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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.

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Comparison of F2, F5 and merged linkage maps for GBS SNP markers for Glycine latifolia linkage groups 1 and 20.Orders of SNP markers were very similar between the F2 and F5 populations. In some cases, markers that segregated in the F2 population co-localized in the F5 population, which may have resulted from errors in calling heterozygous loci in the F2 population. While linkage group 1 showed a high level of collinearity with G. max chromosome 1, linkage group 20 had regions of collinearity with multiple G. max chromosomes. Even so, there was good agreement in marker order between the F2 and F5 populations for linkage group 20. Markers were named for the G. max chromosome and the nucleotide position on the chromosome (×10−6) to which the SNP-containing sequences aligned. Markers that did not align to a G. max chromosome were named for the G. latifolia scaffold containing the SNP.
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pone-0099427-g001: Comparison of F2, F5 and merged linkage maps for GBS SNP markers for Glycine latifolia linkage groups 1 and 20.Orders of SNP markers were very similar between the F2 and F5 populations. In some cases, markers that segregated in the F2 population co-localized in the F5 population, which may have resulted from errors in calling heterozygous loci in the F2 population. While linkage group 1 showed a high level of collinearity with G. max chromosome 1, linkage group 20 had regions of collinearity with multiple G. max chromosomes. Even so, there was good agreement in marker order between the F2 and F5 populations for linkage group 20. Markers were named for the G. max chromosome and the nucleotide position on the chromosome (×10−6) to which the SNP-containing sequences aligned. Markers that did not align to a G. max chromosome were named for the G. latifolia scaffold containing the SNP.

Mentions: Genotyping by sequencing of the F2 population produced a total of 4.00×108 100-nt reads, of which 1.70×108 passed all quality controls and uniquely aligned to PI 559300 sequences. After barcodes were removed, 90 nt were used for SNP discovery. In the F2 population, 5,160 markers could be reliably scored between the parental lines PI 559298 and PI 559300. Linkage maps constructed from that initial data set represented over 13,000 centimorgans (cM), which was significantly larger than G. max (2,296 to 2,550 cM) and previous G. latifolia (1972 cM) linkage maps [19], [43]–[46] and likely resulted from errors in calling heterozygous genotypes because of low coverage at some loci. The data set was reprocessed to exclude markers with more than 30% missing data and with segregation ratios that differed significantly from 1∶2∶1 (P>0.05), which resulted in 2,377 markers (Table S1). The average depth of coverage for the selected SNPs was 32 reads per locus and ranged from 0 to 270 reads. The markers formed 20 large LGs (Figure S1), with an average of 119 markers per LG (Table 1), and a total length of 2,305 cM. To confirm marker orders, an F5 population was analyzed by the same procedures. The analysis produced a total of 1.92×108 100-nt reads, of which 1.05×108 passed all quality controls and uniquely aligned to PI 559300 sequences. The data produced 7,081 SNPs between the parental lines, from which 3,110 GBS markers (Table S2) were selected using similar criteria and analyzed in an F5 population. Average depth of coverage for the selected SNPs was 21 reads and ranged from 0 to 264 reads. As with the F2 population, most of the markers formed 20 large LGs (Figure S2), with an average of 155 markers per LG and a total map length of 3,110 cM. A total of 1,777 markers were shared between the two populations with 600 markers unique to the F2 population and 1,333 markers unique to the F5 population. The orders of shared markers were very similar in linkage maps constructed from the F2 and F5 populations (Figure 1). In some cases, markers that appeared to segregate in the F2 population did not segregate in the F5, presumably caused by errors in calling heterozygous loci in the F2 population. The shared markers were used as a framework to construct consensus linkage maps for G. latifolia (Figures 1 & S3). The merged consensus maps contained 3,710 markers (Table 1).


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 F2, F5 and merged linkage maps for GBS SNP markers for Glycine latifolia linkage groups 1 and 20.Orders of SNP markers were very similar between the F2 and F5 populations. In some cases, markers that segregated in the F2 population co-localized in the F5 population, which may have resulted from errors in calling heterozygous loci in the F2 population. While linkage group 1 showed a high level of collinearity with G. max chromosome 1, linkage group 20 had regions of collinearity with multiple G. max chromosomes. Even so, there was good agreement in marker order between the F2 and F5 populations for linkage group 20. Markers were named for the G. max chromosome and the nucleotide position on the chromosome (×10−6) to which the SNP-containing sequences aligned. Markers that did not align to a G. max chromosome were named for the G. latifolia scaffold containing the SNP.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0099427-g001: Comparison of F2, F5 and merged linkage maps for GBS SNP markers for Glycine latifolia linkage groups 1 and 20.Orders of SNP markers were very similar between the F2 and F5 populations. In some cases, markers that segregated in the F2 population co-localized in the F5 population, which may have resulted from errors in calling heterozygous loci in the F2 population. While linkage group 1 showed a high level of collinearity with G. max chromosome 1, linkage group 20 had regions of collinearity with multiple G. max chromosomes. Even so, there was good agreement in marker order between the F2 and F5 populations for linkage group 20. Markers were named for the G. max chromosome and the nucleotide position on the chromosome (×10−6) to which the SNP-containing sequences aligned. Markers that did not align to a G. max chromosome were named for the G. latifolia scaffold containing the SNP.
Mentions: Genotyping by sequencing of the F2 population produced a total of 4.00×108 100-nt reads, of which 1.70×108 passed all quality controls and uniquely aligned to PI 559300 sequences. After barcodes were removed, 90 nt were used for SNP discovery. In the F2 population, 5,160 markers could be reliably scored between the parental lines PI 559298 and PI 559300. Linkage maps constructed from that initial data set represented over 13,000 centimorgans (cM), which was significantly larger than G. max (2,296 to 2,550 cM) and previous G. latifolia (1972 cM) linkage maps [19], [43]–[46] and likely resulted from errors in calling heterozygous genotypes because of low coverage at some loci. The data set was reprocessed to exclude markers with more than 30% missing data and with segregation ratios that differed significantly from 1∶2∶1 (P>0.05), which resulted in 2,377 markers (Table S1). The average depth of coverage for the selected SNPs was 32 reads per locus and ranged from 0 to 270 reads. The markers formed 20 large LGs (Figure S1), with an average of 119 markers per LG (Table 1), and a total length of 2,305 cM. To confirm marker orders, an F5 population was analyzed by the same procedures. The analysis produced a total of 1.92×108 100-nt reads, of which 1.05×108 passed all quality controls and uniquely aligned to PI 559300 sequences. The data produced 7,081 SNPs between the parental lines, from which 3,110 GBS markers (Table S2) were selected using similar criteria and analyzed in an F5 population. Average depth of coverage for the selected SNPs was 21 reads and ranged from 0 to 264 reads. As with the F2 population, most of the markers formed 20 large LGs (Figure S2), with an average of 155 markers per LG and a total map length of 3,110 cM. A total of 1,777 markers were shared between the two populations with 600 markers unique to the F2 population and 1,333 markers unique to the F5 population. The orders of shared markers were very similar in linkage maps constructed from the F2 and F5 populations (Figure 1). In some cases, markers that appeared to segregate in the F2 population did not segregate in the F5, presumably caused by errors in calling heterozygous loci in the F2 population. The shared markers were used as a framework to construct consensus linkage maps for G. latifolia (Figures 1 & S3). The merged consensus maps contained 3,710 markers (Table 1).

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