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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (7): 1954-1967.doi: 10.3724/SP.J.1006.2023.24185

• TILLAGE & CULTIVATION·PHYSIOLOGY & BIOCHEMISTRY • Previous Articles     Next Articles

Relationship of “LabelmeP1.0”-derived vascular parameters with agronomic traits in sorghum

LU Meng-Qi1(), XIE Ruo-Han1(), LI Xiang2, YANG Ming-Chong1, HE Zi-Wei1, GAO Jie3, ZHAO Xiao-Yan3, SHEN Xiang-Ling4, CHEN Yan2, WANG Ji-Bin1,5, HU Li-Hua1, DUAN Ming-Zheng1,*(), WANG Ling-Qiang1,*()   

  1. 1State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources / Guangxi Key Laboratory of Sugarcane Biology / College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
    2School of Computer, Electronics and Information, Guangxi University, Nanning 530004, Guangxi, China
    3Guizhou Drought Grain Sorghum Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China
    4Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), China Three Gorges University, Yichang 443002, Hubei, China
    5Moutai Institute, Renhuai 564507, Guizhou, China
  • Received:2022-08-09 Accepted:2022-11-25 Online:2023-07-12 Published:2022-12-07
  • Contact: *E-mail: duanmingzheng@gxu.edu.cn; E-mail: lqwang@gxu.edu.cn E-mail:2117301031@st.gxu.edu.cn;ruohanxie@163.com;duanmingzheng@gxu.edu.cn;lqwang@gxu.edu.cn
  • About author:First author contact:**Contributed equally to this work
  • Supported by:
    The Guizhou Science and Technology Support Project(黔科合支撑[2020]1Y053号)

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Abstract:

Stem vascular bundle plays an important role in the mechanical supporting and material transportation of crops. To extract the vascular bundle parameters from the crop stem slices, we developed a high-throughput method “LabelmeP1.0”, which combined the image-annotation function of commercial software “Labelme” with the Python programming language. A total of 26 parameters including both the primary and secondary parameters related to stem regions and vascular bundles was generated in 92 sorghum germplasm resources. 15 parameters related to the number, size, location, proportion, and the density of vascular bundle were summarized as the core indexes by correlation analysis and principal component analysis. In addition, the number and the density of vascular parameters were positively related to agronomic traits including panicle weight, grain weight, and number of primary rachis branch. The germplasm resources could be divided into three categories, namely, class I with lower plant height, thicker stem, thinner rind, fewer seeds, and more vascular bundles, in contrast class II with higher plant height, thinner stems, fewer seeds and vascular bundles and, class III with lower plant height, thicker stem, more seeds and vascular bundles. This study provides the methodology and new ideas for the study of the stem anatomical parameters in crops.

Key words: sorghum, vascular bundles, anatomical structure, image processing

Table 1

Germplasm resources of this study"

