水稻矮化少蘖突变体dlt3的基因定位和蛋白质组学分析

doi:10.16819/j.1001-7216.2018.8001

摘要/Abstract

摘要：

目的株高是农作物的重要农艺性状之一。导致株高变矮的原因很多,最受关注的是赤霉素(GA)和油菜素内酯(BR)对株高的影响,其调控机制的阐明对于植物科学基础研究及遗传育种研究均具有重要意义。方法利用γ射线诱变水稻材料9311,获得一个矮化少蘖突变体,命名为dlt3 (dwarf and low-tillering 3),通过形态学调查手段分析dlt3突变体的株高、分蘖数、叶夹角、叶形态和结实率等性状,通过叶枕部位的伸直情况和α-淀粉酶活性检测分析其对外源BR和GA应答的敏感性,通过构建遗传群体和筛选分子标记对其进行基因定位,并利用基于iTRAQ的定量蛋白质组学技术分析dlt3突变体的蛋白质组表达谱。结果表型分析显示dlt3突变体具有半矮化、少分蘖、叶夹角减小、叶表面皱褶、叶形变短变宽和结实率降低等多个突变表型;突变体对GA正常应答,而对BR处理表现为不应答。遗传分析显示dlt3突变因单个基因隐性突变导致;利用分子标记将dlt3基因定位在第6染色体标记RM2615和R6M14之间。定量蛋白质组学分析在dlt3突变体中鉴定到330个差异表达蛋白,包括222个上调和108个下调表达蛋白。其中,4个差异表达蛋白与BR信号途径直接相关;多个差异表达蛋白与水稻株高或生长发育调控直接相关;此外,多个差异表达蛋白,如丝氨酸/苏氨酸蛋白激酶、Ca²⁺结合蛋白和锌指结构域蛋白等在dlt3突变体中大量富集。结论 dlt3是一个BR不敏感的矮化少蘖突变体,DLT3基因突变引起BR信号途径的异常,进而可能导致胞内蛋白磷酸化信号转导和转录激活途径受到广泛影响,从而引起植株生长发育等多方面性状异常。

关键词: 水稻, 矮化少蘖, dlt3, 油菜素内脂, 基因定位, 蛋白质组学

Abstract:

【Objective】Plant height is an important agronomic trait for crops because dwarf cultivars are more resistant to lodging. Many factors are responsible for dwarfism in plants, but gibberellin (GA) and brassinosteroid (BR) are the most intensely studied factors, since their molecular mechanism in regulating plant height is important for both basic and applied researches of plant breeding. 【Method】In the present study, we reported the characterization and genetic mapping of a dwarf and low-tillering mutant, dlt3, gained through gamma ray mutagenesis of O. sativa indica 9311. The agronomic traits of the dlt3 mutant including plant height, tiller number, lamina inclination, leaf length and width, and seed-setting rate were analyzed by morphological observation and statistics. The responses to GA and BR were detected based on the changes of leaf angle by exogenous application of BR and GA-induced α-amylase activity. The F₂ population and molecular markers were used for genetic mapping of the dlt3 gene. Furthermore, isobaric tags for the relative and absolute quantitation (iTRAQ)-based proteomic method were applied to determine the proteomics of the dlt3 mutant as compared with wild type. 【Result】The plant height, tiller number, leaf angle, leaf length and seed-setting rate were significantly reduced in dlt3. The mutant also showed increased width of leaf blades, dark green and crinkled leaves. The mutant showed normal response to GA, but no response to exogenous BR. Genetic analysis revealed that the dlt3 phenotype was controlled by a single recessive nuclear gene. The dlt3 gene was mapped on the short arm of chromosome 6 between molecular markers RM2615 and R6M14. The iTRAQ-based proteomic analysis revealed that a total of 330 proteins were differentially expressed in the dlt3 mutant, including 222 up-regulated proteins and 108 down-regulated proteins. It showed that four proteins were directly involved in BR signaling pathway and several proteins involved in plant height and developmental regulation were differentially expressed in the mutant. Furthermore, many proteins especially some kinase and phosphatase related proteins, Ca²⁺ binding related proteins and zinc finger containing proteins were significantly enriched in the mutant. 【Conclusion】These results indicate that the dlt3 is a BR-insensitive dwarf and low-tillering mutant. The DLT3 locus, whose mutation results in abnormal BR signaling, could play important roles in regulating both plant height and other aspects of rice growth and development.

