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Multiple repetitive sequences of authentic genes commonly exist in fungal genomes. AT-biased genotypes of Ophiocordyceps sinensis have been hypothesized as repetitive pseudogenes in the genome of Hirsutella sinensis (GC-biased Genotype #1 of O. sinensis) and are generated through repeat-induced point mutation (RIP), which is charactered by cytosine-to-thymine and guanine-to-adenine transitions, concurrent epigenetic methylation, and dysfunctionality. This multilocus study examined repetitive sequences in the H. sinensis genome and transcriptome using a bioinformatic approach and revealed that 8.2% of the authentic genes had repetitive copies, including various allelic insertions/deletions, transversions, and transitions. The transcripts for the repetitive sequences, regardless of the decreases, increases, or bidirectional changes in the AT content, were identified in the H. sinensis transcriptome, resulting in changes in the secondary protein structure and functional specification. Multiple repetitive internal transcribed spacer (ITS) copies containing multiple insertion/deletion and transversion alleles in the genome of H. sinensis were GC-biased and were theoretically not generated through RIP mutagenesis. The repetitive ITS copies were genetically and phylogenetically distinct from the AT-biased O. sinensis genotypes that possess multiple transition alleles. The sequences of Genotypes #2–17 of O. sinensis, both GC- and AT-biased, were absent from the H. sinensis genome, belong to the interindividual fungi, and differentially occur in different compartments of the natural Cordyceps sinensis insect–fungi complex, which contains >90 fungal species from >37 genera. Metatranscriptomic analyses of natural C. sinensis revealed the transcriptional silencing of 5.8S genes in all C. sinensis-colonizing fungi in natural settings, including H. sinensis and other genotypes of O. sinensis. Thus, AT-biased genotypes of O. sinensis might have evolved through advanced evolutionary mechanisms, not through RIP mutagenesis, in parallel with GC-biased Genotype #1 of H. sinensis from a common genetic ancestor over the long course of evolution. [ABSTRACT FROM AUTHOR]

Abstract Background Single nucleotide polymorphism (SNP) markers play significant roles in accelerating breeding and basic crop research. Several soybean SNP panels have been developed. However, there is still a lack of SNP panels for differentiating between wild and cultivated populations, as well as for detecting polymorphisms within both wild and cultivated populations. Results This study utilized publicly available resequencing data from over 3,000 soybean accessions to identify differentiating and highly conserved SNP and insertion/deletion (InDel) markers between wild and cultivated soybean populations. Additionally, a naturally occurring mutant gene library was constructed by analyzing large-effect SNPs and InDels in the population. Conclusion The markers obtained in this study are associated with numerous genes governing agronomic traits, thus facilitating the evaluation of soybean germplasms and the efficient differentiation between wild and cultivated soybeans. The natural mutant gene library permits the quick identification of individuals with natural mutations in functional genes, providing convenience for accelerating soybean breeding using reverse genetics.

Background: Single nucleotide polymorphism (SNP) markers play significant roles in accelerating breeding and basic crop research. Several soybean SNP panels have been developed. However, there is still a lack of SNP panels for differentiating between wild and cultivated populations, as well as for detecting polymorphisms within both wild and cultivated populations. Results: This study utilized publicly available resequencing data from over 3,000 soybean accessions to identify differentiating and highly conserved SNP and insertion/deletion (InDel) markers between wild and cultivated soybean populations. Additionally, a naturally occurring mutant gene library was constructed by analyzing large-effect SNPs and InDels in the population. Conclusion: The markers obtained in this study are associated with numerous genes governing agronomic traits, thus facilitating the evaluation of soybean germplasms and the efficient differentiation between wild and cultivated soybeans. The natural mutant gene library permits the quick identification of individuals with natural mutations in functional genes, providing convenience for accelerating soybean breeding using reverse genetics. [ABSTRACT FROM AUTHOR]

This study aimed to investigate the genetic polymorphisms and population characteristics of Chinese Mongolian group from northwest China (NCM) through a self-developed panel including 43 autosomal insertion/deletion (A-InDel) polymorphism genetic markers. Herein, 288 unrelated healthy individuals from the NCM group were employed to obtain the genetic data of 43 A-InDels through multiplex PCR amplification and InDel genotyping using capillary electrophoresis platform. In addition, multiplex population genetic analyses were performed between the NCM group and 27 reference populations. There were no deviations at 43 loci from Hardy–Weinberg equilibrium in the NCM group. The observed heterozygosity (Ho) values ranged from 0.312 8 to 0.559 2, and the combined power of discrimination (CPD) and cumulative probability of exclusion (CPE) values in the NCM group were 0.999 999 999 999 999 998 77 and 0.999 814, respectively. The forensic parameter values indicated that this panel was polymorphic and informative in the NCM group and could be used as an effective tool for forensic personal identification. Furthermore, the results of pairwise genetic distances, principal component analysis, multidimensional scaling analysis, phylogenetic tree construction, and admixture analysis among the NCM group and 27 reference populations revealed that there were closer genetic relationships between the NCM group and East Asian populations, especially Chinese Hui group (CHH) from the northwest China, which is consistent with the geographical location. These present findings contributed to the ongoing genetic explorations and insights into the genetic architecture of the NCM group. [ABSTRACT FROM AUTHOR]

Simple Summary: Increasing the fertility of sheep remains one of the crucial issues of modern sheep breeding. Recently, the microtubule associated serine/threonine kinase family member 4 (MAST4) gene has been proposed to have an impact on sheep prolificacy traits. Moreover, the MAST4 gene is known for its role in both male and female reproduction. However, it has not been previously linked to sheep fertility traits. Therefore, the focus of our research was to determine whether this gene affects litter size traits in sheep. To address this problem, whole-genome sequencing (WGS) methodology (n = 1507) in 26 different sheep breeds worldwide and polymerase chain reaction (PCR) genotyping of the MAST4 gene polymorphisms were conducted in (n = 566) Australian white (AUW) sheep. The findings indicated that the detected polymorphisms within this gene were presented in all 26 breeds, except for P5-del-24 bp, which was presented in 24 out of 26 breeds. Notably, all InDel loci were found to be associated with sheep traits (p < 0.05) in AUW sheep, making them effective molecular marker loci for sheep breeding. The economic efficiency of sheep breeding can be improved by enhancing sheep productivity. A recent genome-wide association study (GWAS) unveiled the potential impact of the MAST4 gene on prolificacy traits in Australian White sheep (AUW)). Herein, whole-genome sequencing (WGS) data from 26 different sheep breeds worldwide (n = 1507), including diverse meat, wool, milk, or dual-purpose sheep breed types from China, Europe, and Africa, were used. Moreover, polymerase chain reaction (PCR) genotyping of the MAST4 gene polymorphisms in (n = 566) Australian white sheep (AUW) was performed. The 3 identified polymorphisms were not homogeneously distributed across the 26 examined sheep breeds. Findings revealed prevalent polymorphisms (P3-ins-29 bp and P6-del-21 bp) with varying frequencies (0.02 to 0.97) across 26 breeds, while P5-del-24 bp was presented in 24 out of 26 breeds. Interestingly, the frequency of the P3-ins-29 bp variant was markedly higher in Chinese meat or dual-purpose sheep breeds, while the other two variants also showed moderate frequencies in meat breeds. Notably, association analysis indicated that all InDels were associated with AUW sheep litter size (p < 0.05). These results suggest that these InDels within the MAST4 gene could be useful in marker-assisted selection in sheep breeding. [ABSTRACT FROM AUTHOR]

