Scientia Agricultura Sinica ›› 2025, Vol. 58 ›› Issue (17): 3372-3388.doi: 10.3864/j.issn.0578-1752.2025.17.002

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

Identification of Dwarf Genes and Mining of Plant Height Genetic Loci in Shanxi Wheat

XIANG AiHui1,2(), BAI RongJi2(), HAO YuQiong1, ZHAO JiaJia1, WU BangBang1, LI XiaoHua1, ZHENG XingWei1, GUAN PanFeng3,*(), ZHENG Jun1,2,*()   

  1. 1 Institute of Wheat Research, Shanxi Agriculture University/Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Linfen 041000, Shanxi
    2 College of Agriculture, Shanxi Agricultural University, Taigu 030801, Shanxi
    3 School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001
  • Received:2025-03-06 Accepted:2025-05-01 Online:2025-09-02 Published:2025-09-02
  • Contact: GUAN PanFeng, ZHENG Jun

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Abstract:

【Objective】Dwarf genes play a crucial role in wheat genetics and breeding. Different ecological zones and wheat varieties have varying requirements for plant height. Therefore, understanding the distribution pattern and characteristics of dwarf genes in Shanxi wheat, as well as identifying novel genetic loci related to plant height will contribute to wheat genetic improvement.【Method】Based on the accurate identification of plant height and component traits, a total of 11 known dwarfing gene types were genotyped in 306 Shanxi wheat samples and integrated with a 16K SNP chip to conduct genome-wide association analysis aimed at identifying new loci controlling plant height.【Result】With the exception of spike length, both of the plant height and component traits of Shanxi wheat exhibited a gradual decline over the years of breeding and the various compositional traits associated with plant height were influenced by distinct selection pressures. The distribution frequency of 11 dwarfing genes in Shanxi wheat from high to low was Rht12, Rht24, Rht8, Rht26, Rht13, Rht25, Rht2, Rht5, Rht4, Rht1, and Rht9, among which Rht1, Rht2, and Rht25 have not been found in landraces. Except for Rht2 and Rht25 is more widely distributed in irrigated cultivars than in dryland cultivars, the distribution of other dwarfing genes is relatively similar in dryland cultivars and irrigated cultivars. A total of 125 different dwarf genes combination were identified, of which the combination with the highest distribution frequency was Rht8+Rht12+Rht24. Combined with association analysis, a total of 26 stable genetic loci were identified to be distributed on 14 chromosomes including 1A, 2A, and 2B. Notably, eight loci such as QPH-6D, QPH-7A, and Q3rd IL-1D have not been reported yet. Among these, QPH-6D mainly reduced plant height by shortening the length of the third and fourth internodes by approximately 13.68 %, while QPH-7A reduced the plant height by 16.87 % via shortening the length of the second and third internodes.【Conclusion】The main dwarf genes in Shanxi wheat were mainly Rht12, Rht24, and Rht8. 26 stable genetic loci were located on chromosomes 1A, 2A, and 2B, among which eight loci such as QPH-6D, QPH-7A, and Q3rd IL-1D may be novel loci related to plant height.

Key words: Shanxi wheat, plant height, compositional traits, dwarf gene, genome-wide association study

Table 1

Molecular marker and its primer sequences of different dwarfing genes"

