Table 2 Conditional probabilities of QTL genotype combination on the genotypes of flanking markers in both IF2 and its double-cross offspring plants

From: Mixed linear model approach for mapping quantitative trait loci underlying crop seed traits

IF 2

BC 1

QQ:QQ(QQQ)

Qq:QQ(QQQ)

Qq:Qq(Qqq)

qq:Qq(Qqq)

M1M1M2M2

M1M1M2M2

s 1 2 s 2 2 /s 2

s 1 s 2 r 1 r 2 /s 2

s 1 s 2 r 1 r 2 /s 2

r 1 2 r 2 2 /s 2

M1M1M2m2

M1M1M2M2

s 1 2 s 2 r 2 /rs

s 1 r 1 t 2 /rs

s 1 s 2 r 1 r 2 /rs

r 1 2 r 2 s 2 /rs

M1M1M2m2

M1M1M2m2

s 1 2 s 2 r 2 /rs

s 1 s 2 r 1 r 2 /rs

s 1 r 1 t 2 /rs

r 1 2 r 2 s 2 /rs

M1M1m2m2

M1M1M2m2

s 1 2 r 2 2 /r 2

s 1 s 2 r 1 r 2 /r 2

s 1 s 2 r 1 r 2 /r 2

r 1 2 s 2 2 /r 2

M1m1M2M2

M1M1M2M2

s 1 r 1 s 2 2 /rs

s 2 r 2 t 1 /rs

s 1 s 2 r 1 r 2 /rs

s 1 r 1 r 2 2 /rs

M1m1M2M2

M1m1M2M2

s 1 r 1 s 2 2 /rs

s 1 s 2 r 1 r 2 /rs

s 2 r 2 t 1 /rs

s 1 r 1 r 2 2 /rs

M1m1M2m2

M1M1M2M2

s 1 s 2 r 1 r 2 /t

t 1 t 2 / t

s 1 s 2 r 1 r 2 /t

s 1 s 2 r 1 r 2 /t

M1m1M2m2

M1M1M2m2

s 1 s 2 r 1 r 2 /rs

s 2 r 2 t 1 /rs

s 1 r 1 t 2 /rs

s 1 s 2 r 1 r 2 /rs

M1m1M2m2

M1m1M2M2

s 1 s 2 r 1 r 2 /rs

s 1 r 1 t 2 /rs

s 2 r 2 t 1 /rs

s 1 s 2 r 1 r 2 /rs

M1m1M2m2

M1m1M2m2

s 1 s 2 r 1 r 2 /t

s 1 s 2 r 1 r 2 /t

t 1 t 2 /t

s 1 s 2 r 1 r 2 /t

M1m1m2m2

M1M1M2m2

s 1 r 1 r 2 2 /rs

s 2 r 2 t 1 /rs

s 1 s 2 r 1 r 2 /rs

s 1 r 1 s 2 2 /rs

M1m1m2m2

M1m1M2m2

s 1 r 1 r 2 2 /rs

s 1 s 2 r 1 r 2 /rs

s 2 r 2 t 1 /rs

s 1 r 1 s 2 2 /rs

m1m1M2M2

M1m1M2M2

r 1 2 s 2 2 /r 2

s 1 s 2 r 1 r 2 /r 2

s 1 s 2 r 1 r 2 /r 2

s 1 2 r 2 2 /r 2

m1m1M2m2

M1m1M2m2

r 1 2 r 2 s 2 /rs

s 1 s 2 r 1 r 2 /rs

s 1 r 1 t 2 /rs

s 1 2 s 2 r 2 /rs

m1m1M2m2

M1m1M2M2

r 1 2 r 2 s 2 /rs

s 1 r 1 t 2 /rs

s 1 s 2 r 1 r 2 /rs

s 1 2 s 2 r 2 /rs

m1m1m2m2

M1m1M2m2

r 1 2 r 2 2 /s 2

s 1 s 2 r 1 r 2 /s 2

s 1 s 2 r 1 r 2 /s 2

s 1 2 s 2 2 /s 2

IF 2

BC 2

QQ:Qq(QQq)

Qq:Qq(QQq)

Qq:qq(qqq)

qq:qq(qqq)

