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作物学报 ›› 2025, Vol. 51 ›› Issue (11): 2875-2885.doi: 10.3724/SP.J.1006.2025.55022

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

东南沿海短绒野大豆两种代表性生境自然种群的空间遗传结构特征:种群内取样策略研究

王浩辰1,2(), 王克晶1, 韩娟2,*(), 李向华1,*()   

  1. 1 中国农业科学院作物科学研究所资源中心, 北京 100081
    2 西北农林科技大学农学院, 陕西杨凌 712100
  • 收稿日期:2025-03-21 接受日期:2025-08-13 出版日期:2025-11-12 网络出版日期:2025-08-21
  • 通讯作者: *韩娟, E-mail: hjepost@nwsuaf.edu.cn; 李向华, E-mail: lixianghua@caas.cn
  • 作者简介:E-mail: wanghaochen@nwafu.edu.cn
  • 基金资助:
    国家重点研发计划项目(2021YFD1200103)

Spatial genetic structure characteristics of natural populations of Glycine tomentella in two representative habitats in the southeast coast, China: a study of intrapopulation sampling strategy

WANG Hao-Chen1,2(), WANG Ke-Jing1, HAN Juan2,*(), LI Xiang-Hua1,*()   

  1. 1 Resource Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    2 College of Agriculture, Northwest Agriculture & Forestry University, Yangling 712100, Shaanxi, China
  • Received:2025-03-21 Accepted:2025-08-13 Published:2025-11-12 Published online:2025-08-21
  • Contact: *E-mail: hjepost@nwsuaf.edu.cn; E-mail: lixianghua@caas.cn
  • Supported by:
    National Key Research and Development Program of China(2021YFD1200103)

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摘要：

短绒野大豆为国家二级保护植物, 是我国重要的遗传资源, 对栽培大豆育种有潜在的利用价值。由于自花授粉特性的基因流限制及环境异质性, 短绒野大豆居群内的个体在空间分布格局上往往会出现遗传斑块。为探究短绒野大豆在人为干扰程度低的普通天然居群和干扰程度高的墓地居群中的遗传结构差异, 也为制定受干扰程度不同的居群样本取样策略, 本研究利用24对新开发的物种特异SSR分子标记, 分析了受干扰程度不同的短绒野大豆2个天然居群的遗传多样性和空间遗传结构。结果显示: (1) 干扰程度高的墓地群天然居群(B)平均遗传多样性水平不低于干扰程度低的平地天然居群(A); (2) 空间自相关分析表明, 短绒野大豆居群内个体在遗传背景上存在空间遗传斑块, 2种受干扰程度不同的生境居群遗传斑块大小存在差异: 居群A在17.44 m空间范围内个体有显著亲缘关系, 而居群B在14.59 m空间范围内个体有显著亲缘关系; (3) 空间自相关分析和Mantel检验显示, 人为干扰程度高的居群其植株个体间的遗传亲缘关系在空间距离维度上降低, 空间自相关距离显著缩短; (4) 通过使用Python模拟不同的取样数量, 当Nei氏基因多样性指数、香农信息指数和有效等位基因数均达到居群总体的95%时, 居群A取样至少需要20、30和30株, 而居群B取样需要20、35和50株。根据本文的研究, 建议通常的短绒野大豆种质居群取样时, 取样数量至少保证30株, 株间距离保持15~18 m。

关键词: 取样策略, 遗传结构, 遗传多样性, SSR标记, 短绒野大豆

Abstract:

