Genome-wide response to selection and genetic basis of cold tolerance in rice (Oryza sativaL.)

Zhang, Fan; Ma, Xiu-Fang; Gao, Yong-Ming; Hao, Xian-Bin; Li, Zhi-Kang

doi:10.1186/1471-2156-15-55

BMC Genomic Data

Table 3 Genomic information for 29 functional genetic units (FGUs) (17 single loci and 12 association groups or AGs) for seedling cold tolerance (CT) detected by χ ² tests (single loci) and multi-locus linkage disequilibrium analyses in 30 cold-tolerant introgression lines (ILs) selected from four BC ₂ F ₂ populations derived from crosses between the recurrent parent (C418) and four donors (ZH100, Bg300, Cis, and MNTH)

From: Genome-wide response to selection and genetic basis of cold tolerance in rice (Oryza sativaL.)

Population (code)	χ²test						Z-test⁴		QTL ref.
Population (code)	AG¹	Bin	Marker	IF²	FG³	P-value	BC₂F₂individual	P-value	QTL ref.
C418/ZH100 (A)		7.1	RM4584	0.917	1.000	3.4 × 10⁻¹⁴
	AG _A1	1.11	RM1196	0.583	0.833	2.2 × 10⁻⁴			[11, 13]
	AG _A1	1.15	RM1297	0.500	0.833	1.1 × 10⁻⁴			[7, 9, 16]
	AG _A1	4.12	RM2521	0.750	0.833	5.1 × 10⁻⁹			[7]
	AG _A1	9.6	RM1896	0.750	0.833	5.1 × 10⁻⁹
	AG _A2	6.3	RM5754	0.417	0.667	8.7 × 10⁻³	A-IL5	0.0228	[9]
	AG _A2	6.15	RM5463	0.500	0.667	4.5 × 10⁻³	A-IL5	0.0228	[9, 14, 16, 17]
		7.9	RM6835	0.500	0.833	4.5 × 10⁻³			[11, 17]
		7.12	RM5847	0.583	0.833	2.2 × 10⁻⁴
C418/Bg300 (B)	AG _B1	2.6	RM324	0.500	1.000	7.6 × 10⁻¹⁰
	AG _B1	5.10	RM164	0.583	1.000	3.1 × 10⁻⁷	B-IL5	0.0416	[10]
	AG _B1	12.5	RM101	0.583	1.000	3.1 × 10⁻⁷			[1, 9]
	AG _B2	2.4	RM145	0.500	0.833	1.1 × 10⁻⁴			[7]
	AG _B2	2.11	RM262	0.500	0.833	1.1 × 10⁻⁴			[11, 13, 17]
	AG _B2	7.10	RM432	0.417	0.833	1.0 × 10⁻⁶			[11, 17]
	AG _B2	8.2	RM38	0.417	0.833	1.0 × 10⁻⁶			[13]
	AG _B3	3.5	RM7	0.500	0.833	1.1 × 10⁻⁴	B-IL1	0.0368	[7]
	AG _B3	6.3	RM253	0.583	0.833	2.2 × 10⁻⁴			[9]
	AG _B3	9.9	RM257	0.500	0.833	1.1 × 10⁻⁴			[10, 16]
	AG _B4	1.5	RM579	0.333	0.667	3.1 × 10⁻⁴	B-IL4	0.0289	[13, 14, 17]
	AG _B4	3.12	RM6832	0.333	0.667	3.1 × 10⁻⁴	B-IL5	0.0416	[12]
	AG _B4	5.15	RM334	0.333	0.667	3.1 × 10⁻⁴
	AG _B4	6.12	RM275	0.333	0.667	3.1 × 10⁻⁴	B-IL5	0.0072	[9, 14, 16, 17]
	AG _B4	10.3	RM216	0.333	0.667	3.1 × 10⁻⁴	B-IL4/B-IL5	0.0289/0.0072	[9]
	AG _B4	10.9	RM1375	0.333	0.667	3.1 × 10⁻⁴	B-IL4	0.0480	[10, 16]