基因 Gene 标记 Marker 引物序列 Primer sequence (5′-3′) 参考文献 References
Rht4 WMS317-F TGCTAGCAATGCTCCGGGTAAC [32]
WMS317-R TCACGAAACCTTTTCCTCCTCC
Rht5 BARC102-F GGAGAGGACCTGCTAAAATCGAAGACA [33]
BARC102-R GCGTTTACGGATCAGTGTTGGAGA
Rht8 WMC503-F GCAATAGTTCCCGCAAGAAAAG [34]
WMC503-R ATCAACTACCTCCAGATCCCGT
Rht9 BARC151-F TGAGGAAAATGTCTCTATAGCATCC
BARC151-R CGCATAAACACCTTCGCTCTTCCACTC
Rht12 WMS291-F CATCCCTACGCCACTCTGC [35]
WMS291-R AATGGTATCTATTCCGACCCG
Rht13 WMS577-F ATGGCATAATTTGGTGAAATTG [36]
WMS577-R TGTTTCAAGCCCAACTTCTATT
Rht25 PlzAR1 GAGGCAGCAAAAGTGGAAGG [7]
PlzAF2 CTGTATATGCATGTGTGTCTC
Rht26 KASP518-A GAAGGTGACCAAGTTCATGCTAGTGCCCACTACCGGTTCG [20]
KASP518-B GAAGGTCGGAGTCAACGGATTAGTGCCCACTACCGGTTCA
KASP518-C GGATTGGAAAAGTGACCCGC

Table 2

Phenotypic analysis of plant height and component traits of different types of varieties"

