Genome-Wide Variation Analysis of Four Vegetable Soybean Cultivars Based on Re-Sequencing

Vegetable soybean is a type of value-added specialty soybean, served as a fresh vegetable or snack in China. Due to the difference from other types, it is important to understand the genetic structure and diversity of vegetable soybean for further utilization in breeding programs. The four vegetable cultivars, Taiwan-75, Zhexiandou No. 8, Zhexian No. 9 and Zhexian No. 10 are popular soybean varieties planted in Zhejiang province, and have large pods and intermediate maturity. The clustering showed a close relationship of these four cultivars in simple sequence repeat analysis. To reveal the genome variation of vegetable soybean, these four improved lines were analyzed by whole-genome re-sequencing. The average sequencing depth was 7X and the coverage ratio of each cultivar was at least more than 94%. Compared with the reference genome, a large number of single-nucleotide polymorphisms, insertion/deletions and structure variations were identified with different chromosome distributions. The average heterozygosity rate of the single-nucleotide polymorphisms was 11.99% of these four cultivars. According to the enrichment analysis, there were 23,371 genes identified with putative modifications, and a total of 282 genes were related to carbohydrate metabolic processes. These results provide useful information for genetic research and future breeding, which can facilitate the selection procedures in vegetable soybean breeding.

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Sex Differences in Childhood Associations between DNA Markers and General Cognitive Ability

Journal of Individual Differences ◽

10.1027/1614-0001.28.3.161 ◽

2007 ◽

Vol 28 (3) ◽

pp. 161-164 ◽

Cited By ~ 1

Author(s):

Rosalind Arden ◽

Nicole Harlaar ◽

Robert Plomin

Keyword(s):

Sex Differences ◽

Single Nucleotide Polymorphisms ◽

Cognitive Ability ◽

Dna Markers ◽

Community Sample ◽

Nucleotide Polymorphisms ◽

General Cognitive Ability ◽

Single Nucleotide ◽

The Difference

Abstract. An association between intelligence at age 7 and a set of five single-nucleotide polymorphisms (SNPs) has been identified and replicated. We used this composite SNP set to investigate whether the associations differ between boys and girls for general cognitive ability at ages 2, 3, 4, 7, 9, and 10 years. In a longitudinal community sample of British twins aged 2-10 (n > 4,000 individuals), we found that the SNP set is more strongly associated with intelligence in males than in females at ages 7, 9, and 10 and the difference is significant at 10. If this finding replicates in other studies, these results will constitute the first evidence of the same autosomal genes acting differently on intelligence in the two sexes.

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Tumor necrosis factor (TNF)-α gene +489 polymorphisms: association with psoriatic arthritis

Journal of Biological Research - Bollettino della Società Italiana di Biologia Sperimentale ◽

10.4081/jbr.2013.3674 ◽

2013 ◽

Vol 86 (1) ◽

Author(s):

G. Murdaca ◽

F. Puppo

Keyword(s):

Psoriatic Arthritis ◽

Tumor Necrosis Factor ◽

Single Nucleotide Polymorphisms ◽

Tumor Necrosis ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Tnf Α ◽

The Difference ◽

Necrosis Factor

Objective of this work was to investigate the role of single nucleotide polymorphisms (SNPs) at position +489 of the tumor necrosis factor (TNF)-α gene in generic susceptibility and severity of psoriatic arthritis (PsA). Fifty-seven Caucasian PsA patients diagnosed according to CASPAR criteria and 155 healthy matched controls were studied. PASI score, DAS28 and Disability INdex HAQ were calculated. Genomic DNA was extracted from peripheral blood samples and SNPs +489 G>A (rs 80267959) were amplified by PCR. The SNP +489 genotype was significantly associated with PsA susceptibility (p=0.0136) and severity of clinical and laboratory parameters (p values ranging from 0.016 to 2.908 x 10-12). The difference in severity was accounted for by the difference between the AA and GA genotypes with respect to the GG genotype. These findings suggest that TNF-α gene polymorphisms may influence PsA susceptibility and severity. Psoriatics arthritis (PsA) is a complex immunemediated disease that results from the interplay between multiple genetic and environmental factor [1]. Although the pathogenesis of PsA remains elusive, there is evidence that genetic factors may contribute to the etiology of the disease [2]. Is has been estimated that at least one third of the genetic contribution to PsA resides in the major histocompatibility complex (MHC) region [2]. The tumor necrosis factor (TNF)-α gene, which is located in the short arm of chromosome 6 in the MHC class III region between the HLA-B and HLA-DR genes, has been proposed as a major candidate gene in PsA [3]. This hypothesis is supported by studies which have found high serum, synovial fluid and synovial membrane TNF-α levels in patients with PsA [4,5]. Several single nucleotide polymorphisms (PNPs) have been identified in the TNF-α gene promoter [6]. In particular, two common polymorphisms, namely G to A substitutions at positions -238 and -308 have been studied in patients with PsA. However, association studies of these two TNF-α polymorphisms and genetic susceptibility to PsA have lead to conflicting results [7-12]. Previous studies have indicated the potential role of the SNP at +489 position in the first intron of the TNF-α gene in the susceptibility to some rheumatic autoimmune diseases like rheumatoid arthritis [13], systemic lupus erythematosus [14] and systemic sclerosis [15]. However, to our present knowledge, studies on the association of +489 polymorphism with PsA susceptibility and response to TNF-α inhibitors are not reported in the literature. Is this study we investigated the role of SNPs at +489 within the TNF-α gene in PsA susceptibility and severity.

