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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (5): 1249-1261.doi: 10.3724/SP.J.1006.2023.24122

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

Construction of core collection of sweetpotato based on phenotypic traits and SSR markers

CHEN Yi-Hang1,2(), TANG Chao-Chen1, ZHANG Xiong-Jian1, YAO Zhu-Fang1, JIANG Bing-Zhi1, WANG Zhang-Ying1,*()   

  1. 1Crops Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou 510640, Guangdong, China
    2College of Grassland Agriculture, Northwest A&F University, Yangling 712100, Shaanxi, China
  • Received:2022-05-21 Accepted:2022-09-05 Online:2023-05-12 Published:2022-09-22
  • Contact: *E-mail: wangzhangying@gdaas.cn
  • Supported by:
    National Key Research and Development Program of China(2019YFD1000700);National Key Research and Development Program of China(2019YFD1000701);China Agriculture Research System of MOF and MARA, and the Guangdong Modern Agricultural Industry Technology System(2021KJ111)

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Abstract:

To better preserve, study, and utilize sweet potato collection resources, 1091 sweetpotato germplasms preserved in the National Sweetpotato Germplasm Nursery (Guangzhou) were used as the materials in this study. Euclidean distance and Nei’s distance were used for NJ cluster grouping, respectively, and random sampling was conducted within the group to construct the core collection. Mean, variance, Shannon’s diversity index, coefficient of variation, and other indicators were used to evaluate the representativeness of the core collection based on phenotypic traits data, and effective alleles, Nei’s genetic diversity index, Shannon’s diversity index, and other indicators were used to evaluate the representativeness of the core collection based on SSR markers data. The results showed that the constructed sweetpotato core collection contained 289 materials, accounting for 26.49% of the entire collection. At P < 0.05, there was no significant difference in the related indicators of phenotypic traits and SSR molecular markers between the core collection and the entire collection, and the phenotypic frequency distribution of the two germplasm was basically the same. The principal component analysis revealed that the core collection had similar genetic diversity and population structure to the entire collection. In conclusion, the established core collection of sweetpotato well represented the entire collection’s genetic variation and population structure, which could lay a good foundation for variety improvement, excellent genes mining, and germplasm innovation of sweetpotato.

Key words: sweetpotato, core collection, phenotypic traits, SSR markers, germplasm resource

Table 1

Quantified value of 20 qualitative traits in sweetpotato"

性状
Trait		 缩写
Abbreviation		 赋值
Quantified value
顶叶色
Color of top leaf		 CTL 浅绿=1, 绿=2, 紫绿=3, 褐绿=4, 浅紫=5, 紫=6, 褐=7, 金黄=8, 红=9
Light green=1, Green=2, Purple-green=3, Brown-green=4, Light purple=5, Purple=6, Brown=7, Golden yellow=8, Red=9
顶叶形状
Shape of top leaf		 STL 圆=1, 肾=2, 心=3, 尖心=4, 三角=5, 缺刻=6
Round=1, Reniform=2, Cordate=3, Acuminate-cordate=4, Triangular=5, Incised=6
顶芽色
Color of top bud		 CTB 浅绿=1, 绿=2, 浅紫=3, 紫=4, 深紫=5, 褐=6
Light green=1, Green=2, Light purple=3, Purple=4, Dark purple=5, Brown=6
叶色
Leaf color		 LC 浅绿=1, 绿=2, 紫绿=3, 褐绿=4, 浅紫=5, 紫=6, 褐=7, 金黄=, 红=9
Light green=1, Green=2, Purple-green=3, Brown-green=4, Light purple=5, Purple=6, Brown=7, Golden yellow=8, Red=9
叶片形状
Shape of leaf		 SL 圆=1, 肾=2, 心=3, 尖心=4, 三角=5, 缺刻=6
Round=1, Reniform=2, Cordate=3, Acuminate-cordate=4, Triangular=5, Incised=6

Table 2

Sampling of the core collection"

样本数量
Number of samples		 抽样比例
Sampling ratio
<10 60%-100%
<50 50%-55%
<100 25%-30%
<200 20%-5%
≥200 15%-20%

Fig. 1

Source information of all germplasm resources"

Fig. 2

Cluster dendrogram of the entire collection based on phenotype traits and SSR molecular markers A: cluster dendrogram based on phenotype traits; B: cluster dendrogram based on SSR molecular markers."

Fig. S1

Results of partial SSR molecular marker capillary electrophoresis A-D are the detection peaks of GDAAS0694, GDAAS0338, GDAAS0871, and GDAAS0922 respectively. The abscissas represented the banding site and the ordinates represented the relative intensity fluorescence."

