Difference between BPPs and MPPs

BBPs- Bi-parental Populations

Bi-parental populations – derived from crosses between two inbreds lines. Standard design for genetic mapping. 


  • Relative simplicity of their construction
  • High power to detect QTL because all allele frequencies are typically close to the optimal value of 50% 
  • Low rate of linkage disequilibrium decay within chromosomes – means only one or two recombinants per chromosome arm, hence only a few hundred genotyped markers are needed to map QTL. 


  • Lack of precision mapping due to limited effective recombination. 
  • Low genetic diversity, due to choice two founder parents lines – limit the number of QTL can be identified. 

MPPs- Multi-parental Populations

Multi-parental populations- derived from crossing between many parents. Two popular MPP design –

  • NAM-Nested Association mapping – constructed by series of crosses between a recurrent founder line and a number of alternative founders. 
  • MAGIC – Multi-parent advanced generations inter-cross – several founders are inter-crosses over multiple generation. Simple funnel breeding design. 


  • High mapping power and resolution 
  • Greater genetic diversity 
  • Minimal population structure. 
  • Long term durability 

Scott, M.F., Ladejobi, O., Amer, S. et al. Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding. Heredity (2020). https://doi.org/10.1038/s41437-020-0336-6

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