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Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing

View Article: PubMed Central - PubMed

ABSTRACT

Colossoma macropomum, or tambaqui, is the largest native Characiform species found in the Amazon and Orinoco river basins, yet few resources for genetic studies and the genetic improvement of tambaqui exist. In this study, we identified a large number of single-nucleotide polymorphisms (SNPs) for tambaqui and constructed a high-resolution genetic linkage map from a full-sib family of 124 individuals and their parents using the genotyping by sequencing method. In all, 68,584 SNPs were initially identified using minimum minor allele frequency (MAF) of 5%. Filtering parameters were used to select high-quality markers for linkage analysis. We selected 7,734 SNPs for linkage mapping, resulting in 27 linkage groups with a minimum logarithm of odds (LOD) of 8 and maximum recombination fraction of 0.35. The final genetic map contains 7,192 successfully mapped markers that span a total of 2,811 cM, with an average marker interval of 0.39 cM. Comparative genomic analysis between tambaqui and zebrafish revealed variable levels of genomic conservation across the 27 linkage groups which allowed for functional SNP annotations. The large-scale SNP discovery obtained here, allowed us to build a high-density linkage map in tambaqui, which will be useful to enhance genetic studies that can be applied in breeding programs.

No MeSH data available.


Patterns of marker distribution along the tambaqui linkage groups.The dotted box indicates regions with higher marker density. The red lines indicate gaps without markers.
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f2: Patterns of marker distribution along the tambaqui linkage groups.The dotted box indicates regions with higher marker density. The red lines indicate gaps without markers.

Mentions: The distribution of markers across each linkage group was assessed using the sliding window approach. The number of markers within a window was counted using a sliding window of 10 cM with a step size of 1 cM. The density value for each window was calculated by dividing the total of markers within a window by the window length. As shown in Fig. 2, the SNP markers are evenly distributed across the 27 linkage groups. The linkage groups LG2, LG4, LG6, LG8, LG9, LG12, and LG22 had windows with high density of markers (>8 markers per cM), most of which were clustered at the same genetic positions. LG14 had more windows with low density of markers. LG12 had the window with the highest density (10.4 markers per cM) and also the window with the lowest density (0 markers per cM). In general, the regions with high marker density were located near the centromeres (Fig. 2).


Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing
Patterns of marker distribution along the tambaqui linkage groups.The dotted box indicates regions with higher marker density. The red lines indicate gaps without markers.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5384230&req=5

f2: Patterns of marker distribution along the tambaqui linkage groups.The dotted box indicates regions with higher marker density. The red lines indicate gaps without markers.
Mentions: The distribution of markers across each linkage group was assessed using the sliding window approach. The number of markers within a window was counted using a sliding window of 10 cM with a step size of 1 cM. The density value for each window was calculated by dividing the total of markers within a window by the window length. As shown in Fig. 2, the SNP markers are evenly distributed across the 27 linkage groups. The linkage groups LG2, LG4, LG6, LG8, LG9, LG12, and LG22 had windows with high density of markers (>8 markers per cM), most of which were clustered at the same genetic positions. LG14 had more windows with low density of markers. LG12 had the window with the highest density (10.4 markers per cM) and also the window with the lowest density (0 markers per cM). In general, the regions with high marker density were located near the centromeres (Fig. 2).

View Article: PubMed Central - PubMed

ABSTRACT

Colossoma macropomum, or tambaqui, is the largest native Characiform species found in the Amazon and Orinoco river basins, yet few resources for genetic studies and the genetic improvement of tambaqui exist. In this study, we identified a large number of single-nucleotide polymorphisms (SNPs) for tambaqui and constructed a high-resolution genetic linkage map from a full-sib family of 124 individuals and their parents using the genotyping by sequencing method. In all, 68,584 SNPs were initially identified using minimum minor allele frequency (MAF) of 5%. Filtering parameters were used to select high-quality markers for linkage analysis. We selected 7,734 SNPs for linkage mapping, resulting in 27 linkage groups with a minimum logarithm of odds (LOD) of 8 and maximum recombination fraction of 0.35. The final genetic map contains 7,192 successfully mapped markers that span a total of 2,811 cM, with an average marker interval of 0.39 cM. Comparative genomic analysis between tambaqui and zebrafish revealed variable levels of genomic conservation across the 27 linkage groups which allowed for functional SNP annotations. The large-scale SNP discovery obtained here, allowed us to build a high-density linkage map in tambaqui, which will be useful to enhance genetic studies that can be applied in breeding programs.

No MeSH data available.