Development of simple sequence repeat (SSR) markers for the assessment of gene flow between sea beet (<i>Beta vulgaris</i> ssp. <i>maritima</i>) populations

Cureton, A. N.; Burns, M. J.; Ford‐Lloyd, B. V.; Newbury, H. J.

doi:10.1046/j.1471-8286.2002.00253.x

Cited by 25 publications

(12 citation statements)

References 14 publications

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“…H values ranged from 0.12-0.90, with an average value of 0.57 (table 2). These values are similar to those observed previously in quinoa (Mason et al 2005) as well as in related species such as sugar beet (Beta vulgaris L.) (Rae et al 2000;Cureton et al 2002). According to Ott (1992), a marker is considered polymorphic if H≥0.10 and highly polymorphic if H≥0.70.…”

Section: Ssr Discovery and Analysissupporting

confidence: 86%

Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.)

Jarvis

Kopp

Jellen

et al. 2008

J Genet

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Quinoa is a regionally important grain crop in the Andean region of South America. Recently quinoa has gained international attention for its high nutritional value and tolerances of extreme abiotic stresses. DNA markers and linkage maps are important tools for germplasm conservation and crop improvement programmes. Here we report the development of 216 new polymorphic SSR (simple sequence repeats) markers from libraries enriched for GA, CAA and AAT repeats, as well as 6 SSR markers developed from bacterial artificial chromosome-end sequences (BES-SSRs). Heterozygosity (H) values of the SSR markers ranges from 0.12 to 0.90, with an average value of 0.57. A linkage map was constructed for a newly developed recombinant inbred lines (RIL) population using these SSR markers. Additional markers, including amplified fragment length polymorphisms (AFLPs), two 11S seed storage protein loci, and the nucleolar organizing region (NOR), were also placed on the linkage map. The linkage map presented here is the first SSR-based map in quinoa and contains 275 markers, including 200 SSR. The map consists of 38 linkage groups (LGs) covering 913 cM. Segregation distortion was observed in the mapping population for several marker loci, indicating possible chromosomal regions associated with selection or gametophytic lethality. As this map is based primarily on simple and easily-transferable SSR markers, it will be particularly valuable for research in laboratories in Andean regions of South America.

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Section: Ssr Discovery and Analysissupporting

confidence: 86%

Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.)

Jarvis

Kopp

Jellen

et al. 2008

J Genet

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“…The SSR markers reported in this study add to the four genomic SSR markers developed by Mörchen et al (1996), 57 genomic, restricted‐use SSRs developed by Rae et al (2000), 11 genome‐based SSR markers developed from sea beet ( B. vulgaris spp. maritima ; Cureton et al, 2002; Viard et al, 2002), eight genomic SSR markers developed by Richards et al (2004), 23 newly reported SSR markers used for mapping purposes by McGrath et al (2007), 25 genomic SSR markers developed by Smulders et al (2010), 13 EST‐based SSR markers reported in Simko et al (2012), and the 242 genomic SSRs and 773 EST‐based SSRs reported by Laurent et al (2007), of which 41 genomic SSR marker primer pairs were published.…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2014

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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),

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“…maritima that is not captured in the cultivated crops. Molecular markers have been used extensively to characterize sugar beet and related Beta species (Jung and Herrmann, 1991;Mita et al, 1991;Jung et al, 1993;Senda et al, 1995;Kraft et al, 1997;Shen et al, 1998;McGrath et al, 1999;Wang and Goldman, 1999;Kraft et al, 2000;Cureton et al, 2002;Richards et al, 2004;Poulsen et al, 2007;Fénart et al, 2008). Genetic diversity in cultivated beets is low compared with other beet types , and cultivated beets may contain only a quarter to a third of the genetic diversity present in sea beets (Fénart et al, 2008;Saccomani et al, 2009).…”

Section: Genetic Mapsmentioning

confidence: 99%

Root and Tuber Crops

Bradshaw¹

2010

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Development of simple sequence repeat (SSR) markers for the assessment of gene flow between sea beet (Beta vulgaris ssp. maritima) populations

Cited by 25 publications

References 14 publications

Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.)

Simple sequence repeat marker development and genetic mapping in quinoa (Chenopodium quinoa Willd.)

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

Root and Tuber Crops

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