Key words: rice, dwarf and low-tillering, dlt3, brassinosteroid (BR), genetic mapping, proteomics

中图分类号:

张敏娟, 李帅军, 陈琼琼, 景秀清, 陈坤明, 石春海, 李文强. 水稻矮化少蘖突变体dlt3的基因定位和蛋白质组学分析[J]. 中国水稻科学, 2018, 32(6): 529-537.

Minjuan ZHANG, Shuaijun LI, Qiongqiong CHEN, Xiuqing JING, Kunming CHEN, Chunhai SHI, Wenqiang LI. Genetic Mapping and Proteomic Analysis of the Dwarf and Low-tillering Mutant dlt3 in Rice[J]. Chinese Journal OF Rice Science, 2018, 32(6): 529-537.

图/表 5

参考文献 23

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标记名称 Marker name	正向引物序列(5′-3′) Forward primer sequence	反向引物序列(5′-3′) Reverse primer sequence	染色体 Chromosome	物理位置 Physical position/kb
RM1163	TGGACGCGGATAGGAGGAGACG	TCCTCCGCAAGGTCGGTTTCC	6	4021
RM3408	AGTGAATCCCATCAGATCACTCC	CATATCAAATCGCCGAGAAGG	6	4608
RM19556	TTCTGGCCTATGAGGGATGATCG	ACCAAATATCAAGCCTGCACAGC	6	5249
RM19570	CCCAGATATTCTGTGTGATCATGAGG	GAGTGAATGTGAGCCGTCTATTGG	6	5422
RM2615	ATCTCGTTCATACTGCTTGACC	GACTGGTTTCCTTCATGTTACC	6	5970
RM276	GTCCTCCATCGAGCAGTATCAGC	CTAGCAAGACATGGACCTCAACG	6	6241
RM19638	CCACACTGTACCGGTCGAAGACG	CTCTACAACTTGCAGCCCTGTCAGC	6	6387
R6M14	AAATGTCCATGTGTTTGCTTC	CATGTGTGGAATGTGGTTG	6	7710
RM527	CGGTTTGTACGTAAGTAGCATCAGG	TCCAATGCCAACAGCTATACTCG	6	9874

标记名称 Marker name	正向引物序列(5′-3′) Forward primer sequence	反向引物序列(5′-3′) Reverse primer sequence	染色体 Chromosome	物理位置 Physical position/kb
RM1163	TGGACGCGGATAGGAGGAGACG	TCCTCCGCAAGGTCGGTTTCC	6	4021
RM3408	AGTGAATCCCATCAGATCACTCC	CATATCAAATCGCCGAGAAGG	6	4608
RM19556	TTCTGGCCTATGAGGGATGATCG	ACCAAATATCAAGCCTGCACAGC	6	5249
RM19570	CCCAGATATTCTGTGTGATCATGAGG	GAGTGAATGTGAGCCGTCTATTGG	6	5422
RM2615	ATCTCGTTCATACTGCTTGACC	GACTGGTTTCCTTCATGTTACC	6	5970
RM276	GTCCTCCATCGAGCAGTATCAGC	CTAGCAAGACATGGACCTCAACG	6	6241
RM19638	CCACACTGTACCGGTCGAAGACG	CTCTACAACTTGCAGCCCTGTCAGC	6	6387
R6M14	AAATGTCCATGTGTTTGCTTC	CATGTGTGGAATGTGGTTG	6	7710
RM527	CGGTTTGTACGTAAGTAGCATCAGG	TCCAATGCCAACAGCTATACTCG	6	9874

