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Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps.

Sharma SK, Bolser D, de Boer J, Sønderkær M, Amoros W, Carboni MF, D'Ambrosio JM, de la Cruz G, Di Genova A, Douches DS, Eguiluz M, Guo X, Guzman F, Hackett CA, Hamilton JP, Li G, Li Y, Lozano R, Maass A, Marshall D, Martinez D, McLean K, Mejía N, Milne L, Munive S, Nagy I, Ponce O, Ramirez M, Simon R, Thomson SJ, Torres Y, Waugh R, Zhang Z, Huang S, Visser RG, Bachem CW, Sagredo B, Feingold SE, Orjeda G, Veilleux RE, Bonierbale M, Jacobs JM, Milbourne D, Martin DM, Bryan GJ - G3 (Bethesda) (2013)

Bottom Line: These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes.Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion.The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal "pseudomolecules".

View Article: PubMed Central - PubMed

Affiliation: Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom.

ABSTRACT
The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker-based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal "pseudomolecules".

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Related in: MedlinePlus

Step-wise linkage group assignment and ordering of DM superscaffolds using genetic-anchoring information successively from the DM, RH, and tomato genetic maps.
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fig2: Step-wise linkage group assignment and ordering of DM superscaffolds using genetic-anchoring information successively from the DM, RH, and tomato genetic maps.

Mentions: Co-segregating markers removed during linkage map construction were included in the anchoring process as such genetically redundant markers represent distinct, but physically linked sites in the genome. The complete set of STS markers was filtered for unique and unambiguous marker-assembly sequence alignments as described. The combined sequence and genetic map coordinates for these unique STS markers were used to assign and order superscaffolds for constructing a framework physical map. The integrated genetic and physical anchoring strategy is shown in Figure 2. Using this strategy, we anchored 1730 (1305 DArTs, 345 SNPs, and 80 SSRs) of the 2292 mapped, including co-segregating, STS markers to their unique positions on the DM superscaffolds. This approach anchored 54.2% (394 Mb) of the DM genome assembly arranged into 334 superscaffolds (Table 2). The proportion of genetic markers anchored on the genome sequence from each marker-category was 96% (SNPs), 28% (SSRs), and 76% (DArTs). Mapped AFLP fragments were not used in the anchoring process, due to a lack of sequence information. Table S2 contains genomic positions for all the STS markers used in the study. Genetic and physical coordinates for the DMDD mapped markers, including 718 co-segregating markers, are provided in Table S4.


Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps.

Sharma SK, Bolser D, de Boer J, Sønderkær M, Amoros W, Carboni MF, D'Ambrosio JM, de la Cruz G, Di Genova A, Douches DS, Eguiluz M, Guo X, Guzman F, Hackett CA, Hamilton JP, Li G, Li Y, Lozano R, Maass A, Marshall D, Martinez D, McLean K, Mejía N, Milne L, Munive S, Nagy I, Ponce O, Ramirez M, Simon R, Thomson SJ, Torres Y, Waugh R, Zhang Z, Huang S, Visser RG, Bachem CW, Sagredo B, Feingold SE, Orjeda G, Veilleux RE, Bonierbale M, Jacobs JM, Milbourne D, Martin DM, Bryan GJ - G3 (Bethesda) (2013)

Step-wise linkage group assignment and ordering of DM superscaffolds using genetic-anchoring information successively from the DM, RH, and tomato genetic maps.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3815063&req=5

fig2: Step-wise linkage group assignment and ordering of DM superscaffolds using genetic-anchoring information successively from the DM, RH, and tomato genetic maps.
Mentions: Co-segregating markers removed during linkage map construction were included in the anchoring process as such genetically redundant markers represent distinct, but physically linked sites in the genome. The complete set of STS markers was filtered for unique and unambiguous marker-assembly sequence alignments as described. The combined sequence and genetic map coordinates for these unique STS markers were used to assign and order superscaffolds for constructing a framework physical map. The integrated genetic and physical anchoring strategy is shown in Figure 2. Using this strategy, we anchored 1730 (1305 DArTs, 345 SNPs, and 80 SSRs) of the 2292 mapped, including co-segregating, STS markers to their unique positions on the DM superscaffolds. This approach anchored 54.2% (394 Mb) of the DM genome assembly arranged into 334 superscaffolds (Table 2). The proportion of genetic markers anchored on the genome sequence from each marker-category was 96% (SNPs), 28% (SSRs), and 76% (DArTs). Mapped AFLP fragments were not used in the anchoring process, due to a lack of sequence information. Table S2 contains genomic positions for all the STS markers used in the study. Genetic and physical coordinates for the DMDD mapped markers, including 718 co-segregating markers, are provided in Table S4.

Bottom Line: These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes.Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion.The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal "pseudomolecules".

View Article: PubMed Central - PubMed

Affiliation: Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom.

ABSTRACT
The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker-based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal "pseudomolecules".

Show MeSH
Related in: MedlinePlus