The rs13347 Polymorphism of the CD44 Gene Is Associated with the Risk of Kidney Stones Disease in the Chinese Han Population of Northeast Sichuan, China

Objective. To investigate the association between the rs13347 polymorphism of the CD44 gene and the risk of kidney stone disease (KSD) in the Han population of northeast Sichuan, China, so as to provide a theoretical basis for the treatment of KSD. Methods. We used PCR-restriction fragment length polymorphism (RFLP) technique to perform genotyping at rs13347 locus of the CD44 gene in the KSD group and the gontrol group. SNP Hardy-Weinberg equilibrium (HWE) testing was used to confirm the balance of genetic inheritance. Multivariate logistic regression analysis was used for the assessment of rs13347 polymorphism and the risk of developing KSD and to compare the relationship between the polymorphism of rs13347 and clinical characteristics of patients with KSD. Results. Genotypic results of rs13347 locus of the CD44 gene in the two groups were consistent with the SNP-HWE test, indicating the genetic balance. At the same time, multivariate logistic regression analysis indicated that subjects with CT and TT genotypes at rs13347 in the CD44 gene were more likely to have KSD, and there was a higher prevalence rate in males. Furthermore, carrying allele T at rs13347 was also a risk factor for KSD. In addition, people carrying CT and TT genotypes at rs13347 also have a significantly increased risk of relapsing KSD. Conclusion. The rs13347 polymorphism of the CD44 gene may be associated with the risk of KSD in the Han population of northeast Sichuan in China, and the recurrence rate of KSD in the carriers of CT and TT genotypes is higher.

A (GCC) Repeat in the Untranslated Region of Human SBF1 Departs from Hardy-Weinberg Equilibrium in Human and Links to Late-onset Neurocognitive Disorder.

The human SBF1 (SET binding factor 1) gene, alternatively known as MTMR5, is predominantly expressed in the brain, and its epigenetic dysregulation is linked to late-onset neurocognitive disorders (NCDs), such as Alzheimer’s disease. This gene contains a (GCC)-repeat at the interval between +1 and +60 of the transcription start site (SBF1-202 ENST00000380817.8). Sequencing of the SBF1 (GCC)-repeat in a sample of 542 Iranian individuals, consisting of late-onset NCDs (N=260) and controls (N=282) revealed a predominantly bi-allelic locus for this STR, consisting of 8 and 9 repeats, with allele frequencies ranging from 0.39 to 0.55, and four other alleles with frequencies of <0.03 across the two groups. Overall heterozygosity for the observed alleles was significantly less than expected in the NCD and control groups, at 22.3% and 16.31%, respectively (p=0.000). Specifically, the heterozygous 8/9 genotype was significantly less than expected in both case and control groups (Hardy-Weinberg disequilibrium, p=0.000), and significantly enriched in the NCD group (Yates corrected p=0.001). Skewed heterozygous genotypes were also detected for other allele combinations, such as 6/8 vs 6/9 across groups (p=0.000). Bioinformatics studies revealed that the number of (GCC)-repeats may change the RNA secondary structure and interaction sites across human exon 1. This STR was specifically expanded beyond 2-repeats in primates. In conclusion, we report a novel biological phenomenon in which there is indication of purifying selection against heterozygous genotypes at a STR locus in human, and skewed genotype compartment in late-onset NCD vs. controls. In view of the location of this STR in the 5′ UTR, RNA/RNA or RNA/DNA heterodimer formation of the involved genotypes and possible deleterious downstream events should be considered.

