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 1 Genetic regions significantly associated with resistance to the Magnaporthe oryzae isolate D41-2

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					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
D-01	indica	LT	1	id1010103–id1010205	15,438,604–15,649,252	id1010164	T/C	19.6	4.55	0.16	AQCT001, AQEN001, AQEN011, AQEN018
D-02	indica	DLA	1	id1011342–id1011401	18,821,356–18,925,916	id1011349	C/A	9.28	3.96	0.18	AQCT001, AQEN001, AQEN011, AQEN018
D-03	Full	DLA	2	id2003636–id2003653	7,104,193–7,129,000	id2003651	C/T	11.59	4.88	0.07	–
D-04	Full	DLA	2	id2006540-id2006687	16,209,277–16,648,368	id2006548	G/T	8.28	4.38	0.06	–
D-05	Full	DLA	3	id3010758–ud3001344	23,818,976–24,280,279	id3010813	C/T	32.01	4.86	0.06	AQAF029
D-05	Full	DLA	3	id3010758–ud3001344	23,818,976–24,280,279	ud3001342	T/C	31.91	4.86	0.06	AQAF029
D-06	Full	DLA	3	id3016979–id3017136	34,609,998–34,809,786	id3017114	G/A	12.37	5.41	0.08	–
D-07	Full	DLA	4	id4008106–id4008335	24,437,545–24,950,637	id4008148	T/A	46.8	5.30	0.07	CQAC2, Pikur1
D-08	Full	DLA	4	id4008360–id4008522	25,043,111–25,696,775	id4008464	G/A	7.01	4.87	0.07	CQAC2, Pikur1
D-09	Full	DLA	4	id4008601–id4008681	26,300,907–26,575,531	id4008636	G/A	5.92	4.29	0.06	CQAC2, Pikur1
D-10	Full	DLA	5	id5009568–id5009958	22,335,609–22,650,069	id5009818	G/T	5.96	4.13	0.06	AQAQ024
D-11	Full	DLA	5	id5009967–id5010294	22,654,409–23,102,774	id5010176	A/T	10.2	3.72	0.05	–
D-12	Full	DLA	8	id8005634–ud8001357	20,708,815–20,937,247	id8005717	A/G	34.65	5.21	0.07	Pizh
D-13^e	indica	LT	12	ud12000652–id12004102	10,218,678–10,611,754	wd12001025	T/A	38.04	4.77	0.19	AQCT008, AQEN010, AQEN017, LABR_87, LABR_88, LABR_89, Pi6(t), Pi12, Pi19(t), Pi20, Pi31(t), Pi58(t), Pi62(t), Pi157, Pita2, Pita
D-14	Full	LT	12	id12004113–id12004234	10,669,467–10,900,950	id12004183	A/G	35.64	4.64	0.07	AQCT008, AQEN010, AQEN017, Pi6(t), Pi12, Pi19(t), Pi31(t), Pi58(t), Pi62(t), Pi157, Pita2, Ptr
	Full	DLA				id12004183	A/G	35.64	4.64	0.07
	indica	LT				id12004196	G/A	15.46	5.03	0.07
	indica	LT				id12004196	G/A	37.5	5.09	0.12
D-15^f	Full	DLA	12	id12004251–wd12001183	11,060,008–11,555,556	id12004303	A/G	15.43	5.31	0.08	AQCT008, AQEN010, AQEN017, CQAC4, LABR_90, Pi6(t), Pi12, Pi19(t), Pi31(t), Pi58(t), Pi62(t), Pi157, Pita2
D-16	Full	DLA	12	id12004432–id12004540	12,065,937–12,565,383	id12004538	G/A	16.33	5.37	0.08	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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