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Using microsatellites to understand the physical distribution of recombination on soybean chromosomes.

Ott A, Trautschold B, Sandhu D - PLoS ONE (2011)

Bottom Line: Recent sequencing of the soybean genome resulted in the generation of vast amounts of genetic information.The crossover frequency for the entire soybean genome was 7.2%, with extremes much higher and lower than average.The knowledge of distribution of recombination on chromosomes may be applied in characterizing and targeting genes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Wisconsin-Stevens Point, Stevens Point, Wisconsin, United States of America.

ABSTRACT
Soybean is a major crop that is an important source of oil and proteins. A number of genetic linkage maps have been developed in soybean. Specifically, hundreds of simple sequence repeat (SSR) markers have been developed and mapped. Recent sequencing of the soybean genome resulted in the generation of vast amounts of genetic information. The objectives of this investigation were to use SSR markers in developing a connection between genetic and physical maps and to determine the physical distribution of recombination on soybean chromosomes. A total of 2,188 SSRs were used for sequence-based physical localization on soybean chromosomes. Linkage information was used from different maps to create an integrated genetic map. Comparison of the integrated genetic linkage maps and sequence based physical maps revealed that the distal 25% of each chromosome was the most marker-dense, containing an average of 47.4% of the SSR markers and 50.2% of the genes. The proximal 25% of each chromosome contained only 7.4% of the markers and 6.7% of the genes. At the whole genome level, the marker density and gene density showed a high correlation (R(2)) of 0.64 and 0.83, respectively with the physical distance from the centromere. Recombination followed a similar pattern with comparisons indicating that recombination is high in telomeric regions, though the correlation between crossover frequency and distance from the centromeres is low (R(2) = 0.21). Most of the centromeric regions were low in recombination. The crossover frequency for the entire soybean genome was 7.2%, with extremes much higher and lower than average. The number of recombination hotspots varied from 1 to 12 per chromosome. A high correlation of 0.83 between the distribution of SSR markers and genes suggested close association of SSRs with genes. The knowledge of distribution of recombination on chromosomes may be applied in characterizing and targeting genes.

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Related in: MedlinePlus

Distribution of predicted genes and SSR markers on twenty soybean chromosomes.The Y-axis represents percent genes or markers present in each of the 20 segments per chromosome. The X-axis represents length of the chromosome in Mb. Solid lines indicate gene distribution. Dashed lines represent marker distribution.
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pone-0022306-g002: Distribution of predicted genes and SSR markers on twenty soybean chromosomes.The Y-axis represents percent genes or markers present in each of the 20 segments per chromosome. The X-axis represents length of the chromosome in Mb. Solid lines indicate gene distribution. Dashed lines represent marker distribution.

Mentions: We also graphed the percent of genes and markers in factions of the chromosomes to show the correlation between SSR markers and genes (Figure 2). We used the physical locations of predicted open reading frames from Phytozome to identify the location of all 46,430 protein coding genes [28]. We then divided the total length of the chromosome into 20 sections and calculated the number of genes in each 5% chromosomal region. The number of genes in each region was then converted to a percent of the total number of genes for the chromosome and graphed. The same was done for the number of markers in each 5% chromosomal region.


Using microsatellites to understand the physical distribution of recombination on soybean chromosomes.

Ott A, Trautschold B, Sandhu D - PLoS ONE (2011)

Distribution of predicted genes and SSR markers on twenty soybean chromosomes.The Y-axis represents percent genes or markers present in each of the 20 segments per chromosome. The X-axis represents length of the chromosome in Mb. Solid lines indicate gene distribution. Dashed lines represent marker distribution.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3140510&req=5

pone-0022306-g002: Distribution of predicted genes and SSR markers on twenty soybean chromosomes.The Y-axis represents percent genes or markers present in each of the 20 segments per chromosome. The X-axis represents length of the chromosome in Mb. Solid lines indicate gene distribution. Dashed lines represent marker distribution.
Mentions: We also graphed the percent of genes and markers in factions of the chromosomes to show the correlation between SSR markers and genes (Figure 2). We used the physical locations of predicted open reading frames from Phytozome to identify the location of all 46,430 protein coding genes [28]. We then divided the total length of the chromosome into 20 sections and calculated the number of genes in each 5% chromosomal region. The number of genes in each region was then converted to a percent of the total number of genes for the chromosome and graphed. The same was done for the number of markers in each 5% chromosomal region.

Bottom Line: Recent sequencing of the soybean genome resulted in the generation of vast amounts of genetic information.The crossover frequency for the entire soybean genome was 7.2%, with extremes much higher and lower than average.The knowledge of distribution of recombination on chromosomes may be applied in characterizing and targeting genes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Wisconsin-Stevens Point, Stevens Point, Wisconsin, United States of America.

ABSTRACT
Soybean is a major crop that is an important source of oil and proteins. A number of genetic linkage maps have been developed in soybean. Specifically, hundreds of simple sequence repeat (SSR) markers have been developed and mapped. Recent sequencing of the soybean genome resulted in the generation of vast amounts of genetic information. The objectives of this investigation were to use SSR markers in developing a connection between genetic and physical maps and to determine the physical distribution of recombination on soybean chromosomes. A total of 2,188 SSRs were used for sequence-based physical localization on soybean chromosomes. Linkage information was used from different maps to create an integrated genetic map. Comparison of the integrated genetic linkage maps and sequence based physical maps revealed that the distal 25% of each chromosome was the most marker-dense, containing an average of 47.4% of the SSR markers and 50.2% of the genes. The proximal 25% of each chromosome contained only 7.4% of the markers and 6.7% of the genes. At the whole genome level, the marker density and gene density showed a high correlation (R(2)) of 0.64 and 0.83, respectively with the physical distance from the centromere. Recombination followed a similar pattern with comparisons indicating that recombination is high in telomeric regions, though the correlation between crossover frequency and distance from the centromeres is low (R(2) = 0.21). Most of the centromeric regions were low in recombination. The crossover frequency for the entire soybean genome was 7.2%, with extremes much higher and lower than average. The number of recombination hotspots varied from 1 to 12 per chromosome. A high correlation of 0.83 between the distribution of SSR markers and genes suggested close association of SSRs with genes. The knowledge of distribution of recombination on chromosomes may be applied in characterizing and targeting genes.

Show MeSH
Related in: MedlinePlus