Table 3. Positions and effects of the six cross-specific QTL identified in cross 3D1 × 3D7.

Environment	Colony Age, dpi	QTL Peak Markera	Chromosome	Estimated Position of Peaking Marker, cM	Estimated Position of Peaking Marker, kb	LOD Score at Peak	P Value	Mean 3D1 Allele (Gray Value)	Mean 3D7 Allele (Gray Value)	Mean Difference	Allele Effectb	Percentage of Variance Explained by QTL, %	Estimated Position of Proximal Marker, kbc	Estimated Position of Distal Marker, kbc	Bayes Confidence Interval Length, kb
Cold	8	12_143193	12	5.74	143	4.85	0.002	134.56	129.28	5.27	3D1	9.2	29	305	276
Cold	11	8_1250811	8	140.32	1251	4.07	0.01	101.72	112.39	10.66	3D7	7.1	897	2228	1332
Cold	11	c10.loc108 (p)	10	108.13	649	9.55	< 0.001	116.28	100.17	16.11	3D1	15.6	634	673	39
Control	8	c11.loc82 (p)	11	82.06	581	32.2	< 0.001	118	93.73	24.27	3D1	39.2	560	603	43
Control	11	5_871061	5	157.26	871	4.38	0.003	74.99	85.47	10.48	3D7	7.5	449	2799	2350
Fungicide	14	1_1740191	1	193.5	1740	3.64	0.014	64.87	73.03	8.16	3D7	6.3	1063	4267	3203

LOD, logarithm of odds.

^aA (p) indicates that a pseudomarker provided the greatest LOD score. In all other cases a true marker provided the highest LOD score.

^b3D7 indicates that the parental 3D7 allele provided the greater phenotypic mean then the parental 3D1 allele, whereas 3D1 indicates that the parental 3D1 allele provided the higher phenotypic mean then the parental 3D7 allele.

^cMarkers flanking Bayes confidence interval.