蛋白登录号 Protein accession	水稻基因号 RAP_locus	蛋白质功能描述 Protein description	表达量变化 Ratio (dlt3/WT)	P值 P-value	上（下）调 Regulation
油菜素内酯相关蛋白 Brassinosteroid related proteins
Q6Z730	Os02g0122300	Translation initiation factor eIF3 subunit domain containing protein, Brassinosteroid receptor kinase (BRI1)-interacting protein 121, BIP121	0.651	1.08×10^-2	Down
Q0JBZ3	Os04g0501600	AT hook, DNA-binding, conserved site domain containing protein, brassinosteroid receptor kinase (BRI1)-interacting protein 106, BIP106	1.372	9.26×10^-3	Up
Q6K624	Os02g0612800	AT hook, DNA-binding, conserved site domain containing protein, brassinosteroid receptor kinase (BRI1)-interacting protein 135, BIP135	1.374	4.11×10^-2	Up
Q0J5J5	Os08g0430500	14-3-3 protein, Florigen receptor, G-box factor 14-3-3c protein, OsGF14c	3.355	3.15×10^-3	Up
生长素相关蛋白 Auxin related proteins
Q0DSY8	Os03g0280000	Similar to MDR-like ABC transporter, P-Glycoprotein 13, OsABCB13, OsPGP13	1.329	2.71×10^-2	Up
Q0IR61	Os11g0673200	Similar to Auxin-induced beta-glucosidase	1.828	1.65×10^-2	Up
Q84QW4	Os08g0524400	Protein of unknown function DUF568, DOMON-like domain containing protein, auxin-responsive family protein AIR12	1.857	4.48×10^-2	Up
激酶和磷酸酯酶相关蛋白 Kinase and phosphatase related proteins
Q0D6J6	Os07g0472400	Serine/threonine protein kinase-related domain containing protein	0.548	1.01×10^-2	Down
Q69NF8	Os09g0529900	Pyruvate/Phosphoenolpyruvate kinase, catalytic core domain containing protein	0.716	8.12E-03	Down
Q5Z8F2	Os01g0337600	Suppressor of Mek, PH domain-like protein	0.697	1.38×10^-2	Down
Q0D4F7	Os07g0628700	Similar to Receptor protein kinase	1.328	1.51×10^-2	Up
Q5QLG3	Os01g0682500	Similar to Protein Kinase C630.09c	1.431	1.86×10^-3	Up
Q2R2T6	Os11g0549615	Ser/Thr protein phosphatase family protein, purple acid phosphatase 3a	1.889	2.72×10^-2	Up
Q0IP84	Os12g0236400	Adenylate kinase A (EC 2.7.4.3) (ATP-AMP transphosphorylase)	1.471	1.44×10^-2	Up
Q60DT7	Os05g0190500	Similar to acid phosphatase, HAD superfamily phosphatase, VEGETATIVE STORAGE PROTEIN 2, OsVSP2	1.550	3.50×10^-2	Up
Q6AVA8	Os05g0405000	floury endosperm 4, pyruvate orthophospate dikinase, OsPBDK	1.641	7.29×10^-4	Up
Q6H444	Os09g0279400	Rhodanese-like domain containing protein, Rhodanese / Cell cycle control phosphatase superfamily protein	2.096	8.54×10^-3	Up
Q0IPL3	Os12g0189300	Pyruvate/Phosphoenolpyruvate kinase, catalytic core domain containing protein	2.248	6.06×10^-4	Up
Q6KA61	Os02g0285800	Similar to GTP-binding protein typA (Tyrosine phosphorylated protein A)	3.491	3.91×10^-4	Up
Q7XQZ5	Os04g0661300	ATP/GTP binding protein	1.356	1.09×10^-2	Up
Q0JQ62	Os01g0179700	Similar to GTP-binding protein YPTM2, ras-related protein, OsRab1	1.302	2.27×10^-2	Up
Q0DH67	Os05g0489600	ADP-ribosylation factor, Ras-related small GTP-binding family protein	1.608	3.99×10^-3	Up
