Single Nucleotide Polymorphism Loci Research Articles

[Preimplantation genetic testing for a Chinese pedigree affected with Rett syndrome].

To carry out preimplantation genetic testing (PGT) for a Chinese pedigree affected with Rett syndrome (RTT). A pedigree affected with RTT who had presented at the First Hospital of Jilin University on June 4, 2021 was selected as the study subject. Variant of the MECP2 gene was analyzed by next generation sequencing (NGS) and Sanger sequencing. Direct sequencing was also used to determine the carrier status for the c.925C>T variant of the MECP2 gene in the blastocysts, and Sanger sequencing was used to validate the results. The MECP2 gene and 168 effective single nucleotide polymorphism (SNP) loci within 2 Mb ranges up- and downstream of the gene were used to construct a haplotype for analyzing the variant site in the embryos, and embryos without the variant were subjected to the analysis for chromosomal aneuploidies. PGT analysis revealed that five out of seven blastocysts did not harbor the pathogenic variant. The results of aneuploidy analysis indicated that two out of five blastocysts without the variant were euploid. Following genetic counselling, the couple had opted to transplant the optimal blastocyst. Following clinical pregnancy, prenatal diagnosis showed that the fetus has a normal chromosomal karyotype, and the c.925C>T variant was not detected in the amniotic fluid sample. A healthy girl was born by Cesarean section at full term. NGS can attain efficient PGT detection and reduce the risk of disease recurrence in families affected with RTT.

Variations in Genetic Diversity of Invasive Species Lithobates catesbeianus in China.

The introduction and subsequent range expansion of the American bullfrog (Lithobates catesbeianus) is part of a rising trend of troublesome biological invasions happening in China. This detrimental amphibious invasive species has strong adaptability. After its introduction and spread, it established its own ecological niche in many provinces of China, and its range has continued to expand to more areas. Previous studies recorded the introduction time of bullfrogs and calculated the changes in their genetic diversity in China using mitochondria, but the specific introduction route in China is still unknown. Expanding upon previous research, we employed whole-genome scans (utilizing 2b-RAD genomic sequencing) to examine single nucleotide polymorphisms (SNPs) and microsatellites within Lithobates catesbeianus to screen the genomes of these invasive amphibian species from eight Chinese provinces and two U.S. states, including Kansas, where bullfrogs originate. A total of 1,336,475 single nucleotide polymorphic loci and 17 microsatellite loci were used to calculate the genetic diversity of bullfrogs and their migration pathways. Our results suggest that the population in Hunan was the first to be introduced and to spread, and there may have been multiple introductions of subpopulations. Additionally, the genetic diversity of both the SNP and microsatellite loci in the Chinese bullfrog population was lower than that of the US population due to bottleneck effects, but the bullfrogs can adapt and spread rapidly. This study will offer crucial insights for preventing and controlling future introductions into the natural habitats in China. Additionally, it will assist in devising more precise strategies to manage the existing populations and curtail their continued expansion, as well as aim to improve clarity and originality while mitigating plagiarism risk.

Polymorphisms in the cysteine dioxygenase gene and their association with taurine content in the Pacific oyster Crassostrea gigas

The Pacific oyster Crassostrea gigas is rich in taurine, which is crucial for its adaptation to the fluctuating intertidal environment and presents significant potential in improving taurine nutrition and boosting immunity in humans. Cysteine dioxygenase (CDO) is a key enzyme involved in the initial step of taurine biosynthesis and plays a crucial role in regulating taurine content in the body. In the present study, polymorphisms of CDO gene in C. gigas (CgCDO) and their association with taurine content were evaluated in 198 individuals. A total of 24 single nucleotide polymorphism (SNP) loci were identified in the exonic region of CgCDO gene by direct sequencing. Among these SNPs, c.279G>A and c.287C>A were found to be significantly associated with taurine content, with the GG and AA genotype at the two loci exhibiting enhanced taurine accumulation (p < 0.05). Haplotype analysis revealed that the 279GG/287AA haplotype had the highest taurine content of 29.24 mg/g, while the 279AA/287CC haplotype showed the lowest taurine content of 21.19 mg/g. These results indicated that the SNPs of CgCDO gene could influence the taurine content in C. gigas and have potential applications in the selective breeding of high-taurine varieties.

Genetic diversity, disease resistance, and environmental adaptation of Arachis duranensis L.: New insights from landscape genomics.