RAR related orphan receptor A (RORA), which encodes the retinoid-acid-related orphan receptor alpha (RORα), is a clock gene found in skeletal muscle. Several studies have shown that RORα plays an important role in bone formation, suggesting that RORA gene may take part in the regulation of growth and development. The purpose of this research is to study the insertion/deletion (indel) variations of the RORA gene and investigate the relationship with the growth traits of Shaanbei white cashmere (SBWC) goats. Herein, the current study identified that the P4-11-bp and P11-28-bp deletion sites are polymorphic among 12 pairs of primers within the RORA gene in the SBWC goats (n = 641). Moreover, the P11-28-bp deletion locus was significantly related to the body height (p = 0.046), height at hip cross (p = 0.012), and body length (p = 0.003). Both of P4-11-bp and P11-28-bp indels showed the moderate genetic diversity (0.25

Janus kinase 2 (JAK2) plays a critical role in myoblast proliferation and fat deposition in animals. Our previous RNA-Seq analyses identified a close association between the JAK2 gene and muscle development. To date, research delving into the relationship between the JAK2 gene and growth traits has been sparse. In this study, we sought to investigate the relationship between novel mutations within the JAK2 gene and goat growth traits. Herein, two novel InDel (Insertion/Deletion) polymorphisms within the JAK2 gene were detected in 548 goats, and only two genotypes were designated as ID (Insertion/Deletion) and DD (Deletion/Deletion). The results indicate that the two InDels, the del19008 locus in intron 2 and del72416 InDel in intron 6, showed significant associations with growth traits (p < 0.05). Compared to Nubian and Jianzhou Daer goats, the del72416 locus displayed a more pronounced effect in the Fuqing breed group. In the Nubian breed (NB) group, both InDels showed a marked influence on body height (BH). There were strong linkages observed for these two InDels between the Fuqing (FQ) and Jianzhou (JZ) populations. The DD-ID diplotype was associated with inferior growth traits in chest width (ChW) and cannon circumference (CaC) in the FQ goats compared to the other diplotypes. In the NB population, the DD-DD diplotype exhibited a marked negative impact on BH and HuWI (hucklebone width index), in contrast to the other diplotypes. In summary, our findings suggest that the two InDel polymorphisms within the JAK2 gene could serve as valuable molecular markers for enhancing goat growth traits in breeding programs.

This article presents a study that explores the connection between a particular gene variant and the risk of age-related macular degeneration (AMD). The study involved 121 AMD patients and 108 healthy individuals, and genetic testing was conducted using PCR. The findings revealed a significant correlation between the Del/Del genotype and susceptibility to AMD. The study suggests that this gene variant may contribute to the risk of AMD in the general population. Additionally, the study confirms previous research indicating that smoking and outdoor work are risk factors for AMD. However, further investigation is necessary to validate these findings in larger groups of people. [Extracted from the article]

Osteoporosis (OP) is a common systemic, metabolic bone disease that affects 40% of postmenopausal women. Oxidative stress (OS) ìs caused by reactive oxygen species (ROS), inhibits osteoblast differentiation and causes apoptosis in osteoblastic cells. Superoxide dismutase (SOD) reduces OS by playing a role in the reduction and defense of intracellular ROS. Therefore, the purpose of this study was to investigate the relationship between osteopenia/OP and the SOD1 50-bp insertion/deletion (I/D) variant in Turkish postmenopausal women. A total of 180 women participated in this study includá¸-ng 89 osteopenia/OP postmenopausal women and 91 healthy postmenopausal women. T-score > −1 standard deviation (SD) defined normal bone mass, T-score between −1 and −2.5 SD defined osteopenia, T-score ≥ −2.5 SD was defined as OP. DNA was extracted from all subjects and the SOD1 I/D variant genotyped by PCR. The results of the analyses were evaluated for statistical significance. The mean age of 89 osteopenia/OP patients aged 45 to 74 was 58.57 ± 6.57. There was no D/D homozygous genotype in the patient and control groups. The prevalence of genotypes of I/I, and I/D, profiles for the SOD1 I/D variant were 76.4%, and 23.6% respectively, in patients, and 72.5%, and 27.5% respectively, in the control group. When the patient group and control group were compared, the SOD1 I/D genotype distribution and allele frequencies did not show a significant difference between the groups (p > 0.05). Our results showed that the SOD1 I/D variant may not be considered a determining factor in the development of osteopenia/OP in a Turkish population sample. However, ethnic differences, gene-gene, and gene-environment interactions should not be ignored. [ABSTRACT FROM AUTHOR]

The southern varieties of the American eelgrass, Vallisneria americana, are vital contributors to aquatic ecosystems throughout Florida and other areas within the southeastern United States. Recent discovery of cryptic non-native Vallisneria in natural waterbodies of central and southeast Florida has raised concerns for the biosecurity of native American eelgrass populations, which have been lost from many historical locations and are the subject of multiple, intensive restoration/reintroduction efforts throughout the state. The non-native grasses were found to be derivatives of a hybrid V. spiralis × V. denseserrulata, which is ubiquitous within the global aquarium trade and represents a worldwide invasive threat. Concern for the native taxon and difficulties in visually distinguishing it from non-native taxa prompted the development of a molecular screening assay. The method leverages parsimony-informative insertion/deletion-based variation within a fluorescently labeled amplified segment of the nuclear ribosomal internal transcribed spacer region. Based on comparisons to sequenced specimens (n = 96), fragment length polymorphisms for the amplicon, visualized by capillary electrophoresis, reliably diagnosed the Florida non-native grasses with 100% accuracy, sensitivity, and specificity. With additional ground-truthing to confirm intraspecific stability, this assay has the potential for broader application within the genus, including detection of the invasive V. australis (cf. V. gigantea), another ubiquitous aquarium product, as well as identification of first-generation hybrid forms. [ABSTRACT FROM AUTHOR]

Litter size is a critical economic trait in livestock, but only a few studies have focused on associated indel mutations in BMPR1B, a key regulator of ovulation and litter size in sheep. We evaluated the effects of BMPR1B mutations on the reproductive performance of sheep. We used Hu, East Friesian, and East Friesian/Hu crossbred sheep as experimental subjects and identified a novel 90 bp deletion in BMPR1B, which coincides with the c.746A > G (FecB mutation) genotype. The correlation between the two loci and litter size was then evaluated. We identified three genotypes for the Del-90bp locus, namely, II, ID, and DD, and three genotypes for the c.746A > G locus, namely ++, B+, and BB. Both Del-90bp and c.746A > G significantly affected the litter size of Hu and East Friesian/Hu crossbred sheep. Linkage disequilibrium analysis revealed a strong linkage disequilibrium between these loci in Hu sheep and the F1 population (r2 > 0.33), which suggests that detecting this 90 bp deletion might be a simple method to identify the likely carriers of c.746A > G. However, the function of this 90-bp deletion still needs further exploration. We provide genetic data that can be used as a reference for the breeding of improved prolific traits in sheep. [ABSTRACT FROM AUTHOR]

