Welcome to Acta Agronomica Sinica,

Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (1): 26-36.doi: 10.3724/SP.J.1006.2019.84060


Genetic diversity analysis and distinctness identification of peanut cultivars based on morphological traits and SSR markers

Hong LIU1(),Zhen-Jiang XU1(),De-Hua RAO1,Qing LU2,3,Shao-Xiong LI2,3,Hai-Yan LIU2,3, 2,3,Xuan-Qiang LIANG2,3,Yan-Bin HONG2,3,*()   

  1. 1 College of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong, China
    2 Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, China
    3 Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Guangzhou 510640, Guangdong, China
  • Received:2018-04-27 Accepted:2018-08-20 Online:2018-09-19 Published:2018-09-19
  • Contact: Yan-Bin HONG E-mail:laoliuhongscau@163.com;zhenjiangxu521@scau.edu.cn;hongyanbin@gdaas.cn
  • Supported by:
    This study was supported by the National Natural Science Foundation of China(31771841);2015 Variety Resource Protection Project(2015-18);Science and Technology Plan Project of Guangdong Province(2013B020301014);Science and Technology Plan Project of Guangdong Province(2013B050800021);Science and Technology Plan Project of Guangdong Province(2017A030311007);Science and Technology Plan Project of Guangdong Province(2016B020201003);Science and Technology Plan Project of Guangdong Province(2015A030313565);Modern Agricultural Science and Technology Innovation Alliance Construction Project of Guangdong Province.(2016LM3161)


The genetic diversity and distinctness of 101 peanut varieties participated in the South China peanut field trial were analyzed based on their morphological traits and SSR markers. Among 29 morphological traits seven were no difference while 22 demonstrated diversity indexes ranging from 0.23 to 0.77, with an average of 0.43. The varieties were divided into seven groups at the similarity coefficient of 0.76, and those released by the same breeding institution tended to converge into one cluster. Molecular characterization with 40 highly informative SSRs generated a total of 167 alleles ranging from 2 to 6 (averaged 4.18) alleles per marker. The polymorphism information content (PIC) of these markers varied from 0.79 to 0.26 with an average of 0.55/marker. The varieties were divided into six groups based on the similarity coefficient of 0.70, and those released by the same province tended to converge into one cluster. Mantel testing revealed that the correlations of the similarity coefficient matrixes between the morphological traits and SSR markers were weak (r = 0.36), implying that SSR markers are unable to replace morphological traits to be solely adopted to identify the distinctness of peanut varieties, but the combination of morphological traits and SSR markers will effectively increase the accuracy of distinctiveness identification.

Key words: peanut, morphology, SSR, genetic diversity, DUS

Table 1

Numbers and sources of the peanut varieties"

Breeding unit
YY series
16 广东省农业科学院作物研究所
Crops Research Institute, Guangdong Academy of Agricultural Sciences
HH series
2 广东省农业科学院作物研究所
Crops Research Institute, Guangdong Academy of Agricultural Sciences
SY series
10 汕头市农业科学研究所
Shantou Agricultural Science Research Institute
ZKH series
8 仲恺农业工程学院
Zhongkai University of Agriculture and Engineering
ZY series
9 湛江市农业科学研究院
Zhanjiang Academy of Agricultural Sciences
QH series
8 泉州市农业科学研究所
Quanzhou Agricultural Science Research Institute
MH series
8 福建农林大学
Fujian Agriculture and Forestry University
JH series
2 福建农林大学
Fujian Agriculture and Forestry University
LH series
7 龙岩市农业科学研究所
Longyan Agricultural Science Research Institute
PH series
5 莆田市农业科学研究所
Putian Agricultural Science Research Institute
FH series
3 福建省农业科学院作物研究所
Crops Research Institute, Fujian Academy of Agricultural Sciences
GH series
11 广西农业科学院经济作物研究所
Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences
HY series
8 贺州市农业科学研究所
Hezhou Agricultural Science Research Institute
XH series
2 湖南农业大学
Hunan Agricultural University
YH series
2 云南省农业科学院经济作物研究所
Cash Crops Research Institute, Yunnan Academy of Agricultural Sciences

