H1 Haplotype Research Articles

A new gene for restoring wild abortive-type cytoplasmic male sterility in rice.

The WA-type CMS in rice is widely used in Asia for its stability and adaptability. Li Li's team found that the Rf20 gene enhances the fertility restoration of Rf4. It is recommended to introduce the H3 haplotype of the Rf20 gene into indica or Basmati rice, and high-temperature fertility issues in CMS-WA can be addressed through Rf20 gene editing.

NADPH oxidase 5 is a novel susceptibility gene for type 2 diabetes mellitus.

This pilot study investigated whether single nucleotide polymorphisms (SNP) in the NOX5 gene (NADPH oxidase 5) are associated with the type 2 diabetes (T2D) risk. A total of 1579 patients with T2D and 1627 age- and sex-matched healthy subjects were recruited for this study. Genotyping of common SNPs, namely rs35672233, rs3743093, rs2036343, rs311886, and rs438866, was performed using the MassArray-4 system. SNP rs35672233 was associated with an increased risk of T2D (OR = 1.67, 95% CI 1.29-2.17, FDR = 0.003). The H3 haplotype (rs35672233T-rs3743093G-rs2036343A-rs311886C-rs438866C) increased T2D risk (OR = 1.65, 95% CI 1.27-2.13, FDR = 0.001). The rs35672233 polymorphism and H3 haplotype were found to have an association with T2D risk only in subjects with a body mass index greater than 25 kg/m2 (FDR < 0.01). Environmental risk factors, such as chronic psycho-emotional stress, sedentary lifestyle, high-calorie diet and SNP rs35672233 were jointly associated with T2D susceptibility. A haplotype comprising the allele rs35672233-C and conferring protection against T2D, was associated with elevated levels of antioxidants such as total glutathione and uric acid, as well as reduced levels of two-hour postprandial glucose in the plasma of patients. The NOX5 polymorphisms showed no associations with diabetic complications. The present study is the first to establish associations between polymorphisms in NOX5 and the risk of type 2 diabetes mellitus, and provides a new line of evidence for the crucial role of oxidative stress-related genes in disease susceptibility.

Assessment of antioxidant properties in selected pigmented and non-pigmented rice (Oryza sativa L.) germplasm and determination of its association with Rc gene haplotypes

BackgroundAntioxidant properties of rice provide various health benefits due to its ability to inhibit cellular oxidation. Antioxidant content of rice is known to be linked with the pericarp pigmentation. The Rc gene of rice (Os07g0211500) codes for a basic helix-loop-helix (bHLH) protein, acting as a transcriptional factor in regulating proanthocyanidin biosynthesis. The current study was carried out to evaluate the variation of antioxidant properties in a selected panel of rice accessions and assess the possibility of using haplotypes defined based on the Rc gene to predict pericarp pigmentation and antioxidant content in rice.ResultsThirty-two rice accessions were evaluated for grain pericarp colour and antioxidant properties; total phenolic content (TPC), total flavonoids (TFC), proanthocyanidins (PAC) and radical scavenging activity (RSA). The parameters TPC, TFC and PAC showed significant positive correlation with RSA (r > 0.69; P < 0.01). The study panel showed a wide variation for antioxidant properties and rice accessions such as Sudu Heenati, Deweraddiri, Madathawalu, Masuran, Ld 368, At 311, Kalu Heenati, Bw 272-6B, Pokkali, At 362 and Wanni Dahanala exhibited profound potential with respect to antioxidant properties. Based on three-target sites previously reported as critical for the function of the coded bHLH protein (an A/C SNP at 1,353-bp, a 1-bp insertion/deletion at 1,388-bp, and a 14-bp insertion/deletion at 1,408-1,421-bp positioned in the mRNA corresponding to the exon 6 of rice Rc gene), three haplotypes were defined (H1-H3). Pigmentation of the rice pericarp could be successfully explained based on the defined haplotypes (H1 (C/G/+): red, and H2 (A/G/+) and H3 (C/G/-): white), and the H1 haplotype corresponded to a significantly (P < 0.05) higher TPC, TFC, PAC and RSA compared to the other haplotypes.ConclusionsThe studied rice accessions showed a significant variation with respect to antioxidant properties. Haplotype H1 defined based on the three-target sites in the exon 6 of Rc gene can detect rice accessions with red pigmented pericarp and high antioxidant properties effectively. Hence, its use can be recommended as an alternative to biochemical assays for screening during rice breeding programs.