	AG _B4	11.14	RM224	0.333	0.667	3.1 × 10⁻⁴	B-IL4/B-IL5	0.0082/0.0416
		8.14	RM447	0.333	0.667	3.1 × 10⁻⁴			[9, 11, 16]
		12.2	RM247	0.333	0.667	3.1 × 10⁻⁴
C418/Cis (C)		7.2	RM5711	0.538	1.000	2.1 × 10⁻¹⁷
	AG _C1	6.15	RM3307	0.577	0.846	8.3 × 10⁻⁹			[9, 14, 16, 17]
	AG _C1	10.9	RM1873	0.577	0.846	8.3 × 10⁻⁹			[10, 16]
		12.1	RM6973	0.385	0.692	4.7 × 10⁻⁷
		2.18	RM3850	0.308	0.615	5.7 × 10⁻⁷
		6.3	RM5754	0.539	0.923	2.3 × 10⁻¹²	C-IL2	0.0041	[9]
	AG _C2	3.8	RM6959	0.423	0.769	3.5 × 10⁻⁹
	AG _C2	3.16	RM3199	0.423	0.769	3.5 × 10⁻⁹	C-IL1	0.0228
	AG _C2	9.1	RM3609	0.538	0.769	3.6 × 10⁻⁷	C-IL2	0.0055
		4.17	RM6238	0.462	0.692	1.0 × 10⁻⁷			[9]
		4.12	RM2521	0.308	0.538	1.0 × 10⁻³			[7]
		11.10	RM5349	0.308	0.615	5.7 × 10⁻⁷			[12, 17]
		3.2	RM3126	0.654	0.923	3.7 × 10⁻¹¹
		3.18	RM3329	0.346	0.538	3.1 × 10⁻⁵	C-IL3	0.0283	[9]
	AG _C3	7.8	RM5875	0.500	0.769	4.8 × 10⁻⁷			[11, 17]
	AG _C3	8.2	RM1148	0.462	0.769	1.0 × 10⁻⁷			[13]
	AG _C4	2.12	RM3688	0.346	0.615	3.1 × 10⁻⁵	C-IL2	0.0055	[11, 13, 17]
	AG _C4	11.4	RM3133	0.308	0.615	5.7 × 10⁻⁷
		5.1	RM1200	0.308	0.615	5.7 × 10⁻⁷			[17]
		2.4	RM5459	0.462	0.615	7.8 × 10⁻⁵			[7]
C418/MNTH (D)	AG _D1	4.3	RM3658	0.700	1.000	1.5 × 10⁻⁵			[9, 18]
	AG _D1	9.9	RM6235	0.500	1.000	2.5 × 10⁻⁸			[10, 16]
	AG _D2	6.12	RM6298	0.400	0.800	3.0 × 10⁻⁵			[9, 14, 16, 17]
	AG _D2	7.5	RM5436	0.400	0.800	3.0 × 10⁻⁵			[17]
	AG _D2	9.3	RM5899	0.600	0.800	7.3 × 10⁻⁴
	AG _D2	10.10	RM1146	0.600	0.800	7.3 × 10⁻⁴			[10, 16]
	AG _D2	11.2	RM1812	0.400	0.800	3.0 × 10⁻⁵
	AG _D2	11.9	RM1355	0.400	0.800	3.0 × 10⁻⁵			[12, 17]
		5.12	RM5970	0.400	0.800	3.0 × 10⁻⁵	D-IL5	0.0416	[10]

¹An AG is defined as a group of unlinked but perfectly associated loci showing equal introgression in selected cold-tolerant ILs from each BC population as detected by linkage disequilibrium analysis [28].
²IF = introgression (donor) allelic frequency.
³FG is the frequency of functional genotypes (donor homozygote and the heterozygote).
⁴Two-sample Z tests to compare the proportions of two groups of BC₂F₆ ILs derived from the same BC₂F₂ individual but with significantly different CT phenotypes (SP) was performed using SAS [27].

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