谷子不同发育时期株高性状的变化及动态QTL定位

doi:10.3864/j.issn.0578-1752.2024.18.003

Abstract

Abstract:

【Objective】 Plant height is a trait that plays an important role in the increase of foxtail millet yield. The dynamic changes of foxtail millet plant height at different growth stages were studied, and the QTL loci and effects controlling plant height were identified to provide a theoretical basis for plant type breeding of foxtail millet. 【Method】 In this study, a recombinant inbred line population YRRIL containing 215 lines were used as the research object, and the YRRIL population was planted in two environments, Yulin, Shaanxi and Mizhi, Shaanxi, in May 2023, respectively. The phenotypic values of plant height trait of each family were measured at five stages: seedling, elongation, booting, tasseling, and ripening period, respectively. Combined with the genetic linkage map of the YRRIL population, genetic analysis and dynamic QTL mapping of plant height trait at different growth stages of millet were carried out, and the unconditional QTL and conditional QTL controlling plant height of millet were identified. On this basis, candidate gene prediction for important QTL was carried out using Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis methods. 【Result】 In the entire growth period of the millet plant height growth trend was the “S” type curve, from the elongation stage to the booting stage, the growth rate of plant height was faster, which was the key stage of plant height development. In the two environments, plant height of each family line of the population showed continuous distribution at different periods. A total of 86 QTL related to plant height were detected at five periods in the two environments, which were distributed on all 9 chromosomes of the foxtail millet genome. It contained 48 unconditional QTL and 38 conditional QTL, and the phenotypic contribution rate of unconditional QTL was 1.13%-17.49%, of which 6 could be detected repeatedly at two growth periods, and the rest were detected only at one growth period. The phenotypic contribution rate of conditional QTL was 1.97%-14.69%, of which one could be detected repeatedly at two growth stages, and the rest were detected only at one growth stage. No QTL that can be detected in three or more periods were present in either unconditional QTL analysis or conditional QTL analysis. A total of 12 major QTL were detected by unconditional QTL and conditional QTL analysis in two environments, of which 6 QTL were newly identified as primary loci in this study. Based on the prediction and analysis of genes within the main effect QTL interval combined with functional annotation of homologous genes screened out 14 candidate genes that might be related to foxtail millet plant height, among which Seita.1G242300.1, Seita.6G110200.1, and Seita.7G143300.1 were all able to directly regulate plant height development. 【Conclusion】 In the two environments, a large number of QTL were detected to be involved in the phenotypic regulation of plant height trait during the whole growth and development of foxtail millet, with 79 (91.86%) played a role in one period and 7 (8.14%) played a role in two periods and there were no QTL detected in three or more periods, including 12 major QTL. The QTL detected by unconditional and conditional analysis methods accounted for 55.81% and 44.19%, respectively, and 16 (18.60%) were both unconditional and conditional QTL. The QTL effects controlling plant height development at different stages varied, with smaller effect in the seedling stage and generally larger effects from the elongation to the tasseling stage.

Key words: foxtail millet, RIL, plant height, plant architecture, QTL, candidate genes

LIU DeLong, LI ShiRu, WANG ChuanXing, GUO ShuQing, MA ZhiXiu, WU YongJiang, HAN HuiBing, LI YuJie, ZHANG PanPan, YANG Pu. Phenotypical Variation and Dynamic QTL Mapping of Plant Height in Foxtail Millet at Different Developmental Stages[J].Scientia Agricultura Sinica, 2024, 57(18): 3533-3550.

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Figures/Tables 9

Table 1

Table 2

Fig. 1

Fig. 2

Table 3

Unconditional QTL for plant height detected in YRRIL population at different fertility periods"

