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High-resolution linkage map and chromosome-scale genome assembly for cassava (Manihot esculenta Crantz) from 10 populations.

- G3 (Bethesda) (2014)

Bottom Line: Although native to South America, cassava was brought to Africa 400-500 years ago and is now widely cultivated across sub-Saharan Africa, but it is subject to biotic and abiotic stresses.The composite 2412-cM map integrates 10 biparental maps (comprising 3480 meioses) and organizes 22,403 genetic markers on 18 chromosomes, in agreement with the observed karyotype.We used the map to anchor 71.9% of the draft genome assembly and 90.7% of the predicted protein-coding genes.

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Data analysis pipeline used in this study. Using a combination of publicly available and custom tools (gray text), the pipeline starts with sequence data and generates a map for each population (Pop) through a series of analyses (white text on blue). Finally, the maps are merged using LPmerge to generate a single composite map (Endelman and Plomion 2014).
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fig1: Data analysis pipeline used in this study. Using a combination of publicly available and custom tools (gray text), the pipeline starts with sequence data and generates a map for each population (Pop) through a series of analyses (white text on blue). Finally, the maps are merged using LPmerge to generate a single composite map (Endelman and Plomion 2014).

Mentions: GBS data were analyzed by pipelining several widely used sequence analysis tools with custom scripts to extract markers with parental genotype combinations useful for the cross-pollinated (CP) genetic mapping strategy implemented by JoinMap (v4.1 2013, July 11 release) (Van Ooijen 2011). An outline of the pipeline is shown in Figure 1, and step-by-step command-line instructions are available at https://bitbucket.org/rokhsar-lab/gbs-analysis.


High-resolution linkage map and chromosome-scale genome assembly for cassava (Manihot esculenta Crantz) from 10 populations.

- G3 (Bethesda) (2014)

Data analysis pipeline used in this study. Using a combination of publicly available and custom tools (gray text), the pipeline starts with sequence data and generates a map for each population (Pop) through a series of analyses (white text on blue). Finally, the maps are merged using LPmerge to generate a single composite map (Endelman and Plomion 2014).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4291464&req=5

fig1: Data analysis pipeline used in this study. Using a combination of publicly available and custom tools (gray text), the pipeline starts with sequence data and generates a map for each population (Pop) through a series of analyses (white text on blue). Finally, the maps are merged using LPmerge to generate a single composite map (Endelman and Plomion 2014).
Mentions: GBS data were analyzed by pipelining several widely used sequence analysis tools with custom scripts to extract markers with parental genotype combinations useful for the cross-pollinated (CP) genetic mapping strategy implemented by JoinMap (v4.1 2013, July 11 release) (Van Ooijen 2011). An outline of the pipeline is shown in Figure 1, and step-by-step command-line instructions are available at https://bitbucket.org/rokhsar-lab/gbs-analysis.

Bottom Line: Although native to South America, cassava was brought to Africa 400-500 years ago and is now widely cultivated across sub-Saharan Africa, but it is subject to biotic and abiotic stresses.The composite 2412-cM map integrates 10 biparental maps (comprising 3480 meioses) and organizes 22,403 genetic markers on 18 chromosomes, in agreement with the observed karyotype.We used the map to anchor 71.9% of the draft genome assembly and 90.7% of the predicted protein-coding genes.

View Article: PubMed Central - PubMed

Show MeSH
Related in: MedlinePlus