The genetic diversity that exists in natural populations of Arachis duranensis, the wild diploid donor of the A subgenome of cultivated tetraploid peanut, has the potential to improve crop adaptability, resilience to major pests and diseases, and drought tolerance. Despite its potential value for peanut improvement, limited research has been focused on the association between allelic variation, environmental factors, and response to early (ELS) and late leaf spot (LLS) diseases. The present study implemented a landscape genomics approach to gain a better understanding of the genetic variability of A. duranensis represented in the ex-situ peanut germplasm collection maintained at the U.S. Department of Agriculture, which spans the entire geographic range of the species in its center of origin in South America. A set of 2810 single nucleotide polymorphism (SNP) markers allowed a high-resolution genome-wide characterization of natural populations. The analysis of population structure showed a complex pattern of genetic diversity with five putative groups. The incorporation of bioclimatic variables for genotype-environment associations, using the latent factor mixed model (LFMM2) method, provided insights into the genomic signatures of environmental adaptation, and led to the identification of SNP loci whose allele frequencies were correlated with elevation, temperature, and precipitation-related variables (q < 0.05). The LFMM2 analysis for ELS and LLS detected candidate SNPs and genomic regions on chromosomes A02, A03, A04, A06, and A08. These findings highlight the importance of the application of landscape genomics in ex situ collections of peanut and other crop wild relatives to effectively identify favorable alleles and germplasm for incorporation into breeding programs. We report new sources of A. duranensis germplasm harboring adaptive allelic variation, which have the potential to be utilized in introgression breeding for a single or multiple environmental factors, as well as for resistance to leaf spot diseases.

Genome-wide association study and development of molecular markers for yield and quality traits in peanut (Arachis hypogaea L.)

BackgroundThis study aims to decipher the genetic basis governing yield components and quality attributes of peanuts, a critical aspect for advancing molecular breeding techniques. Integrating genotype re-sequencing and phenotypic evaluations of seven yield components and two grain quality traits across four distinct environments allowed for the execution of a genome-wide association study (GWAS).ResultsThe nine phenotypic traits were all continuous and followed a normal distribution. The broad heritability ranged from 88.09 to 98.08%, and the genotype-environment interaction effects were all significant. There was a highly significant negative correlation between protein content (PC) and oil content (OC). The 10× genome re-sequencing of 199 peanut accessions yielded a total of 631,988 high-quality single nucleotide polymorphisms (SNPs), with 374 significant SNP loci identified in association with the nine traits of interest. Notably, 66 of these pertinent SNPs were detected in multiple environments, and 48 of them were linked to multiple traits of interest. Five loci situated on chromosome 16 (Chr16) exhibited pleiotropic effects on yield traits, accounting for 17.64–32.61% of the observed phenotypic variation. Two loci on Chr08 were found to be strongly associated with protein and oil contents, accounting for 12.86% and 14.06% of their respective phenotypic variations, respectively. Linkage disequilibrium (LD) block analysis of these seven loci unraveled five nonsynonymous variants, leading to the identification of one yield-related candidate gene and two quality-related candidate genes. The correlation between phenotypic variation and SNP loci in these candidate genes was validated by Kompetitive allele-specific PCR (KASP) marker analysis.ConclusionsOverall, molecular markers were developed for genetic loci associated with yield and quality traits through a GWAS investigation of 199 peanut accessions across four distinct environments. These molecular tools can aid in the development of desirable peanut germplasm with an equilibrium of yield and quality through marker-assisted breeding.

Polymorphic locus rs8023580 NR2F2-AS1 is associated with breast cancer risk in residents of Central Russia

