Numerous genetic loci identified for drought tolerance in the maize nested association mapping populations

Li, Chunhui; Sun, Baocheng; Li, Yongxiang; Liu, Cheng; Wu, Xun; Zhang, Dengfeng; Shi, Yunsu; Song, Yanchun; Buckler, Edward S.; Zhang, Zhiwu; Wang, Tianyu; Li, Yu

doi:10.1186/s12864-016-3170-8

BMC Genomics

Table 2 List of SNPs significantly associated with seven drought-related traits and the closest candidate genes with significantly differential expression between the samples under the WW and WS conditions in B73

From: Numerous genetic loci identified for drought tolerance in the maize nested association mapping populations

Chr	Position (bp)^a	BPP	Inside QTL^b	Trait affected	Gene ID	Proximity of SNP to gene (bp)	Gene function	DEG^c
1	4606329	0.28	-	HKW	GRMZM2G341934	1721	Peroxidase superfamily protein	0.05
1	27627382	0.27	+	PH	GRMZM2G111324	Inside gene	O-Glycosyl hydrolases family 17 protein	0.07
1	35465166	0.39	+	HKW	GRMZM2G164562	Inside gene	Chorismate synthase	0.56
1	154107233	0.53	-	KNPR	GRMZM2G056039	25433	Heat shock protein 70	2.01
1	163956308	0.49	-	ASI	GRMZM2G443525	130508	ADR1-like 1	3.92
1	219379659	0.25	+	HKW	GRMZM2G146278	1444	Cytochrome B561-1	0.24
1	269328425	0.36	-	EL	GRMZM2G157727	Inside gene	Phytochrome A	3.15
1	275974364	0.30	-	PH	GRMZM2G173852	590	Acyl-CoA N-acyltransferase with RING/FYVE/PHD-type zinc finger protein	1.52
1	287727328	0.57	-	PH	GRMZM2G133023	4891	Stem-specific protein TSJT1	9.94
2	10624855	0.26	-	EL	GRMZM2G098239	Inside gene	HXXXD-type acyl-transferase family protein	0.05
2	19262986	0.42	-	KNPR	GRMZM2G162333	1756	Pectin lyase-like superfamily protein	0.02
2	236797598	0.38	-	GYPP	GRMZM2G016677	229	Photosystem II subunit P-1/PsbP	0.41
3	17258723	0.56	-	EW	GRMZM5G871336	Inside gene	Expressed protein	4.87
3	165705047	0.51	-	EL	GRMZM2G057823	17923	Aldolase superfamily protein/fructose-bisphospate aldolase isozyme	0.19
3	197321346	0.38	-	HKW	GRMZM2G021704	Inside gene	Pyrimidin 4	0.33
4	26425071	0.27	-	PH	GRMZM2G089995	Inside gene	Ethylene response factor 7/AP2 domain containing protein	4.23
4	172055239	0.62	+	EL	GRMZM2G062084	260	P-loop containing nucleoside triphosphate hydrolases superfamily protein/kinesin motor domain containing protein	0.13
4	204344848	0.38	-	HKW	GRMZM2G117064	1105	Long chain acyl-CoA synthetase 9	0.44
4	218157821	0.31	-	HKW	GRMZM2G422464	2207	HhH-GPD base excision DNA repair family protein	2.24
5	10273708	0.55	-	GYPP	GRMZM5G833140	Inside gene	CHASE domain containing histidine kinase protein	2.59
5	11908448	0.28	-	KNPR	GRMZM2G157147	Inside gene	Phosphatidylinositol-4-phosphate 5-kinase 1	0.16
5	16321609	0.36	-	ASI	GRMZM2G134980	Inside gene	Chaperone protein dnaJ	0.69
5	22556254	0.88	+	PH	GRMZM5G869246	Inside gene	Kinesin motor family protein	0.32
5	85252655	0.50	+	HKW	GRMZM2G104632	14	Glyceraldehyde-3-phosphate dehydrogenase of plastid 1	0.30
5	140093287	0.32	-	HKW	GRMZM2G060253	Inside gene	HMG (high mobility group) box protein	0.03