Background: Spindle cell tumours in the sinonasal area are diagnostically challenging. We identified a neoplasm that defied histopathological classification using current criteria. Methods: The case was subjected to histopathological, immunohistochemical and molecular analysis using a large small variant DNA panel. Results: The tumour comprised cytologically bland epithelioid spindle cells with a rich vasculature, which lack expression of actin and other smooth muscle markers, CD34 and beta-catenin. An activating insertion/deletion in exon 12 of the PDGFRA gene was detected. This alteration has previously been described in gastrointestinal stromal tumours and inflammatory fibroid polyps of the GI tract, but the site, histological, and immunophenotypic features in this tumour are distinct. Conclusion: We describe a novel sinonasal spindle cell tumour characterised by an activating insertion/deletion in exon 12 of PDGFRA. The diagnosis of PDGFRA-activated sinonasal spindle cell tumour should be considered in difficult to classify mesenchymal lesions at this site. [ABSTRACT FROM AUTHOR]

Background: The purpose of this study was to identify the angiotensin-converting enzyme (ACE) gene (I/D) variations in CAD patients and healthy controls in an Iranian population (West Azerbaijan province of Iran).Methods: This cross-sectional study included 95 CAD patients and 203 healthy controls. ACE I/D polymorphisms were assessed using PCR, and their frequency was determined. Results: There were 298 people, 95 CAD patients, and 203 controls, with an average age of 50.96±3.45 and 51.14±10.20. We discovered that the frequency of the D allele was significantly higher in CAD patients than in controls (P = 0.0009). In contrast, the frequency of the I allele was significantly higher in controls than in CAD patients (P = 0.0009). The D allele carriers genotypes (DD + ID) were more frequent in the CAD patients than in the control group (P = 0.008). The ACE II genotype-state carriers were more common in the control group than in CAD patients (P = 0.0084). However, in the case of the ACE ID genotype, no significant differences were not found in the tested groups (P = 0.47).Conclusions: These findings suggest that individuals with the ACE DD genotype are predisposed to CAD, whereas individuals with the ACE II genotype state are protected.

Objective: Familial Mediterranean fever (FMF) is one of the most common inherited autoinflammatory diseases. Angiogenesis is a feature of inflammatory activation and part of pathogenic processes in autoimmune diseases. Therefore, this study aimed to investigate the role of the Vascular endothelial growth factor (VEGF) gene insertion/deletion (I/D) functional variant in FMF Turkish patients. Methods:MEFV gene mutations were detected in all patients. The FMF patients (N:105) and the healthy controls (N:100) were genotyped for the VEGF I/D variant using PCR followed by agarose gel electrophoresis. The results were statistically analyzed by calculating the odds ratios (OR) and their 95% confidence intervals (95% CI) using the χ2-tests. Results: The mean age of patients was 25.46 ± 10.09. Fifty-nine patients (56.2%) had two or more MEFV gene mutations. The most common MEFV mutation was M694V/M694V. The VEGF I/D variant genotype distribution exhibited a statistically significant difference between the patients and the controls. VEGF I/D genotype was higher in controls compared to patients, while D/D genotype was higher in patients compared to the controls (p = 0.003, p = 0.013, respectively). When we examined the clinical findings, joint pain was more common in patients with VEGF D/D and I/D genotypes compared to I/I genotype (p = 0.043). Although not statistically significant, the most common genotype in patients with two or more MEFV mutations was VEGF D/D (28.6%). Conclusion: The results provided evidence supporting that the D/D genotype of the VEGF I/D variant is associated with an increased risk of FMF in a group of Turkish populations. [ABSTRACT FROM AUTHOR]

Due to the rapid growth in the global volume of data, deoxyribonucleic acid (DNA) data storage has emerged. Error correction in DNA data storage is a key part of this storage technology. In this paper, an improved marker code scheme is proposed to correct insertion, deletion, and substitution errors in deoxyribonucleic acid (DNA) data storage. To correct synchronization (i.e., insertion and deletion) errors, a novel base-symbol-based synchronization algorithm is proposed and used. In the improved scheme, the marker bits are encoded as the information part of the LDPC code, and then mapped into marker bases to correct the synchronization errors. Thus marker bits not only assist in regaining synchronization, but also play a role in LDPC decoding to improve decoding performance. An improved low-complexity normalized min-sum (INMS) algorithm is proposed to correct residual substitution errors after regaining synchronization. The simulation results demonstrate that the improved scheme provides a substantial performance improvement over the concatenated marker code scheme and concatenated watermark code scheme. At the same time, the complexity of the INMS algorithm was reduced, while its bit error rate (BER) performance was approximate to that of the belief propagation (BP) algorithm. [ABSTRACT FROM AUTHOR]

The economic efficiency of sheep breeding can be improved by enhancing sheep productivity. A recent genome-wide association study (GWAS) unveiled the potential impact of the MAST4 gene on prolificacy traits in Australian White sheep (AUW)). Herein, whole-genome sequencing (WGS) data from 26 different sheep breeds worldwide (n = 1507), including diverse meat, wool, milk, or dual-purpose sheep breed types from China, Europe, and Africa, were used. Moreover, polymerase chain reaction (PCR) genotyping of the MAST4 gene polymorphisms in (n = 566) Australian white sheep (AUW) was performed. The 3 identified polymorphisms were not homogeneously distributed across the 26 examined sheep breeds. Findings revealed prevalent polymorphisms (P3-ins-29 bp and P6-del-21 bp) with varying frequencies (0.02 to 0.97) across 26 breeds, while P5-del-24 bp was presented in 24 out of 26 breeds. Interestingly, the frequency of the P3-ins-29 bp variant was markedly higher in Chinese meat or dual-purpose sheep breeds, while the other two variants also showed moderate frequencies in meat breeds. Notably, association analysis indicated that all InDels were associated with AUW sheep litter size (p < 0.05). These results suggest that these InDels within the MAST4 gene could be useful in marker-assisted selection in sheep breeding.

A growing number of studies have shown that members of the ankyrin repeat and suppressors of cytokine signaling (SOCS) box-containing protein (ASB) family are extensively involved in biological processes such as cell growth, tissue development, insulin signaling, ubiquitination, protein degradation, and skeletal muscle membrane protein formation, while the specific biological role of ankyrin-repeat and SOCS box protein 9 (ASB9) remains unclear. In this study, a 21 bp indel in the intron of ASB9 was identified for the first time in 2641 individuals from 11 different breeds and an F2 resource population, and differences were observed among individuals with different genotypes (II, ID, and DD). An association study of a cross-designed F2 resource population revealed that the 21-bp indel was significantly related to growth and carcass traits. The significantly associated growth traits were body weight (BW) at 4, 6, 8, 10, and 12 weeks of age; sternal length (SL) at 4, 8, and 12 weeks of age; body slope length (BSL) at 4, 8, and 12 weeks of age; shank girth (SG) at 4 and 12 weeks of age; tibia length (TL) at 12 weeks of age; and pelvic width (PW) at 4 weeks of age (p < 0.05). This indel was also significantly correlated with carcass traits including semievisceration weight (SEW), evisceration weight (EW), claw weight (CLW), breast muscle weight (BMW), leg weight (LeW), leg muscle weight (LMW), claw rate (CLR), and shedding weight (ShW) (p < 0.05). In commercial broilers, the II genotype was the dominant genotype and underwent extensive selection. Interestingly, the ASB9 gene was expressed at significantly higher levels in the leg muscles of Arbor Acres broilers than those of Lushi chickens, while the opposite was true for the breast muscles. In summary, the 21-bp indel in the ASB9 gene significantly influenced the expression of the ASB9 gene in muscle tissue and was associated with multiple growth and carcass traits in the F2 resource population. These findings suggested that the 21-bp indel within the ASB9 gene could be used in marker-assisted selection breeding for traits related to chicken growth. [ABSTRACT FROM AUTHOR]

