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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (8): 2125-2133.doi: 10.3724/SP.J.1006.2022.12052

• RESEARCH NOTES • Previous Articles    

Identification and gene mapping of slender stem mutant sr10 in rice (Oryza sativa L.)

WEI Gang1(), CHEN Dan-Yang1(), REN De-Yong2(), YANG Hong-Xia1, WU Jing-Wen1, FENG Ping1, WANG Nan1,*()   

  1. 1Rice Research Institute, Southwest University / Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
    2State Key Laboratory of Rice Biology / Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture and Rural Affairs / China National Rice Research Institute, Hangzhou 310006, Zhejiang, China
  • Received:2021-07-26 Accepted:2021-11-30 Online:2022-08-12 Published:2021-12-22
  • Contact: WANG Nan E-mail:1345433221@qq.com;cdyccdy@163.com;rendeyong616@163.com;wangnan_xndx@126.com
  • About author:First author contact:

    ** Contributed equally to this work

  • Supported by:
    National Natural Science Foundation of China(31771750)

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Abstract:

The mutant sr10 (slender rice 10) reported in this study was obtained by ethyl methanesulfonate (EMS) from Xinong 1B, an indica maintainer line and it was slender stems and male sterility. Cytological observation indicated that the size of mutant cells became longer while the number of vascular bundles was less than wild type. The frozen section and chlorophyll content measurement manifested that the chlorophyll content of sr10 decreased greatly, resulting in the decreased photosynthetic rate, but the falling of stomatal conductance might improve its drought resistance. The levels of IAA and GA3 were significantly increased, while the content of ABA was sharply decreased in sr10. QRT-PCR analysis manifested that some genes involved in GAs pathway were down-regulated and some of IAA pathway related genes were abnormal. Genetic analysis suggested that the mutant phenotype of sr10 was controlled by a single recessive nuclear gene. The SR10 was located at a 175.7 kb interval between the molecular markers LIND12 and 28.5-4 on chromosome 3. These results laid a foundation for cloning and functional analysis of SR10.

Key words: rice (Oryza sativa L.), gene mapping, plant height, tillering, male sterility, hormone

Table S1

Molecular markers newly designed in this study"

标记
Marker		 正向序列
Forward primer(5'→3')		 反向序列
Reverse primer(5'→3')
ZTQ67 CATGTTCCAAGTATTCCTGGG CGAATGCTAGTGCCCTAGCT
LIND16 TGCGTGACAACAGATACAGGATACA TGAAATGTTAGCGATTCCTCTTTCG
LIND24 TTTGGGAGTCGCTGCACTACA GCGCAAGGGCAAATTTCTA
F41-54 CTGCTTCTGTCGCCACCG GATTCCTTGGTCGCCTGCC
LIND12 TAGGCCCTGCAAACTTGTTTAATAG CCTGCTCGTAGTTATGAGTGCTTG
28.5-4 GAGGATGAACTTCACTTACCCTCAAAG GCAGCGAGACTAGAAACTACTCCTCC
RM186 TCCTCCATCTCCTCCGCTCCCG GACGAAGAAGGCCACCACGCCC

Table S2

Primers used for qRT-PCR analysis"

引物
Primer		 正向序列
Forward primer(5'→3')		 反向序列
Reverse primer(5'→3')
OsActin ACCACTTCGACCGCCACTACT ACGCCTAAGCCTGCTGGTT
OsIAA3 GACGCAGCAGAAGGAGGAT GACGTCCCATTCGAGATGTT
OsIAA6 CCAATTCGATCCTTCAGGAG CACAGCAAGGTGCAGATGAC
OsIAA10 GGTTGCTGGATGGGTGAAGG CCAGCTCACCTACGAGGACAGG
OsIAA11 GCGCTGGTGAAGGTGAGCAT AGAGATGACCTGGAGTACGT
iaa21 GAAGGCACAGGTGGTAGGATG GGTGAATCAAATGGGAAGTCAGG
OsIAA23 GTACCTGCGCAAGGTGGAC GTTCGTCGAGTCCTGCAAG
OsSAUR39 TACAGCTGATGGAGAGCGATT TTGGATTCACAGGTGAGGAAA
OsPIN3t CGGCTCTACCACAAGGGATTG TGTACTACATCCTTCTTGGACTATGA
OsTIR1 ATTACATCCTCTCAGGCTGC CATGAACGATCCTGGAAGGT
GA2ox1 ACCACTACCCTCCATCATGCAACA AGGCTAGCAATGGTGGGAATCTGA
GA2ox4 CTGCAGGTGATGACGAACGG TGGAGCAGAGGATCGCGCCGCT
GA3ox2 CGCCTCTGGCCCAAGT GAGTTGCTGAGGTTGTTCTTGAG
GA20ox2 GCCAATGGGGAGGGTGT TGTCGCTGACGATCATGG
SLR1 TGCCCGCCATGCTTCCAC GCTGACCCGTCGGCTGCT

