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Determining the number of QTL
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The following biplot shows that the markers fall into 5 distinct groups. This suggests that at least 5 QTL are involved in determining the yield difference between the two parents (Harrington and Tr306). Since the linkage groups are known, as indicated by the number preceding the marker names, it is clear that more than 5 QTL are involved, distributed in chromosomes 1, 3, 4, 5, 6 and 7, respectively:
If each QTL is represented by its nearest marker, the marker-by-environment biplot becomes:
which may be called as QTL-by-environment biplot or QQE biplot. Markers abg472 and abg715 were excluded because they were linked on chromosome 4 as shown in the biplot; it was suspected that they were included in the biplot above because of their linkage with marker mwg655c, which had the strongest association with yield.
What can we see from this QQE biplot
Next: Mega-environment classification based on the QQE pattern