expressed sequence tag (EST) or other genomic sequences. EST sequences represent actual genes. Increasing the number of EST sequences available in the database facilitates the development of EST-SSR markers in a batch mode ( Chen et al., 2006 ). EST
Chunxian Chen, Jude W. Grosser, Milica Ćalović, Patricia Serrano, Gemma Pasquali, Julie Gmitter, and Fred G. Gmitter Jr
Cunquan Yuan, Zhiyi Qu, Huitang Pan, Tangren Cheng, Jia Wang, and Qixiang Zhang
; Taheri et al., 2018 ). Expressed sequence tag SSRs have shown advantages because of their inexpensive development, high level of genetic diversity, and high transferability to related taxa ( Taheri et al., 2018 ); however, we previously found that the
Amnon Levi, Angela Davis, Pat Wechter, Alvaro Hernandez, and Jyothi Thimmapuram
A cDNA library was assembled using mRNA of watermelon fruit. The cDNA library was normalized and subtracted by hybridization with leaf cDNA of the same watermelon cultivar (Illini Red). 1,046 cDNA clones were sequenced to identify genes associated with fruit development and quality. Of 1,046 cDNA clones sequenced, 832 were unique sequences and designated as expressed sequenced tags (ESTs). Of the 832 ESTs, 205 (24.6%) have not been reported in any other plant species. Additionally, 186 ESTs (22.4%) correspond to genes with unknown function, while 441 ESTs (53.0%) correspond to genes with known function in other plant species. These ESTs are mainly associated with primary metabolism, membrane transport, cytoskeleton synthesis and structure, cell wall and cell division, signal transduction, nucleic acid binding and transcription factors, and defense and stress response. Differential expression of the ESTs was examined using microarray analysis. About 200 (24%) of the 832 ESTs showed differential expression during the development and ripening of watermelon fruit. The ESTs were also screened for simple sequence repeat (SSR) motifs. Of 832 ESTs screened, 177 contain SSR motifs. Primer pairs are being designed for these ESTs, and will be used for development of EST-SSR markers and for mapping on a genetic linkage map constructed for watermelon. This study provides valuable information on genes controlling watermelon fruit development and quality.
John McCallum, Susan Thomson, Meeghan Pither-Joyce, Fernand Kenel, Andrew Clarke, and Michael J. Havey
-nucleotide polymorphism (SNP) markers have been developed from onion expressed sequence tag (EST) resources ( Kuhl et al., 2004 ; Martin et al., 2005 ) and proved to be readily reproducible for mapping ( McCallum et al., 2006a , 2006b ) and cultivar discrimination
David Jesús Gil-Ariza, Iraida Amaya, José Manuel López-Aranda, José Federico Sánchez-Sevilla, Miguel Ángel Botella, and Victoriano Valpuesta
al., 2001 ; Graham et al., 1996 ; Shimomura and Hirashima, 2006 ). The initial objective of this study was to determine the capacity of 10 expressed sequence tag (EST)-derived SSR markers, selected by their high discriminatory power, for effective
Amnon Levi, William P. Wechter, Karen R. Harris, Angela R. Davis, and Zhangjun Fei
et al., 2001 , 2006b , 2009 ), which may not be readily detected by random primers. In fact, DNA polymorphism among watermelon cultivars could be detected with expressed sequence tag (EST)-polymerase chain reaction (PCR) and sequence
Sunao Hisada, Tomoya Akihama, Tomoko Endo, Takaya Moriguchi, and Mitsuo Omura
A cDNA library was constructed from satsuma mandarin (Citrus unshiu Marc.) fruit tissues during the rapid cell enlargement phase. A total of 950 individual cDNA clones was partially sequenced and compared with GenBank databases for characterizing the gene repertoire expressed during this developmental phase. Among these, 426 cDNA clones (44.8%) showed sequence identity with previously characterized genes with optimized (OPT) scores of ≥200, while 524 clones (55.2%) resulted in low OPT scores (<200) and did not show any significant sequence identity with previously published genes. Based on nucleotide sequence, most clones with OPT scores of ≥200 were assumed to be transcription-, translation-, cell-wall-metabolism-, and stress-response-related genes. Other clones showed homology with published sequences related to housekeeping and stress-response-related genes, including metallothionein-like proteins, late-embryogenesis-abundant (LEA) proteins, and heat-shock proteins. These results suggested that Citrus fruit during rapid cell enlargement were metabolically active and expanding in response to biotic and abiotic stress. For clones with low nucleotide sequence homology, the recurrence was evaluated by aligning nucleotide sequences of each clone and generating contig maps. Expressed sequence tags (ESTs) of 162 clones with OPT scores <200 have not been reported for any other organism. Collectively, randomly sequenced cDNA clones described in this study provided information on types of genes expressed during the rapid cell enlargement phase in Citrus fruit. These genes should be used as candidates for Citrus genome mapping projects.
Yan Xu and Yuejin Wang
Expressed sequence tags (ESTs) constitute a rapid and informative strategy for studying gene-expression profiles of specific stages of annual and perennial plant species. Compared with annual plants, the NCBI database has very little sequence information from perennial plant species. To date, only ∼145 ESTs of Vitis pseudoreticulata W.T. Wang have been deposited in databases. This is insufficient to understand the biology and development of this species. In this report, a cDNA library constructed from young leaf inoculated with powdery mildew pathogen [Uncinula necator (Schw.) Burr.] of Chinese wild Vitis pseudoreticulata. Leaf was harvested at various times after inoculation for total RNA extraction, which was used to generate ESTs. In our study, 107 cDNA clones were sequenced either from 5' or 3' end of the cDNAs. Among them, 60 unigenes (56%) were functionally characterized by the BLASTX matches to known function proteins, and 20 unigenes (18.6 %) matched significantly with those having unknown function in the public databases. The remaining 27 unigenes (25.2%) failed to show significant homology to any proteins in the public databases, suggesting that they represent novel sequences. Some functional genes identified from the cDNA library to be potentially associated with plant defence-related responses are discussed.
Wenting Wang, Chao Feng, Zehuang Zhang, Liju Yan, Maomao Ding, Changjie Xu, and Kunsong Chen
Chinese bayberry (Morella rubra) is an economically important subtropical evergreen fruit crop native to China and other Asian countries. For facilitating cultivar discrimination and genetic diversity analysis, a total of 38 high-quality and highly polymorphic expressed sequence tags-simple sequence repeat (EST-SSR) markers, with little or no polymerase chain reaction (PCR) stutter bands, including 21 screened from those obtained previously and 17 newly developed markers, were developed. The average number of alleles (N a) per locus was 5.6, and polymorphism information content varied from 0.34 to 0.86, with a mean value of 0.57. With these markers, all 42 Chinese bayberry accessions analyzed were successfully discriminated and the phylogenetic relationship between accessions was revealed. The accessions can be separated into two groups with six subgroups. The grouping of four main cultivars in three subgroups and 12 white-fruited accessions, each with little or no anthocyanin accumulation in ripe fruit, into five subgroups suggested the preservation of broad diversity among cultivated populations. These EST-SSR markers and the findings obtained in this study can assist the discrimination of cultivars and lines and contribute to genetic and breeding studies in Chinese bayberry.
Jianfeng Liu, Bowen Yang, Yuetong Ming, Yuchu Zhang, and Yunqing Cheng
desirable genetic attributes, including relative abundance, high polymorphism, codominant inheritance, transferability to related species and genera, and good genome coverage ( Guo et al., 2016 ). The expressed sequence tag (EST)-SSRs are widely used in the