性状
Trait		 环境
Env.		 地方品种Landrace 育成品种<BOLD>C</BOLD>ultivar 旱地品种Dryland cultivar 水地品种Irrigated cultivar 总计Total
变幅
Range		 均值
Mean		 变异系数
CV (%)		 变幅
Range		 均值
Mean		 变异系数
CV (%)		 变幅
Range		 均值
Mean		 变异系数
CV (%)		 变幅
Range		 均值
Mean		 变异系数
CV (%)		 变幅
Range		 均值
Mean		 变异系数
CV (%)
株高
PH
(cm)		 E1 103.20-160.80 131.63 8.90 66.20-165.60 93.36** 17.82 66.94-165.60 98.44 17.73 66.20-139.60 88.76** 16.19 66.20-165.60 97.72 20.69
E2 87.40-151.20 133.24 11.23 60.40-163.20 86.78** 20.24 62.18-163.20 91.63 19.94 60.40-138.60 82.41** 19.09 60.40-163.20 92.62 24.98
E3 87.00-156.60 131.20 13.70 61.40-148.80 89.19** 20.85 61.90-148.80 93.21 20.88 61.40-148.40 85.47** 19.81 61.40-156.60 94.42 24.50
E4 85.20-158.20 133.80 13.31 57.60-161.90 89.60** 20.10 68.46-161.90 94.86 19.48 57.60-147.00 84.84** 19.06 57.60-161.90 95.16 24.37
BLUP 86.56-148.80 129.40 12.35 64.98-158.51 89.92** 18.50 68.27-158.51 94.61 18.25 64.98-140.51 85.73** 17.32 64.98-158.51 95.09 22.35
穗长
SL
(cm)		 E1 5.54-12.04 7.99 16.55 6.40-13.00 9.07** 12.29 6.40-12.48 9.21 11.56 6.46-13.00 8.95 12.85 5.54-13.00 8.95 13.29
E2 4.56-15.38 8.66 24.71 5.64-12.72 8.78 12.76 6.74-11.74 8.93 11.56 5.64-12.72 8.64* 13.68 4.56-15.38 8.76 14.71
E3 5.42-11.20 7.88 15.02 5.76-12.48 9.00** 12.35 6.12-12.04 9.13 12.00 5.76-12.48 8.89 12.54 5.42-12.48 8.87 13.30
E4 5.24-14.54 8.23 20.58 6.36-13.18 8.83** 12.56 6.38-12.22 9.00 11.14 6.36-13.18 8.68* 13.67 5.24-14.54 8.76 13.84
BLUP 5.90-14.08 8.38 18.75 6.34-12.17 8.93** 10.13 6.92-10.90 9.05 8.89 6.34-12.17 8.82* 11.08 5.90-14.08 8.86 11.63
穗叶距
DSL
(cm)		 E1 8.60-33.38 25.11 18.98 4.76-36.10 13.67** 37.04 5.86-27.42 14.77 36.16 4.76-36.10 12.68** 36.14 4.76-36.10 14.97 41.45
E2 5.72-38.46 25.31 25.00 3.52-32.86 13.55** 42.11 4.78-30.04 14.76 40.50 3.52-32.86 12.47** 41.93 3.52-38.46 15.03 46.41
E3 11.44-35.14 23.37 23.44 3.00-30.40 13.34** 41.27 3.00-30.4 14.52 39.30 3.24-28.24 12.24** 41.61 3.00-35.14 14.59 43.99
E4 5.58-38.22 24.57 27.42 3.44-32.46 14.04** 40.71 4.60-29.68 15.38 38.10 3.44-32.46 12.86** 41.20 1.58-38.22 15.37 44.30
BLUP 4.25-33.02 23.34 24.54 5.26-31.82 13.74** 36.64 5.63-26.82 14.88 35.15 5.26-31.82 12.74** 36.34 4.25-33.02 15.00 40.40
穗下节
间长度
UIL
(cm)		 E1 30.68-52.66 45.49 10.79 19.80-55.90 31.84** 19.92 21.72-49.54 33.46 19.46 19.80-55.90 30.38** 19.11 19.80-55.90 33.40 22.65
E2 32.72-59.58 43.85 14.01 18.16-54.88 30.53** 22.71 18.88-49.98 32.21 21.74 18.16-54.88 29.04** 22.47 18.16-59.58 32.21 25.26
E3 28.32-56.80 43.33 14.37 18.74-53.44 31.45** 21.00 22.10-53.44 32.80 20.30 18.74-49.54 30.19** 20.89 18.74-56.80 32.93 23.19
E4 29.02-58.18 43.85 15.21 19.06-53.22 31.60** 22.16 19.58-53.22 33.55 21.76 19.06-51.88 29.84** 20.80 19.06-58.18 33.14 24.30