Glycine tomentella is an important genetic resource in China, classified as a nationally protected plant (second-class), and holds significant potential for use in cultivated soybean breeding. Due to its self-pollinating nature and environmental heterogeneity, gene flow is limited, and individuals within G. tomentella populations often exhibit spatial genetic patchiness. To investigate the genetic structure of two primary habitat types in China—highly human-disturbed populations (cemetery natural populations) and minimally disturbed populations (flatland natural populations)—and to provide a theoretical basis for developing sampling strategies that preserve high levels of genetic diversity, this study employed 24 newly developed species-specific SSR markers to analyze genetic diversity and spatial genetic structure in two natural populations subject to different degrees of disturbance. The results showed that: (1) the average genetic diversity of the highly disturbed cemetery population (B) was not lower than that of the less disturbed natural population (A); (2) spatial autocorrelation analysis revealed that individuals in both populations exhibited genetic patch structures, with differing patch sizes: population A showed significant kinship within 17.44 m, while population B showed significant kinship within 14.59 m; (3) spatial autocorrelation and Mantel tests indicated that in highly disturbed populations, genetic relatedness between individuals declined with spatial distance, and the range of significant autocorrelation was reduced; (4) Python-based sampling simulations showed that to reach 95% of the total population values for Nei’s gene diversity index, Shannon’s information index and effective number of alleles at least 20, 30 and 30 individuals needed to be sampled in population A, and 20, 35, and 50 individuals in population B, respectively. Based on these findings, it is recommended that for routine germplasm collection of G. tomentella, a minimum of 30 individuals should be sampled, with an inter-plant spacing of 15-18 m.

Key words: sampling strategy, genetic structure, genetic diversity, SSR markers, Glycine tomentella

图1

取样单株位置分布示意图 图a、图b分别为居群A和居群B的取样植株分布示意图。"

表1

短绒野大豆天然居群内部取样地理位置信息"

取样行数编号
Number of rows		 居群A Population A 居群B Population B
1 2 3 4 1 2 3 4 5
每行取样株与起始点距离
Distances between the sampled plants from the starting point in each row (m)		 6.0 (1) 7.0 (15) 0 (38) 0.1 (64) 0 (1) 10.8 (22) 2.1 (38) 1.0 (57) 1.1 (84)
15.8 (2) 8.3 (16) 2.0 (39) 2.3 (65) 3.0 (2) 12.6 (23) 4.5 (39) 2.8 (58) 8.5 (85)
17.2 (3) 10.5 (17) 3.1 (40) 4.2 (66) 10.3 (3) 14.2 (24) 11.0 (40) 9.1 (59) 10.6 (86)
19.9 (4) 12.5 (18) 4.3 (41) 5.8 (67) 11.5 (4) 16.6 (25) 12.5 (41) 10.7 (60) 12.0 (87)
21.2 (5) 14.8 (19) 6.5 (42) 7.6 (68) 12.1 (5) 18.5 (26) 13.8 (42) 12.4 (61) 14.0 (88)
29.2 (6) 16.4 (20) 8.6 (43) 9.0 (69) 13.8 (6) 20.0 (27) 15.4 (43) 14.2 (62) 15.7 (89)
30.0 (7) 17.4 (21) 12.5 (44) 12.0 (70) 18.0 (7) 22.0 (28) 16.3 (44) 15.7 (63) 17.1 (90)
32.1 (8) 18.9 (22) 14.1 (45) 13.3 (71) 19.0 (8) 25.5 (29) 18.4 (45) 17.2 (64) 18.6 (91)
34.0 (9) 20.9 (23) 16.3 (46) 15.1 (72) 21.5 (9) 30.0 (30) 20.6 (46) 18.7 (65) 20.3 (92)
42.2 (10) 29.3 (24) 18.0 (47) 16.2 (73) 23.1 (10) 31.8 (31) 22.1 (47) 20.5 (66) 23.0 (93)
44.3 (11) 30.3 (25) 19.7 (48) 18.0 (74) 24.5 (11) 33.6 (32) 27.5 (48) 21.7 (67) 26.5 (94)
46.8 (12) 31.6 (26) 21.0 (49) 19.5 (75) 26.0 (12) 34.5 (33) 32. 5(49) 23.4 (68) 28.6 (95)
47.8 (13) 33.7 (27) 29.2 (50) 29.3(76) 27.1 (13) 36.1 (34) 33.9 (50) 26.9 (69) 30.2 (96)
50.0 (14) 34.7 (28) 31.0 (51) 31.6 (77) 28.0 (14) 37.3 (35) 36.6 (51) 28.5 (70) 31.2 (97)
37.0 (29) 32.9 (52) 32.7 (78) 30.8 (15) 38.3 (36) 42.0 (52) 30.4 (71) 33.2 (98)
38.5 (30) 34.2 (53) 34.7 (79) 31.8 (16) 45.9 (37) 42.6 (53) 31.5 (72) 34.9 (99)
40.6 (31) 35.7 (54) 35.7 (80) 33.5 (17) 43.7 (54) 33.6 (73) 36.8 (100)
42.2 (32) 36.9 (55) 36.7 (81) 35.0 (18) 47.8 (55) 34.8 (74) 38.4 (101)
44.0 (33) 38.4 (56) 38.1 (82) 36.7 (19) 49.0 (56) 36.2 (75) 39.7 (102)
45.5 (34) 39.7 (57) 39.8 (83) 37.9 (20) 38.0 (76) 41.5 (103)
46.5 (35) 41.5 (58) 41.7 (84) 48.5 (21) 40.2 (77) 42.7 (104)
47.7 (36) 42.7 (59) 43.5 (85) 41.5 (78) 44.4 (105)
50.0 (37) 44.0 (60) 44.5 (86) 43.1 (79) 45.5 (106)
45.6 (61) 46.2 (87) 44.7 (80) 50.0 (107)
46.6 (62) 46.6 (88) 46.3 (81)
49.0 (63) 47.9 (82)
50.0 (83)
总个数
Total number		 88 107

