Full Text:   <1907>

CLC number: S643.7

On-line Access: 2013-04-03

Received: 2012-09-09

Revision Accepted: 2013-03-03

Crosschecked: 2013-03-16

Cited: 9

Clicked: 3601

Citations:  Bibtex RefMan EndNote GB/T7714

-   Go to

Article info.
1. Reference List
Open peer comments

Journal of Zhejiang University SCIENCE B 2013 Vol.14 No.4 P.279-288


Determination of the genetic diversity of vegetable soybean [Glycine max (L.) Merr.] using EST-SSR markers

Author(s):  Gu-wen Zhang, Sheng-chun Xu, Wei-hua Mao, Qi-zan Hu, Ya-ming Gong

Affiliation(s):  Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; more

Corresponding email(s):   gongym07@126.com

Key Words:  Expressed sequence tag (EST), Simple sequence repeat (SSR), Genetic diversity, Microsatellites, Vegetable soybean

Gu-wen Zhang, Sheng-chun Xu, Wei-hua Mao, Qi-zan Hu, Ya-ming Gong. Determination of the genetic diversity of vegetable soybean [Glycine max (L.) Merr.] using EST-SSR markers[J]. Journal of Zhejiang University Science B, 2013, 14(4): 279-288.

@article{title="Determination of the genetic diversity of vegetable soybean [Glycine max (L.) Merr.] using EST-SSR markers",
author="Gu-wen Zhang, Sheng-chun Xu, Wei-hua Mao, Qi-zan Hu, Ya-ming Gong",
journal="Journal of Zhejiang University Science B",
publisher="Zhejiang University Press & Springer",

%0 Journal Article
%T Determination of the genetic diversity of vegetable soybean [Glycine max (L.) Merr.] using EST-SSR markers
%A Gu-wen Zhang
%A Sheng-chun Xu
%A Wei-hua Mao
%A Qi-zan Hu
%A Ya-ming Gong
%J Journal of Zhejiang University SCIENCE B
%V 14
%N 4
%P 279-288
%@ 1673-1581
%D 2013
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B1200243

T1 - Determination of the genetic diversity of vegetable soybean [Glycine max (L.) Merr.] using EST-SSR markers
A1 - Gu-wen Zhang
A1 - Sheng-chun Xu
A1 - Wei-hua Mao
A1 - Qi-zan Hu
A1 - Ya-ming Gong
J0 - Journal of Zhejiang University Science B
VL - 14
IS - 4
SP - 279
EP - 288
%@ 1673-1581
Y1 - 2013
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B1200243

The development of expressed sequence tag-derived simple sequence repeats (EST-SSRs) provided a useful tool for investigating plant genetic diversity. In the present study, 22 polymorphic EST-SSRs from grain soybean were identified and used to assess the genetic diversity in 48 vegetable soybean accessions. Among the 22 EST-SSR loci, tri-nucleotides were the most abundant repeats, accounting for 50.00% of the total motifs. GAA was the most common motif among tri-nucleotide repeats, with a frequency of 18.18%. Polymorphic analysis identified a total of 71 alleles, with an average of 3.23 per locus. The polymorphism information content (PIC) values ranged from 0.144 to 0.630, with a mean of 0.386. Observed heterozygosity (Ho) values varied from 0.0196 to 1.0000, with an average of 0.6092, while the expected heterozygosity (He) values ranged from 0.1502 to 0.6840, with a mean value of 0.4616. Principal coordinate analysis and phylogenetic tree analysis indicated that the accessions could be assigned to different groups based to a large extent on their geographic distribution, and most accessions from China were clustered into the same groups. These results suggest that Chinese vegetable soybean accessions have a narrow genetic base. The results of this study indicate that EST-SSRs from grain soybean have high transferability to vegetable soybean, and that these new markers would be helpful in taxonomy, molecular breeding, and comparative mapping studies of vegetable soybean in the future.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article


[1]Anderson, J.A., Churchill, G.A., Autrique, J.E., Tanksley, S.D., Sorrells, M.E., 1993. Optimizing parental selection for genetic linkage maps. Genome, 36(1):181-186.