时期 Periods	环境 Environments	数量性状位点 QTL	染色体 Chromosome	标记区间 Marker interval	物理区间 Physical interval (bp)	LOD	加性效应 Additive effect	贡献率 R² (%)
T1	E1	qPH-3-1	Chr.3	c03b143-c03b144	49232103-49249434	5.20	0.70	4.13
		qPH-3-2	Chr.3	c03b144-c03b145	49236212-49263886	5.01	0.71	4.27
		qPH-4-1	Chr.4	c04b091-c04b092	32103966-32392762	4.90	0.55	2.60
		qPH-7-1	Chr.7	c07b111-c07b112	28718452-28977042	10.15	0.97	7.85
		qPH-8-1	Chr.8	c08b154-c08b155	35794684-36110021	3.78	-0.91	7.20
		qPH-8-2	Chr.8	c08b176-c08b177	38668781-38953634	6.36	0.86	6.29
		qPH-9-1	Chr.9	c09b120-c09b121	41372093-41585138	4.49	-0.54	2.44
	E2	qPH-4-2	Chr.4	c04b111-c04b112	34316068-34803353	2.98	1.48	2.95
	E2	qPH-7-2	Chr.7	c07b143-c07b144	34974931-35164751	2.52	2.37	7.56
T2	E1	qPH-3-3	Chr.3	c03b135-c03b136	48347192-48472348	7.06	2.64	5.75
		qPH-3-4	Chr.3	c03b136-c03b137	48422155-48788896	8.51	2.68	5.78
		qPH-5-1	Chr.5	c05b044-c05b045	8175113-9040955	3.58	1.50	1.79
		qPH-7-3	Chr.7	c07b113-c07b114	29002989-29630484	7.98	2.49	5.13
		qPH-9-2	Chr.9	c09b009-c09b010	1065098-1132102	7.18	-1.79	2.64
		qPH-9-3	Chr.9	c09b039-c09b040	7371255-7920890	3.02	-1.40	1.66
		qPH-9-4	Chr.9	c09b166-c09b167	49092452-49697847	6.47	2.65	5.85
		qPH-9-5	Chr.9	c09b167-c09b168	49697847-50189164	4.93	2.75	6.38
	E2	qPH-3-5	Chr.3	c03b106-c03b107	40990588-42411342	5.57	2.97	4.83
	E2	qPH-4-3	Chr.4	c04b125-c04b126	36452291-36506711	2.74	5.03	14.41
		qPH-7-4	Chr.7	c07b082-c07b083	21476252-21704756	3.48	2.29	3.00
		qPH-9-6	Chr.9	c09b015-c09b016	1903164-1983343	4.67	-2.71	4.02
T3	E1	qPH-5-2	Chr.5	c05b028-c05b029	6388870-6398535	5.00	3.92	3.35
		qPH-7-5	Chr.7	c07b114-c07b115	29307823-30059669	3.48	7.54	12.49
		qPH-9-7	Chr.9	c09b008-c09b009	988753-1082109	3.53	-3.22	2.27
	E2	qPH-1-1	Chr.1	c01b083-c01b084	26758853-27387031	4.75	3.50	7.65
		qPH-3-6	Chr.3	c03b046-c03b047	7367554-7576946	3.51	-2.64	4.35
		qPH-3-1	Chr.3	c03b143-c03b144	49232103-49249434	3.75	-2.31	3.42
		qPH-4-4	Chr.4	c04b041-c04b042	6913490-7153895	2.96	-2.04	2.68
		qPH-7-6	Chr.7	c07b055-c07b056	17909787-18105601	3.60	2.74	4.23
		qPH-7-7	Chr.7	c07b090-c07b091	23079209-23253415	8.07	5.22	17.49
T4	E1	qPH-1-2	Chr.1	c01b109-c01b110	31914666-32213218	7.64	5.68	13.60
		qPH-2-1	Chr.2	c02b089-c02b090	27836775-28229243	4.38	-5.74	13.79
		qPH-3-7	Chr.3	c03b053-c03b054	9220324-9287696	6.40	-3.54	5.02
		qPH-5-3	Chr.5	c05b041-c05b042	7885959-8086611	3.01	2.48	2.30
		qPH-8-3	Chr.8	c08b057-c08b058	8950445-9240501	2.84	2.26	2.16
		qPH-9-8	Chr.9	c09b002-c09b003	526353-660290	4.09	2.77	3.14
	E2	qPH-2-2	Chr.2	c02b142-c02b143	44084471-44171197	6.84	6.47	16.32
		qPH-5-4	Chr.5	c05b023-c05b024	5494776-5555640	4.14	3.16	3.73
		qPH-7-8	Chr.7	c07b084-c07b085	21714345-21892410	7.39	3.53	4.87
		qPH-9-9	Chr.9	c09b007-c09b008	983209-988753	3.31	2.35	2.07
		qPH-9-10	Chr.9	c09b165-c09b166	49049868-49379087	3.42	6.12	14.41
T5	E1	qPH-1-3	Chr.1	c01b107-c01b108	31556531-31855243	8.23	5.22	7.57
		qPH-2-1	Chr.2	c02b089-c02b090	27836775-28229243	6.45	-5.11	7.19
		qPH-2-3	Chr.2	c02b115-c02b116	37968852-38141819	4.14	2.67	1.90
		qPH-3-7	Chr.3	c03b053-c03b054	9220324-9287696	9.78	-4.16	4.57
		qPH-5-5	Chr.5	c05b052-c05b053	12174846-13011016	5.45	3.99	4.15
		qPH-7-9	Chr.7	c07b100-c07b101	26617489-26678123	6.11	5.24	7.68
		qPH-8-3	Chr.8	c08b057-c08b058	8950445-9240501	2.59	2.01	1.13
		qPH-9-11	Chr.9	c09b006-c09b007	803316-983209	8.99	4.02	4.38
		qPH-9-12	Chr.9	c09b146-c09b147	45421642-45469731	4.13	-4.85	6.43
		qPH-9-13	Chr.9	c09b175-c09b176	54557509-54694792	4.65	4.58	5.76
	E2	qPH-2-2	Chr.2	c02b142-c02b143	44084471-44171197	5.42	5.93	12.09
		qPH-5-6	Chr.5	c05b073-c05b074	30713393-30861542	3.07	5.19	9.14
		qPH-7-8	Chr.7	c07b084-c07b085	21714345-21892410	8.55	4.52	7.03