Table 2

Morphological traits of the tested varieties"

Morphological trait
Code of traits
Simpson’s index
1 开花期 Flowering stage 3/4/5 0.31
2 植株: 开花习性 Plant: flowering general pattern 2 0
3 主茎: 开花习性 Main stem: flowering general pattern 3 0
4 叶: 小叶形状 Leaflet :shape 2 0
5 叶: 绿色程度 Leaflet: green degree 5/6/7 0.29
6 花: 花冠颜色 Flower: corolla color 2 0
7 植株: 生长习性 Plant: growth habit 1 0
8 叶: 小叶大小 Leaflet: size 5/6/7 0.36
9 主茎: 花青甙显色 Main stem: anthocyanin coloration 1/9 0.32
10 主茎: 茸毛密度 Main stem: pubescence density 1/2/3/5/6 0.37
11 植株: 主茎高度 Plant: main stem height 4/5/6 0.44
12 植株: 分枝数量 Plant: branching 3/4 0.38
13 植株: 侧枝长度 Plant: side branch length 4/5/6/7 0.43
14 成熟期 Mature period 4/5/6 0.31
15 荚果: 籽仁率Pod: rate of seed produced 2 0
16 植株: 荚果数 Plant: pods number 3/4/5 0.61
17 籽仁: 休眠期 Kernel: dormancy period 2/3/4/5 0.41
18 荚果: 长度 Pod: length 4/5/6 0.59
19 荚果: 缢缩程度 Pod: constrictions degree 3/4/5/6 0.48
20 荚果: 果嘴明显程度 Pod: prominence of beak 1/2/3/4/5/6 0.73
21 荚果: 果嘴形状 Pod: beak shape 1/2 0.24
22 荚果: 表面质地 Pod: surface texture 2/3/4/5 0.46
23 荚果: 出仁率 Pod: kernel percentage 3/4/5/6 0.67
24 籽仁: 百仁重 Kernel: weight per 100 kernels 1/2/3/4/5/6/7 0.77
25 籽仁: 形状 Kernel: shape 1/2 0.23
26 籽仁: 种皮颜色数量 Kernel: testa color number 1 0
27 籽仁: 种皮颜色 Kernel: testa color 2/4 0.38
28 籽仁: 种皮裂纹 Kernel: testa crack 1/2/3/4/5 0.52
29 籽仁: 种皮内表面颜色 Kernel: endortesta color 1/2 0.23

Fig. 1

Cluster dendrogram based on the morphological traits"

Table 3

Result of amplifying by selcted primers"

Fig. 3

Comparison of genetic similarity coefficient matrix between morphological traits and SSR markers"

Fig. 2

Cluster dendrogram based on the SSR markers"