Genetic Variability Trend of Lusitano Horse Breed Reared in Italy

The Lusitano Horse (LH) originates from Portugal, but is reared worldwide. Since 1994, the University of Milan has routinely tested the LHs bred in Italy for parentage control. This study aims to assess the genetic variability of the LH reared in Italy using 16 microsatellites markers. Moreover, the genetic variability changes over the years in the total population (n.384) and in unrelated horses (n.47) were evaluated. Horses were grouped according to their date of birth (1975–1990, 1991–2000, 2001–2010, 2010–2019). Standard genetic diversity parameters, including observed (Ho) and expected (He) heterozygosity, Hardy-Weinberg equilibrium (HWE; P-Val), allelic richness, and inbreeding coefficient (Fis) were estimated. In the whole period, the total population showed Ho as high as 0.69, low Fis (0.057), and imbalance for HWE. When considering the unrelated horses, Ho was seen to increase over time (from 0.594 in 1975–1990 to 0.68 in 2010–2019) and frequencies were in HWE, again having low and decreasing values of Fis (from 0.208 in 1975–1990 to 0.019 in 2010–2019). Bottleneck analysis excluded a recent population decline. Principal Coordinate Analysis at the individual level defined two clusters, the major cluster including all the most recent horses. An increasing number of dams (156% more from 2001–2010 to 2011–2019) supports the good variability recorded in the population so far. However, the high number of foals (77.2%) sired by only four stallions in recent years suggests caution in the choice of the sires for the future.

Allele Diversity, Haplotype Frequency and Diversity, and Forensic Genotyping of Fulanis and Yorubas Population in North Central Region of Nigeria

Nigeria is the most populous African nation, comprising over 250 ethnic groups. The Yoruba and Fulani are the second and fourth largest ethnic groups in Nigeria, respectively. Forensic genotyping of short tandem repeats (STRs) is used in computation of Combined DNA Index System databases of individuals and ethnic groups. We examined allele diversity, haplotype frequency, haplotype diversity, and forensic genotyping data of autosomal STRs in Fulani and Yoruba residents in Ilorin, Kwara State, North Central Nigeria, in-order to further provide forensic genotyping data of these ethnic groups. Samples of 25 Fulani males and 23 Yoruba males whose ethnicity was confirmed by three generations (paternal and maternal) were collected with informed consent using purposive sampling. All individuals in the samples were unrelated. The samples were amplified and then genotyped using the SureID® 21G PCR Amplification Kit containing Amelogenin and 20 autosomal STR loci. Statistical analyses of forensic genotyping parameters confirmed no deviation from expectation of Hardy-Weinberg Equilibrium and no dependence of alleles between loci. All tested loci were polymorphic. Expected Heterozygosity and gene diversity parameters showed lower genetic diversity amongst Fulanis compared to Yorubas. This is possibly due to the prevalent custom of marriage between cousins amongst Fulanis, which is forbidden in Yoruba customs.

Development And Identification of 131 SNP Markers In Sthenoteuthis Pteropus (Steenstrup)

The orangeback flying squid, Sthenoteuthis pteropus, is a species of significant potential value that is widely distributed in the tropical and temperate waters of the Atlantic Ocean. There have been no reports of the population genetics and effective molecular markers for this species due to a lack of reliable information regarding its genetic structure and its many individual differences, as well as its complex and changeable life history. Therefore, the development of auxiliary molecular markers would contribute to the development, sustainable utilization, and protection of the species. In this study, 131 novel single nucleotide polymorphism (SNP) markers were developed by double digest restriction-site associated DNA sequencing (dd-RAD). The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.00 to 0.80 and 0.18 to 0.50, respectively. The polymorphism information content (PIC) value ranged from 0.18 to 0.50. None of the marker locations significantly deviated from the Hardy-Weinberg equilibrium (p >0.05) after a Bonferroni correction. These polymorphic SNPs will be important in the further analysis of the population heredity of S. pteropus and its scientific management.