Multivariate analysis of morphological variability of the initial stock intrabreed type of Sarboyan carp (Cyprinus Carpio L.)

The analysis of morphological variability of the initial stock within the breed type Sarboyan carp (Cyprinus carpio L.) by the principal component method is presented. The research was conducted in 2022, 2023 in the Novosibirsk region. The Sarboyan carp stock (males and females) from the fish breeding farm was studied according to eight valuation measurements: body weight, absolute body length, body length without tail fin, maximum height, width and girth. A comparative analysis of the body features of the Sarboyan carp belonging to four haplotypes (H1, H15, H16, H17) was carried out. The morphometric features of the Sarboyan carp were processed using principal component method. It was found that sexual dimorphism was noted on the basis of total size: females have larger sizes than males. In the fish stock under study, a trend towards the difference between H1 and H16 haplotypes was established. The individuals in the H1 haplotype are relatively thicker and shorter compared to H16. There is a group of fish with unknown haplotypes in the data structure, all of which show a shift towards the third component relative to H1, i.e. they have a higher back and smaller body thickness. No haplotypic differences were found in the component showing an apparent inverse relationship between head length trait, body length and absolute fish length. Multivariate analysis of morphological variability also showed that distribution of the individuals in the three-dimensional space PC2-PC3-PC4, free from size-age variability, allows pre-selection of fish with the required proportions of morphological features for further reproduction.

Association of SLCO1B1 gene variants with angiotensin-converting enzyme inhibitor-induced cough in a Pakistani hypertensive cohort.

Angiotensin-converting enzyme inhibitors (ACEIs) are prescribed for individuals with high cardiovascular (CV) risk; however, persistent cough limits the use of ACEIs in a large number of patients. The current study aimed to identify the genetic variants in the SLCO1B1 gene that might be associated with ACEI-related cough in a Pakistani hypertensive population. A prospective cohort study was conducted at a tertiary care hospital in Pakistan. A total of 74 patients who had been treated with ACEIs were recruited through a convenient sampling method. The study was approved by the Institutional Review Board & Ethics Committee of the Shifa International Hospital, Islamabad. Patients provided 2ml of blood for sequencing after signing informed consent. Partial gene sequencing of SLCO1B1 was carried out to find single nucleotide polymorphisms (SNPs) and haplotypes. It was found, through a structured questionnaire, that thirty-eight (38) patients experienced cough within 2weeks of ACEI administration and were considered as a case group (cough), and thirty-six (36) patients were considered as a control group (no cough). The incidence of cough was 51%. We found six different SNPs and 9 haplotypes in the partial gene sequences of SLCO1B1. Haplotype H4 was associated significantly with cough after adjusting for sex and smoking status. Other SNPs and haplotypes were not significantly associated with ACE-Is-induced cough. These findings emphasize the significance of SLCO1B1 genetic variants, specifically H4, as a potential predictor of ACEI-induced cough. It could be included in clinical practice as a possible risk factor for ACEI-induced cough once confirmed in larger clinical trials with bigger sample sizes. The replication of these findings in larger and more diverse populations is likely to contribute to the therapeutic use of ACEIs by predicting ACEI-induced cough.

