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Single-nucleotide polymorphism identification and genotyping in Camelina sativa.

Singh R, Bollina V, Higgins EE, Clarke WE, Eynck C, Sidebottom C, Gugel R, Snowdon R, Parkin IA - Mol. Breed. (2015)

Bottom Line: The array allowed 533 SNP loci to be genetically mapped in a recombinant inbred population of C. sativa.Alignment of the SNP loci to the C. sativa genome identified the underlying sequenced regions that would delimit potential candidate genes in any mapping project.In addition, the SNP array was used to assess genetic variation among a collection of 175 accessions of C. sativa, identifying two sub-populations, yet low overall gene diversity.

View Article: PubMed Central - PubMed

Affiliation: Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N 0X2 Canada ; School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, 180 009 JK India.

ABSTRACT

Camelina sativa, a largely relict crop, has recently returned to interest due to its potential as an industrial oilseed. Molecular markers are key tools that will allow C. sativa to benefit from modern breeding approaches. Two complementary methodologies, capture of 3' cDNA tags and genomic reduced-representation libraries, both of which exploited second generation sequencing platforms, were used to develop a low density (768) Illumina GoldenGate single nucleotide polymorphism (SNP) array. The array allowed 533 SNP loci to be genetically mapped in a recombinant inbred population of C. sativa. Alignment of the SNP loci to the C. sativa genome identified the underlying sequenced regions that would delimit potential candidate genes in any mapping project. In addition, the SNP array was used to assess genetic variation among a collection of 175 accessions of C. sativa, identifying two sub-populations, yet low overall gene diversity. The SNP loci will provide useful tools for future crop improvement of C. sativa.

No MeSH data available.


Related in: MedlinePlus

GenomeStudio images of SNP markers segregating in the RIL Population. a SNP showing typical 3 cluster segregation pattern; b SNP where the hybridization of one allele was affected perhaps by the presence of an additional SNP in the flanking sequence; c SNP with extremely low cluster separation, requiring manual editing of the clusters; and d dominant SNP for which only one allele could be scored
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Fig1: GenomeStudio images of SNP markers segregating in the RIL Population. a SNP showing typical 3 cluster segregation pattern; b SNP where the hybridization of one allele was affected perhaps by the presence of an additional SNP in the flanking sequence; c SNP with extremely low cluster separation, requiring manual editing of the clusters; and d dominant SNP for which only one allele could be scored

Mentions: A recombinant inbred (RI) population derived from a cross between Lindo and Licalla was used to develop a genetic map for C. sativa. The newly developed GoldenGate array was hybridized with DNA from the two parental lines and 180 RI lines. Eighteen of the probes on the array gave poor signals with normalized R values <0.2 for each sample. Two hundred and seven probes on the array showed no polymorphism between the parental lines. The majority of these monomorphic loci (189) were designed from the 3′ cDNA data, and only 18 of these loci had been designed to specifically target SNP variation between Lindo and Licalla. The cluster distribution for the remaining probes on the array varied in pattern and ease of scoring (Fig. 1). The majority of the SNP assays showed a pattern that was distinguished by three clearly defined clusters representing the three genotypes in the mapping population (Fig. 1a). In some instances, although three clusters were observed, one allele was far less tightly clustered than its counterpart suggesting perhaps additional SNP variation in the flanking DNA could be impacting the efficacy of the hybridization (Fig. 1b). In rare cases both alleles showed loose clustering indicating poor hybridization. Such anomalies could in extreme cases suggest additional clusters; however, mapping of the loci showed normal segregation was occurring. Differences in separation of the clusters was also observed and in some cases the variance in normalized theta value between the two alleles was extremely small, requiring manual cluster calling in the GenomeStudio software (Fig. 1c). A very small subset of SNP loci (7) appeared to be dominant in nature, with only one of the alleles showing significant fluorescence levels (normalized R values). For such loci determination of heterozygous individuals was not possible (Fig. 1d).Fig. 1


Single-nucleotide polymorphism identification and genotyping in Camelina sativa.

