Genome-wide association study of rice genes and loci conferring resistance to Magnaporthe oryzae isolates from Taiwan

Lin, Heng-An; Chen, Szu-Yu; Chang, Fang-Yu; Tung, Chih-Wei; Chen, Yi-Chia; Shen, Wei-Chiang; Chen, Ruey-Shyang; Wu, Chih-Wen; Chung, Chia-Lin

doi:10.1186/s40529-018-0248-4

Botanical Studies

Table 2 Genetic regions significantly associated with resistance to the Magnaporthe oryzae isolate 12YL-DL3-2

From: Genome-wide association study of rice genes and loci conferring resistance to Magnaporthe oryzae isolates from Taiwan

No.	Population	Phenotype	Chr.	Range^a	Physical position (bp)^b	Highest marker information^b					Known R genes/QTLs
No.	Population	Phenotype	Chr.	Range^a	Physical position (bp)^b	Marker ID	Allele	MAF (%)^c	− Log₁₀(P)	R^2d	Known R genes/QTLs
Y-01	indica	DLA	1	id1013754–id1014034	23,732,729–23,934,283	id1013942	T/G	36	4.47	0.21	AQCT001, AQEN001, LABR_10
Y-02	indica	DLA	1	id1015101–id1015282	25,284,622–25,681,092	id1015101	A/G	35.06	6.83	0.31	AQAH002, AQCT001, AQEN001, Pitp(t)
Y-02	indica	LT	1	id1015101–id1015282	25,284,622–25,681,092	id1015101	A/G	35.06	4.85	0.28	AQAH002, AQCT001, AQEN001, Pitp(t)
Y-03	indica	DLA	2	id2007485–id2007516	18,977,320–19,192,422	id2007494	G/T	41.09	5.37	0.26	–
Y-04	indica	DLA	2	id2008594–id2008644	21,493,161–21,607,823	id2008601	A/G	39.24	4.88	0.22	Pid(t)1
Y-05	indica	DLA	2	id2009379–id2009403	23,397,267–23,466,199	id2009379	T/C	34.21	4.42	0.21	–
Y-06	indica	DLA	3	id3017643–id3017725	35,480,048–35,558,427	id3017643	C/G	33.33	4.19	0.19	–
Y-07	indica	DLA	5	id5002016-id5002075	3,483,482-3,586,560	id5002075	C/T	30	4.06	0.18	–
Y-08	indica	DLA	5	wd5001198–wd5001344	10,351,569–10,848,969	id5004839, id5004859	C/T	22.79	4.15	0.19	AQEN004, Pi23
Y-08	indica	DLA	5	wd5001198–wd5001344	10,351,569–10,848,969	id5004839, id5004859	A/G	23.75	4.15	0.18	AQEN004, Pi23
Y-09	indica	DLA	6	id6004112–id6004235	6,458,990–6,636,955	id6004212	C/T	46.15	4.37	0.20	AQCT004, AQEN005, Pii1, Pi8, Pi59(t), Pi27(t)
Y-10	indica	DLA	8	id8000511–id8000544	1,744,391–1,839,119	id8000544	A/G	32.88	4.66	0.23	–
Y-11	indica	DLA	8	id8000658–id8000695	2,130,616–2,184,609	id8000663	C/T	26.67	4.47	0.21	–
Y-12	indica	DLA	12	id12002136–id12002219	4,731,647–4,872,049	id12002210	A/G	11.54	4.52	0.21	Pi6(t), Pi62(t)
Y-13	japonica	DLA	12	id12003134–id12003432	7,827,050–8,296,350	id12003144	T/C	7.64	4.09	0.10	AQCT008, AQEN010, AQEN017, Pi6(t), Pi12, Pi20, Pi31(t), Pi58(t), Pi62(t)
Y-14	japonica	DLA	12	ud12000485–id12003608	8,383,596–8,874,826	id12003547	C/T	7.9	4.04	0.10	AQCT008, AQEN010, AQEN017, Pi6(t), Pi12, Pi19(t), Pi20, Pi31(t), Pi58(t), Pi62(t), Pi157
Y-14	japonica	DLA	12	ud12000485–id12003608	8,383,596–8,874,826	id12003562	A/T	7.9	4.04	0.10
Y-15	japonica	DLA	12	id12003642–ud12000566	8,914,661–9,231,272	id12003728	T/A	8.1	3.93	0.10	AQCT008, AQEN010, AQEN017, Pi6(t), Pi12, Pi19(t), Pi20, Pi31(t), Pi58(t),, Pi62(t), Pi157
Y-16^e	Full	LT	12	id12003919–id12004113	10,058,758–10,669,467	id12004093	G/A	10	5.67	0.11	AQCT008, AQEN010, AQEN017, LABR_87, LABR_88, LABR_89, Pi6(t), Pi12, Pi19(t), Pi20, Pi31(t), Pi58(t), Pi62(t), Pi157, Pita2, Pita
	japonica	LT				id12004007	A/T	7	4.82	0.02
	japonica	DLA				wd12001025	T/A	8.2	4.62	0.13
Y-17^f	Full	LT	12	id12004251–wd12001183	11,060,008–11,555,556	id12004284	C/G	8.52	5.87	0.11	AQCT008, AQEN010, AQEN017, CQAC4, LABR_90, Pi6(t), Pi12, Pi19(t), Pi31(t), Pi58(t), Pi62(t), Pi157, Pita2
Y-18	Full	LT	12	id12004546–id12004685	12,567,686–13,060,942	id12004554	C/A	42.11	5.4	0.10	AQCT008, AQCT009, AQEN010, AQEN017, CQAC4, Pi6(t), Pi12, Pi19(t), Pi51(t), Pi62(t), Pi157, Pita2

^aThe left-border marker and right-border marker of the QTL
^bThe physical map position is based on MSU version 7.0 Nipponbare rice reference genome
^cMAF: minor allele frequency
^dR² represents the proportion of the phenotypic variation explained by the single nucleotide polymorphism
^{e, f}Same or largely overlapped genetic region identified by using D41-2 and 12YL-DL3-2

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