[2]Arikit, S., Yoshihashi, T., Wanchana, S., Tanya, P., Juwattanasomran, R., Srinives, P., Vanavichit, A., 2011. A PCR-based marker for a locus conferring aroma in vegetable soybean (Glycine max L.). Theor. Appl. Genet., 122(2):311-316.

[3]Choudhary, S., Sethy, N.K., Shokeen, B., Bhatia, S., 2009. Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor. Appl. Genet., 118(3):591-608.

[4]Cornelious, B.K., Sneller, C.H., 2002. Yield and molecular diversity of soybean lines derived from crosses of northern and southern elite parents. Crop Sci., 42(2):642-647.

[5]Gong, Y.M., Xu, S.C., Mao, W.H., Hu, Q.Z., Zhang, G.W., Ding, J., Li, Y.D., 2010a. Developing new SSR markers from ESTs of pea (Pisum sativum L.). J. Zhejiang Univ.-Sci. B (Biomed. & Biotechnol.), 11(9):702-707.

[6]Gong, Y.M., Xu, S.C., Mao, W.H., Hu, Q.Z., Zhang, G.W., Ding, J., Li, Z.Y., 2010b. Generation and characterization of 11 novel EST derived microsatellites from Vicia faba (Fabaceae). Am. J. Bot., 97(7):69-71.

[7]Gong, Y.M., Xu, S.H., Mao, W.H., Li, Z.Y., Hu, Q.Z., Zhang, G.W., Ding, J., 2011. Genetic diversity analysis of faba Bean (Vicia faba L.) based on EST-SSR markers. Agric. Sci. China, 10(6):838-844.

[8]Hisano, H., Sato, S., Isobe, S., Sasamoto, S., Wada, T., Matsuno, A., Fujishiro, T., Yamada, M., Nakayama, S., Nakamura, Y., et al., 2007. Characterization of the soybean genome using EST-derived microsatellite markers. DNA Res., 14(6):271-281.

[9]Keatinge, J.D.H., Easdown, W.J., Yang, R.Y., Chadha, M.L., Shanmugasundaram, S., 2011. Overcoming chronic malnutrition in a future warming world: the key importance of mungbean and vegetable soybean. Euphytica, 180(1):129-141.

[10]Kuroda, Y., Tomooka, N., Kaga, A., Wanigadeva, S.M.S.W., Vaughan, D.A., 2009. Genetic diversity of wild soybean (Glycine soja Sieb. et Zucc.) and Japanese cultivated soybeans [G. max (L.) Merr.] based on microsatellite (SSR) analysis and the selection of a core collection. Genet. Resour. Crop Evol., 56(8):1045-1055.

[11]Li, A.Q., Zhao, C.Z., Wang, X.J., Liu, Z.J., Zhang, L.F., Song, G.Q., Yin, J., Li, C.S., Xia, H., Bi, Y.P., 2010. Identification of SSR markers using soybean (Glycine max) ESTs from globular stageembryos. Electron. J. Biotechnol., 13(5):1-11.

[12]Li, G., Ra, W.H., Park, J.W., Kwon, S.W., Lee, J.H., Park, C.B., Park, Y.J., 2011. Developing EST-SSR markers to study molecular diversity in Liriope and Ophiopogon. Biochem. Syst. Ecol., 39(4-6):241-252.

[13]Li, Y.H., Guan, R.X., Liu, Z.X., Ma, Y.S., Wang, L.X., Li, L.H., Lin, F.Y., Luan, W.J., Chen, P.Y., Yan, Z., et al., 2008. Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China. Theor. Appl. Genet., 117(6):857-871.

[14]Liu, Y.L., Li, Y.H., Zhou, G.A., Uzokwe, N., Chang, R.Z., Chen, S.Y., Qiu, L.J., 2010. Development of soybean EST-SSR markers and their use to assess genetic diversity in the Subgenus soja. Agric. Sci. China, 9(10):1423-1429.

[15]Lu, Y.B., Yang, Y.W., Wu, P.D., 2006. Separation of phosphatidylcholine from soybean phospholipids by simulated moving bed. J. Zhejiang Univ.-Sci. B, 7(7):559-564.

[16]Metzgar, D., Bytof, J., Wills, C., 2000. Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res., 10(1):72-80.