POLIMORPHIC CHARACTERIZATION OF ESR1 AND FOXL2 GENES AND THE ASSOCIATION OF THEIR INTERACTION WITH PRODUCTIVE TRAITS OF BROWN LOCAL IRAQI CHICKENS

The estrogen receptor 1(ESR1) and fork-head box L2 (FOX L2) genes play a pivotal role in regulation of egg formation in poultry. this study aimed to investigate interaction between ESR1 and FOXL2 in the productive performance of brown local Iraqi chickens (BLIC). A total of 104 BLIC represented from the F4th generation of local chicken selected for high egg productions were used. Two novel single nucleotide polymorphism (SNPs), one of them in ESR1 (T57198C) intron 3, and another of FOX L2 (C919T) gene within encoding region were identified through PCR-DNA sequencing. Six haplotypes (H1=TTCC, H2=TTCT, H3=TCCC, H4=TCCT, H5=CCCC, H6=CCCT) were obtained due to interaction between these two SNPs. Chi-square analysis showed no significant in genotypic and allelic frequencies for each SNP which revealed that both genes were agreement with Hardy-Weinberg equilibrium. Association analysis of haplotypes with production traits revealed that individuals have H4 genotype achieved higher body weight at sexual maturity, at 60 weeks of age and egg weight at 45 and 60 weeks of age, whereas, the higher number of eggs were exhibited in individual with H6 from onset egg till 60 weeks of age. The two haplotypes; H4(TCCT) and H6(CCCT) showed better combination than others with respect to production performance. In conclusion, our findings provided new evidence that the two genes (ESR1 and FOXLl2) with special interaction may have potential effects on productive traits of chickens and beneficial effects in laying breeding programs.

ASSOCIATION OF NOVEL POLYMORPHISM OF ESR2 GENE (G40100A) WITH PRODUCTION TRAITS OF BROWN LOCAL IRAQI CHICKEN

The estrogen receptor 2 (ESR2) plays a crucial role in the growth and development of follicles and ovulation in chickens. The aim of this study was detect the association of estrogen receptor 2(ESR2) gene polymorphisms with the production performance of brown local Iraqi chicken. A total of 104 hens from the F4th generation of local chicken selected for high egg yield were used. The novel SNP(G40100A) transition within third prime untranslated region (3 prime UTR) of ESR2 gene. Three genotypes were found: Wild(GG), Heterozygous(GA), and Homozygous(AA) through (PCR-DAN sequencing). Chi-square analysis showed no significant in genotypic and allelic frequencies for SNP which were agreement with Hardy-Weinberg equilibrium. The genotypes GG and GA were significantly superior with age at sexual maturity compared to AA genotype. The genotype GA was significantly associated with hen day egg production (HDEP) at 30 weeks compared to genotype AA, as well as the genotype GA highest significant variance was reported comparing with the GG genotype in HDEP at 45 and 60 weeks, thus, the study recommends to exploit this ESR2 gene polymorphism (G40100A) as promising marker in breeding program via, the selection of individuals carrying the genotype GA, characterized by the high egg production.

Single nucleotide polymorphism in Interleukin 1 alpha gene might be involved in the Oral Herpes recurrent episodes in Brazilian Para-Athletes

The main goal of this study was to investigate if there is an association between Oral Herpes (OH) recurrent episodes and Single Nucleotide Polymorphisms (SNPs) in IL1A, IL10, and IL1RN genes in a group of Brazilian Para-athletes. This transversal study was prepared according to the STrengthening the REporting of Genetic Association Studies (STREGA) guidelines. Oral examination and DNA collection for genotyping were performed in a non-probabilistic convenience sampling composed of Brazilian para-athletes who participated in a Brazilian selective competition. Data referring to the general characterization of sample were collected through a self-reported questionnaire. Candidate genes were chosen with the UCSC Genome Browser and SNPs in IL1A gene (rs17561, rs1304037), IL10 gene (rs1800871), and IL1RN gene (rs9005) were selected and investigated in allelic, genotypic, dominant, and recessive models. Hardy-Weinberg equilibrium was evaluated in each SNP. The sample was composed of 273 para-athletes (63 (23.4%) practice swimming, 61 (22.3%) powerlifting and 145 (63.7%) athletics). OH recurrent episodes was related by 47 (17.2%) para-athletes and the presence of T allele in the rs1304037 increased chance of OH. These findings suggest that rs1304037 in IL1A gene is associated with OH recurrent episodes in para-athletes.