M1M1M2M2

M1m1M2m2

s 1 2 s 2 2 /s 2

s 1 s 2 r 1 r 2 /s 2

s 1 s 2 r 1 r 2 /s 2

r 1 2 r 2 2 /s 2

M1M1M2m2

M1m1M2m2

s 1 2 s 2 r 2 /rs

s 1 r 1 t 2 /rs

s 1 s 2 r 1 r 2 /rs

r 1 2 r 2 s 2 /rs

M1M1M2m2

M1m1m2m2

s 1 2 s 2 r 2 /rs

s 1 s 2 r 1 r 2 u 2 /rs

s 1 r 1 t 2 /rs

r 1 2 r 2 s 2 /rs

M1M1m2m2

M1m1m2m2

s 1 2 r 2 2 /r 2

s 1 s 2 r 1 r 2 /r 2

s 1 s 2 r 1 r 2 /r 2

r 1 2 s 2 2 /r 2

M1m1M2M2

M1m1M2m2

s 1 r 1 s 2 2 /rs

s 2 r 2 t 1 /rs

s 1 s 2 r 1 r 2 /rs

s 1 r 1 r 2 2 /rs

M1m1M2M2

m1m1M2m2

s 1 r 1 s 2 2 /rs

s 1 s 2 r 1 r 2 /rs

s 2 r 2 t 1 /rs

s 1 r 1 r 2 2 /rs

M1m1M2m2

M1m1M2m2

s 1 s 2 r 1 r 2 /t

t 1 t 2 /t

s 1 s 2 r 1 r 2 /t

s 1 s 2 r 1 r 2 /t

M1m1M2m2

M1m1m2m2

s 1 s 2 r 1 r 2 /rs

s 2 r 2 t 1 /rs

s 1 r 1 t 2 /rs

s 1 s 2 r 1 r 2 /rs

M1m1M2m2

m1m1M2m2

s 1 s 2 r 1 r 2 /rs

s 1 r 1 t 2 /rs

s 2 r 2 t 1 /rs

s 1 s 2 r 1 r 2 /rs

M1m1M2m2

m1m1m2m2

s 1 s 2 r 1 r 2 /t

s 1 s 2 r 1 r 2 /t

t 1 t 2 /t

s 1 s 2 r 1 r 2 /t

M1m1m2m2

M1m1m2m2

s 1 r 1 r 2 2 /rs

s 2 r 2 t 1 /rs

s 1 s 2 r 1 r 2 /rs

s 1 r 1 s 2 2 /rs

M1m1m2m2

m1m1m2m2

s 1 r 1 r 2 2 /rs

s 1 s 2 r 1 r 2 /rs

s 2 r 2 t 1 /rs

s 1 r 1 s 2 2 /rs

m1m1M2M2

m1m1M2m2

r 1 2 s 2 2 /r 2

s 1 s 2 r 1 r 2 /r 2

s 1 s 2 r 1 r 2 /r 2

s 1 2 r 2 2 /r 2

m1m1M2m2

m1m1M2m2

r 1 2 r 2 s 2 /rs

s 1 s 2 r 1 r 2 /rs

s 1 r 1 t 2 /rs

s 1 2 s 2 r 2 /rs

m1m1M2m2

m1m1m2m2

r 1 2 r 2 s 2 /rs

s 1 r 1 t 2 /rs

s 1 s 2 r 1 r 2 /rs

s 1 2 s 2 r 2 /rs

m1m1m2m2

m1m1m2m2

r 1 2 r 2 2 /s 2

s 1 s 2 r 1 r 2 /s 2

s 1 s 2 r 1 r 2 /s 2

s 1 2 s 2 2 /s 2

  1. Abbreviations: IF2, immortalized F2; QTL, quantitative trait locus.
  2. The IF2 indicates the population from random mating of double haploid (DH) lines; BC1 (BC2) indicates the back-cross population of IF2 with P1 (P2); r1, r2 and r are the recombination rates between marker 1 and QTL, between QTL and marker 2 and between the two flanking markers, s=1−r, t=s3+r3, and similarly for s1, s2, t1 and t2. If the IF2 is from random mating of recombinant inbred lines (RILs), instead of the recombination rates, the proportions of recombinant zygote should be used.
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