Genetic Diversity, Population Structure, and Linkage Disequilibrium of a Core Collection of Ziziphus jujuba Assessed with Genome-wide SNPs Developed by Genotyping-by-sequencing and SSR Markers
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Abstract:
Chinese jujube (Ziziphus jujuba Mill) is an economically important fruit species native to China with high nutritious and medicinal value. Genotyping-by-sequencing (GBS) was used to detect and genotype single nucleotide polymorphisms (SNPs) in a core collection of 150 Chinese jujube accessions and further to characterize their genetic diversity, population structure, and linkage disequilibrium (LD). A total of 4,680 high-quality SNPs were identified, of which 38 sets of tri-allelic SNPs were detected. The average polymorphism information content (PIC) values based on bi-allelic SNPs and tri-allelic SNPs were 0.27 and 0.38, respectively. STRUCTURE and principal coordinate analyses based on SNPs revealed that the 150 accessions could be clustered into two groups. However, neighbor-joining trees indicated the accessions should be grouped into three major clusters. Our data confirm that the resolving power for genetic diversity was similar for the SSRs and SNPs. In contrast, regarding population structure, the resolving power was higher for SSRs than for SNPs. The linkage disequilibrium (LD) pattern in Chinese jujube was investigated for the first time. We observed a relatively rapid LD decay with a short range (approximately 10 kb) for all pseudo-chromosomes and for individual pseudo-chromosomes. Our findings provide important information for future genome-wide association analyses and marker-assisted selective breeding of Chinese jujube.Keywords:
Linkage Disequilibrium
Ziziphus jujuba
Summary The immunoglobulin superfamily 6 gene ( IGSF6 ) on chromosome 16p11‐p12 has been investigated as a positional and functional candidate for inflammatory bowel disease (IBD) susceptibility. Screening of the six exons of IGSF6 for single nucleotide polymorphisms (SNPs) detected four novel SNPs, and validated three of six SNPs listed in the international SNP database (dbSNP). The seven SNPs in IGSF6 formed five distinct linkage disequilibrium groups. There was no evidence for association of the common SNPs with disease in a large cohort of patients with IBD. The novel SNPs and the linkage disequilibrium map will be a useful resource for the analysis of IGSF6 in other immune disorders.
Linkage Disequilibrium
dbSNP
Tag SNP
Genetic Association
SNP
Candidate gene
SNP genotyping
SNP array
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Linkage Disequilibrium
Linkage (software)
Candidate gene
Genetic linkage
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Ziziphus jujuba
Rhamnaceae
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The anatomical characteristics of four varieties of species Ziziphus jujuba leaves species, consisting of Z. jujuba var. junzao, Z. jujuba var. pingguozao, Z. jujuba var. lizao and Z. jujuba var. goutouzao, were observed. The results show leaves' structure pattern of four varieties of Z. jujuba belongs to isobilateral leaf, which was anatomically characterized by vascular bundle sheath around the vein in some leaves. Besides, some laticifers occur in the main vein of Z. jujuba var. junzao leaves.
Ziziphus jujuba
Rhamnaceae
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Linkage Disequilibrium
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The fruit of Ziziphus jujuba Mill., also called hongzao in Chinese, has a long history of cultivation in China. From the fruit of Z. jujuba, twenty-seven known compounds were isolated and identified as the main constituents of these fruits. They were 3-O-(trans-p-coumaroyl)-alphitolic acid (1), 3-O-(cis-p-coumaroyl)-alphitolic acid (2), 3β-O-(trans-p-coumaroyl)-maslinic acid (3), pomonic acid (4), 2-oxo-pomolic acid (5), benthamic acid (6), terminic acid (7), oleanic acid (8), betulinic acid (9), quercetin 3-O-rutinoside (10), quercetin 3-O-robinobioside (11), apigenin (12), traumatic acid (13), (Z)-4-oxotetradec-5-enoic acid (14), 7(E)-9-keto-hexadec-7-enoic acid (15), 9(E)-11-oxo-octadecenoic acid (9CI) (16), and magnoflorine (27), etc. The HPLC fingerprint of Z. jujuba fruits was established at the same time. Compounds 4, 5, 7, 11, 14, 15 and 16 were isolated from Z. jujuba for the first time. Compound 14 was isolated from the nature for the first time. Furthermore, cytotoxicity against four human tumor cell lines (MCF-7, A549, HepG2 and HT-29) of the isolated compounds (1-17 and 27) was evaluated. Among these compounds, compounds 1, 2, 3, 6, 7, 9 and 12 had strong growth inhibitory effects on cancer cell lines. These results indicated that jujube extracts exhibited cytotoxicity on these cancer cell lines.
