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Nucleotide diversity patterns of three divergent soybean populations: evidences for population-dependent linkage disequilibrium and taxonomic status of Glycine gracilis.

Wang Y, Shahid MQ, Huang H, Wang Y - Ecol Evol (2015)

Bottom Line: The results indicated that G. max retained only 75.3 (π) and 39% (θ) of the nucleotide polymorphism found in G. soja.Significant genetic differentiation was detected between G. max and G. soja populations and also between G. max and G. gracilis populations; however, nonsignificant genetic differentiation was found between G. gracilis and G. soja populations.The results suggest that LD level depends on genetic background of soybean population, and implicit that G. gracilis should be regarded as the variant of G. soja, not as an independent species.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden Chinese Academy of Science Wuhan Hubei 430074 China ; College of Environment and Life Science Kaili University Kaili Guizhou 556011 China.

ABSTRACT
The level of linkage disequilibrium (LD) is a major factor to determine DNA polymorphism pattern of a population and to construct high-resolution maps useful in localizing and gene cloning of complicated traits. Here, we investigated LD level of three soybean populations with different genetic backgrounds and taxonomic status of G. gracilis by comparing the DNA polymorphism patterns of four high-diversity single-copy nuclear genes. A total of 152, 22, and 77 accessions of G. soja, G. gracilis, and G. max were observed. The results indicated that G. max retained only 75.3 (π) and 39% (θ) of the nucleotide polymorphism found in G. soja. Four gene loci evolved according to neutrality in both G. max and G. gracilis populations, and three gene loci evolved according to neutrality in G. soja population by Tajima's and Fu and Li's test. However, one gene locus deviated from neutrality by Fu and Li's test in the G. soja population. Further, medial level of LD (average r (2) = 0.2426) was found in intragene in G. max and G. gracilis populations, but unexpected low level of LD (r (2) ≤ 0.0539) was found in G. soja population. Significant genetic differentiation was detected between G. max and G. soja populations and also between G. max and G. gracilis populations; however, nonsignificant genetic differentiation was found between G. gracilis and G. soja populations. The results suggest that LD level depends on genetic background of soybean population, and implicit that G. gracilis should be regarded as the variant of G. soja, not as an independent species.

No MeSH data available.


Related in: MedlinePlus

Linkage disequilibrium (r2) versus distance within loci in three divergent soybean populations. The line is a logarithmic trend line fit to the data by SPSS 14.0. (A) A total of 372 pairwise estimates of r2 were calculated from four loci across the genome of G. max; (B) A total of 531 pairwise estimates of r2 were calculated from four loci across the genome of G. gracilis; (C) A total of 1872 pairwise estimates of r2 were calculated from four loci across the genome of G. Soja.
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ece31550-fig-0001: Linkage disequilibrium (r2) versus distance within loci in three divergent soybean populations. The line is a logarithmic trend line fit to the data by SPSS 14.0. (A) A total of 372 pairwise estimates of r2 were calculated from four loci across the genome of G. max; (B) A total of 531 pairwise estimates of r2 were calculated from four loci across the genome of G. gracilis; (C) A total of 1872 pairwise estimates of r2 were calculated from four loci across the genome of G. Soja.

Mentions: Our data indicated 372 pairwise comparisons of all four gene loci in G. max population (Table 3). The LD of 162 pairwise comparisons (43.5%) of segregating sites was significant based on Fisher's exact test, and LD of 175 pairwise comparisons (47.0%) was significant by chi‐square test. The average r2 value of total 372 pairwise comparisons in G. max population was 0.2426 with the minimum and maximum values of 0.0010 (Locus A) and 0.4095 (Locus B), respectively. A total of 531 pairwise comparisons from all four gene loci were found in G. gracilis population, and LD of 125 (23.5%) and 148 (27.9%) pairwise comparisons were found significant by Fisher's exact test and chi‐square test, respectively. The average r2 value of total 531 pairwise comparisons in G. gracilis population was 0.2030. The level of linkage disequilibrium did not decay in intralocus (<500 bp) (Fig. 1A and B) of both G. max and G. gracilis populations; however, low level of linkage disequilibrium was found. In G. soja population(s), 1872 pairwise comparisons were found and LD of 282 (15.2%) and 327 (17.5%) pairwise comparisons were significant based on Fisher's exact test and chi‐square test, respectively. The average r2 values were lower than 0.1 at all loci in G. soja (Fig. 1C), and minimum (0.0348) and maximum (0.0539) r2 values were found at Locus B and Locus C, respectively. It is concluded from above analysis that the level of linkage disequilibrium not only depended on gene loci but also had a strong relationship with the genetic background of soybean populations.


