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Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (4): 556-567.doi: 10.3724/SP.J.1006.2019.82041

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Physiological and biochemical analysis and gene mapping of a novel short radicle and albino mutant sra1 in rice

ZHANG Li-Sha,MI Sheng-Nan,WANG Ling,WEI Gang,ZHENG Yao-Jie,ZHOU Kai,SHANG Li-Na,ZHU Mei-Dan,WANG Nan()   

  1. Rice Research Institute, Southwest University / Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
  • Received:2018-07-29 Accepted:2018-12-24 Online:2019-04-12 Published:2019-01-07
  • Contact: Nan WANG E-mail:wangnan_xndx@126.com
  • Supported by:
    This study was supported by the National Natural Science Foundation of China(31771750);Basic Research and Frontier Exploration Projects of Chongqing City(cstc2018jcyjAX0424)

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Abstract:

The leaf color mutant is an ideal material for studying the process of photosynthesis and the pathways of chlorophyll synthesis and degradation. Studies on rice leaf color mutants are helpful to explain the gene network of chloroplast development and photosynthesis in higher plants. The mutant sra1, derived from the progeny of EMS-treated indica rice Xinong 1B. Leaves of sra1 were white in color from budding to the third leaf, and the radicle of sra1 was significantly shorter than that of wild type in the same stage. The observation of leaves in the same position showed that in Xinong 1B, the chloroplast of mesophyllous cells was abundant and the membrane system was fully developed, while in sra1, the vacuolarization of mesophyll cells was serious, the number of chloroplasts was significantly reduced or absent, and the granule thylakoids were loosely folded. The contents of chlorophyll a, chlorophyll b, and carotenoid in sra1 were close to zero, and the net photosynthetic rate was negative. Genetic analysis indicated that the short-root and albino phenotype was controlled by a single recessive nuclear gene, and SRA1 was localized between the long-arm InDel markers Z-20 and Z-42 of rice chromosome 3. The physical distance between the two InDel markers was about 657 kb. No genes related to chloroplast and root development have been reported in this interval, indicating that sra1 is a novel mutant. The sra1 is a novel mutant with albino and accompanying short roots, suggesting that SRA1 may be involved in regulating chloroplast and root development.

Key words: rice, short radicle and albino mutant, gene mapping

Table 1

Photosynthetic characteristics of the wild type (WT) and the sra1 mutant"

材料
Material		 净光合速率
Net photosynthetic rate
(μmol CO2 m-2 s-1)		 气孔导度
Stomatal conductance
(mol H2O m-2 s-1)		 蒸腾速率
Transpiration rate
(mol H2O m-2 s-1)		 胞间CO2浓度
Intercellular CO2 concentration
(μmol CO2 L-1)
WT 11.77±0.1091 0.30±0.0019 3.29±0.0090 298.44±2.9901
sra1 -3.61±0.0680** 0.18±0.0008** 1.28±0.0070** 424.52±5.7801**

Supplementary table 1

Gene encoding the enzymes in the chlorophyll biosynthetic pathway in angiosperm"

编号
Code		 酶
Enzyme		 基因
Gene		 水稻
Rice
1 谷氨酰-tRNA合成酶 Glutamyl-tRNAsynthetase GltX AK099931
2 谷氨酰-tRNA还原酶 Glutamyl-tRNAreductase HEMA AK099393
3 谷氨酸-1-半醛转氨酶 Glutamate-1-semialdehyde aminotransferase GSA AK064826
4 5-氨基乙酰丙酸脱水酶 5-aminolevulinate dehydratase HEMB AK101836
5 羟甲基后胆色素原合酶 Hydroxymethylbilane synthase HEMC AK060914
6 尿卟啉原III合酶 Uroporphyrinogen III synthase HEMD AK107127
7 尿卟啉原III脱羧酶 Uroporphyrinogen III decarboxylase HEME AK070859
8 粪卟啉原III氧化酶 Copro-porphyrinogen III oxidase HEMF AK070391
9 原卟啉原氧化酶 Protoporphyrinogen IX oxidase HEMG AK108365
10 镁螯合酶D亚基 Mg chelatase D subunit CHLD AK072463
镁螯合酶H亚基 Mg chelatase H subunit CHLH AK067323
镁螯合酶I亚基 Mg chelatase I subunit CHLI AK060389
11 镁原卟啉IX甲基转移酶 Mg-protoporphyrin IX methyltransferase CHLM AK059151
12 镁原卟啉 IX单甲酯环化酶 Mg-protoporphyrinogen IX monomethylester cyclase CHL27 AK069333
13 二乙烯还原酶 3,8-divinyl reductase protochlorophyll a-8-vinyl reductase DVR AK103940
14 原叶绿素酸酯氧化还原酶 Protochlorophyllide oxidoreductase POR AK068143
15 叶绿素合酶 Chlorophyll synthase CHLG AK068855
16 叶绿素a加氧酶1 Chlorophyllide a oxygenase CAO1 AF284781/AK063367

