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Acta Agronomica Sinica ›› 2018, Vol. 44 ›› Issue (11): 1621-1630.doi: 10.3724/SP.J.1006.2018.01621

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Identification and Gene Mapping of sdb1 Mutant with a Semi-dwarfism and Bigger Seed in Rice

Yi-Ran TAO,Yu-Zhen XIONG,Jia XIE,Wei-Jiang TIAN,Xiao-Qiong ZHANG,Xiao-Bo ZHANG,Qian ZHOU,Xian-Chun SANG,Xiao-Wen WANG()   

  1. Basic Experiment Teaching Center of Agronomy / College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
  • Received:2018-03-09 Accepted:2018-07-20 Online:2018-11-12 Published:2018-08-07
  • Contact: Xiao-Wen WANG E-mail:xwwang78@126.com
  • Supported by:
    This study was supported by the Chongqing Research Program of Basic Research and Frontier Technology(cstc2015jcyjA80008);the Project of Chongqing Science & Technology Commission Grants(cstc2016shms- ztzx8007);the Project of Chongqing Science & Technology Commission Grants(cstc2017shms-xdny80057);the College Students’ Innovation and Entrepreneurship Training Scientific Research Project(201710635043)

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Abstract:

Moderate dwarfing is conducive to improving the lodging resistance of rice and further affecting its yield and quality, which is one of the important alternatives in rice breeding. Therefore, it is of great significance to study the molecular mechanism of shortened stem formation. In order to identify new dwarf resources and to explore the molecular regulation mechanism of plant height formation, a semi-dwarf and bigger seed (sdb1) mutant was identified from the progeny of indica restorer line Jinhui 10 with seed treated by ethyl methane sulfonate (EMS). This paper performed systematic studies in phenotypic identification, cytological observation, genetic analysis and gene mapping. At maturity stage, the plant height of sdb1 was only 76.66 cm, significantly shorter than 117.43 cm of wild type, resulting in a 34.72% decrease. It was found from the paraffin sections of the stem that the mutant had no significant change in stem cell length compared with the wild-type cells, it reduced cell width caused significantly smaller cell size, and the number of lateral cells significantly increased. The decrease of longitudinal cells should be the major cause of sdb1 semi-dwarfism. In addition to reduced plant height of sdb1, another typical mutational trait was the larger grain size, the 1000-grain weight increased from wild-type’s 24.83 g to mutant’s 29.00 g, reaching an extremely significant difference. The number of parenchyma cells increased from 666.30 in WT to 813.21 in sdb1, with an increase of 22.05%. The increase of cell number resulted in a significant increase of grain length, width and thickness. The mutant also had increased number of sdb1 mesophyll cells, resulting in significantly higher photosynthetic pigment content than wild type, and dark green leaves. Genetic analysis showed that a recessive nuclear gene regulated the mutant phenotype. Based on the F2 recessive plants of Zhonghua 11/sdb1, the gene was finally mapped between markers RM16632 and J50-7 on chromosome 4, with a physical distance of 406 kb. This research lays a foundation for gene cloning and function research, and is conducive to further understanding the genetic model of rice plant height, which has the potential value for agricultural production research.

Key words: rice (Oryza sativa L.), dwarfism, bigger seeds, gene mapping, sdb1

Table 1

Primer sequences used for gene mapping"

引物名称
Primer name		 上游引物序列
Upstream primer sequence (5'-3')		 下游引物序列
Downstream primer sequence (5'-3')
J50-3 TGCCTCCTTGTGTGTGGAGT TCCAAGCACTGACTTCATAGC
J50-2 CCACCAGTGATCCCTCATACA TCCGAGCGATTCTACTGGTC
J50-7 CCTCGTGTGGAATCTCGTTC GTAACAGTAGGTGCGAAGATGG
J50-53 GCGTTGTGTGCTCACTGG CCACTTGTCAGGTCTCCATC
J50-65 CCGGACGAGCCAATCAG CGGTGGCTTCTCCCAAGG

Fig. 1

Plant phenotype detection of wild type (WT) and sdb1 mutant A: phenotype of the wild type and the sdb1 at the seedling stage, Bar=5 cm; B: phenotype of the wild type and the sdb1 at the heading stage, Bar=10 cm; C: phenotype of the wild type and the sdb1 at the filling stage, Bar=15 cm; D: internodes of the wild type and the sdb1 at the filling stage, Bar=5 cm; E: panicle of the wild type and the sdb1 at the filling stage, Bar=5 cm; F: statistical analysis of panicle and internodes length of the wild type and the sdb1. **Significantly different at P<0.01."