Breast cancer (BC) is the most common hormone-dependent genetically determined cancer among women. The level of “active” sex hormones in the body, the connection of which with breast cancer is beyond doubt, is determined by the content of the protein transporting sex hormones (SHBG).Aim: To study associations of polymorphic loci linked with the level of SHBG at the full-genomic level of significance with the risk of developing breast cancer.Material and Methods. The work was carried out on a sample of 1,498 women, 358 of whom were BC patients, the control was 1140 individuals. Genotyping of four single nucleotide polymorphic loci (SNP) associated with the level of SHBG was performed according to previously performed genome-wide studies (GWAS): rs7910927 JMJD1C, rs4149056 SLCO1B1, rs8023580 NR2F2-AS1, rs12150660 SHBG. The method of logistic regression was used to search for associations.Results and Discussion. SNP rs8023580 of the NR2F2-AS1 gene is associated with the risk of BC developing. The presence of the CC genotype rs8023580 NR2F2-AS1in a woman has a protective value in the formation of the disease (CCvsTC+TT [recessive model]; OR = 0.58; 95%CI = 0.35–0.96; p = 0.033; pperm = 0.042). SNP rs8023580 NR2F2-AS1 is functionally significant in the liver: it is localized in the enhancer region, affects the level of methylation of the cg01739960 (hg38) genome region, affects the expression of the RP11-327J17.2 gene, determines the interaction of DNA with six transcription factors (Fo xd1,Foxl1,Foxq1,Mef2,PLZF,STAT), which are located in the cis-regulatory region of RNA polymerase II, specific for the DNA binding sequence, and determine the activity of DNA-binding transcription factors specific for RNA polymerase II, are involved in the processes of cellular differentiation and tissue development.Conclusion. The SHBG-enhancing CC genotype rs8023580 of the NR2F2-AS1 gene is a protective factor in the development of BC.

Parentage analysis and comparison of cocoa families derived from bi-parental crosses and open-pollination for vigor and precocity in recommended cocoa (Theobroma cacao L.) clones in Ghana

ABSTRACT Bi-parental hybrids (BPHs) are recommended cocoa planting materials in Ghana and other West African countries. However, the inability to produce enough BPHs to meet farmers’ demand makes it almost impossible to avoid open-pollinated families (OPF) in the supply chain. To study the effects of OPF on cocoa production, parentage analysis, vigor, and precocity of seven BPHs generated from a 4 × 2 North Carolina II (NC II) incomplete mating design were compared with eight OPFs. The 15 cocoa progenies together with two checks of Guiana (GU) origin were evaluated in a randomized complete block design with four replications across five contrasting locations for stem diameter increment (SDI) and number of pods per tree (NP). Parentage analyses at 75 single nucleotide polymorphism (SNP) loci of leave samples from the 17 progenies revealed that the BPHs were of the appropriate female and male parents, while the OPF had varying number of male parents. The pollination effect (bi-parental vs open-pollinated progenies) was not significantly different for both traits, but the BPH was relatively better and surpassed on average the OPF by 3.5% for SDI and 7.8% for NP. Crosses involving GU 144/ C, T63/967, and T65/238 as females in both the OPF and BPH showed predominantly higher performance than those with PA 7 and T79/501 for both traits. Among the promising female parents, GU 144/C is the only one that is not in the seed gardens and could be added to parental clones currently used in producing cocoa varieties in the seed garden.

A capture-based method of prenatal cell-free DNA screening for autosomal recessive non-syndromic hearing loss.

This study aimed to develop and validate a prenatal cell-free DNA (cfDNA) screening method that uses capture-based enrichment to genotype fetal autosomal recessive disorders. This method was applied in pregnancies at high risk of autosomal recessive non-syndromic hearing loss (ARNSHL) to assess its accuracy and effectiveness. This assay measured the allele counts in both white blood cell DNA and cfDNA from the blood samples of pregnant women using a capture-based next-generation sequencing method. It then applied a binomial model to infer the fetal genotypes with the maximum likelihood. Ninety-four pregnant couples that were carriers of variants of ARNSHL in GJB2 or SLC26A4 were enrolled. The fetal genotypes deduced using this screening method were compared with the results of genetic diagnosis using amniocentesis. Of the 94 couples, 65 carried more than one variant, resulting in 170 single-nucleotide polymorphism (SNP) loci to be inferred in the fetuses. Of the 170 fetal SNP genotypes, 150 (88.2%) had high confidence calls and 139 (92.7%) of these matched the genotypes obtained by amniocentesis result. Out of the remaining 20 (11.8%) cases with low-confidence calls, only 14 (70.0%) were concordant with genetic diagnosis using amniocentesis. The concordance rate was 100% for sites where the maternal genotype was wild-type homozygous. The discordance was site-biased, with each locus showing a consistent direction of discordance. Genetic diagnosis identified a total of 19 wild-type homozygotes, 46 heterozygotes, 19 compound heterozygotes, and 10 pathogenic homozygotes. This screening method correctly genotyped 81.9% (77/94) of fetuses and demonstrated a sensitivity of 89.7% and a specificity of 89.2% for correctly identifying ARNSHL. This capture-based method of prenatal screening by cfDNA demonstrated strong potential for fetal genotyping of autosomal recessive disorders.