Q84T71	Os03g0854100	Similar to ARF GAP-like zinc finger-containing protein ZIGA2, GTPase-activating protein	1.322	3.38×10^-3	Up
钙结合蛋白 Ca²⁺ binding related proteins
Q6F334	Os05g0491000	EF-Hand type domain containing protein, calmodulin-like protein 9, OsCML9	0.621	1.71×10^-3	Down
Q84VG0	Os08g0117400	Calmodulin-related calcium sensor protein, Ser/Thr kinase/calmodulin, OsCML7, OsSTKC	0.732	7.55×10^-3	Down
Q0DFA8	Os06g0104400	IQ calmodulin-binding motif family protein	1.458	1.17×10^-4	Up
Q0D7H6	Os07g0246200	Similar to calreticulin, CRT	1.325	6.48×10^-6	Up
锌指结构域蛋白 Zinc finger containing proteins
Q6K977	Os02g0831100	Zinc finger CCCH domain-containing protein 19	0.400	4.02×10^-3	Down
Q2R4J4	Os11g0472000	Zinc finger CCCH-type domain containing protein 63	0.436	2.02×10^-3	Down
Q6Z6E6	Os02g0203700	Zinc finger family protein, SRZ1	0.563	5.50×10^-3	Down
Q5NAV3	Os01g0257400	Zinc finger CCCH-type domain containing protein, OsC3H5	0.638	1.30×10^-2	Down
Q6YUR8	Os02g0121100	Zinc finger CCHC-type domain containing protein, cold shock domain protein 1, CSD protein 1	0.679	8.90×10^-3	Down
Q6K4N0	Os02g0789400	Similar to 9G8-like SR protein, RNA recognition motif and CCHC-type zinc finger domains containing protein	1.332	4.31×10^-2	Up
Q75LJ7	Os03g0836200	Similar to RNA-binding protein RZ-1, zinc finger-containing glycine-rich RNA-binding protein 1	1.374	2.39×10^-3	Up
Q6YTY3	Os07g0608400	PHD/F-BOX containing protein, PHD zinc finger protein ALFIN-LIKE 9	1.313	1.73×10^-2	Up
水稻株型调控相关蛋白 Regulation of plant architecture and growth related proteins
Q6EU14	Os02g0672200	Similar to AGO1 homologous protein, OsAGO1a	0.471	1.96×10^-3	Down
Q2QN08	Os12g0583500	Broad Complex BTB domain with non-phototropic hypocotyl 3 NPH3 domain, BTB domain containing protein	0.375	9.84×10^-3	Down
Q0J0F4	Os09g0513000	Similar to TGB12K interacting protein 3, ankyrin repeat domain containing protein, XA21 binding protein 25	0.712	3.06×10^-2	Down
Q10L71	Os03g0356700	Villin/gelsolin superfamily protein, Actin binding protein, Regulation of plant architecture, VLN2	1.350	2.66×10^-2	Up
Q0ITK1	Os11g0247300	Tubulin/FtsZ domain containing protein, Cell elongation and division, TWISTED DWARF 1, Tubulin alpha-2, small and round seed 5, TID1, TubA2, SRS5	2.936	3.45×10^-3	Up
Q0DH37	Os05g0494000	Cytochrome P450	1.507	4.15×10^-3	Up
Q2R176	Os11g0615200	SSXT family protein, GRF-interacting factor 2, protein binding/transcription coactivator	1.428	2.04×10^-2	Up
Q7XHW8	Os07g0681000	Zinc-binding domain of translation initiation factor 2 beta	1.429	4.84×10^-4	Up
Q0JAK9	Os04g0592400	Protein transport protein-related, t-snare domain containing protein	1.574	9.88×10^-4	Up
Q0JP92	Os01g0235400	Similar to Importin-alpha re-exporter, Cellular apoptosis susceptibility protein homolog	2.102	1.54×10^-2	Up