Fig. 2

Stems paraffin sections of the wild type (WT) and sdb1 mutantA and B: longitudinal section of internodes of the wild type and the sdb1, Bar=100 μm; C: enlarged views of the red box in A, Bar=100 μm; D: enlarged views of the red box in B, Bar=100 μm; E:statistics of the cells number of the wild type and the sdb1 in the same area of longitudinal section; F: comparison of the cells size of the wild type and the sdb1 in longitudinal section; G and H: statistics of the cell length and width of the wild type and the sdb1in longitudinal section; I and J: gross section of internodes of the wild type and the sdb1, Bar=100 μm; K: enlarged views of the red box in I, Bar=25 μm; L: enlarged views of the red box in J, Bar=25 μm; M: enlarged views of the black box in I, Bar=50 μm; N: enlarged views of the black box in J, Bar=50 μm; O: statistics of the cells number of the wild type and the sdb1 in the same area of cross section; P:comparison of the cells size of the wild type and the sdb1 in cross section. **Significantly different at P < 0.01."

Fig. 3

Comparison of the grains between the wild-type and the sdb1 mutant A: grains of WT and the sdb1, Bar=0.5 cm; B and C: cross section of the grains of WT and the sdb1, Bar=500 μm; D: enlarged views of the red box in B, Bar=50 μm; E: enlarged views of the red box in C, Bar=50 μm; F: statistical chart of 1000-grain weight of WT and the sdb1; G and H: statistical chart of cell length (G), width (H) and thickness (H) of WT and the sdb1; I: statistical the number of parenchyma cells of WT (B) and the sdb1 (C). **Significantly different at P < 0.01."

Fig. 4

Frozen sections and photosynthetic pigment contents at flowering stage A: the middle of flag leaf of the wild type (WT) and the mutant sdb1 at heading stage; B and C: frozen section of crosscutting leaf of the wild type and the mutant sdb1, Bar=50 μm; D: chlorophyll content of the flag leaf blade; E:chlorophyll content of the second leaf from the top; F: chlorophyll content of the third leaf from the top; Chl a: chlorophyll a; Chl b: chlorophyll b; Car: carotenoid. **Significantly different at P<0.01; *Significantly different at P<0.05."

Fig. 5

Molecular mapping of SDB1 gene on rice chromosome 4"

Table 2

RGAP annotated genes encoding expressed and functional proteins in the restricted region of SDB1 locus"

基因名称
Locus name		 基因注释
Gene annotation
LOC_Os04g23170 Expressed protein
LOC_Os04g23180 Cation efflux family protein, putative, expressed
LOC_Os04g23200 Expressed protein
LOC_Os04g23210 Expressed protein
LOC_Os04g23220 Expressed protein
LOC_Os04g23230 Expressed protein
LOC_Os04g23319 Expressed protein
LOC_Os04g23330 Expressed protein
LOC_Os04g23420 Expressed protein
LOC_Os04g23440 Helix-loop-helix DNA-binding domain containing protein, expressed
LOC_Os04g23460 Expressed protein
LOC_Os04g23550 Basic helix-loop-helix family protein
LOC_Os04g23580 Xylosyltransferase, putative, expressed
LOC_Os04g23600 D-mannose binding lectin family protein, expressed
LOC_Os04g23610 Expressed protein
LOC_Os04g23620 D-mannose binding lectin family protein, expressed
LOC_Os04g23630 Expressed protein
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