Breeding and genetics

• strategies used for livestock improvement:

  • Conventional: selecting between (and within) breeds or strains, creating cross-breeds or strains

   

  • Molecular genetic tools: introducing genes from other breeds or species (GM), genomic selection (via genome mapping), altering existing genes through gene editing
• In industrialised countries there is a dominance of a small number of international breeding companies in each species group. Examples include Avigen for poultry and Benchmark for salmon

  • Primary focus is on economic performance
  • Animal health and growth important
  • Performance of groups is recorded, typically pedigreed
• Breeding pyramid:

  At the very top are the elite/ nucleus flocks or herds which are then cross-bred, descending the pyramid to form commercial flocks or herds which embody the desirable traits of several breeds.

   

  At the top there is comprehensive performance measuring (e.g growth rate, fatness, egg production)

  The highest genetic merit animals are kept for breeding in nucleus groups, second best being bred down for commercial use. This is highly cost effective.
• Estimated breeding value= measurement of genetic potential for a specific trait

  BLUP= best linear unbiased prediction - removes environmental factors from evaluation of genetic potential

  Predicted transmitting abilities= approx. ½ Estimated breeding value

  These are computer statistical procedures which associate genetics with performance of relatives.

  This allows for comparison across flocks and across years
• Performance testing: record the performance of all animals then select the best as parents for widespread use

  Progeny testing: select the most promising potential parents using BLUP, EBVs with ancestors performance. Then create test matings using AI in well recorded herds, recording the performance of their progeny. Update the EBVs to include progeny information then do a final selection of parents for widespread use.
• Desirable traits in pig breeding:

  • Sire lines- selected for growth and carcass traits
  • Dam lines- selected for reproductive ability, growth and carcass traits

  Most commercial producers buy dam line gilts and sire line boars or use AI
• What are the different line specialisations in poultry?

  Meat (broiler chickens, ducks, turkeys) are usually bought as day old chicks from specific breeding companies

  Layer companies usually buy parent stock from a breeding company or point-of-lay pullets from rearing companies
• The sire contributories to balanced poultry breeding are:

  -      Growth rate (G)

  -          Feed conversion rate (F)

  -          Conformation (C)

  -          Breast meat yield (B)

  -          Fertility (F)

  -       Sound legs (L)

  -          Disease resistance (D)

  robustness
• The dam contributories to balanced poultry breeding are:

  • Conformation
  • Rate of lay
  • Fertility/ hatchability
  • Early onset of lay
  • Egg size
  • Sound legs
  • Disease resistance
  • robustness
• Selection objectives in layer hens:

  Direct:

  • egg numbers
  • egg weight
  • egg shell colour/ strength
  • albumin quality and yolk colour
  • production quality

  Indirect:

  • Decreased body weight
  • Residual feed consumption
  • Sexual maturity age
  • Disease resistance
  • Cost/ efficiency
• common commercial pig breeds:

  Dam lines: based on Landrace, Large white, Yorkshire and Meishan

  Sire lines: based on Hampshire, Duroc and Pietrain
• Breeding goals in pigs:

  Dam lines:

  -          Number of piglets born alive, survival rate

  -          Growth rate

  -          Conformation (particularly of legs are mammary glands)

  Sire lines:

  -          Lean growth rate

  -          Feed efficiency

  Carcass traits
• dairy cattle breeding differs from pig or poultry breeding as there is much less of a pedigree nucleus pyramid as commercial farmers have access to top bulls via AI, also creating strong genetic links between herds.

  Most cows are in private ownership and breeding values are in the public domain
• Dairy cattle info:

  • Milk volume, fat%, protein%
  • Average SCC
  • Calving and insemination dates
  • Occurrence of health disorders
  • Culling date and reason
  • Linear type scores and condition scores
• £PLI- Profitable Lifetime Index: Production, survival, fertility, udder health, leg health, calving ability, efficiency.

  £SCI- Spring Calving Index. The same but a greater weighting on fertility and efficiency
• Requirements for genomic selection:

  A large, well-recorded population of the flock/herd with their genotypes is required to calculate the relationship between Single Nucleotide Polymorphisms and performance traits

   

  Wide use in dairy pigs and poultry as GS is valuable for difficult traits such as milk yield and longevity, reproductive traits by sex, carcass information and disease
• Aquaculture breeding:

  Of growing importance, rapid genetic changes are possible as an abundance of offspring is easy to produce (fecundity)

  Large breeding operations with focuses now on growth and disease resistance.
• The main advantage of progeny testing is that it produces accurate predictions of a bull's genetic merit, based on the performance of daughters in commercial herds. The disadvantages are that progeny testing schemes are costly to run, and the results take many years to materialise
• UK distribution of sheep breeds:

  • Hills: mainly pure breeds e.g Scottish blackface, swaledale, welsh mountain
  • Upland and lowland: draft hill breeds crossed to longwool rams to make mules or halfbreds
  • Fat lambs: mules bred to terminal sires such as texel, Suffolk, charollais
• Sheep terminal sires are chosen mainly for their lean growth rate. Modern Tups are now on average 6kg heavier at 20wks, have a lower fat depth but higher muscle depth.
• Selection objectives for hill sheep:

  -          Increase number of lambs reared

  -          Improve ewe milking ability

  -          Improve fleece production

  -          Improve flock lifespan (longevity)

  -          Improve lamb carcass weight  and quality

  -          Increase lamb weaning weight

  Decrease lamb mortality
• Historically, much of terminal beef sire selection was between breeds, however now there is widespread use of european breeds as terminal sires in temperate regions.