序号
No.		 品种名称
Variety name		 来源
Source		 序号
No.		 品种名称
Variety name		 来源
Source
1 川糯粱1号 Chuannuoliang 1 中国四川Sichuan, China 47 RH7.1 中国贵州Guizhou, China
2 川糯粱2号 Chuannuoliang 2 中国四川Sichuan, China 48 V-9 中国贵州Guizhou, China
3 国窖1号 Guojiao 1 中国四川Sichuan, China 49 Q1 中国贵州Guizhou, China
4 红糯15 Hongnuo 15 中国四川Sichuan, China 50 Q14-3 中国贵州Guizhou, China
5 红缨子1号 Hongyingzi 1 中国四川Sichuan, China 51 Q15 中国贵州Guizhou, China
6 机糯粱2号 Jinuoliang 2 中国四川Sichuan, China 52 Q24 中国贵州Guizhou, China
7 金糯粱1号 Jinnuoliang 1 中国四川Sichuan, China 53 Q27 中国贵州Guizhou, China
8 金糯粱2号 Jinnuoliang 2 中国四川Sichuan, China 54 Q4-1 中国贵州Guizhou, China
9 金糯粱5号 Jinnuoliang 5 中国四川Sichuan, China 55 兴湘粱Xingxiangliang 中国湖南 Hunan, China
10 金糯粱6号 Jinnuoliang 6 中国四川Sichuan, China 56 K1781 中国吉林 Jilin, China
11 金糯粱9号 Jinnuoliang 9 中国四川Sichuan, China 57 糯3 Nuo 3 中国吉林 Jilin, China
12 晋杂34 Jinza 34 中国四川Sichuan, China 58 湘糯R Xiangnuo R 中国吉林 Jilin, China
13 辽甜1号 Liaotian 1 中国四川Sichuan, China 59 1269R 中国辽宁Liaoning, China
14 青壳洋1号 Qingkeyang 1 中国四川Sichuan, China 60 1791# 中国辽宁Liaoning, China
15 香谕糯3号 Xiangyunuo 3 中国四川Sichuan, China 61 85061R 中国辽宁Liaoning, China
16 宜糯红5号 Yinuohong 5 中国四川Sichuan, China 62 85063R 中国辽宁Liaoning, China
17 3410 中国四川Sichuan, China 63 LR622 中国辽宁Liaoning, China
18 10098 中国四川Sichuan, China 64 LR625 中国辽宁Liaoning, China
19 10121 中国四川Sichuan, China 65 剑LR Jian LR 中国辽宁Liaoning, China
20 19号 19 中国四川Sichuan, China 66 郑♂ 1 Zheng♂ 1 中国北方 North China
21 吨粮王 Dunliangwang 中国贵州Guizhou, China 67 Early sumac Sorgo 美国 America
22 红壳糯(矮)
Hongkenuo (dwarf)		 中国贵州Guizhou, China 68 HAGEENDYRA 美国 America
23 红缨子2号 Hongyingzi 2 中国贵州Guizhou, China 69 Hegari #750 美国 America
24 茅粱糯2号 Maoliangnuo 2 中国贵州Guizhou, China 70 IS-0114 美国 America
25 黔高7号 Qiangao 7 中国贵州Guizhou, China 71 IS-0170 美国 America
26 黔高8号 Qiangao 8 中国贵州Guizhou, China 72 IS-0223 美国 America
27 青壳洋2号 Qingkeyang 2 中国贵州Guizhou, China 73 IS-0508 美国 America
28 青选2号 Qingxuan 2 中国贵州Guizhou, China 74 IS-0829 美国 America
29 齐杂4号 Qiza 4 中国贵州Guizhou, China 75 IS-0835 美国 America
30 青1 Qing 1 中国贵州Guizhou, China 76 IS-0874 美国 America
31 青2 Qing 2 中国贵州Guizhou, China 77 IS-1159C 美国 America
32 青35 Qing 35 中国贵州Guizhou, China 78 IS-1166C 美国 America
33 8009 中国贵州Guizhou, China 79 IS-1291 美国 America
34 8039 中国贵州Guizhou, China 80 IS-1461 美国 America
35 125# 中国贵州Guizhou China 81 IS-2217 美国 America
36 260# 中国贵州Guizhou, China 82 IS-6439C 美国 America
37 2V-29 中国贵州Guizhou, China 83 IS-8337 美国 America
38 43# 中国贵州Guizhou, China 84 ICSB 51-1 印度 India
39 44# 中国贵州Guizhou, China 85 ICSB 51-2 印度 India
40 92-2V-50 中国贵州Guizhou, China 86 ICSB 55 印度 India
41 G2 中国贵州Guizhou, China 87 ICSB 56 印度 India
42 G216 中国贵州Guizhou, China 88 ICSH 11 印度 India
43 G752 中国贵州Guizhou, China 89 ICSH 12 印度 India
44 G8 中国贵州Guizhou, China 90 ICSH 15 印度 India
45 RH17.1 中国贵州Guizhou, China 91 ICSR 160 印度 India
46 RH28.2 中国贵州Guizhou, China 92 ICSV 1 印度 India

Table 2

Stem vascular bundle parameters generated by “LabelmeP1.0”"