BACKGROUND: The purpose of this study was to identify the angiotensin-converting enzyme (ACE) gene (I/D) variations in CAD patients and healthy controls in an Iranian population (West Azerbaijan province of Iran). METHODS: This cross-sectional study included 95 CAD patients and 203 healthy controls. ACE I/D polymorphisms were assessed using PCR, and their frequency was determined. RESULTS: There were 298 people, 95 CAD patients, and 203 controls, with an average age of 50.96±3.45 and 51.14±10.20. We discovered that the frequency of the D allele was significantly higher in CAD patients than in controls (P = 0.0009). In contrast, the frequency of the I allele was significantly higher in controls than in CAD patients (P = 0.0009). The D allele carriers genotypes (DD + ID) were more frequent in the CAD patients than in the control group (P = 0.008). The ACE II genotype-state carriers were more common in the control group than in CAD patients (P = 0.0084). However, in the case of the ACE ID genotype, no significant differences were not found in the tested groups (P = 0.47). CONCLUSIONS: These findings suggest that individuals with the ACE DD genotype are predisposed to CAD, whereas individuals with the ACE II genotype state are protected. [ABSTRACT FROM AUTHOR]

This paper investigates linear-time decoding algorithms for two classes of error-correcting codes. One of the classes is monotone codes which are known as single deletion error-correcting codes, although they are not known to be single substitution error-correcting codes. The other is azinv codes which are known as single balanced adjacent deletion error-correcting codes, although they are not known to be single balanced adjacent substitution error-correcting codes. As a result, this paper proposes generalizations of Levenshtein's decoding algorithm for Levenshtein's single deletion or single substitution error-correcting codes. This paper points out that it is possible to unify our new two decoding algorithms. Moreover, we provide Python implementations of these algorithms and the graphs of their computational costs at https://github.com/Hokuto496/Decoding_Algorithms_of_monotone_codes_and_azinv_codes. [ABSTRACT FROM AUTHOR]

We investigated whether a functional insertion/deletion (I/D) polymorphism of angiotensin-converting enzyme (ACE) influenced antipsychotic treatment. At baseline, and after 8 weeks of treatment with various antipsychotic medications, we assessed patients' Positive and Negative Syndrome Scale (PANSS) scores, PANSS factors, and metabolic-syndrome-related parameters (fasting plasma lipid and glucose levels, and body mass index). A total of 186 antipsychotic-naïve first-episode psychosis patients or nonadherent chronic psychosis individuals (99 males and 87 females) were genotyped by polymerase chain reaction analysis. The ACE-I/D polymorphism was significantly associated with changes in PANSS psychopathology only (p < 0.05). Compared to ACE-II homozygous males, ACE-DD homozygous and ACE-ID heterozygous males manifested significantly greater decreases in PANSS positive score, PANSS excitement factor, and PANSS cognitive factor. ACE-DD homozygous females manifested higher decreases in PANSS depression factor compared to ACE-II homozygous and ACE-ID heterozygous females. The polymorphism's effect size was estimated as moderate to strong, while its contribution to the PANSS psychopathology ranged from ~5.4 to 8.7%, with the lowest contribution observed for PANSS positive score changes and the highest for PANSS depressive factor changes. Our results indicate that ACE-I/D polymorphism had a statistically significant but weak gender-specific impact on psychopathology data, and showed no association between ACE-I/D polymorphism and metabolic-syndrome-related parameters. [ABSTRACT FROM AUTHOR]

Background: The renin–angiotensin system (RAS), which is important for controlling haemostasis in the body, can increase the development of essential hypertension (HTN). Various surveys have shown that ACE I/D polymorphism that influences ACE activity, a key component of RAS, has been known to be associated with the risk of HTN. The goal of this study was to investigate the correlation between ACE (I/D) polymorphism and HTN. Methods: Blood samples were obtained from 102 patients and 104 healthy individuals. The two groups were matched by age and sex. Informed consent was prepared for the study. The demographic data were collected using a questionnaire. White blood cells (WBCs) and then DNA were extracted from whole blood. After this, the PCR test was performed using specific primers. PCR products were examined using 1% agarose gel. Individuals with genotype II having a band of 490 bp, ID two band of 490 bp and 190 bp, and individuals with DD genotype, have a band in region 190 bp. Results: The average age of the patients was 52.7 ± 7.5 years. A significant difference was seen in the distribution of DD, II and I/D genotypes of ACE polymorphism between the essential hypertensive patients (44.1, 10.8, and 45.1%) and their ethnically matched healthy control (61.5, 3.8, and 24.6%, respectively). Our study showed an increased risk of disease in people with II genotype in comparison to ID and DD genotypes (0.46 (0.1–1.75) and 0.26 (0.05–0.94), respectively). Conclusions: The present study demonstrated that ACEI/D polymorphism is characterised with greater risk of essential HTN in the Lorestan province. II genotype increased the relative risk of essential HTN in the population. In the future, more investigations with more samples size are recommended for the better study of genetic factors in hypertensive patients. [ABSTRACT FROM AUTHOR]

Background: Since the beginning of the pandemic of coronavirus disease 2019 (COVID-19), many countries have experienced a considerable number of COVID-19 cases and deaths. The etiology of a broad spectrum of symptoms is still debated. Host genetic variants might also significantly influence the outcome of the disease. This study aimed to evaluate the association of angiotensin-converting enzyme (ACE1) gene Insertion/Deletion (I/D) polymorphism (rs1799752) and ACE2 gene rs1978124 single nucleotide polymorphism with the COVID-19 severity. Methods: This study was conducted on 470 COVID-19 patients and a control group of 56 healthy individuals across several major cities in Iran. The blood sample and clinical data were collected from the participants, and their ACE1 I/D and ACE2 rs1978124 polymorphisms were determined using polymerase chain reaction and PCR-RFLP, respectively. Serum levels of C-reactive protein (CRP), interleukin 6 (IL-6), and ACE1 were measured in the blood samples. Results: We found that the ACE1 DD genotype frequency was inversely correlated with the risk of intubation (p = 0.017) and mortality in COVID-19 patients (p = 0.049). Even after adjustment, logistic regression demonstrated that this significant inverse association remained constant for the above variables at odds ratios of (OR) = 0.35 and Odds Ratio = 0.49, respectively. Also, in the expired (p = 0.042) and intubated (p = 0.048) groups with II + ID genotypes, the mean level of CRP was significantly higher than in the DD genotype group. Furthermore, in both intubated and expired groups, the mean serum level of ACE1 was higher compared with non-intubated and survived groups with II or II + ID genotypes. The results also indicated that ACE2 rs1978124 TT + CT genotypes in females have a significant positive role in susceptibility to COVID-19; however, in females, the TT + CT genotypes had a protective effect (OR = 0.098) against the severity of COVID-19. Conclusion: These findings suggest that ACE1 I/D and ACE2 rs1978124 polymorphism could potentially influence the outcome of COVID-19 in the Iranian population. [ABSTRACT FROM AUTHOR]

The economic efficiency of sheep breeding, aiming to enhance productivity, is a focal point for improvement of sheep breeding. Recent studies highlight the involvement of the Early Region 2 Binding Factor transcription factor 8 ( E2F8) gene in female reproduction. Our group's recent genome-wide association study (GWAS) emphasizes the potential impact of the E2F8 gene on prolificacy traits in Australian White sheep (AUW). Herein, the purpose of this study was to assess the correlation of the E2F8 gene with litter size in AUW sheep breed. This work encompassed 659 AUW sheep, subject to genotyping through PCR-based genotyping technology. Furthermore, the results of PCR-based genotyping showed significant associations between the P1-del-32bp bp InDel and the fourth and fifth parities litter size in AUW sheep; the litter size of those with genotype ID were superior compared to those with DD and II genotypes. Thus, these results indicate that the P1-del-32bp InDel within the E2F8 gene can be useful in marker-assisted selection (MAS) in sheep.

