Association and linkage mapping to unravel genetic architecture of phenological traits and lateral bearing in Persian walnut (Juglans regia L.)

Bernard, Anthony; Marrano, Annarita; Donkpegan, Armel; Brown, Patrick J.; Leslie, Charles A.; Neale, David B.; Lheureux, Fabrice; Dirlewanger, Elisabeth

doi:10.1186/s12864-020-6616-y

Table 4 Summary of association and linkage mapping results related to heterodichogamy and male flowering dates

From: Association and linkage mapping to unravel genetic architecture of phenological traits and lateral bearing in Persian walnut (Juglans regia L.)

Dataset	GWAS using FarmCPU model						QTLs detection using MIM method
Dataset	SNP	Chr ^a	Physical position	Significance ^b	R^{2 c}	Alleles/Effect ^d	Peak SNP ^e	LG ^f	Physical position	Confidence interval ^g	LOD ^h	P.E.V. ⁱ	d ^j
Heterodichogamy
1989–2016	AX-171595404	11	31,887,506	2.22E-42	69.6	C/G (2.7)
2018–2019	AX-171218000	11	31,885,611	8.97E-49	77.2	A/G (− 2.7)
Beginning male flowering date
2018–2019	AX-171121884	2	21,247,915	1.74E-09	7.2	C/T (−2.5)	AX-171521263	F1	201,441	4.1–9.1	14.4	32.6	4.5
	AX-171578684	4	5,966,307	2.41E-10	6.0	C/T (4.5)	AX-170771092	U1	5,814,444	< 0.5	27.6	52.4	−5.3
	AX-170614801	4	3,642,466	2.78E-10	20.2	C/T (3.6)	AX-170983192	U9	22,032,363	23.6–57.3	5.5	4.9	2.2
	AX-171490851	7	37,022,231	3.56E-10	17.8	C/G (−2.3)
	AX-170625459	10	10,656,433	2.73E-09	20.2	G/T (−2.4)
	AX-171147588	11	31,874,617	1.58E-10	2.0	A/G (3.1)
	AX-170794443	14	10,691,227	2.22E-09	< 0.1	C/T (−2.2)
	AX-170692084	16	3,578,209	1.94E-08	18.2	G/T (−2.5)
2018	AX-171589348	3	27,241,886	1.24E-10	< 0.1	C/G (−2.9)	AX-171521263	F1	201,441	2.1–10.4	7.6	36.0	3.8
	AX-171559197	6	13,733,426	9.96E-17	20.7	C/T (3.6)	AX-170771092	U1	5,814,444	0.0–2.0	17.5	50.9	−4.6
	AX-170937789	7	30,051,478	2.70E-12	18.0	C/T (−3.7)
	AX-170625459	10	10,656,433	4.08E-09	20.6	G/T (−2.2)
2019	AX-171147582	11	31,882,831	6.23E-13	1.7	C/T (6.2)	AX-171521263	F1	201,441	0.7–13.4	6.4	28.1	5.5
	AX-171525706	14	28,381,698	1.38E-10	10.1	C/G (4.9)	AX-170771092	U1	5,814,444	0.0–5.7	9.2	33.5	−5.9
	AX-170692024	16	3,630,320	1.27E-08	22.8	C/T (−4.2)
Peak male flowering date
2018–2019	AX-171578684	4	5,966,307	2.17E-09	6.1	C/T (6.8)	AX-171180038	F1	177,178	3.4–10.2	17.1	32.2	5.4
	AX-171147588	11	31,874,617	1.34E-10	1.9	A/G (4.1)	AX-170771092	U1	5,814,444	< 0.5	30.2	47.0	−6.2
							AX-170869355	F2	35,198,358	14.5–67.9	4.6	6.6	−2.3
							AX-170615140	U4	3,291,736	0.0–24.4	6.2	5.0	2.4
							AX-171478663	U5	7,984,929	30.6–64.9	9.2	9.7	3.0
							AX-171548959	U6	12,747,130	0.0–80.5	6.1	5.5	−2.4
							AX-171214747	U9	18,177,182	23.7–57.3	5.1	5.1	2.2
							AX-171030926	U11	33,195,441	2.3–49.4	4.8	5.2	1.8
							AX-170818106	F14	9,871,222	0.0–58.2	5.6	8.3	2.8
2018	AX-170672894	1	1,835,862	4.05E-11	20.6	G/T (3.1)	AX-171180038	F1	177,178	0.0–12.9	7.2	30.1	4.2
	AX-170802286	4	414,952	8.03E-10	< 0.1	A/G (−3.0)	AX-170771092	U1	5,814,444	0.0–5.1	15.8	49.8	−5.5
