A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

被引：147

作者：

Durand, Jerome ^{[1
,2
]}

Bodenes, Catherine ^{[1
,2
]}

Chancerel, Emilie ^{[1
,2
]}

Frigerio, Jean-Marc ^{[1
,2
]}

Vendramin, Giovanni ^{[3
]}

Sebastiani, Federico ^{[3
]}

Buonamici, Anna ^{[3
]}

Gailing, Oliver ^{[4
,5
]}

Koelewijn, Hans-Peter ^{[6
]}

Villani, Fiorella ^{[7
]}

Mattioni, Claudia ^{[7
]}

Cherubini, Marcello ^{[7
]}

Goicoechea, Pablo G. ^{[8
]}

Herran, Ana ^{[8
]}

Ikaran, Ziortza ^{[8
]}

Cabane, Cyril ^{[9
]}

Ueno, Saneyoshi ^{[1
,2
,10
]}

Alberto, Florian ^{[1
,2
]}

Dumoulin, Pierre-Yves ^{[1
,2
]}

Guichoux, Erwan ^{[1
,2
]}

de Daruvar, Antoine ^{[9
]}

Kremer, Antoine ^{[1
,2
]}

Plomion, Christophe ^{[1
,2
]}

机构：

[1] INRA, BIOGECO, UMR1202, F-33610 Cestas, France

[2] Univ Bordeaux, UMR1202, BIOGECO, F-33610 Cestas, France

[3] CNR, Plant Genet Inst, I-50019 Sesto Fiorentino, FI, Italy

[4] Univ Gottingen, Forest Genet & Forest Tree Breeding Busgen Inst, Fac Forest Sci & Forest Ecol, D-37077 Gottingen, Germany

[5] Michigan Technol Univ, Sch Forest Resources & Environm Sci 07, Houghton, MI 49931 USA

[6] ALTERRA Wageningen UR, NL-6700 AA Wageningen, Netherlands

[7] CNR, Ist Biol Agroambientale & Forestale, I-05010 Porano, TR, Italy

[8] NEIKER, Dpto Biotecnol, Vitoria 01080, Spain

[9] Univ Victor Segalen Bordeaux 2, CBiB, F-33076 Bordeaux, France

[10] Forestry & Forest Prod Res Inst, Dept Forest Genet, Tree Genet Lab, Tsukuba, Ibaraki 3058687, Japan

来源：

BMC GENOMICS | 2010年 / 11卷

关键词：

Amplify Fragment Length Polymorphism; Genomic SSRs; Amplify Fragment Length Polymorphism Marker; Trimeric SSRs; Dimeric SSRs;

D O I：

10.1186/1471-2164-11-570

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Background: Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut). Results: A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher. Conclusion: We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.

引用

页数：13

共 19 条

[1]

ALBERTO F, MOL ECOL

[2]

[Anonymous], 1987, Science, Philosophy, and Human Behavior in the Soviet Union

[3] Construction of a dense genetic linkage map for apple rootstocks using SSRs developed from Malus ESTs and Pyrus genomic sequences [J].

Celton, J. -M. ;

Tustin, D. S. ;

Chagne, D. ;

Gardiner, S. E. .

TREE GENETICS & GENOMES, 2009, 5 (01) :93-107

[4] A set of EST-SNPs for map saturation and cultivar identification in melon [J].

Deleu, Wim ;

Esteras, Cristina ;

Roig, Cristina ;

Gonzalez-To, Mireia ;

Fernandez-Silva, Iria ;

Gonzalez-Ibeas, Daniel ;

Blanca, Jose ;

Aranda, Miguel A. ;

Arus, Pere ;

Nuez, Fernando ;

Monforte, Antonio J. ;

Belen Pico, Maria ;

Garcia-Mas, Jordi .

BMC PLANT BIOLOGY, 2009, 9

[5] EST-SSRs as a resource for population genetic analyses [J].

Ellis, J. R. ;

Burke, J. M. .

HEREDITY, 2007, 99 (02) :125-132

[6]

Goudet J., FSTAT PROGRAM ESTIMA

[7]

GRATTAPAGLIA D, 1994, GENETICS, V137, P1121

[8]

GREEN P, 1999, SWAT CROSSMATCH PHRA

[9]

Green P., 1996, Documentation for Phrap

[10]

Iseli C, 1999, Proc Int Conf Intell Syst Mol Biol, P138

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