BLUP 31.25-52.19 42.87 12.33 20.44-50.54 31.46** 19.38 22.36-47.92 33.03 18.77 20.44-50.54 30.07** 18.79 20.44-52.19 32.95 21.61
第2节
间长度
2nd IL		 E1 22.48-38.78 33.49 10.81 14.56-39.74 23.87** 19.74 15.96-39.74 25.41 19.10 14.56-37.26 22.47** 18.32 14.56-39.74 24.97 22.12
E2 21.44-41.34 32.82 16.60 14.74-38.08 22.66** 20.26 14.74-38.08 23.92 20.20 14.84-35.22 21.54** 18.84 14.74-41.34 23.94 24.16
E3 20.78-41.82 34.59 14.49 9.48-38.78 22.96** 22.66 13.74-38.78 24.18 22.33 9.48-35.76 21.83** 21.78 9.48-41.82 24.41 26.40
E4 20.26-45.88 34.59 18.25 13.06-41.44 23.07** 21.10 14.14-41.44 24.73 20.63 13.06-34.62 21.57** 19.01 13.06-45.88 24.52 25.88
BLUP 20.94-40.41 32.80 15.29 15.39-37.35 23.19** 19.30 15.39-37.35 24.57 18.88 15.46-34.48 21.94** 17.90 15.39-40.41 24.44 22.83
第3节
间长度
3rd IL
(cm)		 E1 14.88-26.32 21.84 14.67 8.02-31.58 13.69** 22.80 9.62-31.58 14.49 22.47 8.02-20.62 12.96** 21.71 8.02-31.58 14.62 27.78
E2 13.46-25.56 20.75 17.63 7.46-32.20 12.39** 24.79 8.52-32.20 13.00 25.84 7.46-23.34 11.84** 22.66 7.46-32.20 13.44 31.21
E3 11.22-30.78 22.44 22.15 5.44-26.55 13.05** 27.76 7.50-25.90 13.56 28.23 5.44-26.55 12.58* 26.74 5.44-30.78 14.22 34.54
E4 11.72-30.08 21.43 21.24 6.32-31.20 13.13** 24.54 8.84-31.20 13.91 24.75 6.32-25.94 12.41** 22.81 6.32-31.20 14.17 30.93
BLUP 12.88-26.12 21.77 14.15 8.88-29.44 13.12** 21.87 9.57-29.44 13.78 22.10 8.88-21.90 12.54** 20.55 8.88-29.44 14.25 28.83
第4节
间长度
4th IL
(cm)		 E1 8.82-17.90 14.15 15.86 5.48-22.24 9.45** 25.94 6.00-22.24 10.02 25.70 5.48-15.68 8.92** 24.86 5.48-22.24 9.99 28.54
E2 5.84-17.00 12.82 21.48 3.38-19.84 8.15** 28.37 4.54-19.84 8.64 29.04 3.38-14.00 7.70** 26.38 3.38-19.84 8.74 32.39
E3 8.36-20.54 14.49 23.06 1.45-20.38 8.66** 31.42 4.36-16.94 9.11 30.76 1.45-20.38 8.24** 31.41 1.45-20.54 9.39 36.21
E4 7.28-22.93 13.56 24.31 4.06-19.02 8.59** 26.92 4.06-19.02 9.15 27.58 4.34-15.70 8.07** 24.48 4.06-22.93 9.22 32.07
BLUP 8.30-17.88 13.15 16.82 5.51-17.69 8.76** 22.65 6.45-17.69 9.24 22.53 5.51-14.91 8.33** 21.55 5.51-17.88 9.34 26.76
第5节
间长度
5th IL
(cm)		 E1 4.42-14.16 8.93 25.47 1.23-14.76 5.15** 38.39 2.25-14.76 5.47 38.90 1.23-11.15 4.86* 36.74 1.23-14.76 5.58 42.01
E2 2.07-11.78 7.38 30.75 1.50-13.98 4.18** 41.08 1.50-13.98 4.43 43.70 1.50-9.26 3.96* 37.14 1.50-13.98 4.59 45.50
E3 3.70-14.44 9.14 33.32 0.35-15.08 4.43** 49.19 0.35-10.96 4.53 48.47 0.35-15.08 4.35* 49.67 0.35-15.08 5.03 55.44
E4 2.66-15.68 7.69 40.19 1.15-12.74 4.48** 39.73 1.15-12.74 4.77 41.00 1.20-12.02 4.22* 37.12 1.15-15.68 4.89 46.18
BLUP 3.94-11.93 7.64 23.84 2.13-11.08 4.61** 28.03 2.74-11.08 4.81 29.06 2.13-10.04 4.44* 26.24 2.13-11.93 5.01 34.12