Background: Since the beginning of the pandemic of coronavirus disease 2019 (COVID-19), many countries have experienced a considerable number of COVID-19 cases and deaths. The etiology of a broad spectrum of symptoms is still debated. Host genetic variants might also significantly influence the outcome of the disease. This study aimed to evaluate the association of angiotensin-converting enzyme (ACE1) gene Insertion/Deletion (I/D) polymorphism (rs1799752) and ACE2 gene rs1978124 single nucleotide polymorphism with the COVID-19 severity.Methods: This study was conducted on 470 COVID-19 patients and a control group of 56 healthy individuals across several major cities in Iran. The blood sample and clinical data were collected from the participants, and their ACE1 I/D and ACE2 rs1978124 polymorphisms were determined using polymerase chain reaction and PCR-RFLP, respectively. Serum levels of C-reactive protein (CRP), interleukin 6 (IL-6), and ACE1 were measured in the blood samples.Results: We found that the ACE1 DD genotype frequency was inversely correlated with the risk of intubation (p = 0.017) and mortality in COVID-19 patients (p = 0.049). Even after adjustment, logistic regression demonstrated that this significant inverse association remained constant for the above variables at odds ratios of (OR) = 0.35 and Odds Ratio = 0.49, respectively. Also, in the expired (p = 0.042) and intubated (p = 0.048) groups with II + ID genotypes, the mean level of CRP was significantly higher than in the DD genotype group. Furthermore, in both intubated and expired groups, the mean serum level of ACE1 was higher compared with non-intubated and survived groups with II or II + ID genotypes. The results also indicated that ACE2 rs1978124 TT + CT genotypes in females have a significant positive role in susceptibility to COVID-19; however, in females, the TT + CT genotypes had a protective effect (OR = 0.098) against the severity of COVID-19.Conclusion: These findings suggest that ACE1 I/D and ACE2 rs1978124 polymorphism could potentially influence the outcome of COVID-19 in the Iranian population.

Background: Androgenetic alopecia (AGA) is a prevalent condition with a complex etiopathogenesis. Angiotensin‐converting enzyme (ACE) gene located on the chromosome 17q23 contains an insertion (I) and deletion (D) polymorphism in the intron 16. This gene polymorphism plays a role in multiple inflammatory disorders. However, there are no studies investigating its association with AGA susceptibility. Objectives: In this work, we aimed at exploring the association of ACE gene I/D polymorphism in AGA susceptibility in a group of Egyptian patients. Methods: This study included 100 AGA patients, and 100 apparently healthy controls. The ACE gene I/D polymorphism was analyzed by polymerase chain reaction. Results: The DD, ID genotypes, and D allele showed higher frequent distribution among studied AGA patients than controls (p < 0.05 each). Positive family history and ACE gene I/D polymorphism were considered AGA susceptibility predictors in both uni‐ and multivariable analyses [p < 0.05 each (OR (95% CI)] on applying logistic regression analysis for risk factors prediction. Conclusions: This study highlights the possible contribution of the suspected genetic polymorphism as a susceptibility indicator for AGA development in the examined group of patients. [ABSTRACT FROM AUTHOR]

Due to the rapid growth in the global volume of data, deoxyribonucleic acid (DNA) data storage has emerged. Error correction in DNA data storage is a key part of this storage technology. In this paper, an improved marker code scheme is proposed to correct insertion, deletion, and substitution errors in deoxyribonucleic acid (DNA) data storage. To correct synchronization (i.e., insertion and deletion) errors, a novel base-symbol-based synchronization algorithm is proposed and used. In the improved scheme, the marker bits are encoded as the information part of the LDPC code, and then mapped into marker bases to correct the synchronization errors. Thus marker bits not only assist in regaining synchronization, but also play a role in LDPC decoding to improve decoding performance. An improved low-complexity normalized min-sum (INMS) algorithm is proposed to correct residual substitution errors after regaining synchronization. The simulation results demonstrate that the improved scheme provides a substantial performance improvement over the concatenated marker code scheme and concatenated watermark code scheme. At the same time, the complexity of the INMS algorithm was reduced, while its bit error rate (BER) performance was approximate to that of the belief propagation (BP) algorithm.

In China, there are two subspecies of the chestnut tiger butterfly, Parantica sita (Kollar) (Lepidoptera: Nymphalidae), P. s. sita in southwest China and P. s. niphonica on Taiwan Island. Our previous study found substantial genetic divergence between both subspecies. This paper reports a novel haplotype of the mitochondrial genome from the specimens in Leshan, Sichuan Province, China (P. sita LS), which is located within the distribution range of P. s. sita. The length of the complete mitochondrial genome is 15,202 bp, and its general characteristics match those published before. However, genetically, P. sita LS diverges substantially from both P. s. sita and P. s. niphonica. First, the COI gene of P. sita LS differs from the COI genes of P. s. sita and P. s. niphonica by 4.7% and 2.5%, respectively. Second, consistent with the difference between P. s. sita and P. s. niphonica, the AT-rich region of P. sita LS shows a fragment deletion. Third, these three haplotypes of P. sita are not forming a monophyly in phylogenetic trees. Instead, P. luzonensis, a related species, mixes in the cluster of P. sita. Based on these results, this paper proposes the division of P. sita into three independent species, which needs to be corroborated by further evidence. [ABSTRACT FROM AUTHOR]

An ideal cancer therapeutic strategy involves the selective killing of cancer cells without affecting the surrounding normal cells. However, researchers have failed to develop such methods for achieving selective cancer cell death because of shared features between cancerous and normal cells. In this study, we have developed a therapeutic strategy called the cancer-specific insertions–deletions (InDels) attacker (CINDELA) to selectively induce cancer cell death using the CRISPR-Cas system. CINDELA utilizes a previously unexplored idea of introducing CRISPR-mediated DNA double-strand breaks (DSBs) in a cancer-specific fashion to facilitate specific cell death. In particular, CINDELA targets multiple InDels with CRISPRCas9 to produce many DNA DSBs that result in cancer-specific cell death. As a proof of concept, we demonstrate here that CINDELA selectively kills human cancer cell lines, xenograft human tumors in mice, patient-derived glioblastoma, and lung patient-driven xenograft tumors without affecting healthy human cells or altering mouse growth. [ABSTRACT FROM AUTHOR]

Global classification of bovine genes is important for studies of biology and tissue-specific gene editing. Herein, we classified the tissue-specific expressed genes and uncovered an important variation in the promoter region of an adipose tissue-specific lncRNA gene. Statistical analysis demonstrated that the number of genes specifically expressed in the brain was the highest, while it was lowest in the adipose tissues. A total of 1,575 genes were found to be significantly higher expressed in adipose tissues. Bioinformatic analysis and qRT-PCR were used to uncover the expression profiles of the 23 adipose tissue-specific and highly expressed genes in 8 tissues. The results showed that most of the 23 genes have higher expression level in adipose tissue. Besides, we detected a 12 bp insertion/deletion (indel) variation (rs720343880) in the promoter region of an adipose tissue-specific lncRNA gene (LOC100847835). The different genotypes of this variation were associated with carcass traits of cattle. Therefore, the outcomes of the present study can be used as a starting point to explore the development of cattle organs and tissues, as well as to improve the quality of cattle products.