MAPT haplotype-associated transcriptomic changes in progressive supranuclear palsy

Progressive supranuclear palsy (PSP) is a neurodegenerative movement and cognitive disorder characterized by abnormal accumulation of the microtubule-associated protein tau in the brain. Biochemically, inclusions in PSP are enriched for tau proteoforms with four microtubule-binding domain repeats (4R), an isoform that arises from alternative tau pre-mRNA splicing. While preferential aggregation and reduced degradation of 4R tau protein is thought to play a role in inclusion formation and toxicity, an alternative hypothesis is that altered expression of tau mRNA isoforms plays a causal role. This stems from the observation that PSP is associated with common variation in the tau gene (MAPT) at the 17q21.31 locus which contains low copy number repeats flanking a large recurrent genomic inversion. The complex genomic structural changes at the locus give rise to two dominant haplotypes, termed H1 and H2, that have the potential to markedly influence gene expression. Here, we explored haplotype-dependent differences in gene expression using a bulk RNA-seq dataset derived from human post-mortem brain tissue from PSP (n = 84) and controls (n = 77) using a rigorous computational pipeline, including alternative pre-mRNA splicing. We found 3579 differentially expressed genes in the temporal cortex and 10,011 in the cerebellum. We also found 7214 differential splicing events in the temporal cortex and 18,802 in the cerebellum. In the cerebellum, total tau mRNA levels and the proportion of transcripts encoding 4R tau were significantly increased in PSP compared to controls. In the temporal cortex, the proportion of reads that expressed 4R tau was increased in cases compared to controls. 4R tau mRNA levels were significantly associated with the H1 haplotype in the temporal cortex. Further, we observed a marked haplotype-dependent difference in KANSL1 expression that was strongly associated with H1 in both brain regions. These findings support the hypothesis that sporadic PSP is associated with haplotype-dependent increases in 4R tau mRNA that might play a causal role in this disorder.

A selection breeding pattern for sexually dimorphic breast plumage color in Guangxi Yao chickens

The breast plumage color of Guangxi Yao chickens shows obvious sexual dimorphism, with roosters showing black and black with red, and hens displaying partridge and red. Black plumage in roosters is considered a sign of quality, necessitating the purification of plumage color. Here, we developed an effective method based on genetic variations within MC1R and plumage characteristics. We clarified the distribution of 5 single nucleotide polymorphisms (SNP) and 3 haplotypes (H1, H2, and H3) of MC1R gene, and revealed potential associations between haplotype H1 and black breast plumage in the F2 resource population derived from a backcross between Guangxi Yao and Yellow chickens. Subsequently, using H1/H1 diplotype roosters and hens to construct families (n = 1,244) notably increased the proportion of offspring with black plumage. Further analysis suggested that red plumage in hens may be the putative phenotype of black plumage in roosters, driven by haplotype H1 of the MC1R gene, as verified by genotype and phenotype analysis. As expected, we found that almost all male offspring of hens with red breast plumage showed black plumage. In short, we established a selection pattern based on the combination of black-plumage roosters and red-plumage hens can significantly purify the sexually dimorphic plumage color and improve the efficiency of breeding programs in Guangxi Yao chickens. Our findings provide a novel technical framework to accelerate the breeding process for plumage trait in poultry.