The Heart of Silk Road “Xinjiang,” Its Genetic Portray, and Forensic Parameters Inferred From Autosomal STRs

The Xinjiang Uyghur Autonomous Region of China (XUARC) harbors almost 50 ethnic groups including the Uyghur (UGR: 45.84%), Han (HAN: 40.48%), Kazakh (KZK: 6.50%), Hui (HUI: 4.51%), Kyrgyz (KGZ: 0.86%), Mongol (MGL: 0.81%), Manchu (MCH: 0.11%), and Uzbek (UZK: 0.066%), which make it one of the most colorful regions with abundant cultural and genetic diversities. In our previous study, we established allelic frequency databases for 14 autosomal short tandem repeats (STRs) for four minority populations from XUARC (MCH, KGZ, MGL, and UZK) using the AmpFlSTR® Identifiler PCR Amplification Kit. In this study, we genotyped 2,121 samples using the GoldenEye™ 20A Kit (Beijing PeopleSpot Inc., Beijing, China) amplifying 19 autosomal STR loci for four major ethnic groups (UGR, HAN, KZK, and HUI). These groups make up 97.33% of the total XUARC population. The total number of alleles for all the 19 STRs in these populations ranged from 232 (HAN) to 224 (KZK). We did not observe any departures from the Hardy–Weinberg equilibrium (HWE) in these populations after sequential Bonferroni correction. We did find minimal departure from linkage equilibrium (LE) for a small number of pairwise combinations of loci. The match probabilities for the different populations ranged from 1 in 1.66 × 1023 (HAN) to 6.05 × 1024 (HUI), the combined power of exclusion ranged from 0.999 999 988 (HUI) to 0.999 999 993 (UGR), and the combined power of discrimination ranged from 0.999 999 999 999 999 999 999 983 (HAN) to 0.999 999 999 999 999 999 999 997 (UGR). Genetic distances, principal component analysis (PCA), STRUCTURE analysis, and the phylogenetic tree showed that genetic affinity among studied populations is consistent with linguistic, ethnic, and geographical classifications.

Association of BTNL2 gene single nucleotide polymorphism with knee osteoarthritis

Relevance. Osteoarthritis (OA) is one of the chronic debilitating condition mostly seen in the aged population. The etiology behind the OA is multifactorial and the exact cause of the disease often remains uncertain. Apart from the conventional risk factors, there are the speculations of role of genetics playing a pivotal role in the causation of OA. The available literature showed BTNL2 gene polymorphism association with risk of Osteoarthritis whether the same relation is present in north Indian population needs to be elucidated. Objective. To find the association between single nucleotide polymorphism (SNP) (rs10947262) in BTNL2 gene and the susceptibility in knee Osteoarthritis (OA) subjects from northern Indian population. Materials and Methods. Blood samples of 100 patients of knee osteoarthritis and 100 healthy subjects were collected after institutional ethical clearance and participants consent. The BTNL2 gene fragment was amplified using Amplification Refractory Mutation System (ARMS-PCR) with predesigned primers after DNA extraction. The corresponding product bands were identified on the gel electrophoresis for 200 samples and the results were statistically analyzed. Results and Discussion. The genotypic distribution of the SNP followed Hardy-Weinberg Equilibrium. The genotype frequency analysis of the polymorphism was statistically significant (2=7.788; P=0.005) with Odds Ratio of CT+TT/CC: OR=2.303; P=0.008 revealing association of BTNL2 polymorphism with risk of Knee Osteoarthritis. Conclusion. The SNP (rs10947262) in the BTNL2 gene region is associated with risk of knee osteoarthritis.