Limits...
Comparative mapping of the wild perennial Glycine latifolia and soybean (G. max) reveals extensive chromosome rearrangements in the genus Glycine.

Chang S, Thurber CS, Brown PJ, Hartman GL, Lambert KN, Domier LL - PLoS ONE (2014)

Bottom Line: The remaining eight G. latifolia linkage groups appeared to be products of multiple interchromosomal translocations relative to G. max.These experiments are the first to compare genome organizations among annual and perennial Glycine species and common bean.The development of molecular resources for species closely related to G. max provides information into the evolution of genomes within the genus Glycine and tools to identify genes within perennial wild relatives of cultivated soybean that could be beneficial to soybean production.

View Article: PubMed Central - PubMed

Affiliation: Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America.

ABSTRACT
Soybean (Glycine max L. Mer.), like many cultivated crops, has a relatively narrow genetic base and lacks diversity for some economically important traits. Glycine latifolia (Benth.) Newell & Hymowitz, one of the 26 perennial wild Glycine species related to soybean in the subgenus Glycine Willd., shows high levels of resistance to multiple soybean pathogens and pests including Alfalfa mosaic virus, Heterodera glycines Ichinohe and Sclerotinia sclerotiorum (Lib.) de Bary. However, limited information is available on the genomes of these perennial Glycine species. To generate molecular resources for gene mapping and identification, high-density linkage maps were constructed for G. latifolia using single nucleotide polymorphism (SNP) markers generated by genotyping by sequencing and evaluated in an F2 population and confirmed in an F5 population. In each population, greater than 2,300 SNP markers were selected for analysis and segregated to form 20 large linkage groups. Marker orders were similar in the F2 and F5 populations. The relationships between G. latifolia linkage groups and G. max and common bean (Phaseolus vulgaris L.) chromosomes were examined by aligning SNP-containing sequences from G. latifolia to the genome sequences of G. max and P. vulgaris. Twelve of the 20 G. latifolia linkage groups were nearly collinear with G. max chromosomes. The remaining eight G. latifolia linkage groups appeared to be products of multiple interchromosomal translocations relative to G. max. Large syntenic blocks also were observed between G. latifolia and P. vulgaris. These experiments are the first to compare genome organizations among annual and perennial Glycine species and common bean. The development of molecular resources for species closely related to G. max provides information into the evolution of genomes within the genus Glycine and tools to identify genes within perennial wild relatives of cultivated soybean that could be beneficial to soybean production.

Show MeSH

Related in: MedlinePlus

Comparison of genetic distances in Glycine latifolia to physical distances in G. max for linkage groups/chromosomes 1 and 18.Glycine latifolia linkage groups 1 and 18 showed a high degree of collinearity with the corresponding G. max chromosomes. The genetic distances in G. latifolia were plotted against the physical locations of the SNP markers on the G. max chromosomes 1 and 18. As in G. max, the predicted ratios of genetic and physical distances varied along G. latifolia linkage groups. The slopes were steeper near the ends of linkage groups and flatter near the center in regions predicted to correspond to centromeres, where recombination is lower.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4061007&req=5

pone-0099427-g003: Comparison of genetic distances in Glycine latifolia to physical distances in G. max for linkage groups/chromosomes 1 and 18.Glycine latifolia linkage groups 1 and 18 showed a high degree of collinearity with the corresponding G. max chromosomes. The genetic distances in G. latifolia were plotted against the physical locations of the SNP markers on the G. max chromosomes 1 and 18. As in G. max, the predicted ratios of genetic and physical distances varied along G. latifolia linkage groups. The slopes were steeper near the ends of linkage groups and flatter near the center in regions predicted to correspond to centromeres, where recombination is lower.

Mentions: As with molecular markers in G. max, comparison of the genetic distances between GBS markers in G. latifolia and the physical distances between positions to which the SNP-containing sequences aligned on G. max chromosomes, indicated that there was reduced recombination in regions that corresponded to G. latifolia centromeres (Figure 3). Points deviating from the main line may represent mis-aligned, or mis-mapped sequences or intrachromosomal rearrangements. No G. latifolia markers were identified that aligned to 13.7 Mb and 15.0 Mb in the central regions of G. max chromosomes 5 and 20, respectively, which may have been caused by low GBS marker density (i.e., lack of PstI cutting sites) or low sequence conservation in highly repetitive pericentromeric regions.


