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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

Genetic linkage map of twenty chromosomes (Cas1-20) of C. sativa. SNP loci (locus names have been shortened for brevity) are indicated in black (reduced representation of genomic DNA) and green (3′ cDNA); additional SSR loci are indicated in red. The ancestral blocks are indicated by colour of AK chromosome of origin and by letter (A–X). Asterisks to right of locus name indicate significant segregation distortion (p < 0.01). (Color figure online)
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Fig2: Genetic linkage map of twenty chromosomes (Cas1-20) of C. sativa. SNP loci (locus names have been shortened for brevity) are indicated in black (reduced representation of genomic DNA) and green (3′ cDNA); additional SSR loci are indicated in red. The ancestral blocks are indicated by colour of AK chromosome of origin and by letter (A–X). Asterisks to right of locus name indicate significant segregation distortion (p < 0.01). (Color figure online)

Mentions: After manual editing of the GenomeStudio cluster file it was possible to score and map 533 SNP loci. These were arranged over twenty linkage groups, representing the haploid chromosome number of C. sativa (Table 1; Fig. 2). Forty-six EST-SSR loci that had previously been mapped on 90 lines of the same population were added to give a final genetic map composed of 579 loci distributed over 1,808.7 cM. There were at least 4 instances where significant (>20 cM) gaps in the linkage map (Cas 4, 15, 17 and 18) were observed. These regions were not associated with the four regions where segregation ratios for multiple linked loci were significantly (p < 0.01) imbalanced (Cas 1, 6, 17 and 20).Table 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)

Genetic linkage map of twenty chromosomes (Cas1-20) of C. sativa. SNP loci (locus names have been shortened for brevity) are indicated in black (reduced representation of genomic DNA) and green (3′ cDNA); additional SSR loci are indicated in red. The ancestral blocks are indicated by colour of AK chromosome of origin and by letter (A–X). Asterisks to right of locus name indicate significant segregation distortion (p < 0.01). (Color figure online)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Genetic linkage map of twenty chromosomes (Cas1-20) of C. sativa. SNP loci (locus names have been shortened for brevity) are indicated in black (reduced representation of genomic DNA) and green (3′ cDNA); additional SSR loci are indicated in red. The ancestral blocks are indicated by colour of AK chromosome of origin and by letter (A–X). Asterisks to right of locus name indicate significant segregation distortion (p < 0.01). (Color figure online)
Mentions: After manual editing of the GenomeStudio cluster file it was possible to score and map 533 SNP loci. These were arranged over twenty linkage groups, representing the haploid chromosome number of C. sativa (Table 1; Fig. 2). Forty-six EST-SSR loci that had previously been mapped on 90 lines of the same population were added to give a final genetic map composed of 579 loci distributed over 1,808.7 cM. There were at least 4 instances where significant (>20 cM) gaps in the linkage map (Cas 4, 15, 17 and 18) were observed. These regions were not associated with the four regions where segregation ratios for multiple linked loci were significantly (p < 0.01) imbalanced (Cas 1, 6, 17 and 20).Table 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