[1] 中华人民共和国农业农村部种子管理局. 中国种业大数据平台. 北京:中华人民共和国农业农村部, 2017[2018-04-01]. .
Bureau of Seed Management of Ministry of Agriculture and Rural Affairs of the People’s Republic of China. China Seed Industry Big Data Platform. Beijing: Ministry of Agriculture and Rural Affairs of the People’s Republic of China, 2017 [2018-04-01]. .
[2] 中华人民共和国国务院. 中华人民共和国植物新品种保护条例. 北京: 中国农业出版社, 1997. pp 4-5.
The State Council of the People’s Republic of China. Regulations of the People’s Republic of China Plant Variety Protection. Beijing: China Agriculture Press, 1997. pp 4-5(in Chinese).
[3] 鲁清, 李少雄, 陈小平, 周桂元, 洪彦彬, 李海芬, 梁炫强 . 我国南方产区花生育种现状、存在问题及育种建议. 中国油料作物学报, 2017,39:556-566.
doi: 10.7505/j.issn.1007-9084.2017.04.019
Lu Q, Li S X, Chen X P, Zhou G Y, Hong Y B, Li H F, Liang X Q . Current situation, problems and suggestions of peanut breeding in southern China. Chin J Oil Crop Sci, 2017,39:556-566 (in Chinese with English abstract).
doi: 10.7505/j.issn.1007-9084.2017.04.019
[4] Hayward A C, Tollenaere R, Dalton-Morgan J, Batley J . Molecular marker applications in plants. Methods Mol Biol, 2015,1245:13-27.
doi: 10.1007/978-1-4939-1966-6
[5] Cockram J, Jones H, Norris C, O'Sullivan D M . Evaluation of diagnostic molecular markers for DUS phenotypic assessment in the cereal crop, barley (Hordeum vulgare ssp. vulgare L.). Theor Appl Genet, 2012,125:1735-1749
[6] Jones H, Norris C, Smith D, Cockram J, Lee D, O’Sullivan D M, Mackay I . Evaluation of the use of high-density SNP genotyping to implement UPOV Model 2 for DUS testing in barley. Theor Appl Genet, 2013,126:901-911.
doi: 10.1007/s00122-012-2024-2 pmid: 23232576
[7] Tommasini L, Batley J, Arnold G M, Cooke R J, Donini P, Lee D, Law J R, Lowe C, Moule C, Trick M, Edwards K J . The development of multiplex simple sequence repeat (SSR) markers to complement distinctness, uniformity and stability testing of rape (Brassica napus L.) varieties. Theor Appl Genet, 2003,106:1091-1101.
doi: 10.1007/s00122-002-1125-8 pmid: 12671758
[8] Arens P, Mansilla C, Deinum D, Cavellini L, Moretti A, Rolland S, van der Schoot H, Calvache D, Ponz F, Collonnier C, Mathis R, Smilde D, Caranta C, Vosman B . Development and evaluation of robust molecular markers linked to disease resistance in tomato for distinctness, uniformity and stability testing. Theor Appl Genet, 2010,120:655-664.
doi: 10.1007/s00122-009-1183-2 pmid: 19855951
[9] Jones H, Mackay I . Implications of using genomic prediction within a high-density SNP dataset to predict DUS traits in barley. Theor Appl Genet, 2015,128:2461-2470.
doi: 10.1007/s00122-015-2601-2
[10] 滕海涛, 吕波, 赵久然, 徐岩, 王凤格, 堵苑苑, 杨坤, 唐浩, 李祥羽 . 利用DNA指纹图谱辅助植物新品种保护的可能性. 生物技术通报, 2009, (1):1-6.
Teng H T, Lyu B, Zhao J R, Xu Y, Wang F G, Du Y Y, Yang K, Tang H, Li X Y . DNA fingerprint profile involved in plant variety protection practice. Biotechnol Bull, 2009, (1):1-6 (in Chinese with English abstract).
[11] 中华人民共和国农业农村部. 植物新品种特异性、一致性和稳定性测试指南:花生. 北京: 中国农业出版社, 2012. pp 4-7.
Ministry of Agriculture and Rural Affairs of the People’s Republic of China. Guidelines for the Conduct of Tests for Distinctness, Uniformity and Stability:Peanut (Arachis hypogaea L.). Beijing: China Agriculture Press, 2012. pp 4-7(in Chinese).
