Genome-wide association analysis unveils novel QTLs for seminal root system architecture traits in Ethiopian durum wheat

Alemu, Admas; Feyissa, Tileye; Maccaferri, Marco; Sciara, Giuseppe; Tuberosa, Roberto; Ammar, Karim; Badebo, Ayele; Acevedo, Maricelis; Letta, Tesfaye; Abeyo, Bekele

doi:10.1186/s12864-020-07320-4

Table 3 List of major and nominal QTLs for RSA traits identified in 192 Ethiopian durum wheat accessions

From: Genome-wide association analysis unveils novel QTLs for seminal root system architecture traits in Ethiopian durum wheat

QTL	Trait^a	Marker^b	Chr	Position (cM)	P-value	– log₁₀P	R² (%)	Sig. SNPs^c	CI (cM)^d	Allele (SNP base)	Effect	Allele count (No.)	Allele (SNP base)	Allele count (No.)
EPdwTRL-1B	TRL	IWB60732	1B	33.75	0.000349	3.46	6.75	0	31.5–36	A	16.08	41	G	151
EPdwTRL-4B^e	TRL	IWB23476	4B	114.43	0.000761	3.12	5.67	0	112.18–116.68	A	8.8	154	G	38
EPdwTRL-5A	TRL	IWA3196	5A	16.83	0.000845	3.07	5.57	1	14.58–19.08	C	39.84	126	T	66
EPdwARL-2A^e	ARL	IWB53380	2A	35.63	0.001	3	5.72	3	33.38–37.88	A	4.76	159	G	33
EPdwRGA-6A	RGA	IWB71119	6A	122.43	1.42E-07	6.85	16.08	8	120.18–124.68	C	−22.31	113	T	79
EPdwRGA-4A^e	RGA	IWB69385	4A	167.15	0.000703	3.15	6.38	1	164.90–169.94	G	13.44	78	T	114
EPdwTRN-1A.1	TRN	IWB8696	1A	5.2	0.00085	3.07	5.71	0	2.95–7.45	A	0.78	31	G	161
EPdwTRN-1A.2	TRN	IWB12589	1A	13.62	0.00046	3.34	6.32	2	11.37–15.87	A	0.57	16	G	176
EPdwTRN-1B	TRN	IWB35568	1B	27.21	0.00041	3.39	6.43	1	24.96–29.46	A	0.54	111	G	81
EPdwTRN-4A	TRN	IWB21309	4A	17.01	0.000204	3.69	7.13	3	14.76–19.26	C	−0.43	87	T	105
EPdwTRN-4B.1	TRN	IWB10265	4B	44.92	0.000724	3.14	5.87	1	42.67–47.17	A	0.39	138	G	54
EPdwTRN-4B.2	TRN	IWB35047	4B	80.4	0.000256	3.59	6.90	0	78.15–82.65	C	−0.44	91	G	101
EPdwTRN-4B.3	TRN	IWB66095	4B	91.74	0.000429	3.37	6.39	4	89.49–93.99	C	0.52	47	T	145
EPdwTRN-7A	TRN	IWB3767	7A	146.9	0.000844	3.07	5.72	3	144.65–149.15	C	0.5	171	T	21
EPdwRDW-1B	RDW	IWB60732	1B	33.75	0.00028	3.55	6.72	1	31.50–36.00	A	10.59	41	G	151
EPdwRDW-3A^e	RDW	IWB67049	3A	80.8	0.000682	3.17	5.76	54	78.55–83.05	A	−14.1	15	G	177
EPdwRDW-4A^e	RDW	IWB21309	4A	17.01	4.59E-05	4.34	8.41	3	14.76–19.26	C	−9.81	87	T	105
EPdwSDW-1A	SDW	IWB29244	1A	123.21	0.000465	3.33	6.27	2	120.96–125.46	C	−9.18	138	T	54
EPdwSDW-1B	SDW	IWB60732	1B	33.75	0.000419	3.38	6.58	0	31.50–36.00	A	13.4	41	G	151