Fig. 1

Phenotype identification of sr10 a1-a6: phenotype observation of WT and sr10 in 4-60 days, Bars are 17.5, 41, 69.2, 102, 191, and 309 mm, respectively; b: plant height of WT and sr10in 4-60 days; c: root length of WT and sr10 in 4-60 days; d: leaf length of WT and sr10 at mature stage; e: leaf width of WT and sr10 at mature stage; f: tiller number of WT and sr10; First: the first leaf-blade; Second: the second leaf-blade; Third: the third leaf-blade; *: P < 0.05; **: P < 0.01."

Fig. 2

Cytological observation of sr10 a: WT upper epidermis of leaves, bar: 35 μm; b: upper epidermis of leaf of sr10, bar: 35 μm; c: WT lower epidermis of leaves, bar: 35 μm; d: lower epidermis of leaf of sr10, bar: 35 μm; e: WT sheath outer skin, bar: 35 μm; f: Outer sheath skin of sr10, bar: 35 μm; g: WT sheath inner epidermis, bar: 35 μm; h: Inner sheath epidermis of sr10, bar: 35 μm; i: the inverted intersegmental cross section of WT and sr10, bar: 1.1 mm; j: the vascular bundle number of WT and sr10. White arrow indicates guard cell, red arrow indicates cell length, and red ellipse indicates vascular bundles; **: P < 0.01."

Fig. 3

Fertility identification of sr10 a: spikes of WT and sr10, bar: 2.1 mm; b, c: anthers of WT and sr10, bar: 2.8 mm (b) and bar: 3.5 mm (c); d: pollen iodine staining of WT, bar: 115 μm; e: pollen iodine staining of sr10, bar: 115 μm; f: pollen fertility of WT and sr10; g: seed setting rate of WT and sr10; **: P < 0.01."

Fig. 4

Determination of chlorophyll content and photosynthetic index of sr10 a: frozen section and fluorescence observation of leaves of WT and sr10, bars: 26 μm; b: the content of chlorophyll a; c: the content of chlo-rophyll b; d: the content of the total chlorophyll; e: the content of Car; f: net photosynthetic rate (Pn); g: stomatal conductance (Gs); h: inter-cellular CO2 concentration (Ci); i: transpiration rate (Tr); First: the first leaf-blade; Second: the second leaf-blade; Third: the third leaf-blade; *: P < 0.05; **: P < 0.01."

Table S3

Genetic analysis of ssr1"

组合
Combinations		 F1代表型
F1 phenotype		 F2代表型
F2 population numbers		 野生型数
WT numbers		 突变体数
Mutant numbers		 分离比
Separation ratio
J10/ sr10 正常normal 4005 3015 990 χ2=0.909<χ20.05,1=3.84

Fig. 5

Molecular mapping of SR10 on rice chromosome 3 N = 229: F2 recessive population used in primary mapping; n = 990: F2 recessive population used in fine mapping."

Table S4

The annotated genes in the mapping region"

基因编号
Locus name		 基因注释
Gene annotation
LOC_Os03g49830 expressed protein
LOC_Os03g49840 hypothetical protein
LOC_Os03g49850 hypothetical protein
LOC_Os03g49860 expressed protein
LOC_Os03g49870 transposon protein, putative, Mariner sub-class, expressed
LOC_Os03g49880 TCP family transcription factor
LOC_Os03g49890 hypothetical protein
LOC_Os03g49900 zinc finger, C3HC4 type domain containing protein, expressed
LOC_Os03g49910 retrotransposon protein, putative, Ty1-copia subclass, expressed
LOC_Os03g49920 expressed protein
LOC_Os03g49930 pentatricopeptide, putative, expressed
LOC_Os03g49940 integral membrane protein, putative, expressed
LOC_Os03g49960 expressed protein
LOC_Os03g49970 expressed protein
LOC_Os03g49980 retrotransposon protein, putative, unclassified, expressed
LOC_Os03g49990 slender rice 1, GRAS-domain protein
LOC_Os03g50010 toc64, putative, expressed
LOC_Os03g50020 retrotransposon, putative, centromere-specific
LOC_Os03g50030 phospholipase A2, putative, expressed
LOC_Os03g50040 phytanoyl-CoA dioxygenase, putative, expressed