Genomic responses to climate: Understanding local adaptation in the Andean tree species Nothofagus pumilio and implications for a changing world

Societal Impact StatementForest trees tend to be strongly genetically adapted to their local environments, but climate change will probably subject trees to novel combinations of precipitation, temperature, and photoperiod. Local adaptation was investigated in the ecologically and economically important Patagonian tree species Nothofagus pumilio by characterizing its genetic diversity in relation to the varied environmental conditions across its range. These insights are useful for conservation and management decisions, for example by identifying suitable populations to establish seed source plantations for restoration and characterizing relationships with environmental drivers of selection to better understand how this species will respond to climate change.SummaryNothofagus pumilio is a foundation tree species that inhabits a 2000‐km‐long range in the southern Andes, a region with two perpendicular environmental gradients: temperature and photoperiod (North–South), and precipitation (West–East). We investigated local adaptation patterns by searching for relationships between environmental clines and signatures of adaptation in candidate genes related to stress response, growth, and phenology. Using a paired site sampling design within a landscape genome analysis, we analyzed 493 adult N. pumilio trees in 20 sampling sites across the species' latitudinal range. We screened 47,336 single nucleotide polymorphism (SNP) loci in 1632 contigs (i.e., coding regions along the genome). Population structure and genetic diversity analyses preceded four genome scan analyses using genetic and environmental data. Population structure and genetic diversity are mainly oriented along the latitude axis. Genome scans identified 445 outlier SNPs, which are loci showing signatures of selection. Temperature and photoperiod variables were associated with notably more outliers than precipitation. However, the most frequent biological functions among genes were water deprivation response and cold response, suggesting that stress response is comprised of complex and polygenic traits that are affected by many environmental variables. Our findings suggest that N. pumilio shows signatures of local adaptation to extant climate conditions, including temperature, photoperiod, and precipitation. However, climate change is likely to alter existing relationships among environmental conditions to which this species is currently adapted. These changes may have unpredictable consequences for the species' future survival, adaptation potential, and the people who depend upon these forests.

Appropriate whole genome amplification and pathogenic loci detection can improve the accuracy of preimplantation genetic diagnosis for deletional α-thalassemia.

To improve the accuracy of preimplantation genetic testing (PGT) in deletional α-thalassemia patients. Article. fifty-two deletional α-thalassemia couples. Whole genome amplification (WGA), Next-generation sequencing (NGS) and PCR mutation loci detection. WGA, Single nucleotide polymorphism (SNP) and PCR mutation loci detection results; Analysis of embryo chromosome copy number variation (CNV). Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) methods for PGT for deletional α-thalassemia. Blastocyst biopsy samples (n = 253) were obtained from 52 deletional α-thalassemia couples. The results of the comparison of experimental data between groups MALBAC and MDA are as follows: (i) The average allele drop-out (ADO) rate, MALBAC vs. MDA = 2.27% ± 3.57% vs. 0.97% ± 1.4%, P=0.451); (ii) WGA success rate, MALBAC vs. MDA = 98.61% vs. 98.89%, P=0.851; (iii) SNP haplotype success rate, MALBAC vs. MDA = 94.44% vs. 96.68%, P=0.409; (iv) The result of SNP haplotype analysis is consistent with that of Gap-PCR/Sanger sequencing results, MALBAC vs. MDA = 36(36/72, 50%) vs. 151(151/181, 83.43%), P=0; (v) Valid SNP loci, MALBAC vs. MDA = 30 ± 9 vs. 34 ± 10, P=0.02; (vi) The mean CV values, MALBAC vs. MDA = 0.12 ± 0.263 vs. 0.09 ± 0.40, P=0.916; (vii) The average number of raw reads, MALBAC vs. MDA =3244259 ± 999124 vs. 3713146 ± 1028721, P=0; (viii) The coverage of genome (%), MALBAC vs. MDA = 5.02 ± 1.09 vs. 5.55 ± 1.49, P=0.008. Our findings indicate that MDA is superior to MALBAC for PGT of deletional α-thalassemia. Furthermore, SNP haplotype analysis combined with PCR loci detection can improve the accuracy and detection rate of deletional α-thalassemia.

