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Molecular marker of high glycyrrhizic acid content based on the SNPs of liquorice IPT gene.

ABSTRACT: Previous studies found that cytokinins (CTKs) are able to significantly promote glycyrrhizic acid (GA) accumulation. This study analyzed the correlation between the contents of GA and CTKs in 98 one-year-old liquorice plants by the combination of high-performance liquid chromatography and enzyme-linked immunosorbent assay. The full length of the liquorice IPT gene was cloned and the Single-nucleotide polymorphisms (SNPs) of the IPT gene in the samples were obtained. The molecular marker of high GA content was found by performing correlation analysis on the SNPs of the IPT gene. Results indicated that the contents of GA and CTKs were positively correlated. The full-length sequence of the IPT gene was 1002 bps, and five SNPs were found in the 98 liquorice samples. One of five SNPs was 348 bps, exhibiting missense mutation and the rest displaying synonymous mutations. In the five SNPs, 348 bps was primarily associated SNP, whereas 821 and 848 bps were auxiliary associated SNP. The findings of this study provided insight into the molecular mechanism of GA genetic variation, serving as basis for improving the GA content in cultivated liquorice and the good varieties breeding.

SUBMITTER: Li Y

PROVIDER: S-EPMC5796932 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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Molecular marker of high glycyrrhizic acid content based on the SNPs of liquorice IPT gene.

Li Yanpeng Y Geng Lu L Chen Jing J Huang Ying Y Qiao Jing J Ren Guangxi G Liu Chunsheng C

3 Biotech 20180115 2

Previous studies found that cytokinins (CTKs) are able to significantly promote glycyrrhizic acid (GA) accumulation. This study analyzed the correlation between the contents of GA and CTKs in 98 one-year-old liquorice plants by the combination of high-performance liquid chromatography and enzyme-linked immunosorbent assay. The full length of the liquorice IPT gene was cloned and the Single-nucleotide polymorphisms (SNPs) of the IPT gene in the samples were obtained. The molecular marker of high ...[more]

PMID: 29430343

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Project description:BACKGROUND:The availability of high-density (HD) marker panels, genome wide variants and sequence data creates an unprecedented opportunity to dissect the genetic basis of complex traits, enhance genomic selection (GS) and identify causal variants of disease. The disproportional increase in the number of parameters in the genetic association model compared to the number of phenotypes has led to further deterioration in statistical power and an increase in co-linearity and false positive rates. At best, HD panels do not significantly improve GS accuracy and, at worst, reduce accuracy. This is true for both regression and variance component approaches. To remedy this situation, some form of single nucleotide polymorphisms (SNP) filtering or external information is needed. Current methods for prioritizing SNP markers (i.e. BayesB, BayesC?) are sensitive to the increased co-linearity in HD panels which could limit their performance. RESULTS:In this study, the usefulness of FST, a measure of allele frequency variation among populations, as an external source of information in GS was evaluated. A simulation was carried out for a trait with heritability of 0.4. Data was divided into three subpopulations based on phenotype distribution (bottom 5%, middle 90%, top 5%). Marker data were simulated to mimic a 770 K and 1.5 million SNP marker panel. A ten-chromosome genome with 200 K and 400 K SNPs was simulated. Several scenarios with varying distributions for the quantitative trait loci (QTL) effects were simulated. Using all 200 K markers and no filtering, the accuracy of genomic prediction was 0.77. When marker effects were simulated from a gamma distribution, SNPs pre-selected based on the 99.5, 99.0 and 97.5% quantile of the FST score distribution resulted in an accuracy of 0.725, 0.797, and 0.853, respectively. Similar results were observed under other simulation scenarios. Clearly, the accuracy obtained using all SNPs can be easily achieved using only 0.5 to 1% of all markers. CONCLUSIONS:These results indicate that SNP filtering using already available external information could increase the accuracy of GS. This is especially important as next-generation sequencing technology becomes more affordable and accessible to human, animal and plant applications.

Dataset Information

Molecular marker of high glycyrrhizic acid content based on the SNPs of liquorice IPT gene.

Publications

Molecular marker of high glycyrrhizic acid content based on the SNPs of liquorice IPT gene.

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