Initiating Breeding Programs By: Seyed Hossein Moradyan The Fundamental Basis of a Breeding Program fundamental objective of a breeding program sustainable aquaculture production utilize feed, water and land resources far more efficiently the potential for increased production efficiency through systematic genetic improvement is enormous A key benefit of selective breeding is that genetic improvement obtained is permanent. The Fundamental Basis of a Breeding Program Breeding programs have long-term goals and objectives Changes implemented in the current generation are first realized in the next generation typical changes or responses tend to be around 10–15% per generation for many traits, requiring accurate measurements. The Fundamental Basis of a Breeding Program Experience from the Atlantic salmon breeding program in Norway that commenced in 1975 the farmers did not necessarily see positive results from the first generation of selection but did so in the second That meant that in reality, it took eight years from the commencement of selection until the farmers realized the benefits of the breeding program The Fundamental Basis of a Breeding Program To secure necessary capital for investment in a breeding program mainly because the genetic gain is cumulative over generations It must be clearly explained to investors patient investors for return of profit are required that there is a very favourable benefit/cost ratio of such investments Summary of main elements in a breeding plan A breeding plan is never a final document should be continuously revised and improved as new knowledge is obtained through experience and research. Summary of main elements in a breeding plan The main elements in a complete breeding plan are: 1. Define the breeding goal 2. Form a base population with broad genetic variation 3. Select breeding strategies 4. Chose selection methods 5. Identification of animals 6. Select mating design 7. Protocol for testing strategies Summary of main elements in a breeding plan 8. Protocol for recording of all traits in the breeding goal 9. Describe systems for selection procedures 10. Estimate breeding values 11. Protocol for selection of broodstock 12. Protocol for control populations 13. Avoid constraints and negative effects of selection 14. Plan for dissemination of organization of breeding work improved stock and Establishment of a Base Population broad genetic diversity failed breeding programs formation of a population maximise the likelihood of long-term genetic response The first, vital and one of the most important steps ensure avoided rapid inbreeding Establishment of a Base Population since all the genetic variability for the traits included originally in the breeding goal and those to be included in the future is contained in the initial founders The success of an aquaculture breeding program depends on the way that base population is formed Also, the decisions taken when creating the base population will have consequences on the genetic progress for any other additional trait that may be part of future breeding goals, whatever production or fitness related traits. Defination The initial population that is used is often called the base population or founder population Similar to the base population, the initial generation is often called the base generation The base population may be considered as generation 0 with no inbreeding alternative ways to establish a good base population broodstock should be selected from at least four genetically diverse strains (Holtsmark et al. 2006) If only wild animals are available, 1 broodstock of farmed fish with no information of pedigree 2 3 broodstock with known pedigree could be highly inbred the level of inbreeding and their effective population sizes should be assessed other farmed strains or wild stocks should be included to decide if it is necessary to include broodstock from other farmed or wild populations Background Traditionally, base populations were created from a number of wild strains by sampling equal numbers from each strain. But for some aquaculture species improved strains are already available mean phenotypic values can be used as a criterion to optimize the sampling when creating base populations Also, genome-wide genotype information could help to assess relationships within and between candidate strains Base Population Considerations The genetic variability in the base population may be secured by forming a synthetic population (Skjervold, 1982). The first step should be to compare productivity in available populations A base population should combine characteristics of the subpopulations. Base Population Considerations For practical reasons the first mating can be random within the strains However, in the next generation, complete crosses between all strains should be performed ► form a synthetic base population in order to ► reduce possible inbreeding at the same time Base Population Considerations (Eknath et al. 2007) It is generally recommended to apply low selection intensity in the initial generations that may secure the maintenance of broad genetic variability for future selection Holtsmark et al. (2007) concluded that prompt, strong selection resulted in greater gain and consistent advantage in the fraction of fixed positive alleles Numbers of a Base Population no single figure for the number of broodstock to form the base population a minimum of at least 100 males and 100 females higher numbers would be advantageous if feasible Although these basic principles apply to the commencement of a novel breeding program The actual formation of the base population of present breeding programs in aquaculture species have been quite different Base Population For Atlantic salmon started in 1971 genetic material was sampled from 40 river strains no restriction was placed on strain contribution during the first generations This resulted in an initial selection between strains reflecting the four year generation interval of the species four base populations were produced Base Population For Atlantic salmon Each included broodstock originating from eight to 24 river strains From each strain, the aim was to use four males and 12 females to produce 12 full-sib groups and 4 half-sib groups however these target numbers were not reached for all river strains The base populations were formed by random mating between and within strains Base Population For Atlantic salmon Progeny from the base population were selected for body weight at harvest both across and within families under the restriction of not mating closely related animals (full- and half-sibs) F1 generations for the four populations were produced in the years 1975–1978 for subsequent generations, selected breeders have been mated randomly Selection intensity for growth rate has been intense from the first generation of selection Base Population for Nile tilapia An alternative is to primarily mate animals from different strains before starting selection and apply low selection intensity during the first generations of selection This strategy was used in GIFT (Genetic Improvement of Farmed Tilapias) in the Philippines This may secure the maintenance of a broad genetic variability (allelic diversity) that allow long-term selection response and a stepwise inclusion of new traits in the breeding goal. Base Population for Nile tilapia the situation was quite different formed from eight unrelated strains The first mating was performed within strains 4 wild strains from Africa 4 strains farmed in the Philippines while in the second, a complete 8×8 diallel cross was made The base population was subsequently made up of 25 strain combinations, allowing selection with low intensity to maintain all the strains in the base Base Population for Rohu Carp In India carried out at CIFA (Central Institute of Freshwater Aquaculture) mating was performed both between and within river strains and the mating was at random. six river strains Base Population for Rohu Carp Base Population for Rohu Carp • It is worth noting that molecular measures of genetic diversity using neutral markers do not seem to be informative about the magnitude of quantitative genetic variation for traits of economic importance in a population (Reed and Frankham, 2001). • Assessment of the magnitude of genetic variation for economic important traits applicable for farmed fish therefore should be obtained from traits recorded on fish raised in a commercial farm environment.
