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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Publications at this Location » Publication #322825

Research Project: Genomics and Bioinformatics Research in Agriculturally Important Organisms

Location: Genomics and Bioinformatics Research

Title: Application of genomic, transcriptomic and metabolomic technologies in Arachis species

Author
item CHU, YE - University Of Georgia
item CLEVENGER, JOSH - University Of Georgia
item HOVAV, RAN - Agricultural Research Organization, Volcani Center
item WANG, JIANPING - University Of Florida
item Scheffler, Brian
item JACKSON, SCOTT - University Of Georgia
item OZIAS-AKINS, PEGGY - University Of Georgia

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 12/1/2015
Publication Date: 12/30/2016
Citation: Chu, Y., Clevenger, J., Hovav, R., Wang, J., Scheffler, B.E., Jackson, S., Ozias-Akins, P. 2016. Peanuts: genetics, processing, and utilization. In: Elsevier. Application of genomic, transcriptomic and metabolomic technologies in Arachis species. San Diego, CA. p.209-239.

Interpretive Summary: Geminiviruses represent one of the most challenging types of viruses in cropping systems. Besides the detrimental impact on crop production, geminiviruses exhibit a high rate of genetic change which can result in alterations of pathogenicity of the existing virus strain or in the development of a new strain. Such changes can be in the main body of virus’ DNA or in satellite DNAs. While some genetic changes are individual nucleotides, many geminiviruses exchange larger portions of DNA through some method of recombination or through the inclusion of different satellite DNAs. The ability to identify viral DNA changes is critical to understanding their behavior in nature and the alterations they cause in plants due to infection. The analysis tool for characterizing these DNA changes has been historically the isolation and enrichment of circular DNA from whole DNA samples collected from plants. This is then followed by cloning the circular DNA and subsequent sequencing of individual clones. This whole process is time consuming, expensive and limited in scope. In this study, a papaya plant exhibiting leaf curling, similar to cotton leaf curl virus, was examined for geminivirus infection using traditional methods and high throughput DNA sequencing, also known as next generation sequencing (NGS). Analysis of the data showed that NGS is a valid replacement for traditional methods. In addition, NGS offers a valuable tool for viral diversity studies. Comparative studies of existing DNA sequences and data from this study showed that the Indian subcontinent is a hotspot for geminiviruses that infect papaya. Also papaya is host for an array of viruses which poses a problem since it is a long living plant.

Technical Abstract: Peanut genetic improvement is approaching the cusp of rapidly accelerating gains due to application of genomic, transcriptomic, and metabolomic tech¬nologies. Yield is a primary target trait for improvement, but is impacted by biotic and abiotic stresses, and quality traits specific to different cultural and industrial sectors that must be taken into account. Arachis genomic and transcriptomic resources, both for cultivated tetraploid peanut, Arachis hypogaea L., and its diploid ances¬tors, Arachis duranensis Krapov. & W. C. Gregory (A genome) and Arachis ipaënsis Krapov. & W. C. Gregory (B genome), have been greatly enriched since their status was documented in 2012, leading to an in-depth understanding of genomic architecture based on comparative sequence analyses. Identifying genes underlying important disease resis¬tance or quality traits requires knowledge of gene action at the level of phe¬notypic response as well as genetic markers within (direct) or near (indirect) genes. Once direct or indirect marker–trait linkages have been validated, markers can be used as surrogates to select for a trait. The efficacy of a marker for selection of a trait is greatest when the marker is within an identi¬fied gene; therefore, targeting gene regions for development of high density molecular maps is desirable. The density of molecular maps in cultivated peanut has been constrained by low molecular polymorphism rates among genotypes and the limited amount of sequence data from which polymor¬phisms could be mined, although in spite of these limitations considerable progress has been made to develop and integrate genetic maps. The peanut genome project has gener¬ated sequence and phenotype data that vastly improve our ability to cre¬ate dense genetic maps encompassing traits of interest, thereby positioning markers in or near genes with functional significance for peanut growth, productivity and sustainability.