Transcript A L.I.S.P Program to Estimate Equine Phenotypes

A L.I.S.P Program to Estimate
Equine Phenotypes
By
Susan. H. Melville
AaBbCcCRcrDdEeFfGgOoPpRrRBrbSTYstyTtWw
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The above 15 standard pairs of genes could
generate 230 or 1,073,741,824 different
combinations!
We can eliminate C, W, F, P, and RB
AaBbCRcrDDEeGgOoRrSTYstyTtOo
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This still leaves us with 10 pairs, we are
down to 220 or 1,048,576 possible
combinations… still too high
The Dominant Gene
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For each pair of genes we have 4 possible
pairings, consider just gene “A”
Foal 1 (AA)
Foal 2 (A a)
Foal 3 (a A)
Foal 4 (a a)
Foals 1, 2, 3 have different GENOTYPES
but the same PHENOTYPE (appearance)
because the dominant A is expressed
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This means we only need to check for
the dominant condition in either parent,
thus reducing our 4 checks to 2
• 1. (Dominant)
• 2. (Recessive, Recessive)
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The exceptions are the genes O, R, and
CR which will still need 4 rules each
• OO or RR produces a stillborn foal
• CRCR produces an unregisterable foal
AaBbEeSTYstyCRcrDdGgRrTtOo
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PHENOTYPE is the key here….
When the genes are rearranged by function
we find
• 4 pairs produce 6 base colors AaBbEeSTYsty
• 4 pairs affect the 6 base colors CrcrDdRrGg
• 2 pairs produce patterns TtOo
Only 97 Rules cover 1,048,576 Genotypes!
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Can this be reduced further?
We can reduce processing time!
• Since we are processing the genes as three
separate subtypes (base, secondary, and pattern)
there is no reason to LOAD all the rules at
the same time.
The Algorithm
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Load base color input rules
Input parents base color genes
Load base color output rules & Process
Load secondary input rules
Input parents secondary color genes
Load secondary output rules & Process
Load pattern input rules
Input parents pattern genes
Load pattern output rules & Process
The Base genes in LISP
AaBbEeSTYsty
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A
a
E
e
(POINTS)
(~POINTS)
(BLACK)
(~BLACK)
B (~LIVER)
b (LIVER)
STY (SOOTY)
sty (~SOOTY)
The Secondary Genes in LISP
CRcrDdGgRr
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CR (CRÈME)
cr (~CRÈME)
CRCR (2 CRÈME)
G (GREY)
g (~GREY)
R
r
RR
D
d
(ROAN)
(~ROAN)
(LETHAL)
(DUN)
(~DUN)
The Pattern genes in LISP
TtOo
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O
o
OO
T
t
(OVERO)
(~OVERO)
(LETHAL)
(TOBIANO)
(~TOBIANO)