Table 3

Sampling results based on phenotypic traits and SSR markers"

类别
Class		 组别
Group		 样本数量
Number of samples		 抽样比例
Sampling ratio (%)		 抽取样本数
Number of samples extracted
表型
Trait		 1 230 17.83 41
2 24 50.00 12
3 16 50.00 8
4 57 28.07 16
5 189 22.75 43
6 42 50.00 21
7 23 52.17 12
8 96 27.08 26
类别
Class		 组别
Group		 样本数量
Number of samples		 抽样比例
Sampling ratio (%)		 抽取样本数
Number of samples extracted
9 1 100.00 1
10 413 17.43 72
共计Sum 251
SSR分子标记
SSR marker		 1 639 17.53 112
2 90 27.78 25
3 200 17.50 35
4 22 50.00 11
5 42 50.00 21
6 37 51.35 19
7 4 75.00 3
8 19 52.63 10
9 4 75.00 3
10 34 50.00 17
共计Sum 256
合计 Total 289

Fig. S2

Cluster dendrogram of the core collection based on phenotype traits and SSR molecular markers A: based on phenotype traits; B: based on SSR molecular markers."

Table 4

Comparison of means, variances, range, coefficient of variation, and H′, and frequency distribution for 20 traits in the entire collections and core collections"

性状
Trait		 级数
Number of classes		 平均值Mean 方差Variance 极差Range 变异系数CV(%) 香农多样性指数(H’) t-test显著性
Significance
全部种质
Entire collection		 核心种质
Core collection		 全部种质
Entire collection		 核心种质
Core collection		 F-值
F-value		 全部种质
Entire collection		 核心种质
Core collection		 全部种质
Entire collection		 核心种质
Core collection		 全部种质
Entire collection		 核心种质
Core collection
CTL 9 3.31 3.09 3.72 3.61 2.79 1-9 1-8 58.32 61.46 1.69 1.65 NS
STL 6 4.6 4.54 2.03 1.88 0.54 2-6 3-6 30.93 30.19 1.68 1.15 NS
CTB 6 2.64 2.55 1.96 1.76 0.86 1-6 1-6 53.07 51.99 1.43 1.41 NS
LC 9 2.02 2.1 0.35 0.65 3.58 1-9 1-9 29.33 38.39 0.55 0.73 NS
SL 6 4.65 4.65 2.14 2.10 0.00 1-6 2-6 31.42 31.15 1.04 1.02 NS
MVP 6 3.98 3.89 2.66 2.68 0.69 1-6 1-6 41.03 42.15 1.57 1.53 NS
SVP 6 3.55 3.47 2.69 2.93 0.49 1-6 1-6 46.21 49.31 1.52 1.56 NS
PBLV 5 3.47 3.45 0.97 1.15 0.09 1-5 1-5 28.41 31.14 1.24 1.35 NS
LAS 3 1.41 1.33 0.25 0.23 5.59 0-2 0-2 35.45 35.90 0.70 0.66 *
PPC 5 2.24 2.22 0.50 0.46 0.19 1-5 1-5 31.55 30.62 0.76 0.63 NS
PBP 5 3.02 3.02 0.97 1.14 0.01 1-5 1-5 32.50 35.36 1.19 1.25 NS
CV 6 2.53 2.53 1.40 1.47 0.06 1-6 1-6 46.72 47.51 0.77 0.87 NS
PCV 7 2.63 2.62 1.71 1.80 0.00 1-7 1-7 49.78 51.14 0.81 0.87 NS
SCV 5 1.75 1.63 2.26 2.19 1.48 0-4 0-4 86.13 91.05 1.33 1.26 NS
VTP 4 1.14 1.19 0.98 1.01 0.59 0-3 0-3 86.79 84.37 1.32 1.33 NS
PT 4 2.65 2.62 0.26 0.27 0.58 1-4 1-4 19.28 19.85 0.74 0.76 NS
VP 3 1.74 1.6 0.35 0.38 12.83 1-3 1-3 34.13 38.61 0.88 0.90 ***
SRS 9 4.19 4.18 2.91 2.78 0.00 1-9 1-9 40.73 39.85 1.60 1.55 NS
SCSR 10 5.66 5.74 7.17 7.93 0.24 1-10 1-10 47.36 49.02 2.09 2.09 NS
PFC 10 3.2 3.46 5.60 6.10 2.55 1-10 1-10 73.85 71.43 1.82 1.86 NS

Fig. 3

Frequency distribution diagram for 20 traits of the entire collections and core collections Abbreviations are the same as those given in Table 1. In this figure, the black and light gray represent the frequency distribution of the core collection and the frequency distribution of the entire collection, respectively."

Table 5

Comparison of genetic diversity of the entire collection and core collection"

指标
Index		 全部种质
Entire collection		 核心种质
Core collection
样本数量Number of samples 1091 289
平均等位基因数Average number of alleles (Na) 1.88 1.92
平均有效等位基因数Average number of effective alleles (Ne) 1.25 1.32
总条带数Total number of strips 135 101
多态性条带数Number of polymorphic bands 119 93
多态性条带百分率Percentage of polymorphic bands (%) 88.15 92.08
Nei’s遗传多样性指数Nei’s genetic diversity index (He) 0.15 0.19
Shannon’s多样性指数Shannon’s diversity index (I) 0.24 0.30

Fig. 4

Principal component plots for the entire collection and core collection based on phenotype traits and SSR molecular markers A: principal component plot based on phenotype traits; B: principal component plot based on SSR markers. In this figure, the red and light gray represent the frequency distribution of the core collection and the frequency distribution of the entire collection, respectively."

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