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Association of Single Nucleotide Polymorphisms on Locus 18q21.1 in the Etiology of Nonsyndromic Cleft Lip Palate (NSCLP) in Indian Multiplex Families

Global Medical Genetics ◽

10.1055/s-0041-1723087 ◽

2021 ◽

Vol 08 (01) ◽

pp. 024-031

Author(s):

Praveen Kumar Neela ◽

Gosla Srinivas Reddy ◽

Akhter Husain ◽

Vasavi Mohan ◽

Sravya Thumoju ◽

...

Keyword(s):

High Risk ◽

Single Nucleotide Polymorphisms ◽

Cleft Lip ◽

Genetic Research ◽

P Value ◽

Allelic Association ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Cleft Lip Palate ◽

Multiplex Families

Abstract Background Cleft lip palate (CLP) is a common congenital anomaly with multifactorial etiology. Many polymorphisms at different loci on multiple chromosomes were reported to be involved in its etiology. Genetic research on a single multigenerational American family reported 18q21.1 locus as a high-risk locus for nonsyndromic CLP (NSCLP). However, its association in multiple multiplex families and Indian population is not analyzed for its association in NSCLP. Aim This study was aimed to evaluate whether high-risk single nucleotide polymorphisms (SNPs) on chromosome 18q21.1 are involved in the etiology of NSCLP in multiplex Indian families. Materials and Methods Twenty multigenerational families affected by NSCLP were selected for the study after following inclusion and exclusion criteria. Genomic DNA was isolated from the affected and unaffected members of these 20 multiplex families and sent for genetic analysis. High-risk polymorphisms, such as rs6507872 and rs8091995 of CTIF, rs17715416, rs17713847 and rs183559995 of MYO5B, rs78950893 of SMAD7, rs1450425 of LOXHD1, and rs6507992 of SKA1 candidate genes on the 18q21.1 locus, were analyzed. SNP genotyping was done using the MassARRAY method. Statistical analysis of the genomic data was done by PLINK. Results Polymorphisms followed the Hardy–Weinberg equilibrium. In the allelic association, all the polymorphisms had a p-value more than 0.05. The odds ratio was not more than 1.6 for all the SNPs. Conclusion High-risk polymorphisms, such as rs6507872 and rs8091995 of CTIF, rs17715416, rs17713847 and rs183559995 of MYO5B, rs78950893 of SMAD7, rs1450425 of LOXHD1, and rs6507992 of SKA1 in the locus 18q21.1, are not associated with NSCLP in Indian multiplex families.

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The association between gsto1 polymorphisms and arsenic methylation of prenatal arsenic exposed infants

Vietnam Journal of Biotechnology ◽

10.15625/1811-4989/15/2/12337 ◽

2018 ◽

Vol 15 (2) ◽

pp. 223-230

Author(s):

Tạ Thị Bình Tạ Thị Bình Tạ Thị Bình ◽

Trần Phương Thảo ◽

Nguyễn Khắc Hải ◽

Nguyễn Huy Hoàng

Keyword(s):

Single Nucleotide Polymorphisms ◽

Arsenic Exposure ◽

Nucleotide Polymorphisms ◽

Glutathione S Transferase ◽

Negative Effects ◽

Single Nucleotide ◽

Arsenic Methylation ◽

Urinary Arsenic ◽

The Difference ◽

High Level

The trace element arsenic naturally presents in the environment. Arsenic is the essential factor to the human body at low level, however it causes environmental pollution and have negative effects to health at high level. Recently, arsenic contamination as well as its effects on public health, especially infants and children is increasingly becoming important and serious issues in worldwide. Glutathione S-transferase omega-1 (GSTO1) is a phase II enzymatic detoxification of xenobiotics in variety of animals including humans; to catalyze the arsenic methylation. The difference of urinary arsenic component in each individual may relate to the genetic polymorphism. To evaluate the variations of single nucleotide polymorphisms of GSTO1, PCR-RFLP technology was ultilized. Single nucleotide polymorphisms (SNPs) genotype of 150 cohort blood samples at GSTO1 Thr->Asn (rs15032), GSTO1 Ala->Val (rs11509439) and GSTO1 Ala->Asp (rs4925) were detected. The association between GSTO1 polymorphisms and prenatal arsenic exposure was evaluated by statistical analysis such as SPSS software version 20, t-test and oneway ANOVA. The results showed that GSTO1 Ala->Asp (rs4925) was statistically associated with MMA/iAs (p = 0.041). Differences between ratio of MMA/iAs and genotypes were checked by Tukey-Kramer method, along with oneway ANOVA showed that Individuals taking the AA genotype had higher MMA/ iAs ratio than individuals carrying the CC genotype, with a statistically significant association (p = 0.044), also clearly higher than the individuals carrying AC genotype, significant at p = 0.046. Therefore, it is possible that individuals carrying the AA genotype in the polymorphism have higher arsenic excretion than individuals with CC and AC genotypes

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