表2

短绒野大豆24对SSR遗传标记的遗传多样性参数"

标记
Marker		 Na Gt Ne He Ho PIC Gst Nm Fis ts (%)
DR_2 8 9 6.77 0.86 0 0.839 0.024 8.418 1.000 0
DR_23 4 4 2.71 0.63 0 0.556 0.630 0.145 1.000 0
DR_38 7 8 3.34 0.70 0 0.670 0.318 0.525 1.000 0
DR_45 13 14 5.46 0.82 0 0.804 0.237 0.785 1.000 0
DR_46 12 17 6.39 0.85 0.28 0.829 0.185 1.070 0.530 0.31
DR_49 8 9 5.00 0.80 0 0.776 0.046 4.629 1.000 0
DR_55 11 12 4.05 0.76 0 0.736 0.063 3.421 1.000 0
DR_57 12 13 7.37 0.87 0 0.855 0.070 3.091 1.000 0
DR_58 11 12 7.31 0.87 0.01 0.849 0.110 1.930 0.985 0.01
DR_85 9 10 3.91 0.75 0 0.707 0.001 37.702 1.000 0
DR_114 15 16 7.88 0.88 0 0.863 0.144 1.430 1.000 0
DR_120 5 5 3.64 0.73 0 0.677 0.192 1.017 1.000 0
DR_149 11 11 9.15 0.89 0 0.881 0.102 2.084 1.000 0
DR_151 10 11 6.51 0.85 0 0.833 0.095 2.249 1.000 0
DR_184 10 11 3.69 0.73 0 0.705 0.164 1.226 1.000 0
DR_213 7 8 3.33 0.70 0 0.665 0.020 9.540 1.000 0
DR_219 13 13 7.74 0.87 0 0.858 0.061 3.527 1.000 0
DR_231 5 7 2.60 0.62 0.01 0.562 0.377 0.406 0.984 0.01
DR_251 8 11 4.12 0.76 0.13 0.722 0.169 1.189 0.801 0.11
DR_278 10 13 7.42 0.87 0.01 0.854 0.050 4.290 0.986 0.01
DR_306 12 13 7.55 0.87 0 0.856 0.133 1.561 1.000 0
DR_324 11 11 6.24 0.84 0 0.821 0.157 1.292 1.000 0
DR_336 7 8 4.21 0.77 0 0.735 0.167 1.204 1.000 0
DR_383 7 9 4.41 0.78 0.03 0.749 0.213 0.895 0.958 0.02
平均Mean 9.42 10.63 5.45 0.79 0.02 0.767 0.155 1.393 0.969 0.02

