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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

Patterns of molecular variation in 175 C. sativa accessions. a STRUCTURE analyses showing population membership of each line (y-axis) based on Q value (x-axis) indicated in red (population 1) and green (population 2). b Phylogenetic relationship among 175 C. sativa accessions based on the unweighted neighbour joining method. (Color figure online)
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Fig3: Patterns of molecular variation in 175 C. sativa accessions. a STRUCTURE analyses showing population membership of each line (y-axis) based on Q value (x-axis) indicated in red (population 1) and green (population 2). b Phylogenetic relationship among 175 C. sativa accessions based on the unweighted neighbour joining method. (Color figure online)

Mentions: Population structure analysis was completed using STRUCTURE (Pritchard et al. 2000) for 175 accessions. Since the estimated log-likelihood values appeared to be an increasing function of K for all examined values of K, inferring the exact value of K was not straightforward (Supplementary Figure 2a). Using the program Structure Harvester (Evanno et al. 2005) maximal ∆K revealed that at a K value of 2 the accessions were clustered into two sub-populations (Supplementary Figure 2b). Using a minimum value of 70 % ancestry, 152 accessions were assigned to one of the two sub-populations, 61 accessions to Population I and 91 accessions to Population II (Fig. 3a). The remaining 23 accessions appeared to be admixtures or have ancestry from more than one population, with qK values <70 % for both populations (Supplementary Table 1). The population clusters did not group according to the available geographical information. A similar pattern was observed for the relationship as determined by the unweighted Neighbour-Joining method, which clustered accessions into two major groups. In Fig. 3b, the red and green branches on the tree represent Populations I and II, respectively as determined by STRUCTURE; all accessions defined as admixtures are shown in black. Similar to the STRUCTURE analysis, the resultant phylogenetic tree did not cluster the accessions based on geographical origin, with the lines derived from each country being evenly distributed between the populations.Fig. 3


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)

Patterns of molecular variation in 175 C. sativa accessions. a STRUCTURE analyses showing population membership of each line (y-axis) based on Q value (x-axis) indicated in red (population 1) and green (population 2). b Phylogenetic relationship among 175 C. sativa accessions based on the unweighted neighbour joining method. (Color figure online)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig3: Patterns of molecular variation in 175 C. sativa accessions. a STRUCTURE analyses showing population membership of each line (y-axis) based on Q value (x-axis) indicated in red (population 1) and green (population 2). b Phylogenetic relationship among 175 C. sativa accessions based on the unweighted neighbour joining method. (Color figure online)
Mentions: Population structure analysis was completed using STRUCTURE (Pritchard et al. 2000) for 175 accessions. Since the estimated log-likelihood values appeared to be an increasing function of K for all examined values of K, inferring the exact value of K was not straightforward (Supplementary Figure 2a). Using the program Structure Harvester (Evanno et al. 2005) maximal ∆K revealed that at a K value of 2 the accessions were clustered into two sub-populations (Supplementary Figure 2b). Using a minimum value of 70 % ancestry, 152 accessions were assigned to one of the two sub-populations, 61 accessions to Population I and 91 accessions to Population II (Fig. 3a). The remaining 23 accessions appeared to be admixtures or have ancestry from more than one population, with qK values <70 % for both populations (Supplementary Table 1). The population clusters did not group according to the available geographical information. A similar pattern was observed for the relationship as determined by the unweighted Neighbour-Joining method, which clustered accessions into two major groups. In Fig. 3b, the red and green branches on the tree represent Populations I and II, respectively as determined by STRUCTURE; all accessions defined as admixtures are shown in black. Similar to the STRUCTURE analysis, the resultant phylogenetic tree did not cluster the accessions based on geographical origin, with the lines derived from each country being evenly distributed between the populations.Fig. 3

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