A preliminary report on the exploration of salivary bacterial diversity by the multiplex SNaPshot assay

Salivary bacterial community composition is associated with the host’s internal and environmental factors, which have potential applications in forensic practice. The 16S rRNA gene sequencing is the most commonly used strategy for detecting salivary bacterial diversity; however, its platforms are not compatible with capillary electrophoresis (CE) platforms commonly used for forensic applications. Therefore, we attempted to detect the salivary bacterial diversity using a single nucleotide polymorphism (SNP) assay. Salivary bacterial diversity varies among diverse geographic locations, making it a potential supplementary biomarker for forensic geographic sourcing. To evaluate the performance of the multiplex SNaPshot assay, saliva samples from three geographic locations in China were analyzed using the multiplex SNaPshot assay and 16S rRNA gene sequencing. We screened SNPs from two high-relative-abundance salivary genera (Streptococcus and Veillonella) to construct a multiplex SNaPshot system that can be used on the CE platform. The stability and sensitivity of the multiplex SNaPshot system were also tested. A random forest classification model was used to classify samples from different regions to explore the ability of salivary bacteria to discriminate between geographic sources. Six bacterial SNPs were screened and a multiplex SNaPshot system was constructed. The stability results showed that the typing of salivary stains that were placed indoors for different days was not affected in this study. Two-thirds of mocked salivary stain samples showed more than 90% of typing results obtained for salivary stain samples with an input of 0.1 µl saliva. The results of principal coordinate analysis based on salivary bacterial diversity showed significant differences between samples from the three different geographic locations. The accuracy of the random forest classification was 66.67% based on the multiplex SNaPshot assay and 83.33% based on the 16S rRNA gene sequencing. In conclusion, this is the first attempt to detect salivary bacterial diversity using a multiplex SNaPshot bacterial SNP assay. The geographic difference in human salivary bacterial community composition was significant, as revealed by the multiplex SNaPshot assay; however, its performance in discriminating geographic sources was lower than that of 16S rRNA gene sequencing. This strategy based on bacterial SNP loci may favor the detection of human bacterial diversity in common forensic laboratories but requires further exploration in larger sample sizes and more bacterial SNP loci.

Identification of molecular markers and candidate regions associated with grain number per spike in Pubing3228 using SLAF-BSA.

Grain number per spike, a pivotal agronomic trait dictating wheat yield, lacks a comprehensive understanding of its underlying mechanism in Pubing3228, despite the identification of certain pertinent genes. Thus, our investigation sought to ascertain molecular markers and candidate regions associated with grain number per spike through a high-density genetic mapping approach that amalgamates site-specific amplified fragment sequencing (SLAF-seq) and bulked segregation analysis (BSA). To facilitate this, we conducted a comparative analysis of two wheat germplasms, Pubing3228 and Jing4839, known to exhibit marked discrepancies in spike shape. By leveraging this methodology, we successfully procured 2,810,474 SLAF tags, subsequently resulting in the identification of 187,489 single nucleotide polymorphisms (SNPs) between the parental strains. We subsequently employed the SNP-index association algorithm alongside the extended distribution (ED) association algorithm to detect regions associated with the trait. The former algorithm identified 24 trait-associated regions, whereas the latter yielded 70. Remarkably, the intersection of these two algorithms led to the identification of 25 trait-associated regions. Amongst these regions, we identified 399 annotated genes, including three genes harboring non-synonymous mutant SNP loci. Notably, the APETALA2 (AP2) transcription factor families, which exhibited a strong correlation with spike type, were also annotated. Given these findings, it is plausible to hypothesize that these genes play a critical role in determining spike shape. In summation, our study contributes significant insights into the genetic foundation of grain number per spike. The molecular markers and candidate regions we have identified can be readily employed for marker-assisted breeding endeavors, ultimately leading to the development of novel wheat cultivars possessing enhanced yield potential. Furthermore, conducting further functional analyses on the identified genes will undoubtedly facilitate a comprehensive elucidation of the underlying mechanisms governing spike development in wheat.