  There is widespread use of performance recording and genetic evaluation within these breeds for their improvement.

   

  In specialised or suckler herds there is wide use of British breeds, with rotational crosses or composites, replacing the traditional beef x dairy suckler model. This is because cross cows producing cross calves have the greatest increase in performance
• Systems of testing and genetic evaluation in beef cattle:

  • On farm performance recording such as through breed societies and breed plans. The accumulation of these records is slow, especially with natural matings
  • Central performance progeny testing
  • Co-operative breeding schemes (fallen out of favour)
  • Genetic evaluation with BLUP EBVs
• Modern sources of data for breeding:

  • Objective carcass/ meat quality evaluation of offspring
  • Fitness trials such as neonate vigour, survival, management and disease
  • Molecular genetic information especially for disease traits, reproduction and meat quality.
• There is less uptake of genomic testing in dog and horse breeding because it is easy to make early changes through better nutrition, environment and training

  There is also a lack of ‘organised’ breeding programmes

  • Particularly in thoroughbreds and pedigrees there is a very narrow genetic base (but many generations of mutation)
• There are Estimated Breeding Value tests for hip and elbow dysplasia in dogs, common since 2014 based on BVA and Kennel Club scoring schemes

   

  Although the assessment is under development, EBVs are scored from low to high risk. Animals are not EBV scored THEMSELVES for elbows but are for hips (so lower accuracy)
• Positives of farm animal breeding selection:

  • Economic contributions- apex of sector contributes about 40% of global output
  • Contribution to livelihoods
  • Efficiency of resource use (less feed, land, GHGs per unit)
  • Food and nutritional security
  • Improve/ halt decline in health and welfare
• Negatives of farm animal breeding selection:

  • Acceleration of livestock revolution and associated environmental / health challenges
  • Loss of farmed/ local breeds
  • Loss of genetic variability within breeds
  • Risk to functional fitness as production or fashion become primary breeding goals
  • Low use of genetic improvement in some sectors and LMICs
  • Inappropriate use of breeds in some places
• Explain why deleterious consequences of animal breeding arise

  ·       Chance – unfavourable genes or traits in the founder population

  ·       Small or inbred populations which increase homozygosity and frequency of homozygous recessive disorders

  ·       Direct or indirect consequences of the breeding goal
• How can deleterious consequences of animal breeding be managed?

  • Sufficient (effective) population sizes
  • Minimising inbreeding
  • Screen for and manage genetic disorders
• Inbreeding is the mating of two related animals resulting in inbreeding depression (reduction in performance, especially fitness; more animals being homozygous for bad recessive genes; 0.3-1% performance decline per 1% inbreeding)

  Inbreeding is relatively inevitable in closed population, so is usually limited in breeding programmes
• Inbreeding calculation:

  (F) probability that two alleles are identical by descent from common ancestor = sum [(1/2)n]

  n = number of individuals in each path from animal through the common ancestor

  father-daughter: n=2, F=25%

  full siblings: n=3+3, F=25%

  half siblings: n=3, F=12.5%

  full cousins: n=5+5, F=6.25%
• Inbreeding can be managed informally by avoiding mating of close relatives

  Formally using decision support software to optimize mate selection and long term genetic contributions
• Common undesirable side effects of selection in poultry:

  • Ascites (waterbelly)
  • Skeletal and mobility issues (low bone density)
  • Broiler breeder hunger (keeping breeding broilers hungry to prenatally programme offspring to have reduced satiety .’. eat more)
• Common undesirable side effects of selection in pigs:

  • Stillbirths and piglet mortality in large litter size lines
  • Sow hunger (keeping breeding sows hungry so offspring eat more)
  • Sudden death syndrome (malignant hyperthermia)
  • Tail biting and aggression
• Common undesirable side effects of selection in dairy cattle:

  • Unfavourable genetic association between yield and fertility
  • Mastitis
  • Lameness
• Calving difficulty, particularly in highly muscled breeds or lines is a common undesirable side effect of selection in beef cattle
• Syringomyelia is an undesirable selection side effect in brachycephalic dog breeds.

  Causes a CSF flow obstruction as the cerebellum is pushed into the foramen magnum, causing pain and neurological effects. Common in CKCS