Fig. 6

Determination of hormone contents and the relative expression of related genes in sr10 *: P < 0.05; **: P < 0.01."

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[1] WANG Li-Yan;ZHAO Ke-Fu. Some Physiological Response of Zea mays under Salt-stress[J]. Acta Agron Sin, 2005, 31(02): 264 -268 .
[2] Qi Zhixiang;Yang Youming;Zhang Cunhua;Xu Chunian;Zhai Zhixi. Cloning and Analysis of cDNA Related to the Genes of Secondary Wall Thickening of Cotton (Gossypium hirsutum L.) Fiber[J]. Acta Agron Sin, 2003, 29(06): 860 -866 .
[3] NI Da-Hu;YI Cheng-Xin;LI Li;WANG Xiu-Feng;ZHANG Yi;ZHAO Kai-Jun;WANG Chun-Lian;ZHANG Qi;WANG Wen-Xiang;YANG Jian-Bo. Developing Rice Lines Resistant to Bacterial Blight and Blast with Molecular Marker-Assisted Selection[J]. Acta Agron Sin, 2008, 34(01): 100 -105 .
[4] DAI Xiao-Jun;LIANG Man-Zhong;CHEN Liang-Bi. Comparison of rDNA Internal Transcribed Spacer Sequences in Oryza sativa L.[J]. Acta Agron Sin, 2007, 33(11): 1874 -1878 .
[5] WANG Bao-Hua;WU Yao-Ting;HUANG Nai-Tai;GUO Wang-Zhen;ZHU Xie-Fei;ZHANG Tian-Zhen. QTL Analysis of Epistatic Effects on Yield and Yield Component Traits for Elite Hybrid Derived-RILs in Upland Cotton[J]. Acta Agron Sin, 2007, 33(11): 1755 -1762 .
[6] WANG Chun-Mei;FENG Yi-Gao;ZHUANG Li-Fang;CAO Ya-Ping;QI Zeng-Jun;BIE Tong-De;CAO Ai-Zhong;CHEN Pei-Du. Screening of Chromosome-Specific Markers for Chromosome 1R of Secale cereale, 1V of Haynaldia villosa and 1Rk#1 of Roegneria kamoji[J]. Acta Agron Sin, 2007, 33(11): 1741 -1747 .
[7] Zhao Qinghua;Huang Jianhua;Yan Changjing. A STUDY ON THE POLLEN GERMINATION OF BRASSICA NAPUS L.[J]. Acta Agron Sin, 1986, (01): 15 -20 .
[8] ZHOU Lu-Ying;LI Xiang-Dong;WANG Li-Li;TANG Xiao;LIN Ying-Jie. Effects of Different Ca Applications on Physiological Characteristics, Yield and Quality in Peanut[J]. Acta Agron Sin, 2008, 34(05): 879 -885 .
[9] ZHENG Tian-Qing;XU Jian-Long;FU Bing-Ying;GAO Yong-Ming;Satish VERUKA;Renee LAFITTE;ZHAI Hu-Qu;WAN Jian-Min;ZHU Ling-Hua;LI Zhi-Kang. Preliminary Identification of Genetic Overlaps between Sheath Blight Resistance and Drought Tolerance in the Introgression Lines from Directional Selection[J]. Acta Agron Sin, 2007, 33(08): 1380 -1384 .
[10] YANG Yan;ZHAO Xian-Lin; ZHANG Yong;CHEN Xin-Min;HE Zhong-Hu;YU Zhuo;XIA Lan-Qin
. Evaluation and Validation of Four Molecular Markers Associated with Pre-Harvest Sprouting Tolerance in Chinese Wheats[J]. Acta Agron Sin, 2008, 34(01): 17 -24 .
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