表3

取样数量对短绒野大豆居群遗传多样性的影响"

遗传参数
Genetic index		 观测等位基因数 Na 有效等位基因数 Ne Nei氏基因多样性指数 H 香农信息指数 I
A B A B A B A B
取样数量
Sampling size		 5 2.60±0.27 3.20±0.22 2.26±0.24 2.82±0.23 0.47±0.06 0.60±0.04 0.79±0.11 1.04±0.09
10 3.40±0.22 4.61±0.26 2.62±0.18 3.69±0.24 0.53±0.03 0.68±0.02 0.97±0.07 1.33±0.07
15 3.74±0.20 5.41±0.28 2.75±0.13 3.96±0.20 0.55±0.02 0.71±0.02 1.00±0.05 1.45±0.06
20 3.40±0.22 5.95±0.24 2.82±0.16 4.14±0.20 0.56±0.02 0.72±0.02 1.05±0.05 1.51±0.05
25 4.21±0.16 6.25±0.25 2.88±0.13 4.24±0.19 0.56±0.01 0.73±0.01 1.06±0.03 1.53±0.04
30 4.32±0.17 6.57±0.24 2.91±0.12 4.37±0.14 0.57±0.02 0.73±0.01 1.09±0.04 1.56±0.03
35 4.47±0.15 6.79±0.24 2.96±0.10 4.39±0.15 0.57±0.01 0.74±0.01 1.10±0.03 1.57±0.04
40 4.59±0.15 6.99±0.22 2.98±0.10 4.44±0.14 0.58±0.01 0.74±0.01 1.12±0.03 1.59±0.03
45 4.68±0.11 7.10±0.22 2.98±0.08 4.47±0.12 0.57±0.01 0.74±0.01 1.12±0.02 1.59±0.03
50 4.73±0.14 7.31±0.20 2.99±0.07 4.52±0.13 0.58±0.01 0.74±0.01 1.12±0.02 1.61±0.03
55 4.78±0.14 7.46±0.14 3.00±0.06 4.57±0.09 0.58±0.01 0.74±0.01 1.12±0.02 1.62±0.02
60 4.86±0.13 7.59±0.17 3.01±0.06 4.59±0.11 0.58±0.01 0.75±0.01 1.13±0.02 1.63±0.02
65 4.92±0.12 7.66±0.12 3.02±0.05 4.61±0.07 0.58±0.01 0.75±0.01 1.13±0.02 1.63±0.02
70 4.99±0.09 7.73±0.12 3.04±0.04 4.61±0.08 0.58±0.00 0.75±0.01 1.14±0.01 1.63±0.02
75 5.01±0.10 7.84±0.11 3.04±0.04 4.64±0.06 0.58±0.01 0.75±0.00 1.14±0.01 1.64±0.01
80 5.06±0.07 7.88±0.12 3.04±0.03 4.64±0.05 0.58±0.00 0.75±0.00 1.14±0.01 1.64±0.01
A、B遗传多样性
Genetic diversity for A and B		 5.13 8.21 3.04 4.70 0.58 0.75 1.14 1.66

图2

抽样群体遗传参数平均值占总体的百分率随取样量变化的S拟合曲线图 缩写同表2和表3。a: 居群A的S拟合曲线图; b: 居群B的S拟合曲线图。"

图3

基于取样植株遗传距离和株间距离的Mantel检验 图a、图b分别代表居群A和居群B的Mantel检验结果。"

图4

短绒野大豆取样居群内各植株的空间自相关分析 r: 空间自相关系数; U: 置信区间上限; L: 置信区间下限; a: 居群A的空间自相关分析; b: 居群B的空间自相关分析。横轴: 植株取样距离; 纵轴: 自相关系数。"

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