Supplementary table 2

Sequences of some discrepant primers for gene mapping"

标记
Marker		 正向引物序列
Forward primer sequence (5′-3′)		 反向引物序列
Reverse primer sequence (5′-3′)
Z-12 ACGCCGTCTCCTTGGTAATC CTTACATTGGAAAGCGGAGG
Z-20 TTGTAGTGCGGGCAGTTCTC GTACTGTTTGCCTCTGCTTGC
Z-42 CCTTAATCTTGTCGCACAAC GCTTCTCTCCATCAACCATAT
Z-78 ACGCAGGAGAAGCTAGATAGG AACCATCTTTTAGTGTCGGGT
Z-83 TACCCTTGGAGCACATATAGTTAA TTGGTCACCAACATATCTTGAA
Z-112 GGCTCTGCTAGCGAAATACTAG GCTCACCATACTCACCAATTACT
ZMD5-18 TCAGGTCTTACGACGGTATGG GGACACACTAGAATCTACGCACG
ZMD5-44 GAAGCTATTAGCCGGGATCG GCCAAGGCAAAGCTCTCTT
ZTQ43 TGCAGAGACAAGGAAGCGG TCCTGATCGTTGAGCAGGC
RM8208 TGTAAATGCCTGAGTGCCTACCC AGCTAAACCGCTAGGGCCTTCC
RM3400 GGGTGCACCTTTGTATCTGTGC TGACAGAGGTAAAGCAGCAGTAGTCG
RM15177 TCCTGTGTTGGACGGAGTATGC GCCTCAGAGGTTAGAAGACAGACAGC
RM405 TATGCTTTCTGTCAGCTTCC CTGCTGTGAAAGAGTTGACG
RM18053 GAGACCAGAGGGAGACAAAGAGAGG CTTAGGTCTCCCGACAGTCACG

Supplementary table 3

Related quantitative gene description"

基因
Gene		 基因产物
Product		 RAP位点
RAP_locus
OsPOLP PolI-like DNA polymerase, plastidal DNA polymerase 1 Os08g0175300
FtsZ Plastid division protein FtsZ1 Os04g0665400
OsRPOTP RNA polymerase Os06g0652000
RpoB RNA polymerase beta subunit CAA33986
V2 Virscent 2 Os03g0320900
V3 Virscent 3 Os06g0168600
HEMA1 Glutamyl-tRNA reductase 1 Os10g0502400
HEMD Uroporphyrinogen-III synthase Os03g0186100
CHLD Magnesium chelatase subunit Os03g0811100
CHLM Mg-protoporphyrin IX methyltransferase Os06g0132400
CAO1 Chlorophyll a oxygenase 1 Os10g0567400
PSY1 Phytoene Synthase 1 Os06g0729000
PSY2 Phytoene synthase 2 Os12g0626400
carb1R Chlorophyll A/B binding protein 1R Os09g0346500
carb2R Chlorophyll A/B binding protein 2R Os01g0600900
petA petA, cytochrome f CAA33961
petB petB, cytochrome B6 CAA33977
psaA psaA, PSI P700 apoprotein A1 CAA33996
psbA psbA, PSII 32 kDa protein CAA34007
RbcL RbcL, Ribulose bisphosphate carboxylase large chain CAA34004
RbcS Rubisco small subunit Os12g0274700

Supplementary table 4

Sequences of primers for RT-PCR"