Common garden experiments and SNP genotyping at the extremes of a steep precipitation gradient suggest local adaptation in a Patagonian conifer

Abstract Plants inhabiting contrasting physical conditions might develop local adaptations overriding the homogenizing effects of gene flow. Hypotheses of local adaptation on phenotypic, genomic, and environmental variation under extreme precipitation regimes were tested in the Patagonian conifer Austrocedrus chilensis. Common garden experiments on progeny and genotype-to-environment association analysis on adults were conducted. Samples consisting of seeds and leaves from adult trees were collected from contrasting dry (DF) and humid (HF) forests along a steep but short precipitation gradient. Seeds were germinated and seedlings were grown under common garden conditions for 24 months. DNA was extracted from 75 randomly selected trees from DF and HF, and genotyped by sequencing to obtain single-nucleotide polymorphisms (SNPs). Seedlings from HF outgrew DF ones suggesting genetically based differences. Twenty-four outlier SNP loci differed between DF and HF, whereas neutral genes (3242) showed high levels of admixture. Eight out of the 24 outlier SNPs aligned with transcripts, half of them related to drought stress responses, and principal component analysis identified four precipitation-related marker–climate associations. Quantitative and genomic traits suggested that natural selection maintains divergence under contrasting climatic conditions regardless high gene flow. This underscores the importance of dry forests as reservoirs of drought-tolerant variants to cope with forecasted climate change.

Influence of molecular marker type on estimating effective population size and other genetic parameters in a critically endangered parrot

AbstractGenetics is a fast‐moving field, and for conservation practitioners or ecologists, it can be bewildering. The choice of marker used in studies is fundamental; in the literature, preference has recently shifted from microsatellites to single nucleotide polymorphism (SNP) loci. Understanding how marker type affects estimates of population genetic parameters is important in the context of conservation, especially because the accuracy of estimates has a bearing on the actions taken to protect threatened species. We compare parameter estimates between seven microsatellites, 3761 SNP loci, and a random subset of 100 SNPs for the exact same 324 individual swift parrots, Lathamus discolor, and also use 457 additional samples from subsequent years to compare SNP estimates. Both marker types estimated a lower HO than HE. We show that microsatellites and SNPs mainly indicate a lack of spatial genetic structure, except when a priori collection locations were used on the SNP data in a discriminant analysis of principal components (DAPC). The 100‐SNP subset gave comparable results to when the full dataset was used. Estimates of effective population size (Ne) were comparable between markers when the same individuals were considered, but SNPs had narrower confidence intervals. This is reassuring because conservation assessments that rely on population genetic estimates based on a few microsatellites are unlikely to be nullified by the general shift toward SNPs in the literature. However, estimates between markers and datasets varied considerably when only adult samples were considered; hence, including samples of all age groups is recommended to be used when available. The estimated Ne was higher for the full SNP dataset (2010–2019) than the smaller comparison data (2010–2015), which might be a better reflection of the species status. The lower precision of microsatellites may not necessarily be a barrier for most conservation applications; however, SNPs will improve confidence limits, which may be useful for practitioners.

Polymorphisms in ENAM, AMBN, and KLK4 predispose Egyptian adults to dental caries: A cross-sectional study

ObjectiveThis study investigates the distributional discrepancies of four single-nucleotide polymorphic loci as correlatives and causatives of dental caries susceptibility among Egyptians. MethodWe conducted a cross-sectional study through the genotyping of enamelin (ENAM rs3796703), ameloblastin (AMBN rs4694075), tuftelin 1 (TUFT1 rs78802584), and kallikrein 4 (KLK4 rs2242670) in 132 adults (males = 74, females = 58) and 72 controls (males = 40, females = 32) referred from various Egyptian hospitals. For each participant, the number of decayed, missing, and filled teeth was charted, and the presence of biofilm/gingivitis/fluorosis was assessed. Bitewing radiographs were taken to detect interproximal caries. In addition, statistical analysis was conducted using Chi-square test, odds ratios, and corresponding P-values. ResultsThe alleles and genotypes of ENAM rs3796703, AMBN rs4694075, and KLK4 rs2242670 correlated strongly with dental caries susceptibility. However, TUFT1 rs78802584 did not exhibit such associations. ConclusionThese findings suggest the potential role of ENAM, AMBN, and KLK4 as determinants of dental caries susceptibility among Egyptian adults. The role of ENAM, AMBN, and KLK4 genetic variants is determinant in influencing susceptibility to dental caries in the Egyptian population, providing valuable insights into the genetic aspects of oral health. However, the lack of associations of caries susceptibility with TUFT1 rs78802584 contradicts its cariogenic role in many ethnicities.