Table 3

Table 4

Conditional QTL for plant height detected in YRRIL population at different fertility periods"

阶段 Stages	环境 Environments	数量性状位点 QTL	染色体 Chromosome	标记区间 Marker interval	物理区间 Physical interval (bp)	LOD	加性效应 Additive effect	贡献率 R² (%)
0—T1	E1	qPH-3-1	Chr.3	c03b143-c03b144	49232103-49249434	5.20	0.70	4.13
		qPH-3-2	Chr.3	c03b144-c03b145	49236212-49263886	5.01	0.71	4.27
		qPH-4-1	Chr.4	c04b091-c04b092	32103966-32392762	4.90	0.55	2.60
		qPH-7-1	Chr.7	c07b111-c07b112	28718452-28977042	10.15	0.97	7.85
		qPH-8-1	Chr.8	c08b154-c08b155	35794684-36110021	3.78	-0.91	7.20
		qPH-8-2	Chr.8	c08b176-c08b177	38668781-38953634	6.36	0.86	6.29
		qPH-9-1	Chr.9	c09b120-c09b121	41372093-41585138	4.49	-0.54	2.44
	E2	qPH-4-2	Chr.4	c04b111-c04b112	34316068-34803353	2.98	1.48	2.95
	E2	qPH-7-2	Chr.7	c07b143-c07b144	34974931-35164751	2.52	2.37	7.56
T1—T2	E1	qPH-3-8	Chr.3	c03b132-c03b133	47561089-47780734	4.74	1.87	8.16
		qPH-5-7	Chr.5	c05b043-c05b044	8131712-8175114	2.56	1.05	2.41
		qPH-5-8	Chr.5	c05b108-c05b109	43783548-44258277	2.56	1.02	2.35
		qPH-9-2	Chr.9	c09b009-c09b010	1065098-1132102	8.38	-1.87	8.16
		qPH-9-14	Chr.9	c09b170-c09b171	51639430-52289028	4.58	1.39	4.56
		qPH-9-15	Chr.9	c09b171-c09b172	51729253-52624644	3.45	1.21	3.47
	E2	qPH-3-5	Chr.3	c03b106-c03b107	40990588-42411342	6.34	2.16	10.16
		qPH-7-10	Chr.7	c07b088-c07b089	22843640-23052954	3.35	1.52	5.21
		qPH-9-16	Chr.9	c09b014-c09b015	1849233-1941826	6.51	-2.22	10.60
T2—T3	E1	qPH-5-9	Chr.5	c05b019-c05b020	4766716-4845453	3.32	3.39	6.97
	E2	qPH-1-4	Chr.1	c01b106-c01b107	31517802-31614766	6.25	6.27	14.24
		qPH-1-3	Chr.1	c01b107-c01b108	31556531-31855243	6.53	6.37	14.69
		qPH-3-9	Chr.3	c03b043-c03b044	6910556-7238657	4.80	-2.86	2.92
		qPH-3-5	Chr.3	c03b106-c03b107	40990588-42411342	7.11	-3.62	4.41
		qPH-3-10	Chr.3	c03b140-c03b141	49122420-49193085	3.29	-2.34	1.97
		qPH-7-11	Chr.7	c07b052-c07b053	17638287-17791653	5.67	3.31	3.41
		qPH-8-4	Chr.8	c08b072-c08b073	12913834-13599376	3.89	2.54	2.33
		qPH-9-7	Chr.9	c09b008-c09b009	988753-1082109	6.42	3.46	4.22
T3—T4	E1	qPH-3-11	Chr.3	c03b126-c03b127	46785100-47002469	3.63	-3.55	3.20
		qPH-6-1	Chr.6	c06b032-c06b033	3556319-3630370	10.48	-6.06	9.86
		qPH-6-2	Chr.6	c06b065-c06b066	12542879-17978220	5.69	6.13	10.09
		qPH-8-5	Chr.8	c08b044-c08b045	6087263-6623116	2.58	3.04	2.46
		qPH-9-11	Chr.9	c09b006-c09b007	803316-983209	8.96	5.75	8.54
	E2	qPH-5-6	Chr.5	c05b073-c05b074	30713393-30861542	3.69	2.51	3.53
		qPH-6-3	Chr.6	c06b119-c06b120	32486143-32533796	5.62	3.29	6.40
		qPH-9-17	Chr.9	c09b164-c09b165	49027777-49049868	3.35	2.49	3.42
		qPH-9-10	Chr.9	c09b165-c09b166	49049868-49379087	3.40	2.42	3.31
T4—T5	E1	qPH-7-12	Chr.7	c07b103-c07b104	27561783-27659941	3.00	2.47	7.00
	E1	qPH-9-18	Chr.9	c09b177-c09b178	54969651-55252443	3.35	2.82	7.98
	E2	qPH-1-5	Chr.1	c01b122-c01b123	34477733-34973198	3.02	-1.06	6.28