5	143975579	0.51	-	HKW	GRMZM2G158313	1348	Basic-leucine zipper (bZIP) transcription factor family protein	0.01
5	208637679	0.95	+	EL	GRMZM2G081214	Inside gene	Phosphate-responsive 1 family protein	6.03
6	9710805	0.26	-	KNPR	GRMZM2G055238	60720	Ureide permease 5	5.40
6	58454978	0.50	-	HKW	GRMZM2G473788	4959	Expressed protein	1.87
6	82185973	0.66	+	PH	GRMZM2G430680	Inside gene	Glucan synthase-like 12	0.34
6	85797877	0.25	+	PH	GRMZM2G365961	52	Prephenate dehydrogenase family protein	0.15
6	88935877	0.40	+	PH	GRMZM2G150302	13001	Nucleotide-diphospho-sugar transferases superfamily protein/glycosyltransferase family 43 protein	0.41
6	119695193	0.50	-	HKW	GRMZM2G368678	Inside gene	Binding/expressed protein	1.80
6	121945548	0.49	-	EL	GRMZM2G142409	Inside gene	VIRB2-interacting protein 2/reticulon domain containing protein	5.21
6	150839908	0.41	-	EL	GRMZM2G178797	1986	Guanylyl cyclase 1	2.11
6	155438561	0.28	+	GYPP	GRMZM2G117344	12391	Expressed protein	0.18
7	135573138	0.64	-	PH	GRMZM2G130959	140	Bug22p-like protein	2.47
7	152001464	0.27	-	EL	GRMZM2G105750	36998	ATP binding;protein kinases;protein serine/threonine kinases	3.08
7	157758647	0.33	+	HKW	GRMZM2G129354	Inside gene	ARF-GAP domain 5/GTPase-activating protein	3.00
7	160601468	0.37	+	HKW	GRMZM2G058197	Inside gene	C2H2-like zinc finger protein	1.85
8	129080393	0.61	+	ASI	GRMZM2G171781	4780	MYB domain protein 61	0.03
8	148509016	0.56	-	KNPR	GRMZM2G013625	Inside gene	Associated molecule with the SH3 domain of STAM 2	3.20
8	166653395	0.26	+	ASI	GRMZM2G143640	Inside gene	MYB family transcription factor	20.26
8	166781122	0.30	+	ASI	GRMZM5G805609	Inside gene	Glycosyl hydrolase superfamily protein	4.33
9	24062413	0.35	+	KNPR	GRMZM2G082855	565	ERECTA-like 2/receptor-like protein kinase 5 precursor	0.34
9	24062931	0.61	-	PH	GRMZM2G082855	47	ERECTA-like 2/receptor-like protein kinase 5 precursor	0.34
9	31283082	0.26	-	GYPP	GRMZM2G308595	76352	Nudix hydrolase homolog 21	8.39
9	78421440	0.32	+	HKW	GRMZM2G094497	Inside gene	ATPase, V1 complex, subunit B protein	0.58
9	133586941	0.31	-	HKW	GRMZM2G317262	252	F-box family protein	6.68
9	134721582	0.94	-	PH	GRMZM2G033846	250	Ca2 + -binding protein 1/EF hand family protein	0.05
10	6398185	0.37	+	PH	GRMZM2G057753	Inside gene	Ovate family protein 13/DUF623 domain containing protein	0.10
10	15549436	0.64	-	PH	GRMZM2G088689	Inside gene	Thiamin diphosphate-binding fold (THDP-binding) superfamily protein/dehydrogenase E1 component domain containing protein	5.47

^aphysical position based on B73 maize reference genome v2
^b “+” repesents that significantly assiciated SNP is located in QTL support interval; “-” repesents that significantly assiciated SNP is not located in QTL support interval
^cdifferential expressed genes (DEG),expression level ratios of candidate genes between WS and WW from B73

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ISSN: 1471-2164

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