Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus

Swamy, BP Mallikarjuna; Vikram, Prashant; Dixit, Shalabh; Ahmed, HU; Kumar, Arvind

doi:10.1186/1471-2164-12-319

BMC Genomics

Table 3 Candidate genes reported in the identified MQTL region.

From: Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus

S. no.	MQTL	Candidate genes (no. within MQTL)	Candidate genes	Candidate genes (no. in total)
1	MQTL_1.1	1	Calcineurin-related phosphoesterase-like	14
2		2	ERECTA-like kinase 1-like	35
3		3	Putative ankyrin-kinase	69
4		4	Putative NAC transcription factor	135
5		5	Putative pectin acetylesterase precursor	139
6		6	Putative signal recognition particle	160
7		7	QUAKING isoform 5-like	179
8		8	Tetratricopeptide repeat (TPR)-containing protein-like	193
9	MQTL_1.2	1	ABC transporter subunit-like	1
10		2	F-box domain-containing protein-like	39
11		3	Glutaredoxin-like	43
12		4	Leucine zipper protein-like	51
13		5	Lustrin A-like	52
14		6	Nodulin-like protein	57
15		7	Ovate family protein-like	59
16		8	Pentatricopeptide repeat (PPR)-containing protein-like	60
17		9	Protein kinase-like	66
18		10	Putative auxin-independent growth promoter	76
19	MQTL_1.3	1	Cell wall protein-like	21
20		2	Cytochrome P450 monooxygenase	30
21		3	F-box domain-containing protein-like	39
22		4	hAT dimerisation domain-containing protein-like	45
23		5	HGWP repeat-containing protein-like	48
24		6	Leucine zipper protein-like	51
25		7	Nucleoporin-like protein	58
26		8	Pentatricopeptide repeat (PPR)-containing protein-like	60
27		9	pr1-like protein	65
28		10	Sucrose-phosphatase-like protein	192
29		11	Zinc knuckle domain-containing protein-like	206
30	MQTL_1.4	1	Polyprotein-like	64
31		2	Putative aspartic proteinase nepenthesin II	74
32		3	Putative cytokinin oxidase	97
33		4	Putative lectin-like receptor kinase 1:1	130
34		5	Putative vacuole membrane protein 1	172
35	MQTL_2.1	1	Ethylene-responsive family protein-like	37
36		2	Putative cytochrome P450	94
37		3	Putative DREPP2 protein	106
38		4	Putative F-box protein	111
39		5	Putative flavin-containing monooxygenase	114
40		6	Putative GTP-binding protein	120
41		7	Putative kaurene synthase	128
42		8	Putative pentatricopeptide repeat (PPR)-containing protein	140
43		9	Putative sugar transporter	164
44		10	Aquaporin	7
45	MQTL_2.2	1	Cell wall protein	21
46		2	Dehydration-responsive family protein-like	33
47		3	F-box protein-like	39
48		4	Growth-regulating factor 1-like	44
49		5	HGWP repeat-containing protein-like	48
50		6	Pentatricopeptide repeat (PPR)-containing protein-like	60
51		7	Putative anther-specific protein	70
52		8	Putative anthocyanin biosynthetic gene regulator	72
53		9	Putative basic-helix-loop-helix transcription factor	77
54		10	Putative cell division control protein	85
55		11	Putative cold acclimation protein	90
56		12	Putative CRT/DRE binding factor 1	93
57		13	Putative cytochrome P450	94
58		14	Putative growth-regulating factor 1	119
59		15	Putative high-mobility group protein	124
60		16	Putative pectin methylesterase	138
61		17	Putative photoperiod-independent early flowering	145
62		18	Putative sexual differentiation process protein	158
63		19	Root-specific protein	184
64		20	Sexual differentiation process protein-like	187
65		21	Trehalose-6-phosphate phosphatase	194
66		22	UDP-glycosyltransferase-like	194
67		23	Vesicle-associated membrane protein-like	199
68		24	Zinc finger (C3HC4-type RING finger)-like	201
69	MQTL_3.1	1	Adapitin protein-like	4
70		2	Cell division control protein 2-like	18
71		3	Cyclin 2 interactor-like	26
72		4	F-box domain-containing protein-like	39
73		5	Flavanone 3-hydroxylase-like	40
74		6	HGWP repeat-containing protein-like	48
75		7	MADS-box transcription factor	53
76		8	NAC domain-containing protein-like	54
77		9	Photomorphogenic	63
78		10	Putative callose synthase 1	81
79		11	Putative cell cycle switch protein	84
80		12	Putative cell division control protein 2	86