Table 4

Fig. 3

Fig. 4

Table 5

Candidate genes within the confidence interval of major QTL for plant height"

数量性状位点 QTL	染色体 Chromosome	候选基因 Candidate genes	GO注释 GO annotation	拟南芥同源基因 Homologous genes in Arabidopsis	功能注释 Functional annotation
qPH-2-2	Chr.2	Seita.2G366600.1	GO:0016020, GO:0009765	AT3G61470.1	捕光天线蛋白；叶绿素a/b结合蛋白2 LHCA2; light-harvesting complex I chlorophyll a/b binding protein 2
qPH-1-2	Chr.1	Seita.1G242300.1	GO:0055114, GO:0016491	AT4G21200.1	赤霉素2-氧化酶8 Gibberellin 2-oxidase 8
qPH-1-3	Chr.1	Seita.1G240300.1		AT2G37040.1	PHE解氨酶1 PHE ammonia lyase 1
		Seita.1G240400.1		AT2G37040.1	PHE解氨酶1 PHE ammonia lyase 1
		Seita.1G240500.1		AT2G37040.1	PHE解氨酶1 PHE ammonia lyase 1
		Seita.1G240600.1		AT2G37040.1	PHE解氨酶1 PHE ammonia lyase 1
		Seita.1G240200.1		AT2G37040.1	PHE解氨酶1 PHE ammonia lyase 1
		Seita.1G238300.1	GO:0008152, GO:0003824	AT2G20420.1	ATP柠檬酸裂解酶（ACL）家族蛋白 ATP citrate lyase (ACL) family protein
qPH-2-1	Chr.2	Seita.2G183600.1	GO:0006412, GO:0005840, GO:0003735	AT2G36170.1	泛素超群；核糖体蛋白L40e Ubiquitin supergroup; Ribosomal protein L40e
		Seita.2G183800.1	GO:0006412, GO:0005840, GO:0003735, GO:0005515	AT2G36170.1	泛素超群；核糖体蛋白L40e Ubiquitin supergroup; Ribosomal protein L40e
		Seita.2G183700.1	GO:0006412, GO:0005840, GO:0003735	AT2G36170.1	泛素超群；核糖体蛋白L40e Ubiquitin supergroup; Ribosomal protein L40e
		Seita.2G185400.1	GO:0009058, GO:0008909	AT1G18870.1	异分支酸合酶2 Isochorismate synthase 2
qPH-3-5	Chr.3	Seita.3G329200.1		AT2G16920.1	泛素结合酶 23 Ubiquitin-conjugating enzyme 23
		Seita.3G329400.1		AT2G16920.1	泛素结合酶 23 Ubiquitin-conjugating enzyme 23
		Seita.3G329600.1		AT2G16920.1	泛素结合酶 23 Ubiquitin-conjugating enzyme 23
		Seita.3G329800.1		AT2G16920.1	泛素结合酶 23 Ubiquitin-conjugating enzyme 23
		Seita.3G329900.1		AT2G16920.1	泛素结合酶 23 Ubiquitin-conjugating enzyme 23
qPH-6-2	Chr.6	Seita.6G105300.1	GO:0055114, GO:0051287, GO:0016616	AT5G15490.1	UDP-葡萄糖6-脱氢酶家族蛋白 UDP-glucose 6-dehydrogenase family protein
		Seita.6G110200.1	GO:0016157, GO:0005985	AT5G20280.1	蔗糖磷酸合酶1F Sucrose phosphate synthase 1F
		Seita.6G105100.1	GO:0055114, GO:0016616, GO:0006694, GO:0003854	AT1G15950.1	肉桂酰基辅酶a还原酶1 Cinnamoyl coa reductase 1
qPH-7-5	Chr.7	Seita.7G234000.1	GO:0055114, GO:0016491, GO:0008270	AT4G39330.1	肉桂醇脱氢酶9 Cinnamyl alcohol dehydrogenase 9
qPH-7-7	Chr.7	Seita.7G143300.1	GO:0031625, GO:0006511	AT2G04660.1	后期促进复合体/环体2 Anaphase-promoting complex/cyclosome 2
qPH-9-10	Chr.9	Seita.9G439100.1	GO:0008641	AT5G06460.1	泛素激活酶2 Ubiquitin activating enzyme 2
qPH-9-10	Chr.9	Seita.9G440900.1	GO:0006529, GO:0004066	AT5G65010.1	天冬酰胺合成酶2 Asparagine synthetase 2