Fig. 1

Classification of plant height and evolution characteristics of plant height composition traits of wheat in Shanxi A:Shanxi wheat plant height polymorphism; B: Classification of plant height of Shanxi Wheat Varieties; C-J: Plant height and plant height composition traits phenotypes and the percentage of plant height composition traits in plant height.Yellow dots and solid lines indicate the percentage of plant height composition traits in plant height and its trend, and blue dots and dashed lines indicate trait phenotypic values and their trends; K: Analysis of the percentage of plant height composition traits in plant height for different types. SL: Spike length; DSL: Distance from base of the spike to the flag leaf ligule; UIL: Uppermost internode length; 2nd IL: 2nd internode length; 3rd IL: 3rd internode length; 4th IL: 4th internode length; 5th IL: 5th internode length. PH: Plant height. ***: Significant difference at 0.001. The same as below"

Fig. 2

Detection results of dwarf genes in some varieties A: Detection result of dwarfing gene Rht4; B: Detection result of dwarfing gene Rht5; C: Detection result of dwarfing gene Rht8; D: Detection result of dwarfing gene Rht9; E: Detection result of dwarfing gene Rht12; F: Detection result of dwarfing gene Rht13; G: Detection result of dwarfing gene Rht25; H: Rht26 gene KASP molecular marker genotyping results. A and C: A-CK: 02-38; C-CK: Xinong890; 1: Jinmai66; 2: Dahongmai; 3: Jinmai32; 4: Jinmai1; 5: Jinmai19; 6: Jinmai20; 7: Jinmai21; 8: Jinmai70; 9: Qisuimai. B, D and E: M: 50bp DNA Marker; B-CK: 06-6-5-3-4; D-CK: Xinong891; E-CK: 06-6-5-24; 1: Dahongmai; 2: Yulanmai; 3: Jinmai31; 4: Jinmai29; 5: Jinmai53; 6: Jinmai47; 7: Hongtumai; 8: Shunmai1718; 9: Hongxiaomai. F andG: M: 50bp DNA Marker; F-CK: Xinong887; G-CK: Nonglin10; 1: Yunhan20410; 2: Jinmai11; 3: Jinmai20; 4: Jinmai59; 5: Jinmai19; 6: Xianmai; 7: Hongxiaomai; 8: Dahongmai; 9: Baixianmai. + indicates the presence of a dwarf gene; -indicates the absence of dwarf gene"

Fig. 3

Distribution of dwarf genes and effect of number of dwarf genes on plant height A: A single dwarf gene is distributed in Shanxi wheat; B: Dwarf gene combinations are distributed in Shanxi wheat; C: Effect of thenumber of dwarf genes on plant height; D: The distribution frequency of dwarf genes in cultivar in different periods. Different letters indicate significant differences at P<0.05"

Table 3

QTL loci for plant height and composition traits"