蛋白登录号 Protein accession	水稻基因号 RAP_locus	蛋白质功能描述 Protein description	表达量变化 Ratio (dlt3/WT)	P值 P-value	上（下）调 Regulation
油菜素内酯相关蛋白 Brassinosteroid related proteins
Q6Z730	Os02g0122300	Translation initiation factor eIF3 subunit domain containing protein, Brassinosteroid receptor kinase (BRI1)-interacting protein 121, BIP121	0.651	1.08×10^-2	Down
Q0JBZ3	Os04g0501600	AT hook, DNA-binding, conserved site domain containing protein, brassinosteroid receptor kinase (BRI1)-interacting protein 106, BIP106	1.372	9.26×10^-3	Up
Q6K624	Os02g0612800	AT hook, DNA-binding, conserved site domain containing protein, brassinosteroid receptor kinase (BRI1)-interacting protein 135, BIP135	1.374	4.11×10^-2	Up
Q0J5J5	Os08g0430500	14-3-3 protein, Florigen receptor, G-box factor 14-3-3c protein, OsGF14c	3.355	3.15×10^-3	Up
生长素相关蛋白 Auxin related proteins
Q0DSY8	Os03g0280000	Similar to MDR-like ABC transporter, P-Glycoprotein 13, OsABCB13, OsPGP13	1.329	2.71×10^-2	Up
Q0IR61	Os11g0673200	Similar to Auxin-induced beta-glucosidase	1.828	1.65×10^-2	Up
Q84QW4	Os08g0524400	Protein of unknown function DUF568, DOMON-like domain containing protein, auxin-responsive family protein AIR12	1.857	4.48×10^-2	Up
激酶和磷酸酯酶相关蛋白 Kinase and phosphatase related proteins
Q0D6J6	Os07g0472400	Serine/threonine protein kinase-related domain containing protein	0.548	1.01×10^-2	Down
Q69NF8	Os09g0529900	Pyruvate/Phosphoenolpyruvate kinase, catalytic core domain containing protein	0.716	8.12E-03	Down
Q5Z8F2	Os01g0337600	Suppressor of Mek, PH domain-like protein	0.697	1.38×10^-2	Down
Q0D4F7	Os07g0628700	Similar to Receptor protein kinase	1.328	1.51×10^-2	Up
Q5QLG3	Os01g0682500	Similar to Protein Kinase C630.09c	1.431	1.86×10^-3	Up
Q2R2T6	Os11g0549615	Ser/Thr protein phosphatase family protein, purple acid phosphatase 3a	1.889	2.72×10^-2	Up
Q0IP84	Os12g0236400	Adenylate kinase A (EC 2.7.4.3) (ATP-AMP transphosphorylase)	1.471	1.44×10^-2	Up
Q60DT7	Os05g0190500	Similar to acid phosphatase, HAD superfamily phosphatase, VEGETATIVE STORAGE PROTEIN 2, OsVSP2	1.550	3.50×10^-2	Up
Q6AVA8	Os05g0405000	floury endosperm 4, pyruvate orthophospate dikinase, OsPBDK	1.641	7.29×10^-4	Up
Q6H444	Os09g0279400	Rhodanese-like domain containing protein, Rhodanese / Cell cycle control phosphatase superfamily protein	2.096	8.54×10^-3	Up
Q0IPL3	Os12g0189300	Pyruvate/Phosphoenolpyruvate kinase, catalytic core domain containing protein	2.248	6.06×10^-4	Up
Q6KA61	Os02g0285800	Similar to GTP-binding protein typA (Tyrosine phosphorylated protein A)	3.491	3.91×10^-4	Up
Q7XQZ5	Os04g0661300	ATP/GTP binding protein	1.356	1.09×10^-2	Up
Q0JQ62	Os01g0179700	Similar to GTP-binding protein YPTM2, ras-related protein, OsRab1	1.302	2.27×10^-2	Up
Q0DH67	Os05g0489600	ADP-ribosylation factor, Ras-related small GTP-binding family protein	1.608	3.99×10^-3	Up
