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Title of Journal: Theor Appl Genet

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Abbravation: Theoretical and Applied Genetics

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Springer-Verlag

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DOI

10.1007/bf01019957

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1432-2242

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Development of 1030 genomic SSR markers in switch

Authors: Y W Wang T D Samuels Y Q Wu
Publish Date: 2010/10/27
Volume: 122, Issue: 4, Pages: 677-686
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Abstract

Switchgrass Panicum virgatum L a native to the tall grass prairies in North America has been grown for soil conservation and herbage production in the USA and recently widely recognized as a promising dedicated cellulosic bioenergy crop A large amount of codominant molecular markers including simple sequence repeats SSRs are required for the construction of linkage maps and implementation of molecular breeding strategies to develop superior switchgrass cultivars The objectives of this study were 1 to identify SSRcontaining clones and to design PCR primer pairs PPs in SSRenriched genomic libraries and 2 to validate and characterize the designed SSR PPs Five genomic SSR enriched libraries were constructed using genomic DNA of ‘SL93 7 × 15’ a switchgrass genotype selected in an Oklahoma State University OSU southern lowland breeding population A total of 3046 clones from four libraries enriched in CA/TGn GA/TCn CAG/CTGn and AAG/CTTn SSR repeats were sequenced at the OSU Core Facility From the sequences we isolated 1300 unique SSRcontaining clones from which we designed 1398 PPs using SSR Locator V1 software Among the designed PPs 1030 737 amplified reproducible and strong bands with expected fragment size and 802 detected polymorphic alleles in SL93 7 × 15 and ‘NL94 16 × 13’ two parents of one mapping population All of the four libraries contained a high rate of perfect SSR repeat types ranging from 627 to 762 Polymorphism of the effective SSR markers was also tested in two lowland and two upland switchgrass cultivars encompassing ‘Alamo’ and ‘Kanlow’ and ‘Blackwell’ and ‘Dacotah’ respectively The developed SSR markers should be useful in genetic and breeding research in switchgrassWe gratefully thank Sharon Williams Pu Feng and Gary Williams for maintenance of plant materials used in this study in greenhouse Dr Ming Su from Oklahoma State University for helping format the Electronic Supplementary Material and Ms Yan Song and Dr Peter Hoyt of the OSU Microarray and Bioinformatics Core Facility for trimming the sequences This work has been supported in part by the NSF EPSCoR award EPS 0814361 We are also grateful to the China Scholarship Council No 2006 3142 and Quality Forage Products Promotion Program 2006G38 funded by the Ministry of Agriculture of China for supporting a visiting research stay of Yunwen Wang at Oklahoma State University


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