81		13	Putative cytochrome p450	94
82		14	Putative dihydrodipicolinate reductase	103
83		15	Putative dihydrofolate synthetase	104
84	MQTL_3.2	1	ABC transporter-like protein-like	2
85		2	c-type cytochrome synthesis 1	25
86		3	Pentatricopeptide repeat (PPR)-containing protein-like	60
87		4	Pherophorin-dz1 protein-like	62
88		5	Putative cleavage stimulation factor subunit 1-like protein	89
89		6	Putative cold acclimation protein	90
90		7	Putative peroxidase	142
91		8	Putative phytochrome C	146
92		9	Putative prolamin	148
93		10	Putative prolyl 4-hydroxylase	149
94		11	Putative protein kinase SPK-2	150
95		12	Putative protein phosphatase 2C	151
96		13	Putative UDP-glucose 6-dehydrogenase	171
97		14	Putative zinc-finger protein	177
98		15	Receptor protein kinase	181
99		16	Senescence downregulated leo1	185
100	MQTL_4.1	1	Auxin-related protein-like	11
101		2	Cell division cycle	20
102		3	Cytochrome c oxidase	28
103		4	Hydroxyproline-rich glycoprotein	49
104		5	Integral membrane transporter-like	50
105		6	Lustrin A-like	52
106		7	Protoporphyrinogen IX oxidase	67
107		8	Putative calcium-binding protein	79
108		9	Putative cell cycle checkpoint protein MAD2 homolog	83
109		10	Putative chitinase	88
110		11	Putative CONSTANS-like protein	92
111		12	Putative ER33 protein	108
112		13	Putative LRR receptor-like kinase	131
113		14	Putative salt-tolerance protein	154
114		15	Stress-inducible protein	191
115		16	Zinc finger (C3HC4-type RING finger)-like protein	202
116	MQTL_4.2	1	ABC-1-like	3
117		2	Auxin response factor	9
118		3	Calcium-dependent protein kinase	15
119		4	CCAAT-box binding factor HAP5	17
120		5	Cytochrome P450 monooxygenase	29
121		6	Cytokinin-induced apoptosis inhibitor 1	32
122		7	Heat shock protein binding	47
123		8	HGWP repeat-containing protein	48
124		9	Pentatricopeptide repeat (PPR)-containing protein	60
125		10	Pherophorin-C1 protein precursor-like	61
126		11	Putative calcium-dependent protein kinase	80
127		12	Putative dehydration-responsive element-binding protein	101
128		13	Putative ethylene response factor	109
129		14	Putative floricaula	115
130		15	Putative flowering locus D	116
131		16	Putative growth-regulating factor	118
132		17	Putative IAA24	125
133		18	Putative inositol 1,3,4,5,6-pentakisphosphate 2-kinase	126
134		19	Putative jasmonate O-methyltransferase	127
135		20	Putative late embryogenesis abundant protein	129
136		21	Putative wall-associated kinase 1	175
137		22	RCP1 (ROOT CAP 1)-like	180
138		23	Stress-related-like protein interactor-like	190
139		24	Wall-associated protein kinase-like	200
140		25	Zinc finger (C3HC4-type RING finger)-like	201
141	MQTL_8.1	1	Heat shock protein	46
142		2	Vesicle-associated membrane protein	197
143		3	Auxin efflux carrier protein-like	8
144		4	Cell division control protein-like	19
145		5	Cellulose synthase-1-like protein	22
146		6	CLAVATA1 receptor kinase (CLV1)-like protein	23
147		7	CONSTANS-like protein	24
148		8	Cytochrome b5-like	27
149		9	Ethylene-responsive elongation factor EF-Ts precursor-like	36
150		10	F-box domain-containing protein-like	39
151		11	Germin protein type 1	42
152		12	HGWP repeat-containing protein-like	49
153		13	NAC2 protein-like	55
154		14	Nam-like protein	56
155		15	Nodulin-like protein	57
156		16	Pentatricopeptide repeat (PPR)-containing protein-like	60
157		17	Polyprotein-like protein	64
158		18	Putative ABC transporter	68
159		19	Putative anthocyanin 5-aromatic acyltransferase	71
160		20	Putative AP2/EREBP transcription factor LEAFY PETIOLE	73
161		21	Putative CCAAT box binding factor/transcription factor Hap2a	82
162		22	Putative chaperone GrpE	87
163		23	Putative cold shock protein-1	91
164		24	Putative cytokinin-regulated kinase 1	98
165		25	Putative death receptor interacting protein	99
166		26	Putative DEFECTIVE IN ANTHER DEHISCENCE1	100
167		27	Putative farnesylated protein	110
168		28	Putative fertility restorer homolog	113