Comparative mapping of the wild perennial Glycine latifolia and soybean (G. max) reveals extensive chromosome rearrangements in the genus Glycine.

Chang S, Thurber CS, Brown PJ, Hartman GL, Lambert KN, Domier LL - PLoS ONE (2014)

Comparison of genetic distances in Glycine latifolia to physical distances in G. max for linkage groups/chromosomes 1 and 18.Glycine latifolia linkage groups 1 and 18 showed a high degree of collinearity with the corresponding G. max chromosomes. The genetic distances in G. latifolia were plotted against the physical locations of the SNP markers on the G. max chromosomes 1 and 18. As in G. max, the predicted ratios of genetic and physical distances varied along G. latifolia linkage groups. The slopes were steeper near the ends of linkage groups and flatter near the center in regions predicted to correspond to centromeres, where recombination is lower.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4061007&req=5

pone-0099427-g003: Comparison of genetic distances in Glycine latifolia to physical distances in G. max for linkage groups/chromosomes 1 and 18.Glycine latifolia linkage groups 1 and 18 showed a high degree of collinearity with the corresponding G. max chromosomes. The genetic distances in G. latifolia were plotted against the physical locations of the SNP markers on the G. max chromosomes 1 and 18. As in G. max, the predicted ratios of genetic and physical distances varied along G. latifolia linkage groups. The slopes were steeper near the ends of linkage groups and flatter near the center in regions predicted to correspond to centromeres, where recombination is lower.
Mentions: As with molecular markers in G. max, comparison of the genetic distances between GBS markers in G. latifolia and the physical distances between positions to which the SNP-containing sequences aligned on G. max chromosomes, indicated that there was reduced recombination in regions that corresponded to G. latifolia centromeres (Figure 3). Points deviating from the main line may represent mis-aligned, or mis-mapped sequences or intrachromosomal rearrangements. No G. latifolia markers were identified that aligned to 13.7 Mb and 15.0 Mb in the central regions of G. max chromosomes 5 and 20, respectively, which may have been caused by low GBS marker density (i.e., lack of PstI cutting sites) or low sequence conservation in highly repetitive pericentromeric regions.

Bottom Line: The remaining eight G. latifolia linkage groups appeared to be products of multiple interchromosomal translocations relative to G. max.These experiments are the first to compare genome organizations among annual and perennial Glycine species and common bean.The development of molecular resources for species closely related to G. max provides information into the evolution of genomes within the genus Glycine and tools to identify genes within perennial wild relatives of cultivated soybean that could be beneficial to soybean production.

View Article: PubMed Central - PubMed

Affiliation: Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America.

ABSTRACT
Soybean (Glycine max L. Mer.), like many cultivated crops, has a relatively narrow genetic base and lacks diversity for some economically important traits. Glycine latifolia (Benth.) Newell & Hymowitz, one of the 26 perennial wild Glycine species related to soybean in the subgenus Glycine Willd., shows high levels of resistance to multiple soybean pathogens and pests including Alfalfa mosaic virus, Heterodera glycines Ichinohe and Sclerotinia sclerotiorum (Lib.) de Bary. However, limited information is available on the genomes of these perennial Glycine species. To generate molecular resources for gene mapping and identification, high-density linkage maps were constructed for G. latifolia using single nucleotide polymorphism (SNP) markers generated by genotyping by sequencing and evaluated in an F2 population and confirmed in an F5 population. In each population, greater than 2,300 SNP markers were selected for analysis and segregated to form 20 large linkage groups. Marker orders were similar in the F2 and F5 populations. The relationships between G. latifolia linkage groups and G. max and common bean (Phaseolus vulgaris L.) chromosomes were examined by aligning SNP-containing sequences from G. latifolia to the genome sequences of G. max and P. vulgaris. Twelve of the 20 G. latifolia linkage groups were nearly collinear with G. max chromosomes. The remaining eight G. latifolia linkage groups appeared to be products of multiple interchromosomal translocations relative to G. max. Large syntenic blocks also were observed between G. latifolia and P. vulgaris. These experiments are the first to compare genome organizations among annual and perennial Glycine species and common bean. The development of molecular resources for species closely related to G. max provides information into the evolution of genomes within the genus Glycine and tools to identify genes within perennial wild relatives of cultivated soybean that could be beneficial to soybean production.

Show MeSH
Related in: MedlinePlus