Adaptive selection of founder segments and epistatic control of plant height in the MAGIC winter wheat population WM-800

Table 4 Significant epistatic interaction effects for plant height in WM-800

Epistatic Interaction^a	SNP M1^b	Chr^c	Pos^d	SNP M2^b	Chr^c	Pos^d	FDR^e	R^2f	J/J^g	N/N^h	J/Nⁱ	N/J^j	aa^k
EpiHEI.WM-800.1	Kukri_c67601_267	1A	71.5	TA001269–1282	5A	62.7	3.23E-13	17.0	81.4	83.6	90.4	75.3	0.70
EpiHEI.WM-800.2	BS00050522_51	1B	5.3	Kukri_c21008_657	2A	151.3	2.35E-03	6.4	80.6	81.8	81.8	72.2	8.40
EpiHEI.WM-800.3	Excalibur_c92298_213	1D	171.3	wsnp_Ex_c539_1072859	4A	60.4	1.24E-02	5.4	81.3	81.1	78.1	82.3	1.80
EpiHEI.WM-800.4	BobWhite_c11022_78	2A	11.5	TA004056–0809	4A	48.5	1.38E-02	3.4	80.3	80.6	87.4	79.9	−6.40
EpiHEI.WM-800.5	RAC875_c47161_100	2A	47.2	TA004556–0473	5B	176.6	3.44E-04	8.6	82.0	78.6	81.8	80.1	−1.40
EpiHEI.WM-800.6	RAC875_c9523_328	2A	144.2	BS00095061_51	3B	67.5	1.35E-02	4.5	81.5	81.1	78.0	81.9	2.60
EpiHEI.WM-800.7	TA002989–0535	2B	157.2	RAC875_rep_c78007_425	7B	135.4	5.95E-09	9.8	78.4	96.2	81.3	79.6	13.70
EpiHEI.WM-800.8	BS00067499_51	3A	68.7	Tdurum_contig57370_82	7B	53.8	4.67E-04	9.7	79.8	77.4	81.9	86.7	−11.40
EpiHEI.WM-800.9	TG0010a	4B	56.0	TG0011a	4D	69.2	6.32E-44	45.1	73.9	77.7	89.0	NA	−13.20
EpiHEI.WM-800.10	wsnp_Ra_rep_c69221_665	5A	42.0	Tdurum_contig17062_221	7A	202.2	3.58E-06	11.5	82.4	77.0	90.0	78.4	−9.00
EpiHEI.WM-800.11	TA001269–1282	5A	62.7	wsnp_Ex_c1880_3545329	5A	104.9	3.49E-11	15.2	76.9	82.8	82.4	88.7	−11.50
								84.1

^aName of epistatic interaction including prefix Epi, trait, population and a consecutive number
^bInteracting SNP markers M1 and M2
^cChromosomal location of SNP [36]
^dGenetic position in cM of SNP [36]
^eFDR corrected p value of marker 1*marker 2 interaction
^fProportion of explained epistatic variance in % of marker 1*marker 2 interaction (in %)
^gMean plant height (in cm) of WM lines carrying homozygous Julius alleles (J) at both loci
^hMean plant height (in cm) of WM lines carrying homozygous Non-Julius alleles (N) at both loci
ⁱMean plant height (in cm) of WM lines carrying a homozygous Julius allele (J) and a Non-Julius allele (N) at loci 1 and 2, respectively
^jMean plant height (in cm) of WM lines carrying a homozygous Non-Julius allele (N) and a Julius allele (J) at loci 1 and 2, respectively
^kEstimated additive by additive epistatic interaction effect (aa) [45]
Bold letters indicate markers located in regions containing main QTL for plant height (Table 3)
NA = data not available, in this case, the epistatic interaction effect was estimated by adding twice the mean plant height of the JN group

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