性状
Traits		 QTL标记
QTL marker		 染色体
Chr.		 位置
Position (Mb)		 标记
Marker		 环境
Environment		 P值
<BOLD>P</BOLD> value (×10-5)		 表型贡献率
R2 (%)		 参考文献
References
株高
PH		 QPH-2A 2A 59.28-115.28 2A_87283474 E1, E2, E3, E4, BLUP 1.63-6.10 4.88-5.78 [52]
QPH-2D 2D 29.47-36.47 2D_32970833 E2, E4, BLUP 0.76-4.70 4.96-6.40 Rht8[6]
QPH-4A 4A 618.36-670.86 4A_644613024 E2, E4, BLUP 2.18-6.18 4.85-5.47 [53]
QPH-4B 4B 30.82-55.82 4B_48317177 E4 9.82 3.64 Rht1[3]
QPH-4D 4D 0.92-20.92 4D_10917137 E1 1.47 5.88 Rht2[3]
QPH-5A 5A 560.95-608.95 5A_608950417 E2, E3, E4, BLUP 1.14-4.30 5.12-6.21 Rht9[43]
QPH-6D 6D 387.78-392.08 6D_389928252 E2, E4, BLUP 1.72-7.30 3.56-6.75
QPH-7A 7A 682.23-702.23 7A_692232694 E1, E3, E4, BLUP 2.59-7.75 4.63-7.58
穗长SL QSL-1A 1A 12.22-16.72 1A_14467852 E2, E4, BLUP 0.80-5.88 5.18-6.34 [61]
穗叶距
DSL		 QDSL-5A 5A 318.46-336.24 5A_324460015 E1, E4, BLUP 0.31-8.95 4.62-6.99 [55]
QDSL-4D 4D 0.92-20.92 4D_10917137 E1 9.77 4.76 Rht2[3]
QDSL-6A 6A 76.49-129.49 6A_102993644 E3 1.04 5.22 Rht25[18]
穗下节间长度UIL QUIL-6A 6A 76.49-129.49 6A_102993644 E3 1.49 5.04 Rht25[18]
第2节间长度
2nd IL		 Q2nd IL-2D 2D 29.47-36.47 2D_32970833 E4 9.69 4.64 Rht8[6]
Q2nd IL-4B 4B 40.82-55.82 4B_48317177 E1, E2, E3, BLUP 1.10-3.92 4.26-4.99 Rht1[3]
Q2nd IL-7A 7A 682.23-702.23 7A_692232694 E1, E2, E3, E4, BLUP 1.17-6.66 4.76-6.17
第3节间长度
3rd IL		 Q3rd IL-1D 1D 262.94-274.14 1D_268540306 E1, E2, E4, BLUP 0.29-8.27 4.55-7.00
Q3rd IL-2A 2A 59.28-115.28 2A_87283474 E2, E4, BLUP 1.18-3.60 5.01-5.93 [46]
Q3rd IL-2B 2B 197.11-202.11 2B_202107777 E1, E2, BLUP 3.01-7.68 5.42-6.08 [58]
Q3rd IL-2D 2D 29.47-36.47 2D_32970833 E2, E4, BLUP 1.34-4.35 4.89-5.95 Rht8[6]
Q3rd IL-3B 3B 0-42.16 3B_10662726 E2 9.87 4.54 Rht5[57]
Q3rd IL-4B 4B 30.82-55.82 4B_48317177 E1, E4, BLUP 4.82-9.57 3.48-3.85 Rht1[3]
Q3rd IL-4D 4D 18.55-38.55 4D_28547729 E4 1.17 6.15 Rht2[3]
Q3rd IL.6A 6A 558.85-611.85 6A_585345446 E2, E4, BLUP 3.14-7.49 4.99-5.37 [59]
Q3rd IL-6D 6D 387.78-392.08 6D_389928252 E1, E2, E3, BLUP 4.35-7.25 3.77-5.04
Q3rd IL-7A 7A 682.23-702.23 7A_692232694 E2, E3, E4, BLUP 0.54-2.72 5.47-6.56
Q3rd IL-7B 7B 233.63-245.13 7B_239379204 E1, E4, BLUP 0.84-8.93 4.48-6.34 [62]
第4节间长度
4th IL		 Q4th IL-2A 2A 59.28-115.28 2A_87283474 E1, E2, BLUP 1.99-8.31 4.62-5.72 [46]
Q4th IL-2D 2D 29.47-36.47 2D_32970833 E2, E3, E4, BLUP 0.18-2.65 5.33-7.41 Rht8[6]
Q4th IL-3B 3B 9.28-72.28 3B_40776268 E4 2.05 5.50 Rht5[57]
Q4th IL-4B 4B 30.82-55.82 4B_48317177 E4 7.02 3.60 Rht1[3]
Q4th IL-4D 4D 18.55-38.55 4D_28547729 E4 2.00 5.57 Rht2[3]
Q4th IL-6D 6D 387.78-392.08 6D_389928252 E1, E2, BLUP 2.77-8.08 4.75-5.35
第5节间长度
5th IL		 Q5th IL-1B 1B 544.60-558.35 1B_546854696 E1, E4, BLUP 1.53-3.23 4.70-5.63 [60]
Q5th IL-2B 2B 419.99-429.99 2B_424009984 E1, E2, E4 1.87-8.05 4.52-5.34
Q5th IL-5A.2 5A 552.57-564.57 5A_558574163 E2 1.00 7.52 Rht9[54]
Q5th IL-5A.4 5A 687.64-699.64 5A_693635094 E3 8.38 5.02 Rht12[56]
Q5th IL-5D 5D 494.40-496.40 5D_495395359 E1, E2, E3, BLUP 0.05-2.11 5.24-5.67 [63]
Q5th IL-7A 7A 212.95-232.95 7A_222945332 E1, E4, BLUP 1.84-2.10 4.18-5.35 [4]

Fig. 4

Effect of QPH-6D and QPH-7A on plant height and constitutive traits A: Manhattan plot of genome-wide association analysis for plant height; B: Manhattan map of QPH-7A authenticated by GWAS; C: Manhattan map of QPH-6D authenticated by GWAS; D: QPH-7A distribution frequency; E: QPH-6D distribution frequency; F: Effect of QPH-7A on plant height and compositional traits; G: Effect of QPH-6D on plant height and compositional traits. E1, E2, E3, and E4 represent plant heights measured from Hongtong in 2022-2023, Hancun in 2022-2023, Hongtong in 2023-2024, and Hancun in 2023-2024, respectively; BLUP: best linear unbiased prediction. *, ** and *** indicate significant difference at the 0.05, 0.01 and0.001 probability levels; respectively. NS: No significant difference"

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