EST sequencing and gene expression profiling of cultivated peanut (Arachis hypogaea L.)

Bi, Yu-Ping; Liu, Wei; Xia, Han; Su, Lei; Zhao, Chuan-Zhi; Wan, Shu-Bo; Wang, Xing-Jun
October 2010
Genome;Oct2010, Vol. 53 Issue 10, p832
Academic Journal
Peanut (Arachis hypogaea L.) is one of the most important oil crops in the world. However, biotechnological based improvement of peanut is far behind many other crops. It is critical and urgent to establish the biotechnological platform for peanut germplasm innovation. In this study, a peanut seed cDNA library was constructed to establish the biotechnological platform for peanut germplasm innovation. About 17 000 expressed sequence tags (ESTs) were sequenced and used for further investigation. Among which, 12.5% were annotated as metabolic related and 4.6% encoded transcription or post-transcription factors. ESTs encoding storage protein and enzymes related to protein degradation accounted for 28.8% and formed the largest group of the annotated ESTs. ESTs that encoded stress responsive proteins and pathogen-related proteins accounted for 5.6%. ESTs that encoded unknown proteins or showed no hit in the GenBank nr database accounted for 20.1% and 13.9%, respectively. A total number of 5066 EST sequences were selected to make a cDNA microarray. Expression analysis revealed that these sequences showed diverse expression patterns in peanut seeds, leaves, stems, roots, flowers, and gynophores. We also analyzed the gene expression pattern during seed development. Genes that were upregulated (>=twofold) at 15, 25, 35, and 45 days after pegging (DAP) were found and compared with 70 DAP. The potential value of these genes and their promoters in the peanut gene engineering study is discussed. L'arachide (Arachis hypogaea L.) est l'une des oléagineuses les plus importantes dans le monde. Malgré cela, la contribution des biotechnologies à l'amélioration génétique chez cette espèce a été beaucoup moindre que chez d'autres espèces. Il est ainsi critique et urgent d'établir une plateforme biotechnologique permettant l'innovation au sein des ressources génétiques de l'arachide. Dans ce travail, une banque d'ADNc de graines de l'arachide a été produite pour fonder l'assise d'une plateforme biotechnologique d'innovation chez l'arachide. Environ 17 000 EST ont été séquencés et employés lors d'analyses subséquentes. Parmi ceux-ci, 12,5% ont été annotés comme étant liés au métabolisme et 4,6% des EST codaient pour des facteurs transcriptionnels ou post-transcriptionnels. Les EST codant pour des protéines de réserve ou pour des enzymes impliquées dans la dégradation des protéines formaient le plus grand groupe et représentaient 28,8% des EST annotés. Les EST codant pour des protéines de réponse aux stress ou aux pathogènes constituaient 5,6% du total. Les EST codant pour des protéines inconnues et ceux codant pour des protéines sans homologues au sein de GenBank constituaient respectivement 20,1% et 13,9% du total. Une collection de 5066 séquences d'EST a été retenue pour fabriquer une puce d'ADNc. Une analyse transcriptomique a révélé que ces séquences montraient divers motifs d'expression chez les graines, les feuilles, les tiges, les racines, les fleurs et les gynophores de l'arachide. Les auteurs ont également analysé l'expression génique au cours du développement des graines. Des gènes qui étaient sur-exprimés (>2 fois) à 15, 25, 35 et 45 jours après fécondation par rapport au niveau enregistré à 70 jours ont été identifiés. Les auteurs discutent de l'utilité potentielle de ces gènes et de leurs promoteurs pour des fins d'ingénierie génétique chez l'arachide.


Related Articles

  • A novel method to identify the DNA motifs recognized by a defined transcription factor. Ji, Xiaoyu; Wang, Liuqiang; Nie, Xianguang; He, Lin; Zang, Dandan; Liu, Yujia; Zhang, Bing; Wang, Yucheng // Plant Molecular Biology;Nov2014, Vol. 86 Issue 4-5, p367 

    The interaction between a protein and DNA is involved in almost all cellular functions, and is vitally important in cellular processes. Two complementary approaches are used to detect the interactions between a transcription factor (TF) and DNA, i.e. the TF-centered or protein-DNA approach, and...