Objective To investigate the population genetic data of 47 autosomal insertion/deletion （InDel） polymorphism genetic markers involved in AGCU InDel 50 kit in Guangdong Han, Guangxi Zhuang, Guangxi Yao, Guangxi Jing, and Guangxi Mulam, and to evaluate their application in forensic DNA identification. Methods Multiplex amplification of the 768 unrelated individuals from the 5 ethnic groups mentioned above was performed with the AGCU InDel 50 kit. Genotyping was carried out by 3500xL gene analyzer, population genetic parameters were gathered and polymorphism analysis was performed. Results No linkage disequilibrium was found among 47 autosomal InDel loci in the 5 ethnic groups. The distribution of genotype frequency of 47 autosomal InDel loci confirmed to the Hardy-Weinberg equilibrium in Guangdong Han and Guangxi Zhuang. Except for rs139934789, the other 46 loci confirmed to the Hardy-Weinberg equilibrium in Guangxi Yao, Guangxi Jing, and Guangxi Mulam. The results of genetic variation analysis among the populations showed that 1.12% of genetic variation was caused by ethnic group differences. The cumulative discrimination power of 47 autosomal InDel loci for the 5 ethnic groups were all above 0.999 999 999 999 999. The cumulative probability of exclusion for each ethnic group was less than 0.999 9. The two Y-InDels were identified in all male individuals and were absent in all female individuals. Conclusion Except for rs139934789, the other 46 InDel loci have a relatively good genetic polymorphism in the 5 Chinese ethnic groups, and can be used for forensic individual identification and as effective supplements for paternity testing.

Differential pulse-position modulation (DPPM) shows significant power and bandwidth efficiency, but suffers from serious insertion/deletion and substitution errors if the DPPM soft-decision symbol-by-symbol detection method is used. In this paper, based on the DPPM transmission scheme combining the watermark with the low-density parity-check (LDPC) code, and the equivalent source and channel models, we propose an efficient decoding scheme using hidden Markov model (HMM). Specifically, with the known watermark and the equivalent source and channel models, a hidden markov model is first established to estimate the insertion/deletion errors of the received symbols. Then, a hard-decision forward-backward algorithm is used to recover synchronization and output the estimate of the codeword. Finally, Belief-Propagation (BP) decoding algorithm in the logarithmic domain is performed to correct the residual substitution errors. Simulation results reveal that compared with the decoding scheme using the dynamic programming (DP) and Viterbi algorithms, the proposed decoding scheme has superior performance in correcting insertion, deletion and substitution errors in DPPM transmission.

Janus kinase 2 ( JAK2 ) plays a critical role in myoblast proliferation and fat deposition in animals. Our previous RNA-Seq analyses identified a close association between the JAK2 gene and muscle development. To date, research delving into the relationship between the JAK2 gene and growth traits has been sparse. In this study, we sought to investigate the relationship between novel mutations within the JAK2 gene and goat growth traits. Herein, two novel InDel (Insertion/Deletion) polymorphisms within the JAK2 gene were detected in 548 goats, and only two genotypes were designated as ID (Insertion/Deletion) and DD (Deletion/Deletion). The results indicate that the two InDels, the del19008 locus in intron 2 and del72416 InDel in intron 6, showed significant associations with growth traits ( p < 0.05). Compared to Nubian and Jianzhou Daer goats, the del72416 locus displayed a more pronounced effect in the Fuqing breed group. In the Nubian breed (NB) group, both InDels showed a marked influence on body height (BH). There were strong linkages observed for these two InDels between the Fuqing (FQ) and Jianzhou (JZ) populations. The DD-ID diplotype was associated with inferior growth traits in chest width (ChW) and cannon circumference (CaC) in the FQ goats compared to the other diplotypes. In the NB population, the DD-DD diplotype exhibited a marked negative impact on BH and HuWI (hucklebone width index), in contrast to the other diplotypes. In summary, our findings suggest that the two InDel polymorphisms within the JAK2 gene could serve as valuable molecular markers for enhancing goat growth traits in breeding programs.

Insulin-like growth factor 1 receptor (IGF1R) is a cell surface receptor, belonging to the tyrosine kinase receptor superfamily. IGF1R plays a role not only in normal cell development but also in malignant transformation, which has become a candidate therapeutic target for the treatment of human cancer. This study aimed to explore insertions and deletions (indels) in IGF1R gene and investigate their association with growth traits in four Chinese cattle breeds (Xianan cattle, Jinnan cattle, Qinchuan cattle and Nanyang cattle). The current paper identified a 28-bp indel by polymerase chain reaction within IGF1R gene. The analysis showed that there was a significant correlation between the locus and the hucklebone width of Nanyang cattle in four periods, in which it was highly correlated at 6, 12 and 18 months. At the age of 6 months, it was also significantly correlated with body height, body weight and body length. Association analysis showed that the locus in Jinnan cattle was extremely significantly correlated with body slanting length and body weight, and significantly correlated with chest circumference. There was no significant correlation between this locus and growth traits of Xianan cattle and Qinchuan cattle. The detected indel in the IGF1R gene was significantly associated with growth traits in Jinnan and Nanyang cattle, and could be used as a molecular marker for growth trait selection. [ABSTRACT FROM AUTHOR]

We investigated whether a functional insertion/deletion (I/D) polymorphism of angiotensin-converting enzyme (ACE) influenced antipsychotic treatment. At baseline, and after 8 weeks of treatment with various antipsychotic medications, we assessed patients’ Positive and Negative Syndrome Scale (PANSS) scores, PANSS factors, and metabolic-syndrome-related parameters (fasting plasma lipid and glucose levels, and body mass index). A total of 186 antipsychotic-naïve first-episode psychosis patients or nonadherent chronic psychosis individuals (99 males and 87 females) were genotyped by polymerase chain reaction analysis. The ACE-I/D polymorphism was significantly associated with changes in PANSS psychopathology only (p < 0.05). Compared to ACE-II homozygous males, ACE-DD homozygous and ACE-ID heterozygous males manifested significantly greater decreases in PANSS positive score, PANSS excitement factor, and PANSS cognitive factor. ACE-DD homozygous females manifested higher decreases in PANSS depression factor compared to ACE-II homozygous and ACE-ID heterozygous females. The polymorphism’s effect size was estimated as moderate to strong, while its contribution to the PANSS psychopathology ranged from ~5.4 to 8.7%, with the lowest contribution observed for PANSS positive score changes and the highest for PANSS depressive factor changes. Our results indicate that ACE-I/D polymorphism had a statistically significant but weak gender-specific impact on psychopathology data, and showed no association between ACE-I/D polymorphism and metabolic-syndrome-related parameters.