[17]Mimura, M., Coyne, C.J., Bambuck, M.W., Lumpkin, T.A., 2007. SSR diversity of vegetable soybean [Glycine max (L.) Merr.]. Genet. Resour. Crop Evol., 54(3):497-508.

[18]Moe, K.T., Zhao, W.G., Song, H.S., Kim, Y.H., Chung, J.W., Cho, Y.I., Park, P.H., Park, H.S., Chae, S.C., Park, Y.J., 2010. Development of SSR markers to study diversity in the genus Cymbidium. Biochem. Syst. Ecol., 38(4):585-594.

[19]Morgante, M., Hanafey, M., Powell, W., 2002. Microsatellites are preferentially associated with non-repetitive DNA in plant genomes. Nat. Genet., 30(2):194-200.

[20]Roy, J.K., Lakshmikumaran, M.S., Balyan, H.S., Gupta, P.K., 2004. AFLP-based genetic diversity and its comparison with diversity based on SSR, SAMPL, and phenotypic traits in bread wheat. Biochem. Genet., 42(1/2):43-59.

[21]Saldivar, X., Wang, Y.J., Chen, P., Mauromoustakos, A., 2010. Effects of blanching and storage conditions on soluble sugar contents in vegetable soybean. LWT Food Sci. Technol., 43(9):1368-1372.

[22]Shultz, J.L., Kazi, S., Bashir, R., Afzal, J.A., Lightfoot, D.A., 2007. The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. Theor. Appl. Genet., 114(6):1081-1090.

[23]Song, Q.J., Marek, L.F., Shoemaker, R.C., Lark, K.G., Concibido, V.C., Delannay, X., Specht, J.E., Cregan, P.B., 2004. A new integrated genetic linkage map of the soybean. Theor. Appl. Genet., 109(1):122-128.

[24]Temnykh, S., Park, W.D., Ayres, N., Cartinhour, S., Hauck, N., Lipovich, L., Cho, Y.G., Ishii, T., McCouch, S.R., 2000. Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor. Appl. Genet., 100(5):697-712.

[25]Varshney, R.K., Graner, A., Sorrells, M.E., 2005. Genic microsatellite markers in plants: features and applications. Trends Biotechnol., 23(1):48-55.

[26]Wang, X.B., Mulock, B., Guus, B., McCallum, B.T., 2010. Development of EST-derived simple sequence repeat markers for wheat leaf rust fungus, Puccinia triticina Eriks. Can. J. Plant Pathol., 32(1):98-107.

[27]Wen, Z.X., Ding, Y.L., Zhao, T.J., Gai, J.Y., 2009. Genetic diversity and peculiarity of annual wild soybean (G. soja Sieb. et Zucc.) from various eco-regions in China. Theor. Appl. Genet., 119(2):371-381.

[28]Xia, Z.J., Tsubokura, Y., Hoshi, M., Hanawa, M., Yano, C., Okamura, K., Ahmed, T., Anai, T., Watanabe, S., Hayashi, M., et al., 2007. An integrated high-density linkage map of soybean with RFLP, SSR, STS, and AFLP markers using a single F2 population. DNA Res., 14(6):257-269.

[29]Yinbo, G., Peoples, M.B., Rerkasem, B., 1997. The effect of N fertilizer strategy on N2 fixation, growth and yield of vegetable soybean. Field Crop Res., 51(3):221-229.

[30]Young, G., Mebrahtu, T., Johnson, J., 2000. Acceptability of green soybeans as a vegetable entity. Plant Food Hum. Nutr., 55(4):323-333.

[31]Zhou, X., Carter, J.T.E., Cui, Z., Miyazaki, S., Burton, J.W., 2002. Genetic diversity patterns in Japanese soybean cultivars based on coefficient of parentage. Crop Sci., 42(4):1331-1342.

Open peer comments: Debate/Discuss/Question/Opinion


Please provide your name, email address and a comment

Journal of Zhejiang University-SCIENCE, 38 Zheda Road, Hangzhou 310027, China
Tel: +86-571-87952783; E-mail: cjzhang@zju.edu.cn
Copyright © 2000 - Journal of Zhejiang University-SCIENCE