COPD RISK IN PAKISTANI PUNJABI POPULATION: ROLE OF GATM, PSMA4, AND CHRNA5-A3-B4 GENE VARIANTS

Background: Chronic obstructive pulmonary disease (COPD) is a complex, multifactorial and polygenic disease concerning genetic and environmental factors. Objectives: The selected single nucleotide polymorphisms (SNPs) within or between potential candidate genes were studied to find the association with the onset of COPD disease in the Punjabi population of Pakistan. Methods: 254 COPD patients and 219 control subjects were enrolled for this case-control study. After a literature review and with the help of bioinformatics tools, risk-associated deleterious SNPs residing within or among genes GATM, PSMA4, CHRNA3, CHRNA5, and CHRNB4 were selected to evaluate their association with COPD. Following the mini-sequencing technique, the disease’s association analysis was done using PLINK v1.9 and SHEsis Plus. Results: The mean age of cases was 48.9 ± 9.04 years (N=254), comprising 55.1% males and 44.9% females with 36.6% positive family history of COPD. ‘C’ alleles for rs200551904, rs199547652 and rs1288775 are associated with COPD (p-value 9.70x10-9, 1.14x10-5 and 7.45x10-4 respectively), whereas the ‘CC’ genotype of rs8053 seems to be a protective factor for the disease. The variants rs1288775 and rs199547652 remained associated even with adjusting results for smoking exposure (p-value 0.002 and 1.22 x10-6, respectively). Haplotype analysis for rs1145086, rs1288775, rs8053, rs77994111, rs16969968, rs200551904, rs199547652, rs19968256, and rs181037724 shows that four of the haplotypes H4, H9, H10 and H14, (GATAGGACC; CACAAGACC; CATAGGACC; GACAAGACC respectively), are associated with the disease, while two haplotypes, H1 and H11 (CACAGGCCC and CGCAGGACC respectively), are protective factors against the disease. Conclusion: The association of COPD with chromosome 15 variants in the Punjabi population is reported in this study.

Characterizing the Phan Rang Sheep: A First Look at the Y Chromosome, Mitochondrial DNA, and Morphometrics.

The Phan Rang sheep, considered the sole indigenous breed of Vietnam, are primarily concentrated in the two central provinces of Ninh Thuan and Binh Thuan, with Ninh Thuan accounting for more than 90% of the country's sheep population. These provinces are known for their high temperatures and frequent droughts. The long-standing presence of the Phan Rang sheep in these regions suggests their potential resilience to heat stress-a trait of increasing interest in the face of global climate change. Despite the breed's significance, a critical knowledge gap hinders conservation and breeding programs. To address this, our study employed a two-pronged approach. First, we collected body conformational data to aid in breed identification. Second, we analyzed mitochondrial DNA (D-loop) and Y chromosome markers (SRY and SRYM18) to elucidate the maternal and paternal lineages. Among the 68 Phan Rang sheep analyzed for their D-loop, 19 belonged to mitochondrial haplogroup A, while 49 belonged to haplogroup B. The haplogroups can be subdivided into 16 unique haplotypes. All 19 rams surveyed for their paternal lineages belonged to haplotypes H5 and H6. These findings strongly support the hypothesis of dual origins for the Phan Rang sheep. This study presents the first genetic data for the Phan Rang breed, providing crucial insights for future research and conservation efforts.

Phylogeography of Morella nana: The Wumeng Mountains as a natural geographical isolation boundary on the Yunnan-Guizhou Plateau.

The Yunnan-Guizhou Plateau (YGP) is characterized by the distinctive isolated habitat of the limestone Karst Islands and features the Wumeng Mountains, which divide the YGP into the two Plateaus of Yunnan and Guizhou. This study aimed to assess the effects of geographic isolation and past climate fluctuation on the distribution of flora in the YGP. To achieve this, we carried out the phylogeographical pattern and genetic structure based on chloroplast and nuclear ribosomal DNA sequence in relation to past (Last Glacial Maximum) and present distributions based on ecological niche modeling for Morella nana, an important wild plant resource and endemic to the YGP once considered a vulnerable species. The results suggest that the genetic and chlorotype network structures of M. nana are divided into at least two groups: cpDNA chlorotype H2 (or dominant nrDNA haplotypes h1 and h2), distributed primarily to the east of the Wumeng Mountains, and cpDNA chlorotypes H1 and H3-H10 (or dominant nrDNA haplotype h2 and h3), distributed to the west of the Wumeng Mountains. A deep genetic split was noted within the two groups to reach 25 steps, especially for the cpDNA fragment variation. This east-west divergence reveals the existence of a natural geographical isolation boundary in the form of the Wumeng Mountains, and supports the existence of at least two glacial refuges during the Quaternary glacial period, along with two genetic diversity center, and at least two large geographic protection units for the important species of M. nana. This study indicates that the phylogeographical pattern of M. nana can be attributed to geographic/environmental isolation caused by the Wumeng Mountains and climate fluctuation during the last glacial maximum, and proposes an effective strategy to protecting this important plant resource.

