Generation and Characterization of a Sugarbeet Transcriptome and Transcript‐Based SSR Markers

Abstract

Sugarbeet is a major source of refined sucrose and increasingly grown 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 transcriptome of expressed genes from leaf and root tissues at varying stages of development and production, and after elicitation with jasmonic acid (JA) or salicylic acid (SA), was constructed and used to generate simple sequence repeat (SSR) markers. The transcriptome was generated via paired-end RNA sequencing and contains 82,404 unigenes. A total of 37,207 unigenes were annotated, of which 9480 were functionally classified using clusters of orthologous groups (COG) annotations, 17,191 were classified into biological process, molecular function, or cellular component using gene ontology (GO) terms, and 17,409 were assigned to 126 metabolic pathways using Kyoto Encyclopedia of Genes and Genomes (KEGG) identifiers. A SSR search of the transcriptome identified 7680 SSRs, including 6577 perfect SSRs, of which 3834 were located in unigenes with ungapped sequence. Primer-pairs were designed for 288 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 B. vulgaris genotypes. The transcriptome and SSR markers provide additional, public domain genomic resources for an important crop plant and can be used to increase understanding of the functional elements of the sugarbeet genome, aid in discovery of novel genes, facilitate RNA-sequencing based expression research, and provide new tools for sugarbeet genetic research and selective breeding. Sugarbeet (Beta vulgaris L.) is an herbaceous dicotyledon and member of the Amaranthaceae family. Grown primarily for the production of refined sucrose, sugarbeet provides approximately 22% of the world's sugar (Südzucker, 2013). It is also the source of two highenergy animal feeds (beet molasses and beet pulp), and is increasingly grown for biofuel production (Harland et al., 2006;Panella, 2010). Sugarbeet is grown in 42 countries on five continents, with Europe and North America producing more than 60% of the crop. Other economically important members of the species include table beet, chard, and fodder beet. Sugarbeet production is challenged by an array of abiotic and biotic stresses that reduce biomass and sucrose content. Insufficient water, excessively hot or cold temperatures, and saline soils prevent the crop from reaching its full genetic potential and can reduce yield by as much as 50% (Boyer, 1982;Ober and Rajabi, 2010). Insects, including the sugarbeet root maggot (Tetanops myopaeformis von Röder) and root aphid (Pemphigus betae Doane),

Jasmonic acid causes short- and long-term alterations to the transcriptome and the expression of defense genes in sugarbeet roots

“…From these libraries, 283 differentially expressed unigenes were identified in JA-treated roots 2 d after treatment, and 326 differentially expressed unigenes were identified in JA-treated roots 60 d after treatment (Table 2). Of the differentially expressed unigenes, approximately 65% were up-regulated and 35% were down-regulated by JA at both 2 and 60 d. From a BLASTx search against GenBank nr, Swiss-Prot, COG, and KEGG protein databases (Fugate et al, 2014), 139 (49%) of the differentially expressed unigenes 2 d after JA treatment and 178 (54%) of the differentially expressed unigenes 60 d after treatment were annotated. Most annotations indicated putative functions for unigenes.…”

“…A B Table 1 Primer sequences used for qPCR analysis of select sugarbeet genes. Unigene numbers correspond to the unigenes identified in a sugarbeet transcriptome (Fugate, 2013;Fugate et al, 2014). Multiple unigene numbers are presented for unigenes that coalign to different portions of the same gene as determined by alignment of unigenes to the sugarbeet genome (Dohm et al, 2014).…”

SNP discovery and functional annotation in the Panax japonicus var. major transcriptome

“…The discovery of single nucleotide polymorphisms (SNPs) plays key roles in the studies of disease treatment, genetics and evolution in animal and plant breeding. 2 The availability of high-throughput sequencing methods has led to the discovery of thousands to millions of SNPs in diverse organisms, particularly humans, model experimental organisms and agriculturally important plants and animals. Since SNPs provide a powerful tool for the discovery of high-risk groups, identication of disease genes, design and testing of drugs and basic biological research, they have become important in the application of the Human Genome Project.…”

Genetic diversity of sugar beet genotypes evaluated by microsatellite DNA markers

“…Amongst these, microsatellites have always been a matter of choice as they are hyper variable, multiallelic, codominantly inherited, reproducible and abundant, besides being the most appropriate tool to describe genetic diversity at DNA level (Kalia et al, 2011). Several sugar beet specific polymorphic genomic and EST-SSR markers (Mörchen et al, 1996;McGrath et al, 2007;Richards et al, 2004;Smulders et al, 2010) and transcript-based SSR markers (Fugate et al, 2014) have been developed. Despite the availability of such vast literature on the development of SSR markers in sugar beet, their actual use in genetic diversity analysis of elite sugar beet germplasm is limited.…”