Nucleotide diversity patterns of three divergent soybean populations: evidences for population-dependent linkage disequilibrium and taxonomic status of Glycine gracilis.

Wang Y, Shahid MQ, Huang H, Wang Y - Ecol Evol (2015)

Linkage disequilibrium (r2) versus distance within loci in three divergent soybean populations. The line is a logarithmic trend line fit to the data by SPSS 14.0. (A) A total of 372 pairwise estimates of r2 were calculated from four loci across the genome of G. max; (B) A total of 531 pairwise estimates of r2 were calculated from four loci across the genome of G. gracilis; (C) A total of 1872 pairwise estimates of r2 were calculated from four loci across the genome of G. Soja.
© Copyright Policy - creativeCommonsBy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4588648&req=5

ece31550-fig-0001: Linkage disequilibrium (r2) versus distance within loci in three divergent soybean populations. The line is a logarithmic trend line fit to the data by SPSS 14.0. (A) A total of 372 pairwise estimates of r2 were calculated from four loci across the genome of G. max; (B) A total of 531 pairwise estimates of r2 were calculated from four loci across the genome of G. gracilis; (C) A total of 1872 pairwise estimates of r2 were calculated from four loci across the genome of G. Soja.
Mentions: Our data indicated 372 pairwise comparisons of all four gene loci in G. max population (Table 3). The LD of 162 pairwise comparisons (43.5%) of segregating sites was significant based on Fisher's exact test, and LD of 175 pairwise comparisons (47.0%) was significant by chi‐square test. The average r2 value of total 372 pairwise comparisons in G. max population was 0.2426 with the minimum and maximum values of 0.0010 (Locus A) and 0.4095 (Locus B), respectively. A total of 531 pairwise comparisons from all four gene loci were found in G. gracilis population, and LD of 125 (23.5%) and 148 (27.9%) pairwise comparisons were found significant by Fisher's exact test and chi‐square test, respectively. The average r2 value of total 531 pairwise comparisons in G. gracilis population was 0.2030. The level of linkage disequilibrium did not decay in intralocus (<500 bp) (Fig. 1A and B) of both G. max and G. gracilis populations; however, low level of linkage disequilibrium was found. In G. soja population(s), 1872 pairwise comparisons were found and LD of 282 (15.2%) and 327 (17.5%) pairwise comparisons were significant based on Fisher's exact test and chi‐square test, respectively. The average r2 values were lower than 0.1 at all loci in G. soja (Fig. 1C), and minimum (0.0348) and maximum (0.0539) r2 values were found at Locus B and Locus C, respectively. It is concluded from above analysis that the level of linkage disequilibrium not only depended on gene loci but also had a strong relationship with the genetic background of soybean populations.

Bottom Line: The results indicated that G. max retained only 75.3 (π) and 39% (θ) of the nucleotide polymorphism found in G. soja.Significant genetic differentiation was detected between G. max and G. soja populations and also between G. max and G. gracilis populations; however, nonsignificant genetic differentiation was found between G. gracilis and G. soja populations.The results suggest that LD level depends on genetic background of soybean population, and implicit that G. gracilis should be regarded as the variant of G. soja, not as an independent species.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden Chinese Academy of Science Wuhan Hubei 430074 China ; College of Environment and Life Science Kaili University Kaili Guizhou 556011 China.

ABSTRACT
The level of linkage disequilibrium (LD) is a major factor to determine DNA polymorphism pattern of a population and to construct high-resolution maps useful in localizing and gene cloning of complicated traits. Here, we investigated LD level of three soybean populations with different genetic backgrounds and taxonomic status of G. gracilis by comparing the DNA polymorphism patterns of four high-diversity single-copy nuclear genes. A total of 152, 22, and 77 accessions of G. soja, G. gracilis, and G. max were observed. The results indicated that G. max retained only 75.3 (π) and 39% (θ) of the nucleotide polymorphism found in G. soja. Four gene loci evolved according to neutrality in both G. max and G. gracilis populations, and three gene loci evolved according to neutrality in G. soja population by Tajima's and Fu and Li's test. However, one gene locus deviated from neutrality by Fu and Li's test in the G. soja population. Further, medial level of LD (average r (2) = 0.2426) was found in intragene in G. max and G. gracilis populations, but unexpected low level of LD (r (2) ≤ 0.0539) was found in G. soja population. Significant genetic differentiation was detected between G. max and G. soja populations and also between G. max and G. gracilis populations; however, nonsignificant genetic differentiation was found between G. gracilis and G. soja populations. The results suggest that LD level depends on genetic background of soybean population, and implicit that G. gracilis should be regarded as the variant of G. soja, not as an independent species.

No MeSH data available.


Related in: MedlinePlus