序号
No.		 性状和参数
Trait and parameter		 说明
Description
一级参数Primary parameters
1 大维管束数目
Number of large vascular bundles (NLVB)		 labelme 导出的 json 文件中标为大维管束的轮廓总数
Number of contours labeled as large vascular bundles in json file
2 小维管束数目
Number of small vascular bundles (NSVB)		 labelme 导出的 json 文件中标为小维管束的轮廓总数
Number of contours labeled as small vascular bundles in json file
3 总维管束数目
Total number of vascular bundles (TNVB)		 大、小维管束数目之和
The number of LVB plus the number of SVB
4 大(小)维管束面积和
Total area of vascular bundles (TALVB or TASVB) *		 对多边形轮廓, 用cv2.contourArea()格林公式计算面积, 圆形轮廓以圆面积公式πr²计算面积, 最后加总
Total area of vascular bundles was the sum of the area of individual vascular bundle. Area of each LVB (polygon contour) was calculated by Cv2.ContourArea() Green’s formula, whereas the area of each SVB (circular contour) was calculated by the formula πr²
5 大(小)维管束平均面积
Area of vascular bundles (ALVB or ASVB)		 大(小)维管束面积和除以大(小)维管束数目
Total area of LVB (or SVB) divided by the number of LVB (or SVB), respectively
6 大(小)维管束中心
Vascular bundles point (LVBP or SVBP) *		 对多边形轮廓, 用cv2.minEnclosingCircle() 确定轮廓最小包围圆, 以该圆圆心为轮廓中心。圆形轮廓以圆心为轮廓中心
The central point of a circle determined by cv2.minEnclosingCircle() (LVB as the polygon contour) and the central point of a circle (SVB as circular contour)
7 大(小)维管束离心距
Vascular bundle distance (LVBD or SVBD)		 逐一计算大(小)维管束中心与茎中心的距离, 将所有距离加总后除以大(小)维管束数目
The mean values of the distance of the central point of LVB (or SVB) from the stem center point
8 茎直径Stem diameter (SD) 用cv2.minEnclosingCircle()确定茎轮廓的最小包围圆, 以该圆直径为茎直径
The diameter of a circle determined by cv2.minEnclosingCircle() (stem slice as the polygon contour)
9 茎中心Stem center point (SCP) * 用cv2.minEnclosingCircle()确定茎轮廓的最小包围圆, 以该圆圆心为茎中心
The central point of a circle determined by cv2.minEnclosingCircle() (stem slice as the polygon contour)
10 茎周长Stem circumference (SC) 用cv2.arcLength()计算封闭轮廓的周长
Perimeter of the stem (closed contour) was calculated with cv2.arcLength()
11 茎面积Stem area (SA) * 用cv2.contourArea()格林公式计算茎轮廓的面积
Area of stem (closed contour) was calculated with cv2.contourArea()
12 空腔面积Cavity area (CA) 用 cv2.contourArea()格林公式计算空腔轮廓的面积
Area of cavity (closed contour) was calculated with cv2.contourArea()
13 去腔茎面积SA-CA 茎面积减去空腔面积
Stem area minus cavity area
14 皮厚度Rind thickness (RT) 皮指外围厚壁组织, 下同。将大维管束最大离心距和小维管束最小离心距的平均视作内环半径, 茎半径减内环半径
Rind thickness was calculated as the stem semidiameter minus the r of the inner edge of rind. The r was estimated by the average of the maximal LVBD and the minimum SVBD.
15 内环面积Parenchyma area (PA) * 以圆面积计算公式πr²计算得到内环面积
Parenchyma area was calculated with πr²
16 皮面积Rind area (RA) 茎面积减去内环面积
Stem area minus parenchyma area
二级参数Secondary parameter
17 大维管束数目占比
Proportion of NLVB (%)		 大维管束数目占总维管束数目的百分比
Proportion of the number of LVB to the total number of vascular bundles (%)
18 大维管束面积占比
Proportion of TALVB (%)		 大维管束面积和占维管束总面积的百分比
Proportion of the total area of LVB to the total area of all vascular bundles (%)
19 大小维管束平均面积比值
ALVB/ASVB		 大维管束平均面积与小维管束平均面积之比
The ratio of the area of LVB to the area of SVB
20 大(小)维管束面积占茎比
Percentage of TALVB to (SA-CA) (%)		 大(小)维管束面积和占去腔茎面积的百分比
Percentage of the total area of LVB (or SVB) to the stem area (without cavity area) (%)
21 大维管束面积占内环比
Percentage of TALVB to (PA-CA) (%)		 大维管束面积和占内环面积(减空腔后)的百分比
Percentage of the total area of LVB to the parenchyma area (without cavity area) (%)
22 小维管束面积占皮比
Percentage of TASVB to RA (%)		 小维管束面积和占皮面积的百分比
Percentage of the total area of SVB to the rind area (%)
23 大(小)维管束相对离心距LVBD/ SD/2 大(小)维管束到茎中心的平均距离与茎半径的比值
Ratio of the distance of LVB (or SVB) to the stem semidiameter
24 小维管束“周长密度”NSVB/SC 小维管束数目除以茎周长
Number of SVB divided by the length of stem circumference
25 小维管束“面积密度”NSVB/RA 小维管束数目除以皮面积
Number of SVB divided by the rind area
26 大维管束“面积密度”NLVB/(PA-CA) 大维管束数目除以内环面积(减空腔后)
Number of LVB divided by the parenchyma area (without cavity area)
27 空腔面积占茎比
Percentage of CA to SA (%)		 空腔面积占茎面积的百分比
Percentage of the cavity area to stem area (%)

