny together with a large ‘pool’ of young boars. The average number of registered progeny per boar is close to ten, suggesting that the breeds are limiting the loss of genetic diversity. Kinship of boars with progeny all below recent breed inbreeding levels (except MW).

Inbreeding

B 0.12 BSB GOS LB 0.1 MW OSB TAM 0.08

0.06

0.04

0.02

0

1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010

Inbreeding %

Average Min Max TAM 4.6 3.3 6.5 LB 4.9 3.4 6.7 GOS 5.2 4.4 7.7 BSB 5.9 3.9 7.8 B 6.2 4.5 8.7 MW 7.1 4.8 9.7 OSB 8.1 5.4 11.1