  • Wide-scale screening of T-DNA lines for transcription factor genes affecting male gametophyte development in Arabidopsis. Reňák, David; Dupl'áková, Nikoleta; Honys, David // Sexual Plant Reproduction;Mar2012, Vol. 25 Issue 1, p39 

    Male gametophyte development leading to the formation of a mature pollen grain is precisely controlled at various levels, including transcriptional, post-transcriptional and post-translational, during its whole progression. Transcriptomic studies exploiting genome-wide microarray technologies...

  • Computational identification of anthocyanin-specific transcription factors using a rice microarray and maximum boundary range algorithm. Chang Kug Kim; Shoshi Kikuchi; Jang Ho Hahn; Soo Chul Park; Yong Hwan Kim; Byun Woo Lee // Evolutionary Bioinformatics;2010, Issue 6, p133 

    This study identifies 2,617 candidate genes related to anthocyanin biosynthesis in rice using microarray analysis and a newly developed maximum boundary range algorithm. Three seed developmental stages were examined in white cultivar and two black Dissociation insertion mutants. The resultant...

  • Osiris: an integrated promoter database for Oryza sativa L. Robert T. Morris; Timothy R. OConnor; John J. Wyrick // Bioinformatics;Dec2008, Vol. 24 Issue 24, p2915 

    Summary: Rice (Oryza sativa L.) is an important model monocot and cereal crop. While the rice genome sequence has been published and annotated, relatively little is known about the transcriptional networks that regulate rice gene expression. For this reason, we have developed Osiris, a database...

  • Sequence Characterization and Expression Analysis of Three APETALA2-like Genes from Saffron Crocus. Tsaftaris, Athanasios; Pasentsis, Konstantinos; Madesis, Panagiotis; Argiriou, Anagnostis // Plant Molecular Biology Reporter;Apr2012, Vol. 30 Issue 2, p443 

    To further understand flowering and flower organs formation in the monocot crop saffron crocus ( Crocus sativus L.), we cloned three APETALA2-like cDNA sequences of the AP2/ERF transcription factor family designated CsatAP2a/b/c as well as the respective promoter region sequences. Bioinformatics...

  • Isolation and Characterization of Three Cassava Elongation Factor 1 Alpha (MeEF1A) Promoters. Suhandono, Sony; Apriyanto, Ardha; Ihsani, Nisa // PLoS ONE;Jan2014, Vol. 9 Issue 1, p1 

    In plant genetic engineering, the identification of gene promoters leading to particular expression patterns is crucial for the development of new genetically modified plant generations. This research was conducted in order to isolate and characterize several new promoters from cassava (Manihot...

  • Sources of High Variance between Probe Signals in Affymetrix Short Oligonucleotide Microarrays. Jaksik, Roman; Marczyk, Michal; Polanska, Joanna; Rzeszowska-Wolny, Joanna // Sensors (14248220);Jan2014, Vol. 14 Issue 1, p532 

    High density oligonucleotide microarrays present a big challenge for statistical data processing methods which aim to separate changes induced by experimental factors from those caused by artifacts and measurement inaccuracies. Despite huge advances in the field of microarray probe design...

  • Cloning and expression analysis of peanut (Arachis hypogaea L.) CHI gene. Yue Zhang; Han Xia; Mei Yuan; Chuanzhi Zhao; Aiqin Li; Xingjun Wang // Electronic Journal of Biotechnology;1/15/2012, Vol. 15 Issue 1, p1 

    Chalcone isomerase (CHI) is the key enzyme that catalyzes chalcone into (2S)-flavanol or (2S)-5-desoxidation flavanol. The full length cDNA (1050 bp) of AhCHI (Arachis hypogaea CHI gene) was cloned by large scale EST sequencing using a peanut immature seed cDNA library. Sequence analysis results...

  • TILLING by sequencing to identify induced mutations in stress resistance genes of peanut (Arachis hypogaea). Yufang Guo; Abernathy, Brian; Yajuan Zeng; Ozias-Akins, Peggy // BMC Genomics;2015, Vol. 16 Issue 1, p1 

    Background: Targeting Induced Local Lesions in Genomes (TILLING) is a powerful reverse genetics approach for functional genomics studies. We used high-throughput sequencing, combined with a two-dimensional pooling strategy, with either minimum read percentage with non-reference nucleotide or...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics