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| Genetic Diversity Analysis of Faba Bean (Vicia faba L.) Based on EST-SSR Markers |
| GONG Ya-ming1*, XU Sheng-chun1*, MAO Wei-hua2, LI Ze-yun2, HU Qi-zan1, ZHANG Gu-wen1 and DING Ju1 |
1 Institute of Vegetables, Zhejiang Academy of Agricultural Science, Hangzhou 310021, P.R.China
2 Center of Analysis and Measurement, Zhejiang University, Hangzhou 310029, P.R.China |
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摘要 Faba bean (Vicia faba L.), one of the most important legumes in the world, evolved different types of cultivars due to its partial cross-pollination. The development of simple sequence repeat (SSR) markers from expressed sequence tags (EST) provided a useful tool for investigation of its genetic diversity. The purpose of the present study was to investigate the genetic diversity of faba bean from China and Europe using EST-SSR markers. 5 031 faba bean ESTs from the NCBI database were downloaded and assembled into 1 148 unigenes. A total of 107 microsatellites in 96 unigenes were identified, indicating that merely 8.36% of sequences contained SSRs. The most abundant SSR within faba bean was tri-nucleotide repeat motif, and among all the tri-nucleotide repeats, the motif AAG/CTT was the most abundant type. Based on these results, 11 EST-SSR markers were used to assess the genetic diversity of 29 faba bean cultivars from China and Europe with two to three alleles per locus. The polymorphism information content value ranged from 0.0644 to 0.4278 with an average of 0.2919. Principal coordinate analysis (PCA) and phylogenetic clustering based on these 11 EST-SSR markers distinguished these cultivars into different groups. The results indicated that faba bean in China had a narrow genetic basis, and the additional sources of genetic cultivars/accessions should be introduced to enhance the genetic variability. The results of this study proved that the EST-SSR marker is very effective in evaluation of faba bean germplasm.
Abstract Faba bean (Vicia faba L.), one of the most important legumes in the world, evolved different types of cultivars due to its partial cross-pollination. The development of simple sequence repeat (SSR) markers from expressed sequence tags (EST) provided a useful tool for investigation of its genetic diversity. The purpose of the present study was to investigate the genetic diversity of faba bean from China and Europe using EST-SSR markers. 5 031 faba bean ESTs from the NCBI database were downloaded and assembled into 1 148 unigenes. A total of 107 microsatellites in 96 unigenes were identified, indicating that merely 8.36% of sequences contained SSRs. The most abundant SSR within faba bean was tri-nucleotide repeat motif, and among all the tri-nucleotide repeats, the motif AAG/CTT was the most abundant type. Based on these results, 11 EST-SSR markers were used to assess the genetic diversity of 29 faba bean cultivars from China and Europe with two to three alleles per locus. The polymorphism information content value ranged from 0.0644 to 0.4278 with an average of 0.2919. Principal coordinate analysis (PCA) and phylogenetic clustering based on these 11 EST-SSR markers distinguished these cultivars into different groups. The results indicated that faba bean in China had a narrow genetic basis, and the additional sources of genetic cultivars/accessions should be introduced to enhance the genetic variability. The results of this study proved that the EST-SSR marker is very effective in evaluation of faba bean germplasm.
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Received: 10 June 2011
Online: 10 June 2011
Accepted:
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Corresponding Authors:
GONG Ya-ming
E-mail: gongym07@126.com
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| About author: Correspondence GONG Ya-ming, Tel: +86-571-86404179, Fax: +86-571-86404179, E-mail: gongym07@126.com
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Cite this article:
GONG Ya-ming, XU Sheng-chun, MAO Wei-hua, LI Ze-yun, HU Qi-zan, ZHANG Gu-wen and DING Ju.
2011.
Genetic Diversity Analysis of Faba Bean (Vicia faba L.) Based on EST-SSR Markers. Journal of Integrative Agriculture, 10(6): 838-844.