• Severe acute respiratory syndrome coronavirus 2 rapidly spread to all continents. • Genetic seems to be important for the resistance to and mortality of COVID-19. • ACE I/D polymorphism has the potential to affect infection symptoms and mortality. • ACE I/I homozygotes were more common in COVID-19 patients that in controls. • The difference was driven just by the symptomatic subjects. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rapidly spread from China in 2019/2020 to all continents. Significant geographical and ethnic differences were described, and host genetic background seems to be important for the resistance to and mortality of COVID-19. Angiotensin-converting enzyme (ACE) insertion/deletion (I/D) polymorphism (rs4646994) is one of the candidates with the potential to affect infection symptoms and mortality. In our study, we successfully genotyped 408 SARS-CoV-2-positive COVID-19 survivors (163 asymptomatic and 245 symptomatic) and compared them with a population-based DNA bank of 2,559 subjects. The frequency of ACE I/I homozygotes was significantly increased in COVID-19 patients compared with that in controls (26.2% vs. 21.2%; P = 0.02; OR [95% CI] = 1.55 [1.17–2.05]. Importantly, however, the difference was driven just by the symptomatic subjects (29.0% vs. 21.2% of the I/I homozygotes; P = 0.002; OR [95% CI] = 1.78 [1.22–2.60]). The genotype distribution of the ACE genotypes was almost identical in population controls and asymptomatic SARS-CoV-2-positive patients (P = 0.76). We conclude that ACE I/D polymorphism could have the potential to predict the severity of COVID-19, with I/I homozygotes being at increased risk of symptomatic COVID-19. [ABSTRACT FROM AUTHOR]

Objective To explore the genetic background and structure of Urumqi Mongolians, the previously developed 39-AIM-InDels panel for ancestry inference was utilized in the present study. Methods The blood samples of 145 unrelated healthy Urumqi Mongolian individuals were collected and genotyped. The compositions of ancestry information of Urumqi Mongolians were studied with 17 different populations from three continents （East Asia, Europe and Africa） as reference populations. Then, multiple population genetics and bioinformatics analysis methods were applied, the Fst and DA values between matched populations were compared and analyzed, PCA analysis was performed and a phylogenetic tree was constructed. The proportions of ancestry information components of Urumqi Mongolians were analyzed with Structure software, etc. Results The ancestry information components of Urumqi Mongolian group in different intercontinental populations accounted for 89%, 7%, and 3% of East Asian, European, and African populations, respectively. Compared with other intercontinental populations, Urumqi Mongolian group and East Asian populations have lower Fst and DA values, and they were in the same cluster in PCA analysis as well. In a phylogenetic tree, the Urumqi Mongolian group was in the same branch as East Asian populations. Conclusion Urumqi Mongolian group had relatively close genetic relationships with East Asian populations, and the proportion of its East Asian ancestry was about 89%.

A-kinase anchoring protein 12 (AKAP12) plays key roles in male germ cells and female ovarian granulosa cells, whereas its influence on livestock litter size remains unclear. Herein we detected the genetic variants of AKAP12 gene and their effects on litter size as well as alternative splicing variants expression in Shaanbei white cashmere (SBWC) goats, aiming at exploring theoretical basis for goat molecular breeding. We identified two Insertion/deletions (Indels) (7- and 13-bp) within the AKAP12 gene. Statistical analyses demonstrated that the 13-bp indel mutation in the 3′ UTR was significantly associated with litter size (n = 1,019), and the carriers with DD genotypes presented lower litter sizes compared with other carriers (P < 0.01). Bioinformatics analysis predicted that this 13-bp deletion sequence could bind to the seed region of miR-181, which has been documented to suppress porcine reproductive and respiratory syndrome virus (PRRSV) infection by targeting PRRSV receptor CD163 and affect the pig litter size. Therefore, luciferase assay for this 13-bp indel binding with miRNA-181 was performed, and the luciferase activity of pcDNA-miR-181-13bp-Deletion-allele vector was significantly lower than that of the pcDNA-miR-181-13bp-Insertion-allele vector (P < 0.05), suggesting the reduced binding capability with miR-181 in DD genotype. Given that alternative spliced variants and their expression considerably account for the Indel genetic effects on phenotypic traits, we therefore detected the expression of the alternative spliced variants in different tissues and identified that AKAP12-AS2 exhibited the highest expression levels in testis tissues. Interestingly, the AKAP12-AS2 expression levels of homozygote DD carriers were significantly lower than that of individuals with heterozygote ID, in both testis and ovarian tissues (P < 0.05), which is consistent with the effect of the 13-bp deletion on the reduced litter size. Taken together, our results here suggest that this 13-bp indel mutation within goat AKAP12 might be utilized as a novel molecular marker for improving litter size in goat breeding.

A-kinase anchoring protein 12 (AKAP12) plays key roles in male germ cells and female ovarian granulosa cells, whereas its influence on livestock litter size remains unclear. Herein we detected the genetic variants of AKAP12 gene and their effects on litter size as well as alternative splicing variants expression in Shaanbei white cashmere (SBWC) goats, aiming at exploring theoretical basis for goat molecular breeding. We identified two Insertion/deletions (Indels) (7- and 13-bp) within the AKAP12 gene. Statistical analyses demonstrated that the 13-bp indel mutation in the 3′ UTR was significantly associated with litter size (n = 1,019), and the carriers with DD genotypes presented lower litter sizes compared with other carriers (P < 0.01). Bioinformatics analysis predicted that this 13-bp deletion sequence could bind to the seed region of miR-181, which has been documented to suppress porcine reproductive and respiratory syndrome virus (PRRSV) infection by targeting PRRSV receptor CD163 and affect the pig litter size. Therefore, luciferase assay for this 13-bp indel binding with miRNA-181 was performed, and the luciferase activity of pcDNA-miR-181-13bp-Deletion-allele vector was significantly lower than that of the pcDNA-miR-181-13bp-Insertion-allele vector (P < 0.05), suggesting the reduced binding capability with miR-181 in DD genotype. Given that alternative spliced variants and their expression considerably account for the Indel genetic effects on phenotypic traits, we therefore detected the expression of the alternative spliced variants in different tissues and identified that AKAP12-AS2 exhibited the highest expression levels in testis tissues. Interestingly, the AKAP12-AS2 expression levels of homozygote DD carriers were significantly lower than that of individuals with heterozygote ID, in both testis and ovarian tissues (P < 0.05), which is consistent with the effect of the 13-bp deletion on the reduced litter size. Taken together, our results here suggest that this 13-bp indel mutation within goat AKAP12 might be utilized as a novel molecular marker for improving litter size in goat breeding. [ABSTRACT FROM AUTHOR]

Mungbean [Vigna radiata (L.) R. Wilczek var. radiata] is vital grain legume having nutritional and socio-economic importance, especially in the developing countries. We performed whole-genome re-sequencing of three accessions representing the wild progenitor species, released and landrace of mungbean to identify SNPs with relevance to genetic relationships analysis. Approximately 9.3 million raw reads were obtained using Ion Torrent PGM™ platform and more than 92% of the reads were mapped to the reference mungbean genome. We identified a total of 233,799 single-nucleotide polymorphisms in relation to the reference genome (SNPs: 103,341 in wild, 93,078 in released and 37,380 in landrace accessions) and 9544 insertions and deletions (InDels: 4742 in wild, 3608 in released and 1194 in landrace accessions) in the coding and non-coding regions. In all accessions, genomic variants were unevenly distributed within and across the mungbean chromosomes. Among these 5339, 4739 and 1795 SNPs were non-synonymous in 815, 790 and 317 genes of wild, released and landrace accessions, respectively. These polymorphisms might contribute to the variation in important pathways of genes for abiotic and biotic stress tolerance and important agronomic traits, such as seed dormancy, flowering time and seed size in mungbean. Among the randomly selected SNPs, a selected subset was validated using Sanger sequencing technique. The genomic variations among mungbean wild, released and landrace accessions constitute a powerful tool to support genetic research and molecular breeding of mungbean. [ABSTRACT FROM AUTHOR]

