Development of Microsatellite Markers in Tung Tree (Vernicia fordii) Using Cassava Genomic Sequences

Lingling Zhang; Mingcheng Luo; Frank M. You; Eviatar Nevo; Shiyou Lu; Dongfa Sun; Junhua Peng

doi:10.1007/s11105-014-0804-3

Development of Microsatellite Markers in Tung Tree (Vernicia fordii) Using Cassava Genomic Sequences

Lingling Zhang, Mingcheng Luo, Frank M. You, Eviatar Nevo, Shiyou Lu, Dongfa Sun, Junhua Peng

Department of Evolutionary and Environmental Biology

Research output: Contribution to journal › Article › peer-review

Abstract

Tung tree, Vernicia fordii, is a native oil-bearing woody plant of China. Oil extracted from the fruit is an important industrial and biodiesel feedstock. Microsatellite (simple-sequence repeat (SSR)) markers are effective in germplasm evaluation and marker-assisted breeding of plants. The objective of this study was to develop SSR markers in tung tree using cassava genomic sequences and test the effectiveness of the interspecific transferable SSR markers. According to the principle of comparative genomics, SSR markers were designed based on cassava genomic sequences and tested in tung tree and other Euphorbiaceae plant species. Among 255 cassava SSR markers, 104 (41 %) could effectively amplify DNA of tung tree, and a large portion of these transferable SSR markers could work well in other Euphorbiaceae species, Vernicia montana (98 %), castor bean (92 %), and Jatropha curcas (88 %). Genotyping a set of 16 tung tree accessions using the 104 transferable SSRs, a total of 437 alleles were obtained, 162 of which were polymorphic, and the Shannon information index varied from 0.000 to 0.560 with a mean of 0.139. A phylogenetic tree unambiguously distinguished the 32 accessions of the abovementioned five Euphorbiaceae species. Using cassava genomics resources is an effective approach to develop SSR markers for tung tree when its genome sequence is not available. The developed SSR markers should facilitate germplasm evaluation and other molecular-level investigations in tung tree.

Original language	English
Pages (from-to)	893-904
Number of pages	12
Journal	Plant Molecular Biology Reporter
Volume	33
Issue number	4
DOIs	https://doi.org/10.1007/s11105-014-0804-3
State	Published - 6 Aug 2015

Bibliographical note

Funding Information:
This work was supported by the National Natural Science Foundation of China (NSFC) grant nos. 31030055 and 30870233, Chinese Academy of Sciences under the Important Directional Program of Knowledge Innovation Project grant no. KSCX2-YW-Z-0722. We thank Dr. Wenquan Wang at the Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Science, 571101, Haikou, Hainan, China, for providing leaf tissues of cassava; Dr. Liu Aizhong at the Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303, Menglun, Yunnan, China, for providing leaf tissue of castor bean; and Dr. Wu Guojiang at the South China Botanical Garden, Chinese Acedemy of Sciences, 510650, Guangzhou, Guangdong, China, for providing leaf tissues of J. curcas. We sincerely thank the editors and two anonymous reviewers for their suggestion and comments on this manuscript.

Publisher Copyright:
© 2014, Springer Science+Business Media New York.

Keywords

Cassava
Energy plant
SSR marker
Transferability
Tung tree

ASJC Scopus subject areas

Molecular Biology
Plant Science

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10.1007/s11105-014-0804-3

Cite this

@article{ae589d01cdb9496280eb7619205fa811,

title = "Development of Microsatellite Markers in Tung Tree (Vernicia fordii) Using Cassava Genomic Sequences",

abstract = "Tung tree, Vernicia fordii, is a native oil-bearing woody plant of China. Oil extracted from the fruit is an important industrial and biodiesel feedstock. Microsatellite (simple-sequence repeat (SSR)) markers are effective in germplasm evaluation and marker-assisted breeding of plants. The objective of this study was to develop SSR markers in tung tree using cassava genomic sequences and test the effectiveness of the interspecific transferable SSR markers. According to the principle of comparative genomics, SSR markers were designed based on cassava genomic sequences and tested in tung tree and other Euphorbiaceae plant species. Among 255 cassava SSR markers, 104 (41 %) could effectively amplify DNA of tung tree, and a large portion of these transferable SSR markers could work well in other Euphorbiaceae species, Vernicia montana (98 %), castor bean (92 %), and Jatropha curcas (88 %). Genotyping a set of 16 tung tree accessions using the 104 transferable SSRs, a total of 437 alleles were obtained, 162 of which were polymorphic, and the Shannon information index varied from 0.000 to 0.560 with a mean of 0.139. A phylogenetic tree unambiguously distinguished the 32 accessions of the abovementioned five Euphorbiaceae species. Using cassava genomics resources is an effective approach to develop SSR markers for tung tree when its genome sequence is not available. The developed SSR markers should facilitate germplasm evaluation and other molecular-level investigations in tung tree.",

keywords = "Cassava, Energy plant, SSR marker, Transferability, Tung tree",

author = "Lingling Zhang and Mingcheng Luo and You, {Frank M.} and Eviatar Nevo and Shiyou Lu and Dongfa Sun and Junhua Peng",