Table 3

Statistics of vascular bundle parameters and agronomic traits of sorghum germplasm resources"

性状和参数
Trait and parameter		 均值
Mean		 最小值
Min.		 最大值
Max.		 变异系数
CV (%)		 偏度
Skew.		 峰度
Kurt.
大维管束数目NLVB 209.4 89 390 32.5 0.4 -0.6
小维管束数目NSVB 173.5 65 282 29.0 0.0 -0.3
总维管束数目TNVB 382.9 163 672 29.8 0.3 -0.5
大维管束平均面积ALVB (mm2) 0.023 0.013 0.047 27.2 1.3 2.1
小维管束平均面积ASVB (mm2) 0.010 0.003 0.020 45.4 0.6 -0.6
大维管束离心距LVBD (mm) 3.5 2.1 5.2 18.4 0.3 0.1
小维管束离心距SVBD (mm) 4.5 2.9 7.0 17.5 0.4 0.4
茎直径SD (mm) 9.7 6.3 14.6 16.8 0.4 0.4
茎周长SC (mm) 29.6 19.2 45.0 17.1 0.4 0.4
空腔面积CA (mm2) 1.8 0.0 11.9 153.2 2.0 4.2
去腔茎面积SA-CA (mm2) 68.9 28.4 159.8 35.7 1.1 1.7
皮厚度RT (mm) 0.5 0.3 0.9 20.0 0.6 1.0
皮面积RA (mm2) 9.2 4.1 21.0 32.6 1.2 3.0
大维管束数目占比Proportion of NLVB (%) 54.5 43.8 65.2 8.2 -0.2 -0.2
大维管束面积占比Proportion of TALVB (%) 74.7 54.7 88.7 10.5 -0.5 -0.3
大小维管束平均面积比值ALVB/ASVB 2.7 1.5 5.3 37.2 0.8 -0.5
大维管束面积占茎百分比Percentage of ALVB to (SA-CA) (%) 7.2 4.3 11.5 24.7 0.5 -0.4
大维管束面积占内环百分比Percentage of TALVB to (PA-CA) (%) 7.6 4.6 12.2 24.3 0.5 -0.4
小维管束面积占茎百分比Percentage of TASVB to (SA-CA) (%) 2.6 0.8 7.1 52.7 0.9 0.3
小维管束面积占皮面积百分比Percentage of TASVB to RA (%) 19.8 5.9 44.2 56.7 0.5 -1.1
大维管束相对离心距2LVBD/ SD (%) 71.6 65.8 76.6 2.9 -0.3 -0.2
小维管束相对离心距2SVBD/ SD (%) 93.4 90.1 96.2 1.6 -0.2 -0.7
小维管束周长密度NSVB/SC(No. mm-1) 5.8 2.8 8.4 20.9 -0.4 -0.1
小维管束面积密度NSVB/RA(No. mm-2) 19.9 8.4 36.2 32.2 0.5 -0.1
大维管束面积密度NLVB/(PA-CA) (No. mm-2) 3.3 2.0 4.8 17.2 0.1 -0.1
空腔面积占茎百分比Percentage of CA to SA (%) 2.7 0.0 16.3 144.6 1.6 2.3
株高Plant height (cm) 161.5 71.0 278.0 27.8 0.5 -0.2
单株鲜重Plant fresh weight (g) 265.7 79.0 609.7 38.4 1.4 2.3
穗长Panicle length (cm) 25.9 8.7 41.0 19.9 -0.3 0.7
穗重Panicle weight (g) 54.6 10.2 194.6 72.7 1.7 2.7
一级枝梗数No. of primary rachis branches (NPRB) 50.1 27.8 90.8 26.2 1.1 1.2
千粒重1000-grain weight (g) 20.3 7.0 33.1 22.2 0.2 1.1

Fig. 1

Correlation analysis of the primary parameters of stem vascular bundles TALVB: total area of large vascular bundles; CA: cavity area; SA: stem area; LVBD: large vascular bundle distance; SD: stem diameter; NLVB: the number of large vascular bundles; TASVB: total area of small vascular bundles; RA: rind area. df = 90, r0.05 = 0.205."