[12] Shirasawa K, Bertioli D J, Varshney R K, Moretzsohn M C, Leal-Bertioli S C M, Thudi M, Pandey M K, Rami J F, Foncéka D, Gowda M V C, Qin H, Guo B, Hong Y, Liang X, Hirakawa H, Tabata S, Isobe S . Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes. DNA Res, 2013,20:173-184.
doi: 10.1093/dnares/dss042 pmid: 1744303
[13] Heilmann-Clausen J, Christensen M, Frøslev T G, Kjøller R . Taxonomy of Tricholoma in northern Europe based on ITS sequence data and morphological characters. Persoonia, 2017,38:38-57.
doi: 10.3767/003158517X693174 pmid: 5645187
[14] Smykal P, Horacek J, Dostalova R, Hybl M . Variety discrimination in pea (Pisum sativum L.) by molecular, biochemical and morphological markers. J Appl Genet, 2008,49:155-166.
doi: 10.1007/BF03195609 pmid: 18436990
[15] Ebrahimi A, Zarei A, Zamani F M, Lawson S . Evaluation of genetic variability among “Early Mature” Juglans regia using microsatellite markers and morphological traits. Peer J, 2017,5:e3834.
[16] Rebaa F, Abid G, Aouida M, Abdelkarim S, Aroua I, Muhovski Y, Baudoin J P, M’hamdi M, Sassi K, Jebara M . Genetic variability in Tunisian populations of faba bean (Vicia faba L. var. major) assessed by morphological and SSR markers. Physiol Mol Biol Plants, 2017,23:397-409.
doi: 10.1007/s12298-017-0419-x pmid: 28461727
[17] 李瑞峰, 高鹏, 朱子成, 栾非时 . 基于形态学标记及SSR标记的甜瓜主栽品种分类鉴定研究. 中国蔬菜, 2014, ( 6):20-27.
doi: 10.3969/j.issn.1000-6346.2014.06.004
Li R F, Gao P, Zhu Z C, Luan F S . Studies on classification and identification based on morphological markers and SSR markers for elite varieties of Cucumis melo L. China Vegetables, 2014, ( 6):20-27 (in Chinese with English abstract).
doi: 10.3969/j.issn.1000-6346.2014.06.004
[18] 李鹤, 郭世荣, 束胜, 徐扬, 孙锦 . 砧用南瓜种质资源形态学性状与SSR标记分析. 园艺学报, 2014,41:1379-1390.
Li H, Guo S R, Shu S, Xu Y, Sun J . Germplasm resources analysis of rootstock-used pumpkins by phenotype and SSR. Acta Hortic Sin, 2014,41:1379-1390 (in Chinese with English abstract).
[1] XIAO Ying-Ni, YU Yong-Tao, XIE Li-Hua, QI Xi-Tao, LI Chun-Yan, WEN Tian-Xiang, LI Gao-Ke, HU Jian-Guang. Genetic diversity analysis of Chinese fresh corn hybrids using SNP Chips [J]. Acta Agronomica Sinica, 2022, 48(6): 1301-1311.
[2] YANG Huan, ZHOU Ying, CHEN Ping, DU Qing, ZHENG Ben-Chuan, PU Tian, WEN Jing, YANG Wen-Yu, YONG Tai-Wen. Effects of nutrient uptake and utilization on yield of maize-legume strip intercropping system [J]. Acta Agronomica Sinica, 2022, 48(6): 1476-1487.
[3] LI Hai-Fen, WEI Hao, WEN Shi-Jie, LU Qing, LIU Hao, LI Shao-Xiong, HONG Yan-Bin, CHEN Xiao-Ping, LIANG Xuan-Qiang. Cloning and expression analysis of voltage dependent anion channel (AhVDAC) gene in the geotropism response of the peanut gynophores [J]. Acta Agronomica Sinica, 2022, 48(6): 1558-1565.
[4] CHEN Xiao-Hong, LIN Yuan-Xiang, WANG Qian, DING Min, WANG Hai-Gang, CHEN Ling, GAO Zhi-Jun, WANG Rui-Yun, QIAO Zhi-Jun. Development of DNA molecular ID card in hog millet germplasm based on high motif SSR [J]. Acta Agronomica Sinica, 2022, 48(4): 908-919.