Ex situ conservation of two rare oak species using microsatellite and SNP markers.

Plant collections held by botanic gardens and arboreta are key components of ex situ conservation. Maintaining genetic diversity in such collections allows them to be used as resources for supplementing wild populations. However, most recommended minimum sample sizes for sufficient ex situ genetic diversity are based on microsatellite markers, and it remains unknown whether these sample sizes remain valid in light of more recently developed next-generation sequencing (NGS) approaches. To address this knowledge gap, we examine how ex situ conservation status and sampling recommendations differ when derived from microsatellites and single nucleotide polymorphisms (SNPs) in garden and wild samples of two threatened oak species. For Quercus acerifolia, SNPs show lower ex situ representation of wild allelic diversity and slightly lower minimum sample size estimates than microsatellites, while results for each marker are largely similar for Q. boyntonii. The application of missing data filters tends to lead to higher ex situ representation, while the impact of different SNP calling approaches is dependent on the species being analyzed. Measures of population differentiation within species are broadly similar between markers, but larger numbers of SNP loci allow for greater resolution of population structure and clearer assignment of ex situ individuals to wild source populations. Our results offer guidance for future ex situ conservation assessments utilizing SNP data, such as the application of missing data filters and the usage of a reference genome, and illustrate that both microsatellites and SNPs remain viable options for botanic gardens and arboreta seeking to ensure the genetic diversity of their collections.

Development of a high-density sub-species-specific targeted SNP assay for Rocky Mountain bighorn sheep (Ovis canadensis canadensis).

Due to their abundance and relative ease of genotyping, single nucleotide polymorphisms (SNPs) are a commonly used molecular marker for contemporary population genetic and genomic studies. A high-density and cost-effective way to type SNP loci is Allegro targeted genotyping (ATG), which is a form of targeted genotyping by sequencing developed and offered by Tecan genomics. One major drawback of this technology is the need for a reference genome and information on SNP loci when designing a SNP assay. However, for some non-model species genomic information from other closely related species can be used. Here we describe our process of developing an ATG assay to target 50,000 SNPs in Rocky Mountain bighorn sheep, using a reference genome from domestic sheep and SNP resources from prior bighorn sheep studies. We successfully developed a high accuracy, high-density, and relatively low-cost SNP assay for genotyping Rocky Mountain bighorn sheep that genotyped ~45,000 SNP loci. These loci were relatively evenly distributed throughout the genome. Furthermore, the assay produced genotypes at tens of thousands of SNP loci when tested on other mountain sheep species and subspecies.

Association between smoking and alcohol drinking and benign adrenal tumors: a Mendelian randomization study.

In recent years, the detection rate of adrenal tumors has increased, but it is unclear whether smoking and alcohol drinking are risk factors for benign adrenal tumors. The objective of this study is to employ Mendelian randomization (MR) analysis to explore the causal relationship between smoking, alcohol drinking and susceptibility to benign adrenal tumors. We acquired large-scale data from publicly accessible databases on genome-wide association studies (GWAS) pertaining to smoking, alcohol drinking and benign adrenal tumors. A total of 11 sets of instrumental variables (IVs) and 281 associated single nucleotide polymorphic (SNP) loci were identified. The Mendelian randomization analyses were conducted using inverse variance weighting (IVW), MR-Egger regression and weighted median estimation (WME) methods, in addition to sensitivity analyses. There is no causal relationship between smoking status, alcohol drinking status, alcohol intake frequency, alcohol taken with meals, alcohol consumption and benign adrenal tumors, while pack years of smoking and cigarettes per day are risk factors for benign adrenal tumors. The IVW analysis revealed that both the pack years of smoking and cigarettes per day were positively associated with an increased risk of benign adrenal tumors (OR = 2.853, 95%CI = 1.384-5.878, p = 0.004; OR = 1.543, 95%CI = 1.147-2.076, p = 0.004). Two SNPs (rs8042849 in the analysis of pack years of smoking and rs8034191 in the analysis of cigarettes per day) significantly drove the observed causal effects. Two-sample Mendelian randomization analysis showed a causal effect between smoking but not alcohol consumption and benign adrenal tumors.

Identification of Single Nucleotide Polymorphic Loci and Candidate Genes for Seed Germination Percentage in Okra under Salt and No-Salt Stresses by Genome-Wide Association Study.

