Large-scale development of functional markers in<i>Brassica</i>species

An, Zeshan; Gao, Chengwen; Li, Jiana; Fu, Donghui; Tang, Zhongjie; Ortegón, Oscar

doi:10.1139/g11-042

Cited by 9 publications

(10 citation statements)

References 28 publications

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“…We found that 60% of SSR primer pairs exhibited polymorphic bands in the different Brassica species (An et al. ), similar to the 60–73% polymorphism detected for other developed SSR primers in Brassica species (Lowe et al. , Piquemal et al.…”

Section: Discussionsupporting

confidence: 84%

“…We used the same set of experimental materials (15/16 accessions) in another study (An et al. ) to estimate the utility of functional SSR markers developed from assembled unique transcripts. We found that 60% of SSR primer pairs exhibited polymorphic bands in the different Brassica species (An et al.…”

Section: Discussionmentioning

confidence: 99%

“…An et al. () found that the PIC values of SSRs developed and tested across the same set of Brassica accessions ranged from 0.14 to 0.69, with an average value of 0.49. The PIC of 55% of markers exceeded 0.50.…”

Section: Discussionmentioning

confidence: 99%

“…Using the SSR marker system (An et al. ), the 16 accessions could be classified into five clusters based on species: B. oleracea (cluster I), B. napus (cluster II), B. rapa (cluster III), B. juncea (cluster IV) and B. nigra (cluster V), with similarity coefficients ranging from 0.31 to 0.91. However, the two genotypes of B. carinata clustered with B. oleracea and B. napus , respectively, presumably due to the allotetraploid nature of B. napus and B .…”

Section: Discussionmentioning

confidence: 99%

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MicroRNA‐based molecular markers: a novel PCR‐based genotyping technique in Brassica species

Mason

et al. 2013

Plant Breeding

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DNA‐based molecular markers play a significant role in gene mapping, genetic diversity analysis, germplasm evaluation and molecular marker‐assisted selection. A combination of desirable marker characteristics such as abundant polymorphism, good stability, ease of production and high efficiency is difficult to achieve when utilizing traditional molecular marker systems. MicroRNAs are a type of endogenous non‐coding RNAs prevalent in the genomes of many organisms. The high conservation of miRNA and pre‐miRNA sequences provides an opportunity to develop a novel molecular marker type. We downloaded 82 miRNA sequences from the Brassica miRBase database and designed 46 single miRNA‐based primers which could be randomly combined to generate primer pairs. A proportion of these primer pairs were validated for transferability and polymorphism using DNA from 16 varieties of six Brassica species. The percentage of polymorphic primer pairs were 28.1%, and the average polymorphism information content (PIC) value for the 34 primer pairs was 0.43. Good transferability was verified across species. These results indicate that miRNA‐based markers provide a novel genotyping technique with low costs, high efficiency, stability and good transferability.

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Section: Discussionsupporting

confidence: 84%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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MicroRNA‐based molecular markers: a novel PCR‐based genotyping technique in Brassica species

Mason

et al. 2013

Plant Breeding

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“…52 Although several studies have been conducted to develop genic SSR markers from the ESTs/unique transcripts of B. rapa , 29,31,32 B. oleracea 31 and B. napus , 30–32 the total number (<5000) of publicly available genic SSR markers has remained limited in Brassica (). In the current study, a large number of newly developed genome-wide SSR markers (32 648, 33 228 and 58 952 for B. rapa , B. oleracea and B. napus , respectively) were involved in the annotated genes (Supplementary Table S7) and thus belonged to the genic SSR markers.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Microsatellite Characterization and Marker Development in the Sequenced Brassica Crop Species

Shi¹,

Huang²,

Zhan³

et al. 2013

DNA Research

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Although much research has been conducted, the pattern of microsatellite distribution has remained ambiguous, and the development/utilization of microsatellite markers has still been limited/inefficient in Brassica, due to the lack of genome sequences. In view of this, we conducted genome-wide microsatellite characterization and marker development in three recently sequenced Brassica crops: Brassica rapa, Brassica oleracea and Brassica napus. The analysed microsatellite characteristics of these Brassica species were highly similar or almost identical, which suggests that the pattern of microsatellite distribution is likely conservative in Brassica. The genomic distribution of microsatellites was highly non-uniform and positively or negatively correlated with genes or transposable elements, respectively. Of the total of 115 869, 185 662 and 356 522 simple sequence repeat (SSR) markers developed with high frequencies (408.2, 343.8 and 356.2 per Mb or one every 2.45, 2.91 and 2.81 kb, respectively), most represented new SSR markers, the majority had determined physical positions, and a large number were genic or putative single-locus SSR markers. We also constructed a comprehensive database for the newly developed SSR markers, which was integrated with public Brassica SSR markers and annotated genome components. The genome-wide SSR markers developed in this study provide a useful tool to extend the annotated genome resources of sequenced Brassica species to genetic study/breeding in different Brassica species.

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