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Acta Agronomica Sinica ›› 2026, Vol. 52 ›› Issue (1): 316-328.doi: 10.3724/SP.J.1006.2026.51043

• RESEARCH NOTES • Previous Articles    

Phenotypic characterization and transcriptomic analysis of the semi-dwarf mutant sd3 in Tartary buckwheat

Liu Di1(), Li Rui-Yuan2, Shi Mao-Zhu1, Li Hong-You1, Chen Qing-Fu1, Shi Tao-Xiong1,*()   

  1. 1College of Life Sciences, Guizhou Normal University / Guizhou Buckwheat Engineering Technology Research Center, Guiyang 550025, Guizhou, China
    2Key Laboratory of Information and Computing Science of Guizhou Province, Guizhou Normal University, Guiyang 550025, Guizhou, China
  • Received:2025-05-05 Accepted:2025-09-11 Online:2026-01-12 Published:2025-09-19
  • Contact: *E-mail: shitaoxiong@gznu.edu.cn
  • Supported by:
    National Natural Science Foundation of China(32260489);China Agriculture Research System of MOF and MARA(CARS-07-A5);Guizhou Provincial Key Laboratory of Biology and Breeding for Specialty Crops(QKHPT ZSYS [2025] 026)

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Abstract:

Plant height is a key agronomic trait in Tartary buckwheat, closely associated with lodging resistance, photosynthetic efficiency, and yield formation. Dwarfism is generally advantageous for enhancing lodging resistance and thereby improving yield. To explore dwarf stem gene resources, and to provide a theoretical basis for understanding plant height development and its application in breeding, we conducted phenotypic characterization and transcriptomic analysis of the semi-dwarf mutant sd3, previously generated through EMS mutagenesis. The results showed that compared with the wild type, the plant height of the sd3 at the mature stage reduced 28.43%, and the number of nodes on the main stem decreased by 44.44%. The reduction in node number was the primary cause of the dwarfism in sd3. Cytological observations revealed enhanced lateral cell division at the stem nodes in sd3, which has led to significantly thickened stem walls and an increased basal internode diameter. sd3 is sensitive to gibberellin, and exogenous GA3 can restore its phenotype. Transcriptome analysis identified 3067 differentially expressed genes (DEGs), GO and KEGG pathway enrichment revealed 57 genes potentially involved in regulating plant height. Notably, GID1 in the gibberellin signaling pathway was upregulated in sd3, while GID2, UNE10, and PIF1 were downregulated, suggesting these genes may play a key role in the dwarf phenotype of sd3. Overall, our findings provide preliminary insights into the dwarfing mechanisms of sd3 and offer valuable candidate genes for breeding lodging-resistant varieties and improving plant architecture through genetic approaches.

Key words: Tartary buckwheat, semi-dwarf mutant, phenotype identification, transcriptome, differential expression gene

Table 1

Primer sequences used in this study"

基因ID
Gene ID		 正向引物序列
Forward primer sequence (5′-3′)		 反向引物序列
Reverse primer sequence (5′-3′)
FtActin GAGTTATGAGCTTCCTGATG CCGCCACTCAACACAATGTT
FtPinG0006532300.01 TCGGACCAATCAACTCTGCT AACCCACCACAAGAACCCAA
FtPinG0000484500.01 AGTCCAGAAACCAAGCCACA AAACTGGGAAGCAAGGGGAC
FtPinG0001040500.01 ACGATCTATGACGGACGACA GGCATGATTCTCCGTTCTCC
FtPinG0004976300.01 CGCACCACCAAACTCAGAGT GCTCGAATCCACCACAGTCA
FtPinG0006346100.01 GGAGTGCGATAATGGCTGGA ACTCCTCCTTCACCAACTCG
FtPinG0009574600.01 ACAACAGGGTGGGAAAGTGA CGTCGTGCCAAAAACCCTAC
FtPinG0001225500.01 CGTGTCACCAAACCCATTCG GTCGTGAATCCGCTCTCCTT
FtPinG0009795500.01 AGGGTGGAAGGGTGAAGACT TGGAATCAAGCAAAAGCGCA

Fig. 1

Differences in plant height-related traits between the semi-dwarf mutant sd3 and WT of Tartary buckwheat (A): phenotypes of sd3 and WT in seedling stage (left) and mature stage (right); (B): plant height; (C): main stem nodes; (D): internode length; (E): internode thickness. * and ** indicate significant difference of the same trait between wild type and sd3 at the 0.05 and 0.01 levels, respectively. Scale bar = 5.0 cm."