Excessive soil salinity is a major stressor inhibiting crops' growth, development, and yield. Seed germination is a critical stage of crop growth and development, as well as one of the most salt-sensitive stages. Salt stress has a significant inhibitory effect on seed germination. Okra is a nutritious vegetable, but its seed germination percentage (GP) is low, whether under salt stress conditions or suitable conditions. In this study, we used 180 okra accessions and conducted a genome-wide association study (GWAS) on the germination percentage using 20,133,859 single nucleotide polymorphic (SNP) markers under 0 (CK, diluted water), 70 (treatment 1, T1), and 140 mmol/L (treatment 2, T2) NaCl conditions. Using the mixed linear model (MLM) in Efficient Mixed-model Association eXpedated (EMMAX) and Genome-wide Efficient Mixed Model Association (GEMMA) software, 511 SNP loci were significantly associated during germination, of which 167 SNP loci were detected simultaneously by both programs. Among the 167 SNPs, SNP2619493 on chromosome 59 and SNP2692266 on chromosome 44 were detected simultaneously under the CK, T1, and T2 conditions, and were key SNP loci regulating the GP of okra seeds. Linkage disequilibrium block analysis revealed that nsSNP2626294 (C/T) in Ae59G004900 was near SNP2619493, and the amino acid changes caused by nsSNP2626294 led to an increase in the phenotypic values in some okra accessions. There was an nsSNP2688406 (A/G) in Ae44G005470 near SNP2692266, and the amino acid change caused by nsSNP2688406 led to a decrease in phenotypic values in some okra accessions. These results indicate that Ae59G004900 and Ae44G005470 regulate the GP of okra seeds under salt and no-salt stresses. The gene expression analysis further demonstrated these results. The SNP markers and genes that were identified in this study will provide reference for further research on the GP of okra, as well as new genetic markers and candidate genes for cultivating new okra varieties with high GPs under salt and no-salt stress conditions.

Identifying Relationships between Glutathione S-Transferase-2 Single Nucleotide Polymorphisms and Hypoxia Tolerance and Growth Traits in Macrobrachium nipponense.

Investigating hypoxia tolerance and growth trait single nucleotide polymorphisms (SNPs) in Macrobrachium nipponense is conducive to cultivating prawns with hypoxia tolerance and good growth characteristics. The glutathione S-transferase-2 gene (GST-2) has been shown to regulate hypoxia responses in M. nipponense. In this study, we identified a single GST-2 SNP in M. nipponense, and analyzed its regulatory relationship with hypoxia tolerance and growth. The GST-2 sequence was amplified with a polymerase chain reaction from 197 "Taihu Lake No. 3", "Taihu Lake No. 2", and Pearl River population samples to identify SNP loci. The full-length Mn-GST2 sequence was 2317 bp, including three exons and two introns. In total, 38 candidate SNP loci were identified from GST-2 using Mega11.0 comparisons, with most loci moderately polymorphic in terms of genetic diversity. Locus genotypes were also analyzed, and basic genetic parameters for loci were calculated using Popgene32 and PIC_CALC. The expected heterozygosity of the 38 SNP loci ranged from 0.2334 to 0.4997, with an average of 0.4107, while observed heterozygosity ranged from 0.1929 to 0.4721, with an average of 0.3401. The polymorphic information content ranged from 0.21 to 0.37. From SPSS analyses, the G+256A locus was significantly correlated with hypoxia tolerance across all three M. nipponense populations, while the SNP loci A+261C, C+898T, A+1370C, and G+1373T were significantly associated with growth traits. Further analyses revealed that the T+2017C locus was significantly correlated with hypoxia tolerance in "Taihu Lake No. 2" populations, G+256A, A+808T, C+1032T, and A+1530G loci were significantly correlated with hypoxia tolerance in "Taihu Lake No. 3" populations, while no SNP loci were correlated with hypoxia tolerance in Pearl River populations. A+1370C and G+1373T loci, which were associated with growth traits, exhibited a high degree of linkage disequilibrium (r2 = 0.89 and r2 > 0.8), suggesting potential genetic linkage. Our data suggest associations between hypoxia tolerance and growth trait SNP loci in M. nipponense, and provide valuable evidence for the genetic improvement of growth and hypoxia tolerance in this prawn species.