PhD thesis: Optimisation of selective breeding program for Nile tilapia (Oreochromis niloticus)

The  aim  of  this  thesis  was  to  optimise  the  selective  breeding  program  for  Nile tilapia in the Mekong Delta region of Vietnam. Two breeding schemes, the “classic” BLUP scheme following the GIFT method (with pair mating) and a rotational mating scheme  with  own  performance  selection  and  natural  group  spawning,  were investigated.  In  the  latter  scheme,  the  aim  was  to  mimic  natural  spawning conditions  of  Nile  tilapia  to  reduce  the  time  for  family  production;  however reconstruction of pedigrees using DNA markers to monitor inbreeding is required. Parental  assignment  using microsatellites  and  SNPs  showed  that  exclusion-  and likelihood-based methods are equally good for parental assignment, provided that good marker sets with high exclusion power, such as SNPs, are available and that all  parents  are  sampled.  Prolonged  family  production  is  problematic  in  BLUP breeding  value  estimation  and  could  be  a consequence  of  selection  for  harvest weight  in  Nile  tilapia.  Using  a  natural  mating  design  with  single  males  mated  to multiple females in groups, 85% of the successful spawns were collected within 20 days. Genetic correlations between harvest weight and spawning success ranged from 0.48 to  0.52, provided  that the mating period is limited to 20-32 days. We conclude that Nile tilapia favour mating in groups, and that selection for harvest weight in GIFT should improve spawning success of Nile tilapia. Moreover, harvest weight  and  body  weight  at  spawning  have  favourable  genetic  correlations  with number  of  eggs,  relative  fecundity,  and  number  of  swim-up  fry,  which  are  the desired characteristics for Nile tilapia seed production. High-input cages and low-input ponds are the dominant production systems for tilapia in the Mekong Delta. We show that selection in nucleus ponds will produce desired correlated responses in Nile tilapia grown in river-cages. Moreover, they are expected to develop a more rotund  and  thicker  body  shape  at  the  same  length  compared  to  fish  grown  in ponds. In conclusion, we recommend the use of the ‘single male, multiple females’ mating as this will reduce the generation interval by 2 months, thereby increasing genetic gain by about 20%. A rotational mating scheme, with at least 4 cohorts, can be  incorporated  into  the  GIFT  selection  scheme  to  further  reduce  inbreeding,  to estimate  pond  effects  and  to  secure  the  breeding  material.  Finally,  a  reliable multiplier system is important to sustain the current Nile tilapia breeding program, which  can  provide  sufficient  improved  fry  (>50  million  per  year)  for  the  whole Mekong Delta Nile tilapia production.