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United States Department of Agriculture

Agricultural Research Service

Research Project: Physiological and genetic approaches to improving extractable sugar yield in sugarbeet

Location: Sugarbeet and Potato Research

Title: Generation and characterization of a sugarbeet transcriptome and transcript-based SSR markers

Authors
item Fugate, Karen
item Fajardo, Diego -
item Schlautman, Brandon -
item Ferrareze, Jocleita -
item Bolton, Melvin
item Campbell, Larry
item Wiesman, Eric
item Zalapa, Juan

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 23, 2014
Publication Date: June 30, 2014
Citation: Fugate, K.K., Fajardo, D., Schlautman, B., Ferrareze, J.P., Bolton, M.D., Campbell, L.G., Wiesman, E.C., Zalapa, J.E. 2014. Generation and characterization of a sugarbeet transcriptome and transcript-based SSR markers. The Plant Genome. 7(2) doi: 10.3835/plantgenome2013.11.0038.

Interpretive Summary: Sugarbeet is a major source of refined sucrose, as well as a source for high-energy animal feeds and a substrate for biofuel production. Demand for higher productivity for this crop requires greater knowledge of sugarbeet physiology, pathology, and genetics which can be advanced by the development of new molecular tools. Towards this end, a composite dataset of genes expressed in leaf and root tissues at varying stages of development and production and after exposure to the plant hormones, jasmonic acid and salicylic acid, was developed and used to generate molecular markers that can be used by breeders. The generated dataset contains 82,404 gene sequences. A total of 37,207 of these share sequence similarity with identified proteins from sugarbeet or other plant species and identified gene sequences were classified by function, metabolic pathway, or cellular location to which they putatively contribute. The dataset was used to identify 7,680 sites that could be used for the development of molecular markers. PCR primer-pairs were designed for 288 selected sites, and 72 of these primer-pairs were tested for their ability to detect diversity between germplasm. Forty-three of the tested primer-pairs were effective in distinguishing diversity among eight Beta vulgaris genotypes. The newly developed molecular tools provide additional public domain genomic resources for an important crop plant. Their use will potentially further our understanding of the functional elements of the sugarbeet genome, aid in the discovery of novel genes, facilitate expression research, and provide new tools for sugarbeet genetic research and selective breeding.

Technical Abstract: Sugarbeet is a major source of refined sucrose, as well as a source for high-energy animal feeds and a substrate for biofuel production. Demand for higher productivity for this crop requires greater knowledge of sugarbeet physiology, pathology, and genetics which can be advanced by the development of new genomic resources. Towards this end, a sugarbeet reference transcriptome containing expressed genes from leaf and root tissues at varying stages of development and production and after elicitation with jasmonic acid or salicylic acid was developed and used to generate simple sequence repeat markers. The reference transcriptome was generated via Illumina paired-end RNA sequencing. Cleaned raw reads were assembled into 82,404 unigenes. The median unigene length was 424 nucleotides with greater than 83.4% of unigenes containing no gaps in their sequence. A total of 37,207 unigenes were annotated by sequence similarity search against proteins contained in the National Center for Biotechnology Information (NCBI) nonredundant protein (nr) database, Swiss-Prot protein database, Kyoto Encyclopedia of Genes and Genomes (KEGG) protein database, and Clusters of Orthologous Groups (COG) of proteins. Of the annotated unigenes, 9,480 unigenes were functionally classified using COG annotations, 17,191 unigenes were classified into the biological process, molecular function, or cellular component to which they putatively contribute using Gene Ontology terms, and 17,409 unigenes were assigned to 126 metabolic or functional pathways using KEGG identifiers. A SSR search of the transcriptome identified 7,680 SSRs, including 6,577 perfect SSRs, of which 3,834 were located in unigenes with ungapped sequence. Primer-pairs were designed for 288 selected SSR loci, and 72 of these primer-pairs were tested for their ability to detect polymorphisms. Forty-three primer-pairs detected single polymorphic loci and effectively distinguished diversity among eight diverse Beta vulgaris genotypes. The newly developed reference transcriptome and SSR markers provide additional genomic resources in the public domain for an important crop plant. Their use will potentially further our understanding of the functional elements of the sugarbeet genome, aid in the discovery of novel genes, facilitate RNA-seq based expression research, and provide new tools for sugarbeet genetic research and selective breeding.

Last Modified: 9/10/2014
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