Q84T71	Os03g0854100	Similar to ARF GAP-like zinc finger-containing protein ZIGA2, GTPase-activating protein	1.322	3.38×10^-3	Up
钙结合蛋白 Ca²⁺ binding related proteins
Q6F334	Os05g0491000	EF-Hand type domain containing protein, calmodulin-like protein 9, OsCML9	0.621	1.71×10^-3	Down
Q84VG0	Os08g0117400	Calmodulin-related calcium sensor protein, Ser/Thr kinase/calmodulin, OsCML7, OsSTKC	0.732	7.55×10^-3	Down
Q0DFA8	Os06g0104400	IQ calmodulin-binding motif family protein	1.458	1.17×10^-4	Up
Q0D7H6	Os07g0246200	Similar to calreticulin, CRT	1.325	6.48×10^-6	Up
锌指结构域蛋白 Zinc finger containing proteins
Q6K977	Os02g0831100	Zinc finger CCCH domain-containing protein 19	0.400	4.02×10^-3	Down
Q2R4J4	Os11g0472000	Zinc finger CCCH-type domain containing protein 63	0.436	2.02×10^-3	Down
Q6Z6E6	Os02g0203700	Zinc finger family protein, SRZ1	0.563	5.50×10^-3	Down
Q5NAV3	Os01g0257400	Zinc finger CCCH-type domain containing protein, OsC3H5	0.638	1.30×10^-2	Down
Q6YUR8	Os02g0121100	Zinc finger CCHC-type domain containing protein, cold shock domain protein 1, CSD protein 1	0.679	8.90×10^-3	Down
Q6K4N0	Os02g0789400	Similar to 9G8-like SR protein, RNA recognition motif and CCHC-type zinc finger domains containing protein	1.332	4.31×10^-2	Up
Q75LJ7	Os03g0836200	Similar to RNA-binding protein RZ-1, zinc finger-containing glycine-rich RNA-binding protein 1	1.374	2.39×10^-3	Up
Q6YTY3	Os07g0608400	PHD/F-BOX containing protein, PHD zinc finger protein ALFIN-LIKE 9	1.313	1.73×10^-2	Up
水稻株型调控相关蛋白 Regulation of plant architecture and growth related proteins
Q6EU14	Os02g0672200	Similar to AGO1 homologous protein, OsAGO1a	0.471	1.96×10^-3	Down
Q2QN08	Os12g0583500	Broad Complex BTB domain with non-phototropic hypocotyl 3 NPH3 domain, BTB domain containing protein	0.375	9.84×10^-3	Down
Q0J0F4	Os09g0513000	Similar to TGB12K interacting protein 3, ankyrin repeat domain containing protein, XA21 binding protein 25	0.712	3.06×10^-2	Down
Q10L71	Os03g0356700	Villin/gelsolin superfamily protein, Actin binding protein, Regulation of plant architecture, VLN2	1.350	2.66×10^-2	Up
Q0ITK1	Os11g0247300	Tubulin/FtsZ domain containing protein, Cell elongation and division, TWISTED DWARF 1, Tubulin alpha-2, small and round seed 5, TID1, TubA2, SRS5	2.936	3.45×10^-3	Up
Q0DH37	Os05g0494000	Cytochrome P450	1.507	4.15×10^-3	Up
Q2R176	Os11g0615200	SSXT family protein, GRF-interacting factor 2, protein binding/transcription coactivator	1.428	2.04×10^-2	Up
Q7XHW8	Os07g0681000	Zinc-binding domain of translation initiation factor 2 beta	1.429	4.84×10^-4	Up
Q0JAK9	Os04g0592400	Protein transport protein-related, t-snare domain containing protein	1.574	9.88×10^-4	Up
Q0JP92	Os01g0235400	Similar to Importin-alpha re-exporter, Cellular apoptosis susceptibility protein homolog	2.102	1.54×10^-2	Up