Vitis sp. cv. Koshu is indigenous to Japan and used as a table and processing grape. It also constitutes an important grape cultivar in Japanese white wine making and is phylogenetically distinct from European grapes. To understand its genomic information, we compared its small and structural variations with those of the table grape cultivar “Thompson seedless” and European wine grape cultivar “Tannat” via a short-read-based resequencing approach. The Koshu genome exhibited high heterozygosity compared to these cultivars, with this characteristic being particularly prominent on chromosome 7. Furthermore, Koshu structural variation encompassed the most and largest extent of duplications and the fewest and smallest extent of deletions with regard to copy number variation and the fewest absence variations among the compared grape cultivars. Plant disease resistance related to cell death associated with hypersensitive response and environmental stress response, such as water deprivation, oxidative stress, and cell wall organization, was inferred through enrichment analysis of small and structural variations. Variant accumulation levels in Koshu indicated that phenylpropanoid, flavonoid, glutathione, and α-linolenic acid pathways were related to polyphenol and flavor components. Together, this Koshu genomic information provides a foundation for improving the quality of Koshu wine and may facilitate the use of Koshu as a genetic resource.

Pod-shattering causes a significant yield loss in many soybean cultivars. Shattering-tolerant cultivars provide the most effective approach to minimizing this loss. We developed molecular markers for pod-shattering and validated them in soybeans with diverse genetic backgrounds. The genes Glyma.16g141200, Glyma.16g141500, and Glyma.16g076600, identified in our previous study by quantitative trait locus (QTL) mapping and whole-genome resequencing, were selected for marker development. The whole-genome resequencing of three parental lines (one shattering-tolerant and two shattering-susceptible) identified single nucleotide polymorphism (SNP) and/or insertion/deletion (InDel) regions within or near the selected genes. Two SNPs and one InDel were converted to Kompetitive Allele-Specific PCR (KASP) and InDel markers, respectively. The accuracy of the markers was examined in the two recombinant inbred line populations used for the QTL mapping, as well as the 120 varieties and elite lines, through allelic discrimination and phenotyping by the oven-drying method. Both types of markers successfully discriminated the pod shattering-tolerant and shattering-susceptible genotypes. The prediction accuracy, which was as high as 90.9% for the RILs and was 100% for the varieties and elite lines, also supported the accuracy and usefulness of these markers. Thus, the markers can be used effectively for genetic and genomic studies and the marker-assisted selection for pod-shattering tolerance in soybean.

Abstract Background RNA-seq is the most commonly used sequencing application. Not only does it measure gene expression but it is also an excellent media to detect important structural variants such as single nucleotide variants (SNVs), insertion/deletion (Indels) or fusion transcripts. However, detection of these variants is challenging and complex from RNA-seq. Here we describe a sensitive and accurate analytical pipeline which detects various mutations at once for translational precision medicine. Methods The pipeline incorporates most sensitive aligners for Indels in RNA-Seq, the best practice for data preprocessing and variant calling, and STAR-fusion is for chimeric transcripts. Variants/mutations are annotated, and key genes can be extracted for further investigation and clinical actions. Three datasets were used to evaluate the performance of the pipeline for SNVs, indels and fusion transcripts. Results For the well-defined variants from NA12878 by GIAB project, about 95% and 80% of sensitivities were obtained for SNVs and indels, respectively, in matching RNA-seq. Comparison with other variant specific tools showed good performance of the pipeline. For the lung cancer dataset with 41 known and oncogenic mutations, 39 were detected by the pipeline with STAR aligner and all by the GSNAP aligner. An actionable EML4 and ALK fusion was also detected in one of the tumors, which also demonstrated outlier ALK expression. For 9 fusions spiked-into RNA-seq libraries with different concentrations, the pipeline was able to detect all in unfiltered results although some at very low concentrations may be missed when filtering was applied. Conclusions The new RNA-seq workflow is an accurate and comprehensive mutation profiler from RNA-seq. Key or actionable mutations are reliably detected from RNA-seq, which makes it a practical alternative source for personalized medicine.

Genetic markers in forensic DNA typing experienced the variable number of tandem repeats （VNTR） sequences and the short tandem repeats （STR） sequences. With the emerge of sequencing technology, the third generation of genetic markers were found out, which usually have two alleles including single nucleotide polymorphism （SNP） and insertion/deletion （InDel）, also known as biallelic genetic markers. Because of the insertions or deletions of DNA fragments, InDel genetic marker reveals DNA fragment length polymorphism and widely distributes across the whole genome. InDel genetic marker is numerous and has the characteristics of STR and SNP genetic markers, which has been applied in the fields of genetics and anthropology. This review focuses on the research progress of InDel genetic marker in forensic science, aiming to review and summarize the main research findings in recent years and provide clues for future researches.

Vitis sp. cv. Koshu is indigenous to Japan and used as a table and processing grape. It also constitutes an important grape cultivar in Japanese white wine making and is phylogenetically distinct from European grapes. To understand its genomic information, we compared its small and structural variations with those of the table grape cultivar "Thompson seedless" and European wine grape cultivar "Tannat" via a short-read-based resequencing approach. The Koshu genome exhibited high heterozygosity compared to these cultivars, with this characteristic being particularly prominent on chromosome 7. Furthermore, Koshu structural variation encompassed the most and largest extent of duplications and the fewest and smallest extent of deletions with regard to copy number variation and the fewest absence variations among the compared grape cultivars. Plant disease resistance related to cell death associated with hypersensitive response and environmental stress response, such as water deprivation, oxidative stress, and cell wall organization, was inferred through enrichment analysis of small and structural variations. Variant accumulation levels in Koshu indicated that phenylpropanoid, flavonoid, glutathione, and α-linolenic acid pathways were related to polyphenol and flavor components. Together, this Koshu genomic information provides a foundation for improving the quality of Koshu wine and may facilitate the use of Koshu as a genetic resource. [ABSTRACT FROM AUTHOR]

Summary: Parathyroid hormone (PTH) is a crucial regulator of calcium homeostasis and bone remodeling, and the parathyroid hormone 1 receptor (PTH1R) belongs to a class II G‐protein‐coupled receptor. PTH activates PTH1R, which mediates catabolic and anabolic processes in the skeleton. However, the functional mechanism of PTH1R has not been thoroughly elucidated in organisms. This study identified a 51 bp indel mutation in the first intron of the PTH1R gene and elucidated the effect of this gene mutation on the growth and carcass traits in chickens. The results indicated that the 51 bp indel was significantly associated with subcutaneous fat thickness, abdominal fat weight, body weight and daily gain over 4–8 weeks. Furthermore, we found that PTH1R gene expression was highest in the kidney and liver tissues, and it showed a trend of decreasing in leg and breast muscle tissues at different embryonic stages. In addition, we examined the expression of the three genotypes of the PTH1R gene in the liver, breast muscle and abdominal fat and found that the II genotype was significantly higher than the DD and ID genotypes. In summary, these findings suggest that the PTH1R gene can serve as a potential molecular marker for chicken breeding. [ABSTRACT FROM AUTHOR]

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