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| 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, 181-186. Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D,Waugh R. 2000. Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics, 156, 847-854. Choudhary S, Sethy N K, Shokeen B, Bhatia S. 2009.Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theoretical and Applied Genetics, 118, 591-608. Duc G, Bao S Y, Baum M, Redden B, Sadiki M, Suso M J,Vishniakova M, Zong X X. 2010. Diversity maintenance and use of Vicia faba L. genetic resource. Field Crops Research, 115, 270-278. Ellis J R, Burke J M. 2007. EST-SSRs as a resource for population genetic analyses. Heredity, 99, 125-132. Eujayl I, Sorrells M E, Baum M, Wolters P, Powell W. 2002.Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theoretical and Applied Genetics, 104, 399-407. Fu Y B. 2003. Applications of bulking in molecular characterization of plant germplasm: a critical review. Plant Genetic Resources, 1, 161-167. 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.). Journal of Zhejiang University (Science B), 11, 702-707. 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).American Journal of Botany, 97, 69-71. Gupta P K, Rustgi S, Sharma S, Singh R, Kumar N, Balyan H S.2003. Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat.Molecular Genetics and Genomics, 270, 315-323. Hanai L R, de Campos T, Camargo L E, Benchimol L L, de Souza A P, Melotto M, Carbonell S A, Chioratto A F, Consoli L,Formighieri E F, et al. 2007. Development, characterization,and comparative analysis of polymorphism at common bean SSR loci isolated from genic and genomic sources. Genome,50, 266-277. 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 ESTderived microsatellite markers. DNA Research, 14, 271-281. Martin M S. 2000. Crop strength through diversity. Nature,406, 681-682. Metzgar D, Bytof J, Wills C. 2000. Selection against frameshift mutations limits microsatellite expansion in coding DNA.Genome Research, 10, 72-80. Nei M, Li W H. 1979. Mathematical models for studying genetic variation in terms of restriction endonucleases. Proceeding of the National Academy of Sciences of the USA, 76, 5269-5273. Poncet V, Rondeau M, Tranchant C, Cayrel A, Hamon S, de Kochko A, Hamon P. 2006. SSR mining in coffee tree EST databases: potential use of EST-SSRs as markers for the Coffea genus. Molecular Genetics and Genomics, 276, 436-449. Powell W, Machray G C, Provan J. 1996. Polymorphism revealed by simple sequence repeats. Trends in Plant Science, 1, 215-222. Pozarkova D, Koblizkova A, Roman B, Torres A M, Lucretti S,Lysak M, Dolezel J, Macas J. 2002. Development and characterization of microsatellite markers from chromosome 1-specific DNA libraries of Vicia faba. Biologia Plantarum,45, 337-345. Squirrell J, Hollingsworth P M, Woodhead M, Russell J, Lowe A J, Gibby M, Powell W. 2003. How much effort is required to isolate nuclear microsatellites from plants? Molecular Ecology, 12, 1339-1348. Terzopulos P J, Bebeli P J. 2008. Genetic diversity analysis of Mediterranean faba bean (Vicia faba L.) with ISSR markers.Field Crops Research, 108, 39-44. Varshney R K, Graner A, Sorrells M E. 2005. Genic microsatellite markers in plants: features and applications. Trends in Biotechnology, 23, 48-55. Yan Q L, Zhang Y H, Li H B, Wei C H, Niu L L, Guan S, Li S G,Du L X. 2008. Identification of microsatellites in cattle unigenes. Journal of Genetics and Genomics, 35, 261-266. Yeh F C, Yang R C, Boyle T. 1999. POPGENE (ver.1.31):Microsoft Window-Bases Freeware for Population Genetic Analysis. University of Alberta and the Centre for International Forestry Research. Zane L, Bargelloni L, Patarnello T. 2002. Strategies for microsatellite isolation: a review. Molecular Ecology, 11, 1-16. Zeid M, Mitchell S, Link W, Carter M, Nawar A, Fulton T,Kresovich S. 2009. Simple sequence repeats (SSRs) in faba bean: new loci from Orobanche-resistant cultivar ‘Giza 402’.Plant Breeding, 128, 149-155. Zong X X, Liu X J, Guan J P, Wang S M, Liu Q C, Paull J G,Redden R. 2009. Molecular variation among Chinese and global winter faba bean germplasm. Theoretical and Applied Genetics, 118, 971-978. |
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