Table 4

Principal component analysis (PCA) of vascular bundle parameters (27) in sorghum"

性状和参数
Traits and parameters		 PC1
(40.4%)*		 PC2
(21.8%)*		 PC3
(10.2%)*		 PC4
(8.4%)*		 PC5
(7.1%)*
大维管束数目NLVB 7.7 0.5 2.5 1.4 1.8
小维管束数目NSVB 7.7 0.2 2.0 1.4 1.9
总维管束数目TNVB 8.3 0.1 2.5 1.5 0
大维管束平均面积ALVB 4.9 0.2 9.6 0.1 0.1
小维管束平均面积ASVB 4.0 3.4 10.5 3.5 0.1
大维管束离心距LVBD 7.4 3.3 0.3 0.6 0.3
小维管束离心距SVBD 7.3 3.5 0.2 0.3 0.8
茎直径SD 7.1 4.0 0 0.1 0.8
茎周长SC 7.3 3.7 0.1 0.3 0.8
空腔面积CA 0.3 2.5 0.2 23.7 1.6
去腔茎面积SA-CA 7.4 3.1 0 0 1.3
皮厚度RT 0.1 4.3 9.4 7.9 0.1
皮面积RA 3.0 5.6 5.9 0.2 0.8
大维管束数目占比Proportion of NLVB 0.1 4.8 0 0 27.2
大维管束面积占比Proportion of TALVB 0.5 11.4 2.9 3.2 4.7
大小维管束平均面积比值ALVB/ASVB 0.9 7.6 3.6 4.9 0.1
大维管束面积占茎百分比Percentage of ALVB to (SA-CA) 4.8 1.2 2.4 1.0 14.0
大维管束面积占内环百分比Percentage of TALVB to (PA-CA) 4.5 1.2 3.1 1.1 14.7
小维管束面积占茎百分比Percentage of TASVB to (SA-CA) 2.0 10.3 5.0 1.0 0
小维管束面积占皮百分比Percentage of TASVB to RA 3.8 8.8 0.5 1.4 0
大维管束相对离心距2LVBD/SD 3.3 0 8.3 8.5 2.5
小维管束相对离心距2SVBD/SD 2.6 0.6 10.0 8.6 0.3
小维管束“周长密度”NSVB/SC 3.0 5.7 3.5 3.8 2.2
小维管束“面积密度”NSVB/RA 0.8 7.0 13.2 0.4 0.3
大维管束“面积密度”NLVB/(PA-CA) 0.1 4.8 4.3 4.7 20.8
空腔面积占茎百分比Percentage of CA to SA 1.1 2.2 0 20.4 2.9

Fig. 2

Heat map of the correlation between core parameters of stem vascular bundles and agronomic traits in sorghum stem NLVB: the number of large vascular bundles; TALVB: total area of large vascular bundles; LVBD: large vascular bundle distance; SD: stem diameter; NSVB: the number of small vascular bundles; SC: stem circumference; TASVB: total area of small vascular bundles; RA: rind area; CA: cavity area; SA: stem area; PA: parenchyma area. df = 90, r0.05 = 0.205."

Fig. 3

Scatter plots of the significant correlations between vascular bundles parameter and agronomic traits in sorghum stem ***, **, and * indicate significant correlations at the 0.001, 0.01, and 0.05 probability levels, respectively. LVB: large vascular bundles; SVB: small vascular bundles; TVB: total vascular bundles; SC: stem circumference; TASVB: total area of small vascular bundles; RA: rind area."

Fig. 4

Clustering analysis of sorghum resources and the vascular bundle of representative materials"

Fig. 5

Boxplots for the comparison of the characters of three classes of sorghum resources Abbreviations are the same as those given in Table 3."

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