Visualized protein polymorphisms in leaf sheaths and roots of rice assessed by 2-DE analysis

Chen, Fangyu; Jiang, Liangrong; Huang, Rongyu; Chen, Xiaolong; Chen, Zhiming; Wang, Houcong; Huang, Yumin; Zheng, Jingsheng

doi:10.1590/1984-70332019v19n1a15

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Crop Breeding and Applied Biotechnology

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ARTICLE • Crop Breed. Appl. Biotechnol. 19 (01) • Jan-Mar 2019 • https://doi.org/10.1590/1984-70332019v19n1a15 copy

Visualized protein polymorphisms in leaf sheaths and roots of rice assessed by 2-DE analysis

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

To identify potential protein markers associated with tillering in rice, a d10 allelic mutant (JHCA) with a high-tillering dwarf phenotype and a wild-type cultivar (GLA4) with normal numbers of tillers were used to produce a hybrid (F₁), and 2-DE (two-dimensional electrophoresis) analysis was conducted in seedling leaf sheaths and roots of the rice hybrid and its parents. A total of 61 protein spots representing qualitative or quantitative polymorphisms were detected. Among them, 38 spots were successfully identified as 23 different proteins by MALDI-TOF/MS. The identified proteins were further divided into P/As (presence/absence variations), PSs (position shift variations) and qVs (quantitative variations). Most of the identified polymorphic proteins exhibited tissue-specific expression. Two spot families, identified as a putative vitamin B12-independent methionine synthase and a putative phosphoglycerate mutase were found. The profiles of expression abundance of three iso-spots in each spot family showed a reciprocal relationship between the two parents.

Keywords:
Protein polymorphism; rice; leaf sheath; root; proteomics

Spot variation	Protein abundance	Differentially expressed proteins
Spot variation	Protein abundance	Leaf sheaths	Roots
Qualitative	Only in JHCA	L8, L9, L12, L16, L18, L23, L26, L29	R4, R8, R11, R12, R13, R16, R18, R20, R21, R22, R23, R27, R28
Qualitative	Only in GLA4	L7, L10, L11, L13, L14, L19, L20, L21, L22, L24, L25, L28, L30	R5, R7, R10, R14, R15, R17, R19, R25, R29, R30
Quantitative	More in JHCA	L1, L2, L6, L15, L17, L27	R1, R2, R6, R24
Quantitative	More in GLA4	L3, L4, L5	R3, R9, R26, R31

GenBank Acc. No.	Protein name	Mr(Da)/pI^b	Protein Spot	MP^c	SC^d	Scores
Q2QLY5	Putative vitamin B12-independent methionine synthase	84874/5.93	L1/L2/L3	16/21/25	22%/30%/36%	78/124/177
Q5QMK7	Putative phosphoglycerate mutase	60980/5.42	L4/L5/L6	18/19/19	49%/36%/35%	139/160/111
Q93WM3	Putative asparagine-tRNA ligase	62948/5.68	L7/L8	15/16	25%/27%	90/97
ABF99538	methylenetetrahydrofolate reductase, putative, expressed	64656/5.75	L9	12	27%	81
Q6K4Z1	Hypothetical protein OSJNBa0035A24.3	47253/6.05	L10	7	24%	65
Q654U8	Putative pyrophosphate-dependent phosphofructokinase beta subunit	61907/6.01	L11	14	34%	71
Q8W3M9	26S proteasome regulatory particle triple-A ATPase subunit5b	21851/5.51	L14	7	33%	62
Q6YYH5	Hypothetical protein OSJNBa0051E21.10	9480/8.85	L16	4	33%	54
Q6AV21	Putative transcription factor(Auxin response factor)	61577/9.04	L20	7	21v	51
Q6ERW9	Putative cinnamyl alcohol dehydrogenase	38249/6.12	L22	7	24%	65
Q5VS40	Putative glycine-rich protein	15123/11.29	L23	4	33%	31
Q2R339	Citrate synthase 4, mitochondrial, putative, expressed	52557/7.71	L26	10	29%	56
Q2QRE2	Retrotransposon protein, putative, Ty3-gypsy subclass	170578/8.68	L28	13	13%	73
gi\|125558131	protein\|photosystem I reaction center subunit IV A	15440/9.64	L29/L30	7/6	61%/66%	77/74
Q2QLY5	Putative vitamin B12-independent methionine synthase	84874/5.93	R1/R2/R3	15/13/13	24%/27%/17%	87/69/67
Q5QMK7	Putative phosphoglycerate mutase	60980/5.42	R6	21	47%	172
Q93WM3	Putative asparagine-tRNA ligase	62948/5.68	R7/R8	10/11	18%/20%	61/62
Q259D7	H0801D08.15 protein	28229/6.07	R10	7	29%	53
AAR01748	AC139172 NID (Methylenetetrahydrofolate reductase)	42245/6.10	R11	13	43%	96
Q654U8	Putative pyrophosphate-dependent phosphofructokinase beta subunit	61907/6.01	R12/R15	10/20	19%/32%	64/163
JC4395	ferredoxin-nitrite reductase (EC 1.7.7.1) precursor	66671/6.83	R13	26	43%	187
gi\|218188296	hypothetical protein OsI_02106	61129/5.95	R14	17	31%	102
Q2R3Q9	Transferase family protein, putative, expressed	49570/5.04	R16/R17	13/12	41%/32%	112/78
Q2R480	6-phosphogluconate dehydrogenase, decarboxylating, putative, expressed	54494/6.09	R18/R19	14/14	35%/30%	74/107
Q19BJ6	Flavone O-methyltransferase	40066/5.41	R23/R25	17/15	48%/43%	120/81
AJRZQB	glutamate-ammonia ligase (EC 6.3.1.2) beta, cytosolic	39519/5.73	R24	12	25%	87
Q93Y73	Putative dehydrogenase	40438/6.73	R26	10	41%	54

Types of variation	Tissues
Types of variation	Leaf sheaths	Roots
PSs	L7-L8, L29-L30	R7-R8, R12-R15, R16-R17, R18-R19, R23-R25
P/As	L9, L10, L11, L12, L13, L14, L16, L18, L19, L20, L21, L22, L23, L24, L25, L26, L28	R4, R5, R10, R11, R13, R14, R20, R21, R22, R27, R28, R29, R30
qVs	L1-L2-L3, L4-L5-L6, L15, L17, L27	R1-R2-R3, R6, R9, R26, R31, R24

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