	AX-171578684	4	5,966,307	1.04E-08	5.5	C/T (4.3)
	AX-171559197	6	13,733,426	3.12E-12	20.3	C/T (3.2)
	AX-171571158	12	1,647,435	5.48E-09	< 0.1	A/C (−2.4)
2019	AX-171578684	4	5,966,307	5.63E-09	8.0	C/T (9.1)	AX-171180038	F1	177,178	0.0–15.6	6.7	28.3	6.1
	AX-171490851	7	37,022,231	1.13E-10	19.2	C/G (−4.3)	AX-170771092	U1	5,814,444	< 0.5	11.8	40.1	−7.6
	AX-171147582	11	31,882,831	1.47E-10	1.5	C/T (5.1)
	AX-170849618	12	14,608,835	1.85E-08	< 0.1	C/T (−2.9)
	AX-170692024	16	3,630,320	6.46E-15	22.6	C/T (−6.2)
End male flowering date
2018–2019	AX-171578684	4	5,966,307	1.01E-09	5.4	C/T (7.9)	AX-171521263	F1	201,441	4.8–8.1	19.0	33.6	6.5
	AX-171560933	5	604,688	1.30E-08	19.2	C/G (−2.8)	AX-170771092	U1	5,814,444	< 0.5	29.8	43.2	−7.1
	AX-171559197	6	13,733,426	6.50E-10	18.2	C/T (3.3)	AX-171539906	F2	34,841,469	29.2–67.9	5.3	6.3	−2.9
							AX-171002599	U5	20,087,966	43.9–78.7	6.3	3.4	2.6
							AX-170677995	U6	1,908,834	0.0–24.0	8.8	7.8	−3.3
							AX-170901663	U12	19,737,912	12.8–85.3	5.6	3.9	2.4
							AX-170818106	F14	9,871,222	0.0–60.6	6.2	9.2	3.2
2018	AX-171559197	6	13,733,426	5.14E-13	20.0	C/T (4.1)	AX-171180038	F1	177,178	1.5–11.1	7.4	30.7	5.4
	AX-171142468	11	31,834,919	9.09E-11	3.4	A/G (5.3)	AX-170771092	U1	5,814,444	0.0–2.2	13.4	44.3	−6.5
	AX-171531310	11	29,400,625	1.53E-08	0.7	C/T (3.3)
2019	AX-170817347	1	32,640,957	1.07E-09	< 0.1	C/T (4.1)	AX-171180038	F1	177,178	1.2–11.6	9.8	36.1	7.7
	AX-171578684	4	5,966,307	2.05E-09	7.7	C/T (9.9)	AX-170771092	U1	5,814,444	0.0–2.1	18.4	42.6	−8.7
	AX-171217997	11	31,886,671	3.10E-09	0.2	A/G (4.8)	AX-171165000	U5	10,051,966	23.5–78.7	4.1	6.1	3.2
	AX-170692024	16	3,630,320	2.07E-08	23.4	C/T (−4.1)	AX-171583903	U6	2,237,730	0.0–81.0	4.7	6.9	−3.4
							AX-170838105	U11	35,888,157	13.9–49.4	3.7	5.3	2.8
							AX-170901663	U12	19,737,912	25.7–74.8	5.5	8.3	3.8

^a Chr, abbreviation for Chromosome
^b For GWAS panel, the significance value indicated is the p-value, which is significant if lower than the False Discovery Rate
^c For GWAS panel, R² is the percentage explained variance corrected for genome-wide background
^d For GWAS panel, the allelic effect is the difference in mean of measured trait between genotypes with one or other allele
The sign is with respect to the allele that is first mentioned
^e For F₁ progeny using QTLs detection, the indicated SNP is the peak SNP inside the QTL interval
^f LG, abbreviation for Linkage Group with F and U for ‘Franquette’ and ‘UK 6–2’ parental maps respectively
^g For F₁ progeny using QTLs detection, the position in cM indicated in brackets is the 99.9% confidence interval of the QTL
^h For F₁ progeny using QTLs detection, the significance value indicated is the LOD score (LOD = logarithm of the odds ratio)
ⁱ For F₁ progeny using QTLs detection, P.E.V. is for percentage explained variance
^j For F₁ progeny using QTLs detection, d is the estimated substitution effect of the QTL

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