Singh R, Bollina V, Higgins EE, Clarke WE, Eynck C, Sidebottom C, Gugel R, Snowdon R, Parkin IA - Mol. Breed. (2015)

GenomeStudio images of SNP markers segregating in the RIL Population. a SNP showing typical 3 cluster segregation pattern; b SNP where the hybridization of one allele was affected perhaps by the presence of an additional SNP in the flanking sequence; c SNP with extremely low cluster separation, requiring manual editing of the clusters; and d dominant SNP for which only one allele could be scored
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4300397&req=5

Fig1: GenomeStudio images of SNP markers segregating in the RIL Population. a SNP showing typical 3 cluster segregation pattern; b SNP where the hybridization of one allele was affected perhaps by the presence of an additional SNP in the flanking sequence; c SNP with extremely low cluster separation, requiring manual editing of the clusters; and d dominant SNP for which only one allele could be scored
Mentions: A recombinant inbred (RI) population derived from a cross between Lindo and Licalla was used to develop a genetic map for C. sativa. The newly developed GoldenGate array was hybridized with DNA from the two parental lines and 180 RI lines. Eighteen of the probes on the array gave poor signals with normalized R values <0.2 for each sample. Two hundred and seven probes on the array showed no polymorphism between the parental lines. The majority of these monomorphic loci (189) were designed from the 3′ cDNA data, and only 18 of these loci had been designed to specifically target SNP variation between Lindo and Licalla. The cluster distribution for the remaining probes on the array varied in pattern and ease of scoring (Fig. 1). The majority of the SNP assays showed a pattern that was distinguished by three clearly defined clusters representing the three genotypes in the mapping population (Fig. 1a). In some instances, although three clusters were observed, one allele was far less tightly clustered than its counterpart suggesting perhaps additional SNP variation in the flanking DNA could be impacting the efficacy of the hybridization (Fig. 1b). In rare cases both alleles showed loose clustering indicating poor hybridization. Such anomalies could in extreme cases suggest additional clusters; however, mapping of the loci showed normal segregation was occurring. Differences in separation of the clusters was also observed and in some cases the variance in normalized theta value between the two alleles was extremely small, requiring manual cluster calling in the GenomeStudio software (Fig. 1c). A very small subset of SNP loci (7) appeared to be dominant in nature, with only one of the alleles showing significant fluorescence levels (normalized R values). For such loci determination of heterozygous individuals was not possible (Fig. 1d).Fig. 1

Bottom Line: The array allowed 533 SNP loci to be genetically mapped in a recombinant inbred population of C. sativa.Alignment of the SNP loci to the C. sativa genome identified the underlying sequenced regions that would delimit potential candidate genes in any mapping project.In addition, the SNP array was used to assess genetic variation among a collection of 175 accessions of C. sativa, identifying two sub-populations, yet low overall gene diversity.

View Article: PubMed Central - PubMed

Affiliation: Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, S7N 0X2 Canada ; School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, 180 009 JK India.

ABSTRACT

Camelina sativa, a largely relict crop, has recently returned to interest due to its potential as an industrial oilseed. Molecular markers are key tools that will allow C. sativa to benefit from modern breeding approaches. Two complementary methodologies, capture of 3' cDNA tags and genomic reduced-representation libraries, both of which exploited second generation sequencing platforms, were used to develop a low density (768) Illumina GoldenGate single nucleotide polymorphism (SNP) array. The array allowed 533 SNP loci to be genetically mapped in a recombinant inbred population of C. sativa. Alignment of the SNP loci to the C. sativa genome identified the underlying sequenced regions that would delimit potential candidate genes in any mapping project. In addition, the SNP array was used to assess genetic variation among a collection of 175 accessions of C. sativa, identifying two sub-populations, yet low overall gene diversity. The SNP loci will provide useful tools for future crop improvement of C. sativa.

No MeSH data available.


Related in: MedlinePlus