169		29	Putative MADS-box protein	132
170		30	Putative male fertility protein	133
171		31	Putative nucleoporin	137
172		32	Putative pherophorin	143
173		33	Putative senescence-associated protein	155
174		34	Putative osmatic embryogenesis receptor-like kinase 1	178
175		35	Putative sexual differentiation process protein isp4	159
176		36	Putative starch synthase	161
177		37	Putative stress-responsive gene	162
178		38	Putative teosinte branched1 protein	166
179		39	Putative trehalose-6-phosphate synthase	170
180		40	Putative vesicle-associated membrane associated protein	173
181		41	Putative wall-associated kinase	174
182		42	Ripening-related protein-like	182
183		43	Root cap protein 1-like	183
184		44	Senescence-associated protein-like	186
185		45	Stress-inducible protein-like	189
186		46	Zinc finger-like protein	204
187	MQTL_8.2	1	AP2 domain transcription factor-like	6
188		2	Auxin-induced protein-related-like protein	10
189		3	F-box protein family-like protein	39
190		4	Pentatricopeptide repeat (PPR)-containing protein-like	60
191		5	Putative calcineurin B subunit	78
192		6	Putative cytochrome P450 monooxygenase	95
193		7	Putative male fertility protein	133
194		8	Putative NAC domain protein	134
195		9	Putative senescence-associated protein	155
196		10	Putative stromal cell-derived factor 2 precursor	163
197		11	Putative temperature stress-induced lipocalin	165
198		12	Putative teosinte branched1 protein	166
199		13	Putative tethering factor	167
200		14	Putative trehalose-6-phosphate synthase	170
201		15	Somatic embryogenesis receptor kinase-like protein	188
202		16	Zinc finger protein-like	204
203	MQTL_10.1	1	Aminotransferase-like	5
204		2	Putative gibberellin-regulated protein	117
205		3	Putative peptide transporter 1	141
206		4	Putative serine threonine kinase	157
207		5	Putative wall-associated kinase 4	176
208		6	ABC transporter-like	1
209	MQTL_10.2	1	Calcineurin B-like protein	13
210		2	Calcium-dependent protein kinase, isoform 1 (CDPK 1)	16
211		3	Cytochrome p450-like	31
212		4	Dehydration-responsive family protein-like	33
213		5	Elicitor-like protein	34
214		6	Ethylene-responsive protein-like	38
215		7	F-box protein-like	39
216		8	Fringe-related protein-like	41
217		9	Pentatricopeptide repeat (PPR)-containing protein-like	60
218		10	Putative anther-specific protein	70
219		11	Putative auxin response factor 10	75
220		12	Putative cytokinin dehydrogenase	96
221		13	Putative DEFECTIVE IN ANTHER DEHISCENCE1	100
222		14	Putative dehydration-induced protein	102
223		15	Putative DRE binding factor 2	105
224		16	Putative drought-inducible protein	107
225		17	Putative fertility restorer	112
226		18	Putative hairy meristem	121
227		19	Putative heat shock factor RHSF5	122
228		20	Putative hexose carrier protein HEX6	123
229		21	Putative NAM (no apical meristem) gene	136
230		22	Putative pollen-specific kinase partner protein	147
231		23	Putative root cap-specific glycine-rich protein	152
232		24	Putative salt-induced MAP kinase 1	153
233		25	Putative senescence-associated protein DH	156
234		26	Putative tonoplast membrane integral protein	168
235		27	Putative trehalose-6-phosphate phosphatase	169
236		28	Putative zinc finger protein	177
237		29	Ripening-related protein-like	182
238		30	Senescence-associated protein-like	186
239		31	Stress-inducible protein-like	189
240		32	Tetratricopeptide repeat (TPR)-containing protein-like	193
241		33	Universal stress protein-like	195
242	.	34	Vacuolar protein-sorting 13C protein-like	196
243		35	Vesicle-associated membrane associated protein-like	198
244		36	Zinc finger (HIT type)-like	203
245	MQTL_12.1	1	Calcineurin B-like	12
246		2	Cell wall protein-like	21
247		3	HGWP repeat-containing protein-like	48
248		4	Hydroxyproline-rich glycoprotein-like	49
249		5	Putative pherophorin-dz1 protein	144
250		6	Zinc knuckle-containing protein-like	205

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