note = "Funding Information: This work was supported by the National Natural Science Foundation of China (NSFC) grant nos. 31030055 and 30870233, Chinese Academy of Sciences under the Important Directional Program of Knowledge Innovation Project grant no. KSCX2-YW-Z-0722. We thank Dr. Wenquan Wang at the Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Science, 571101, Haikou, Hainan, China, for providing leaf tissues of cassava; Dr. Liu Aizhong at the Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303, Menglun, Yunnan, China, for providing leaf tissue of castor bean; and Dr. Wu Guojiang at the South China Botanical Garden, Chinese Acedemy of Sciences, 510650, Guangzhou, Guangdong, China, for providing leaf tissues of J. curcas. We sincerely thank the editors and two anonymous reviewers for their suggestion and comments on this manuscript. Publisher Copyright: {\textcopyright} 2014, Springer Science+Business Media New York.",

year = "2015",

month = aug,

day = "6",

doi = "10.1007/s11105-014-0804-3",

language = "English",

volume = "33",

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T1 - Development of Microsatellite Markers in Tung Tree (Vernicia fordii) Using Cassava Genomic Sequences

AU - Zhang, Lingling

AU - Luo, Mingcheng

AU - You, Frank M.

AU - Nevo, Eviatar

AU - Lu, Shiyou

AU - Sun, Dongfa

AU - Peng, Junhua

N1 - Funding Information: This work was supported by the National Natural Science Foundation of China (NSFC) grant nos. 31030055 and 30870233, Chinese Academy of Sciences under the Important Directional Program of Knowledge Innovation Project grant no. KSCX2-YW-Z-0722. We thank Dr. Wenquan Wang at the Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Science, 571101, Haikou, Hainan, China, for providing leaf tissues of cassava; Dr. Liu Aizhong at the Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303, Menglun, Yunnan, China, for providing leaf tissue of castor bean; and Dr. Wu Guojiang at the South China Botanical Garden, Chinese Acedemy of Sciences, 510650, Guangzhou, Guangdong, China, for providing leaf tissues of J. curcas. We sincerely thank the editors and two anonymous reviewers for their suggestion and comments on this manuscript. Publisher Copyright: © 2014, Springer Science+Business Media New York.

PY - 2015/8/6

Y1 - 2015/8/6

N2 - Tung tree, Vernicia fordii, is a native oil-bearing woody plant of China. Oil extracted from the fruit is an important industrial and biodiesel feedstock. Microsatellite (simple-sequence repeat (SSR)) markers are effective in germplasm evaluation and marker-assisted breeding of plants. The objective of this study was to develop SSR markers in tung tree using cassava genomic sequences and test the effectiveness of the interspecific transferable SSR markers. According to the principle of comparative genomics, SSR markers were designed based on cassava genomic sequences and tested in tung tree and other Euphorbiaceae plant species. Among 255 cassava SSR markers, 104 (41 %) could effectively amplify DNA of tung tree, and a large portion of these transferable SSR markers could work well in other Euphorbiaceae species, Vernicia montana (98 %), castor bean (92 %), and Jatropha curcas (88 %). Genotyping a set of 16 tung tree accessions using the 104 transferable SSRs, a total of 437 alleles were obtained, 162 of which were polymorphic, and the Shannon information index varied from 0.000 to 0.560 with a mean of 0.139. A phylogenetic tree unambiguously distinguished the 32 accessions of the abovementioned five Euphorbiaceae species. Using cassava genomics resources is an effective approach to develop SSR markers for tung tree when its genome sequence is not available. The developed SSR markers should facilitate germplasm evaluation and other molecular-level investigations in tung tree.

AB - Tung tree, Vernicia fordii, is a native oil-bearing woody plant of China. Oil extracted from the fruit is an important industrial and biodiesel feedstock. Microsatellite (simple-sequence repeat (SSR)) markers are effective in germplasm evaluation and marker-assisted breeding of plants. The objective of this study was to develop SSR markers in tung tree using cassava genomic sequences and test the effectiveness of the interspecific transferable SSR markers. According to the principle of comparative genomics, SSR markers were designed based on cassava genomic sequences and tested in tung tree and other Euphorbiaceae plant species. Among 255 cassava SSR markers, 104 (41 %) could effectively amplify DNA of tung tree, and a large portion of these transferable SSR markers could work well in other Euphorbiaceae species, Vernicia montana (98 %), castor bean (92 %), and Jatropha curcas (88 %). Genotyping a set of 16 tung tree accessions using the 104 transferable SSRs, a total of 437 alleles were obtained, 162 of which were polymorphic, and the Shannon information index varied from 0.000 to 0.560 with a mean of 0.139. A phylogenetic tree unambiguously distinguished the 32 accessions of the abovementioned five Euphorbiaceae species. Using cassava genomics resources is an effective approach to develop SSR markers for tung tree when its genome sequence is not available. The developed SSR markers should facilitate germplasm evaluation and other molecular-level investigations in tung tree.

KW - Cassava

KW - Energy plant

KW - SSR marker

KW - Transferability

KW - Tung tree

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M3 - Article

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SN - 0735-9640

VL - 33

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EP - 904

JO - Plant Molecular Biology Reporter

JF - Plant Molecular Biology Reporter

IS - 4

ER -

Development of Microsatellite Markers in Tung Tree (Vernicia fordii) Using Cassava Genomic Sequences

Abstract

Bibliographical note

Keywords

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