TABLE 4

Summary of predictions from “test” methods 1–3 designed to identify SFPs against “control” method 4 designed to identify all expression-based single-locus polymorphisms (SFPs and GEMs)

Initial predictionsTest methods 1–3 (P ≤ 10−18)Control method 4
Leaf tissue SFPs18532131
Embryo tissue SFPs32833598
Combined and unique SFPs36083953
SFPs common to test and control3354
SFPs common to both leaf and embryo1527 (42%)1776 (45%)
SFPs unique to leaf325 (9%)355 (9%)
SFPs unique to embryo1755 (49%)1822 (46%)
Embedded Image; P = 0.07, NS
SFPs match to SNP genotypes of 30 DHLs208205
Good agreement (>90%)198 (95%)196 (95%)
Poor agreement (≤90%)10 (5%)9 (5%)
Embedded Image; P = 0.84, NS
SFPs match to St/Mx informative features175188
Feature has sequence polymorphism64 (37%)66 (35%)
Feature has no sequence polymorphism111 (63%)122 (65%)
Embedded Image; P = 0.77, NS