EPdwSDW-3B^e	SDW	IWB35437	3B	41.34	0.000796	3.10	5.93	2	39.09–43.59	C	−17.57	36	T	156
EPdwSDW-4A^e	SDW	IWB21309	4A	17.01	0.000151	3.82	7.39	3	14.76–19.26	C	−8.2	87	T	105
EPdwSDW-4B	SDW	IWB23476	4B	114.43	0.000594	3.23	6.03	1	112.18–116.68	A	15.41	154	C	38
EPdwSDW-5B	SDW	IWB8808	5B	190.51	0.000809	3.09	5.73	0	188.26–192.76	A	−9.41	36	C	156
EPdwiTGW-3B.1	iTGW	IWB65507	3B	126.23	7.09E-05	4.15	8.71	2	123.98–128.48	A	−9.84	160	G	32
EPdwiTGW-3B.2	iTGW	IWB11298	3B	129.61	0.000135	3.87	8.01	12	127.36–131.86	A	10.94	160	C	32
EPdwiTGW-7A	iTGW	IWB7752	7A	98.3	0.000448	3.35	6.73	1	96.05–100.55	A	−7.27	173	G	19
EPdwiTGW-7B	iTGW	IWB60	7B	33.71	0.000486	3.31	6.64	1	31.46–35.96	A	3.83	28	C	164
EPdwIRW-1B	IRW	IWB60732	1B	33.75	0.000789	3.10	5.80	0	31.50–36.0	A	1.70	41	G	151
EPdwIRW-2B	IRW	IWB29332	2B	160.51	0.000328	3.48	6.68	0	158.26–162.76	A	4.50	24	G	168
EPdwIRW-5A	IRW	IWA3196	5A	16.83	8.64E-05	4.06	8.03	0	14.58–19.08	C	7.54	26	T	166
EPdwIRW-5B.1^e	IRW	IWB70122	5B	40.39	0.000702	3.15	5.92	7	38.14–12.64	A	2.81	16	C	176
EPdwIRW-5B.2^e	IRW	IWA332	5B	16.73	0.00101	3	5.56	1	14.48–18.89	G	−2.96	15	T	177
EPdwIRW-6B^e	IRW	IWB73456	6B	90.33	0.00046	3.34	6.34	4	88.08–92.58	C	2.94	21	T	171
EPdwIRW-7A^e	IRW	IWB11841	7A	94.72	0.000684	3.17	5.94	0	92.47–96.97	C	−1.43	66	T	126
EPdwRSR-3A	RSR	IWB25948	3A	96.93	0.000947	3.02	4.62	2	94.68–99.18	C	−0.10	170	T	22
EPdwRT6-4B.1^e	RT6	IWB72884	4B	45.01	0.000211	3.68	7.13	7	42.76–47.26	A	0.21	138	G	54
EPdwRT6-4B.2^e	RT6	IWB35047	4B	80.4	0.000351	3.45	6.62	0	78.15–82.65	C	−0.22	91	G	101
EPdwRT6-4B.3^e	RT6	IWB66095	4B	91.74	0.000481	3.32	6.30	3	89.49–93.99	C	0.28	47	T	145

^a RSA trait acronyms: iTGW, initial thousand grain weight; TRL, total root length; ARL, average root length; RGA, root growth angle; TRN, total root number; RDW, root dry weight; IRW, individual root dry weight; SDW, shoot dry weight; RSR, root to shoot ratio; RT6, presence of the sixth root
^b SNP found at the peak of corresponding QTL (QTL-tag SNP)
^c The number of significant SNPs present in the significant interval
^d Confidence interval flanking the QTL-tag SNP based on the tetraploid wheat consensus map of Maccaferri et al. (2015)
^e The fourteen newly discovered RSA QTLs
See Table 6 for trait abbreviations

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