Table 2

Statistical analysis of grain traits in sd3 and WT of Tartary buckwheat"

基因型
Genotype		 千粒重
Thousand grain weight (g)		 粒长
Grain length (mm)		 粒宽
Grain width (mm)		 籽粒长宽比
Grain length to width ratio		 籽粒面积
Grain area
(mm2)		 籽粒周长
Grain perimeter (mm)		 单株粒重
Grain weight per plant (g)
sd3 15.89±1.11** 3.72±0.09** 3.31±0.07 1.13±0.01** 9.07±0.36** 11.68±0.30** 3.17±0.54
WT 17.76±0.90 4.13±0.08 3.33±0.03 1.24±0.02 9.72±0.22 12.21±0.17 4.53±1.15

Fig. 2

Cell morphology of the second internode in the semi-dwarf mutant sd3 and wild type (WT) of Tartary buckwheat (A): cell morphology of the second internode in transverse section; (B): cell morphology of the second internode in longitudinal section; (C): cell length statistics in longitudinal section; (D): cell width statistics in longitudinal section. ** indicates a significant difference between WT and sd3 in the same trait at P < 0.01. Scale bar = 100 μm."

Fig. 3

Effects of different exogenous hormones on plant height and number of main stem nodes in the seme-dwarf mutant sd3 and wild type (WT) GA3: gibberellins; IAA: indole-3-acetic acid; BR: brassinosteroids. * and ** indicate a significant phenotypic difference of the same genotype between H2O and hormones treatments at P < 0.05 and P < 0.01, respectively."

Table 3

Quality statistics of transcriptome sequencing data"

样品
Sample		 原始测序数据
Raw reads		 过滤后的数据
Clean reads		 Q20 (%) Q30 (%) GC含量
GC content (%)		 比对率
Mapped ratio (%)		 表达基因
Expressed genes
WT-1 18,538,986 17,995,672 98.59 95.50 45.45 95.79 22,277
WT-2 29,682,745 28,905,875 98.67 95.77 45.66 95.40 22,461
WT-3 26,856,615 26,208,150 98.79 96.15 45.52 96.15 22,496
sd3-1 25,628,759 25,093,875 98.93 96.56 44.37 96.08 22,990
sd3-2 25,228,748 24,594,866 98.74 95.97 45.51 96.03 22,233
sd3-3 33,559,767 32,565,576 98.70 95.88 45.55 96.06 22,404

Fig. 4

Volcano plot of differentially expressed gene between the semi-dwarf mutant sd3 and wild type (WT) of Tartary buckwheat Red indicates genes with up-regulated expression, blue indicates genes with down-regulated expression, and gray dots indicate genes without significant expression differences. -log10 (FDR): the negative logarithm of the false discovery rate based on 10; log2 (FC): the logarithm of the fold change based on 2."

Fig. 5

Top 20 KEGG-enriched pathways of DEGs between sd3 and WT"

Fig. 6

qRT-PCR validation of the eight genes related to plant hormone signal transduction (A): qRT-PCR validation of the eight genes related to plant hormone signal transduction; (B): correlation analysis between qRT-PCR and RNA-seq. * and ** indicate a significant difference between WT and sd3 at P < 0.05 and P < 0.01, respectively."

Fig. 7

Heatmap of gene expression in the gibberellin signaling pathway"

Table 4

Differentially expressed genes with synonymous or non-synonymous SNP/InDel variations identified in the gibberellins signal pathway"

基因ID
Gene ID		 基因名称
Gene name		 染色体
Chromosome		 外显子
Exon		 突变/核苷酸
Mutation/nucleotide		 突变/蛋白质
Mutation/protein
FtPinG0003219000.01 GID1 Ft3 exon1 c.A1008G p.V336V
FtPinG0000281400.01 UNE10 Ft1 exon2 c.96_97del p.M32fs
exon2 c.798_798del p.R266fs
exon3 c.655_655del p.D219fs
FtPinG0004174900.01 PIF1 Ft3 exon3 c.G362A p.G121E
exon7 c.C1165T p.P389S
exon7 c.C1120T p.R374C
FtPinG0004976300.01 PIF1 Ft1 exon4 c.861_861del p.R287fs
exon7 c.1398_1398del p.P466fs
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