[5] ZHANG Xia, YU Zhuo, JIN Xing-Hong, YU Xiao-Xia, LI Jing-Wei, LI Jia-Qi. Development and characterization analysis of potato SSR primers and the amplification research in colored potato materials [J]. Acta Agronomica Sinica, 2022, 48(4): 920-929.
[6] DING Hong, XU Yang, ZHANG Guan-Chu, QIN Fei-Fei, DAI Liang-Xiang, ZHANG Zhi-Meng. Effects of drought at different growth stages and nitrogen application on nitrogen absorption and utilization in peanut [J]. Acta Agronomica Sinica, 2022, 48(3): 695-703.
[7] SONG Shi-Qin, YANG Qing-Long, WANG Dan, LYU Yan-Jie, XU Wen-Hua, WEI Wen-Wen, LIU Xiao-Dan, YAO Fan-Yun, CAO Yu-Jun, WANG Yong-Jun, WANG Li-Chun. Relationship between seed morphology, storage substance and chilling tolerance during germination of dominant maize hybrids in Northeast China [J]. Acta Agronomica Sinica, 2022, 48(3): 726-738.
[8] HUANG Li, CHEN Yu-Ning, LUO Huai-Yong, ZHOU Xiao-Jing, LIU Nian, CHEN Wei-Gang, LEI Yong, LIAO Bo-Shou, JIANG Hui-Fang. Advances of QTL mapping for seed size related traits in peanut [J]. Acta Agronomica Sinica, 2022, 48(2): 280-291.
[9] WANG Ying, GAO Fang, LIU Zhao-Xin, ZHAO Ji-Hao, LAI Hua-Jiang, PAN Xiao-Yi, BI Chen, LI Xiang-Dong, YANG Dong-Qing. Identification of gene co-expression modules of peanut main stem growth by WGCNA [J]. Acta Agronomica Sinica, 2021, 47(9): 1639-1653.
[10] WANG Jian-Guo, ZHANG Jia-Lei, GUO Feng, TANG Zhao-Hui, YANG Sha, PENG Zhen-Ying, MENG Jing-Jing, CUI Li, LI Xin-Guo, WAN Shu-Bo. Effects of interaction between calcium and nitrogen fertilizers on dry matter, nitrogen accumulation and distribution, and yield in peanut [J]. Acta Agronomica Sinica, 2021, 47(9): 1666-1679.
[11] SHI Lei, MIAO Li-Juan, HUANG Bing-Yan, GAO Wei, ZHANG Zong-Xin, QI Fei-Yan, LIU Juan, DONG Wen-Zhao, ZHANG Xin-You. Characterization of the promoter and 5'-UTR intron in AhFAD2-1 genes from peanut and their responses to cold stress [J]. Acta Agronomica Sinica, 2021, 47(9): 1703-1711.
[12] GAO Fang, LIU Zhao-Xin, ZHAO Ji-Hao, WANG Ying, PAN Xiao-Yi, LAI Hua-Jiang, LI Xiang-Dong, YANG Dong-Qing. Source-sink characteristics and classification of peanut major cultivars in North China [J]. Acta Agronomica Sinica, 2021, 47(9): 1712-1723.
[13] ZHANG He, JIANG Chun-Ji, YIN Dong-Mei, DONG Jia-Le, REN Jing-Yao, ZHAO Xin-Hua, ZHONG Chao, WANG Xiao-Guang, YU Hai-Qiu. Establishment of comprehensive evaluation system for cold tolerance and screening of cold-tolerance germplasm in peanut [J]. Acta Agronomica Sinica, 2021, 47(9): 1753-1767.
[14] XUE Xiao-Meng, WU JIE, WANG Xin, BAI Dong-Mei, HU Mei-Ling, YAN Li-Ying, CHEN Yu-Ning, KANG Yan-Ping, WANG Zhi-Hui, HUAI Dong-Xin, LEI Yong, LIAO Bo-Shou. Effects of cold stress on germination in peanut cultivars with normal and high content of oleic acid [J]. Acta Agronomica Sinica, 2021, 47(9): 1768-1778.
[15] HAO Xi, CUI Ya-Nan, ZHANG Jun, LIU Juan, ZANG Xiu-Wang, GAO Wei, LIU Bing, DONG Wen-Zhao, TANG Feng-Shou. Effects of hydrogen peroxide soaking on germination and physiological metabolism of seeds in peanut [J]. Acta Agronomica Sinica, 2021, 47(9): 1834-1840.
Full text



No Suggested Reading articles found!