基因
Gene		 正向引物
Forward sequence (5′-3′)		 反向引物
Reverse sequence (5′-3′)
Actin GACCCAGATCATGTTTGAGACCT CAGTGTGGCTGACACCATCAC
OsPOLP ACCGGTGCTTTCAGGCTTG GCTGACTGATAATCACACG
FtsZ AAAGGACATAACCTTGCAAG AGTTTTCCTATTGAACCGTG
OsRPOTP TCCTCATGTCGAGCAAGGAT GAAAGAATGTCTGGACTTTG
RpoB TATGGTCTAATTCCGAGCGGT TATGGTCTAATTCCGAGCGG
V2 GAGGAGTTCCTCACGATGAT AGCATCAATGATAGACTCC
V3 GTTAGATGCTTCACTACACAG GTACCATTGCCAACATGGCAAC
HEMA1 CGCTATTTCTGATGCTATGGGT TCTTGGGTGATGATTGTTTGG
HEMD AGGGATGGAAGGCTGCTGGA CAGTGGTCCTTGGAAGCTCTG
CHLD GCTTGCAGAAAGCTACACAAGC AGGCCGTGAGCTAAAGGAGA
CHLM CCATCCATTGGTCTCCTTATGACA GTAGCCTACTTACCATCAATGAGTC
CAO1 GACACCTTCATCTGGGCTTCAA CGAGAGACATCCGGTAGAGC
PSY1 GTGACCGAGCTCAGCCAG TTAATCGGAAGGCAGATGCT
PSY2 GGGCGTTGCGCATCTAGA CAAGAAATCGTGCGAAATCA
carb1R AGATGGGTTTAGTGCGACGAG TTTGGGATCGAGGGAGTATTT
carb2R TGTTCTCCATGTTCGGCTTCT GCTACGGTCCCCACTTCACT
petA TGAATGTGGGTGCTGTTCTTATTT TCGGGCGGCGCTAAT
petB TCCTCGGTTCAATACATAATGACCG CGTGCAGGATCATCATTAGAACCA
psaA GCGAGCAAATAAAACACCTTTC GTACCAGCTTAACGTGGGGAG
psbA CCCTCATTAGCAGATTCGTTTT ATGATTGTATTCCAGGCAGAGC
RbcL CTTGGCAGCATTCCGAGTAA ACAACGGGCTCGATGTGATA
RbcS TCCGCTGAGTTTTGGCTATTT GGACTTGAGCCCTGGAAGG

Fig. 1

Plant morphology of the wide type (WT) and the sra1 mutant A-C: 3-day seeding of the wild type and the sra1; D: 10-day seeding of the wild type and the sra1; E: 20-day seeding of the wild type and the sra1; Scale bars: 1 cm in A, B, and C, 2 cm in D and E."

Fig. 2

Length of roots of the wild type (WT) and the sra1 mutant A: 3-day seeding roots of the wild type and the sra1 mutant; B: 10-day seeding roots of the wild type and the sra1 mutant; C: 20-day seeding roots of the wild type and the sra1 mutant; D-G: the middle of 10-day seeding roots of the wild type and the sra1 mutant; Scale bars: 1 cm in A, B, and C, 0.5 cm in D and E, 0.1 cm in F and G. H: length of radicle of the wild type and the sra1 mutant; I: length of lateral roots on the middle of radicle of the wild type and the sra1 mutant; J: density of lateral roots of the wild type and the sra1 mutant. *Significantly different at P < 0.05 by t-test."

Fig. 3

Chloroplast transmission electron microscope observation in the wild type (WT) and the sra1 mutant 1: chloroplast; 2: cell vacuole; 3: grana lamella; 4: thylakoid; 5: stroma thylakoids-like. A-C: transmission electron microscopy observation of chloroplasts of wild type plants; D-F: transmission electron microscopy observation of chloroplasts of sra1 plants; Scale: 2 μm in A and D, 500 nm in B and E, 200 nm in C and F."

Fig. 4

Photosynthetic pigments contents of the wild type and the sra1 mutant"

Fig. 5

Chlorophyll fluorescence of the wild type and the sra1 mutant A: maximum and minimum fluorescence amounts of wild type and sra1 under dark adaptation; B: maximum and minimum fluorescence of wild type and sra1 under light adaptation conditions."

Fig. 6

Activities of SOD, POD, CAT, and MDA content in sra1 and wild type"

Fig. 7

Gene mapping of SRA1 on rice chromosome 3 The thick black line in the figure represents the chromosome, the SSR markers used for gene mapping are marked above the line, the value below the line represents the genetic distance between the two markers, and n is the total number of F2 localized populations."

Fig. 8

Expression levels of genes associated in the wild type (WT) and sra1 mutant A: expression levels of OsPOLP, FtsZ, OsRpoTp, Rpob, V2, V3 in the wild type and sra1; B: expression levels of HEMA1, HEMD, CHLD, CHLM, CAO1, PSY1, PSY2 in the wild type and sra1; C: expression levels of RbcL, RbcS, Cab1R, Cab2R, PsaA, PsbA, PetA, PetB in the wild type and sra1."

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