Generation of Expressed Sequence Tags (ESTs) for Gene Discovery and Marker Development in Cultivated Peanut

Abstract

Expressed sequence tag (EST) libraries for cultivated peanut (Arachis hypogaea L.) were developed from two cDNA libraries constructed by means of mRNA prepared from leaves of peanut line C34‐24 (resistant to leaf spots and Tomato spotted wilt virus) and immature pods of peanut line A13 (tolerant to drought stress and preharvest aflatoxin contamination). Randomly selected cDNA clones were partially sequenced to generate a total of 1825 ESTs, 769 from the C34‐24 cDNA library and 1056 from the A13 cDNA library, in which 536 and 769 unique ESTs were identified, respectively. Results of BLASTx search showed that 52.8% of the ESTs from leaf tissue and 78.6% of the ESTs from the pod tissue have homology to genes of known function. Approximately 27.3 and 22.1% of ESTs matching homologous sequences in dbEST of GenBank on the basis of BLASTn algorithm have unknown functions. The ESTs were queried against MIPS functional catalog criteria and sorted according to putative function into 15 categories. A total of 1345 ESTs have been released to GenBank1 Four hundred unigenes have been selected from these ESTs and arrayed on glass slides for gene expression analysis, and 44 EST‐derived simple sequence repeat (SSR) markers have been characterized for cultivated peanut, in which over 20% of the SSRs produced polymorphic markers among 24 cultivated peanut genotypes. This is the first report of ESTs in cultivated peanut, and further characterization of resistance and stress genes may explain mechanisms functioning in these two peanut lines.

Identification and functional validation of a unique set of drought induced genes preferentially expressed in response to gradual water stress in peanut

“…This could be because peanut plants are able to maintain turgor driven process as a result of osmotic adjustment, in turn leading to maintenance of cellular metabolism. There are a couple of drought stress cDNA library already generated in A. hypogaea, but they correspond to genes expressed in immature pods (Luo et al 2005;Devaiah et al 2007). There is one library, which catalogues the genes expressed in a wild Arachis species (A. stenosperma) under non-stress condition (Proite et al 2007).…”

Repertoire of leaf expressed sequence tags (ESTs) and partial characterization of stress-related and membrane transporter genes from mulberry (Morus indica L.)

“…Some of the proteins, which did not show any sequence similarity with known proteins, can be considered putatively as genes specific for mulberry. Comparative analysis of expressed sequence tags from different organs as attempted in Populus (Bhalerao et al 2003), maize (Fernandes et al 2002), Vitis vinifera (Moser et al 2005), and peanut (Luo et al 2005) will be highly effective in annotating new expressed sequences in mulberry.…”

Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut

“…Advances in other marker types, such as randomly amplified polymorphic DNA (RAPD) (Halward and Stalker, 1991;Halward et al, 1992), restriction fragment length polymorphism (RFLP) (Halward and Stalker, 1991;Kochert et al, 1996;Burow et al, 2009), amplified fragment length polymorphism (AFLP) (Herselman et al, 2004), simple sequence repeat (SSR) (He et al, 2003;Gimenes et al, 2007;Cuc et al, 2008;Liang et al, 2009), sequence-related amplified polymorphism (SRAP) , single strand conformational polymorphism (SSCP) (Nagy et al, 2010), and single nucleotide polymorphism (SNP) (Nagy et al, 2012), soon replaced the early exploration with proteins. During the past two decades, much effort has been made to develop genetic and genomic tools in cultivated peanut, such as construction of BAC libraries (Yuksel and Paterson, 2005;Guimarães et al, 2008), cDNA libraries (Luo et al, 2005;Proite et al, 2007;Guo et al, 2008Guo et al, , 2009Koilkonda et al, 2012), RNAseq using next generation sequencing technology (Guimaraes et al, 2012;Zhang et al, 2012) and development of DNA markers (see reviews of Feng et al, 2012;Pandey et al, 2012;Zhao et al, 2012; (Table 1). Among the various molecular markers investigated to date, simple sequence repeats (SSR) have emerged as one of the preferred DNA marker system for conducting genetic and genomic studies in cultivated peanut.…”