Analysis of Gene Expression Profiles in Leaf Tissues of Cultivated Peanuts and Development of EST-SSR Markers and Gene Discovery.

Baozhu Guo,Tim Brenneman,Albert Culbreath,Phat Dang,Xuanqiang Liang,Xiaoping Chen,Yanbin Hong,Corley Holbrook

doi:10.1155/2009/715605

Abstract

Peanut is vulnerable to a range of foliar diseases such as spotted wilt caused by Tomato spotted wilt virus (TSWV), early (Cercospora arachidicola) and late (Cercosporidium personatum) leaf spots, southern stem rot (Sclerotium rolfsii), and sclerotinia blight (Sclerotinia minor). In this study, we report the generation of 17,376 peanut expressed sequence tags (ESTs) from leaf tissues of a peanut cultivar (Tifrunner, resistant to TSWV and leaf spots) and a breeding line (GT-C20, susceptible to TSWV and leaf spots). After trimming vector and discarding low quality sequences, a total of 14,432 high-quality ESTs were selected for further analysis and deposition to GenBank. Sequence clustering resulted in 6,888 unique ESTs composed of 1,703 tentative consensus (TCs) sequences and 5185 singletons. A large number of ESTs (5717) representing genes of unknown functions were also identified. Among the unique sequences, there were 856 EST-SSRs identified. A total of 290 new EST-based SSR markers were developed and examined for amplification and polymorphism in cultivated peanut and wild species. Resequencing information of selected amplified alleles revealed that allelic diversity could be attributed mainly to differences in repeat type and length in the SSR regions. In addition, a few additional INDEL mutations and substitutions were observed in the regions flanking the microsatellite regions. In addition, some defense-related transcripts were also identified, such as putative oxalate oxidase (EU024476) and NBS-LRR domains. EST data in this study have provided a new source of information for gene discovery and development of SSR markers in cultivated peanut. A total of 16931 ESTs have been deposited to the NCBI GenBank database with accession numbers ES751523 to ES768453.

Highlights

Peanut (Arachis hypogaea L.), an important source of oil, protein, and other nutrients worldwide, is ranked as the second most important seed legume after soybean
Generation of expressed sequence tags (ESTs) Derived from Peanut Leaf cDNA Libraries
After trimming vector and discarding low-quality sequences from the raw sequences, 16 931 high-quality EST sequences were obtained for further analysis

Summary

Introduction

Peanut (Arachis hypogaea L.), an important source of oil, protein, and other nutrients worldwide, is ranked as the second most important seed legume after soybean. In recent years emphasis has been placed on the improvement of cultivated peanuts and the development of new cultivars with higher levels of resistance to fungal and viral diseases, which have caused reduced levels of peanut production worldwide [1,2,3]. Tomato spotted wilt virus (TSWV), a member of the genus Tospoviruses, causes significant yield loss in many production areas. Both early leaf spot (Cercospora arachidicola) and late leaf spot (Cercosporidium personatum) are severe and widespread diseases of peanut. The improvement of existing cultivars and/or development of new cultivars with greater levels of field resistance is the most effective economical means of controlling these diseases and is a major objective in peanut breeding programs [4].

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Results

Conclusion