Table 5

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时期 Periods	生育期 Growth periods	测定时间 Measuring time	测定方法 Measurement methods	参考文献 Reference
T1	苗期 Seedling stage	播种后40 d 40 days after sowing	自然状态下地面至植株最高叶的距离 The distance from the ground to the highest leaf of the plant under natural conditions	/
T2	拔节期 Elongation stage	播种后56 d 56 days after sowing	地面至植株最上部展开叶叶尖距离 Distance from the ground to the tip of the uppermost unfolded leaf of the plant	/
T3	孕穗期 Booting stage	播种后72 d 72 days after sowing	地面至幼穗顶部距离 Distance from the ground to the top of the spikelet	/
T4	抽穗期 Tasseling stage	田间50%的植株穗子完全伸出旗叶鞘 50% of the plants in the field had spikes fully protruding from the flag leaf sheaths	齐穗后地面至穗子顶端距离 The distance from the ground to the top of the ear after full heading	[32]
T5	成熟期 Ripening period	田间50%的植株穂部籽粒完全硬化转成正常颜色 The grains of 50% plants in the field were completely hardened and turned into normal color	成熟后地面至植株顶端（含穗）距离 The distance from the ground to the top of the plant (including spikes) after ripening	[32]

性状 Trait	时期 Periods	环境 Environments	平均值±标准差 Mean±SD	变异系数 Coefficient of variation (%)	最小值 Min value	最大值 Max value	偏度 Skewness	峰度 Kurtosis
株高 PH (cm)	T1	E1	24.38±2.12	8.70	19.42	30.33	0.30	-0.30
	T1	E2	18.81±3.79	20.15	8.88	27.63	-0.06	-0.43
	T2	E1	45.58±5.57	12.22	32.50	65.00	0.42	0.19
	T2	E2	37.57±9.24	24.59	16.75	65.50	0.26	-0.24
	T3	E1	98.16±12.97	13.21	57.50	133.25	0.11	-0.03
	T3	E2	94.36±10.31	10.93	71.67	119.33	0.12	-0.51
	T4	E1	125.81±11.65	9.26	94.25	150.33	-0.23	-0.32
	T4	E2	98.94±11.45	11.57	72.00	136.00	0.33	-0.29
	T5	E1	131.31±13.44	10.24	97.50	163.00	0.02	-0.27
	T5	E2	100.54±11.79	12.00	75.33	138.00	0.31	-0.22

Phenotypical Variation and Dynamic QTL Mapping of Plant Height in Foxtail Millet at Different Developmental Stages

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