Ziziphus jujuba
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To identify the single nucleotide polymorphisms (SNPs) of the alpha2-Heremans-Schmid glycoprotein (AHSG) gene and assess their association with the AHSG serum level.The SNPs of the AHSG gene were identified from 30 unrelated Han individuals from Guangzhou area by resequencing. Linkage disequilibrium(LD) was performed to observe the linkage disequilibrium pattern. Then tagSNPs were genotyped in 192 Han individuals from Beijing and 424 Han individuals from Guangzhou area. Finally, luciferase reporter gene assay was performed to determine whether the SNPs affected the promoter activity. Serum AHSG concentrations were measured in the 192 subjects from Beijing using ELISA.Eight SNPs were detected in total. The linkage disequilibrium profile in the Guangzhou Han population was different from that in the Beijing Han population. However, the allele and genotype frequencies of tagSNPs between the two Han populations were not significantly different. The reporter gene assay showed that the -799A allele had significantly higher promoter activity than the -799T allele. Multiple regression analysis revealed that only the rs2248690 SNP was an independent contributor to serum AHAG concentration.The rs2248690 SNP in the promoter region of the AHSG gene might affect the AHSG gene transcription.
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Objective:To investigate the distribution characters and linkage disequilibrium of PRF1 and GZMB gene polymorphisms in Han population of Chongqing.Methods:The single nucleotide polymorphisms(SNPs)in PRF1 and GZMB gene of 100 normal subjects in Han population of Chongqing were detected by DNA sequencing analysis.Results:Two SNPs in exon 3 of PRF1 as well as one SNP in exon 2,two SNPs in exon 3,two SNPs in exon 5 of GZMB were identified,but no SNPs were detected in exon 2 of PRF1.Among them,two novel SNPs were identified in GZMB gene.The frequency distribution of these SNPs was different among different races and territory.In addition,linkage disequilibrium in the SNPs of 3877CT and 3955CT of PRF1 gene was found.There was a strong linkage disequilibrium among the SNPs of GZMB.Conclusion:7 SNPs were detected in PRF1 and GZMB genes all together,two of which were first identified. There is apparent linkage disequilibrium among SNPs of PRF1and GZMB gene in Han population of Chongqing.
Linkage Disequilibrium
SNP genotyping
SNP
Tag SNP
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Summary Single‐strand conformational polymorphism (SSCP) was used to identify single nucleotide polymorphisms (SNPs) in the promoter region of the human interleukin‐18 receptor α (IL‐18Rα). Two SNPs were identified at positions −69 and −638 relative to the transcriptional start site. Two‐way comparison of the two SNPs revealed strong linkage disequilibrium (χ 2 = 63.45, P < 0.001). Three haplotypes were identified, namely C −69 C −638 , T −69 C −638 and C −69 T −638 , with frequencies of 0.26, 0.39 and 0.35, respectively.
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Single-strand conformation polymorphism
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Introduction: Age-related macular degeneration (AMD) is a progressive neurodegenerative disease and the leading cause of blindness in developed countries. Current genome-wide association studies (GWAS) for late-stage age-related macular degeneration are mainly single-marker-based approaches, which investigate one Single-Nucleotide Polymorphism (SNP) at a time and postpone the integration of inter-marker Linkage-disequilibrium (LD) information in the downstream fine mappings. Recent studies showed that directly incorporating inter-marker connection/correlation into variants detection can help discover novel marginally weak single-nucleotide polymorphisms, which are often missed in conventional genome-wide association studies, and can also help improve disease prediction accuracy. Methods: Single-marker analysis is performed first to detect marginally strong single-nucleotide polymorphisms. Then the whole-genome linkage-disequilibrium spectrum is explored and used to search for high-linkage-disequilibrium connected single-nucleotide polymorphism clusters for each strong single-nucleotide polymorphism detected. Marginally weak single-nucleotide polymorphisms are selected via a joint linear discriminant model with the detected single-nucleotide polymorphism clusters. Prediction is made based on the selected strong and weak single-nucleotide polymorphisms. Results: Several previously identified late-stage age-related macular degeneration susceptibility genes, for example, BTBD16, C3, CFH, CFHR3, HTARA1, are confirmed. Novel genes DENND1B, PLK5, ARHGAP45, and BAG6 are discovered as marginally weak signals. Overall prediction accuracy of 76.8% and 73.2% was achieved with and without the inclusion of the identified marginally weak signals, respectively. Conclusion: Marginally weak single-nucleotide polymorphisms, detected from integrating inter-marker linkage-disequilibrium information, may have strong predictive effects on age-related macular degeneration. Detecting and integrating such marginally weak signals can help with a better understanding of the underlying disease-development mechanisms for age-related macular degeneration and more accurate prognostics.
Linkage Disequilibrium
SNP
Genome-wide Association Study
Genetic Association
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