Correlation of glutamate dehydrogenase gene polymorphism and mRNA expression level with free glutamate content in the clam Meretrix petechialis

Free glutamate is a characteristic amino acid with a fresh taste. A high free glutamate content can increase the flavour of clams and better meet consumer demands. GDH is involved in the production of glutamate from a-ketoglutarate and determines the speed and direction of reaction in the glutamate metabolic pathway. In this study, we cloned a full-length cDNA of MpGDH homologues in the clam Meretrix petechialis and further investigated the relationship among MpGDH gene polymorphisms, gene expression levels, enzyme activity and glutamate content traits. A significant positive correlation of MpGDH gene expression with free glutamate content was observed (r = 0.62, p < 0.05). The relationship of variation in MpGDH gene expression with its SNP genotype and SNP haplotype was assessed. Five SNPs were found to be significantly associated with MpGDH gene expression (p < 0.05), from which we constructed two main haplotypes due to linkage disequilibrium. The results showed that haplotype H2 may be an effective haplotype associated with high MpGDH gene expression and high free glutamate content. The genetic effect of different haplotypes was validated by different family materials, which showed that MpGDH gene expression level of the H1H2 heterozygous genotype were significantly higher than those of the homozygous genotype H1H1 (p < 0.05). In summary, our findings revealed the potential influence of the MpGDH polymorphism on the free glutamate content and provided molecular biological information for the selective breeding of good-quality traits of M. petechialis.

Genetic variability of Aedes aegypti (Diptera: Culicidae) in El Salvador and Honduras: presence of a widespread haplotype and implications for mosquito control

BackgroundThis study examined population genetics of Aedes aegypti in El Salvador and Honduras, two adjacent countries in Central America. Aedes aegypti is associated with yellow fever, dengue, chikungunya, and Zika. Each year, thousands of cases of dengue are typically reported in El Salvador and Honduras.MethodsIn El Salvador, collections were obtained from five Departments. In Honduras, samples were obtained from six municipalities in four Departments. Mitochondrial DNA cytochrome oxidase I (COI) was sequenced, and consensus sequences were combined with available sequences from El Salvador to determine haplotype number, haplotype diversity, nucleotide diversity, and Tajima’s D. A haplotype network was produced to examine the relationship between genotypes.ResultsIn El Salvador, there were 17 haplotypes, while in Honduras there were 4 haplotypes. In both El Salvador and Honduras, Haplotype 1 is most abundant and widespread. In El Salvador, haplotype H2 was also widespread in 10 of 11 sampled municipalities, but it was not present in Honduras. The capital of El Salvador (San Salvador) and the eastern region of ES had the highest haplotype diversity of regions sampled.ConclusionsHaplotype 1 and H2 each belong to different phylogenetic lineages of Ae. aegypti. The most geographically widespread haplotype (H1) may have been present the longest and could be a remnant from previous eradication programs. These data may contribute to future control programs for Ae. aegypti in the two countries.Graphical

The Role of Glutathione Transferase Omega-Class Variant Alleles in Individual Susceptibility to Ovarian Cancer.

The tumor microenvironment is affected by reactive oxygen species and has been suggested to have an important role in ovarian cancer (OC) tumorigenesis. The role of glutathione transferases (GSTs) in the maintenance of redox balance is considered as an important contributing factor in cancer, including OC. Furthermore, GSTs are mostly encoded by highly polymorphic genes, which further highlights their potential role in OC, known to originate from accumulated genetic changes. Since the potential relevance of genetic variations in omega-class GSTs (GSTO1 and GSTO2), with somewhat different activities such as thioltransferase and dehydroascorbate reductase activity, has not been clarified as yet in terms of susceptibility to OC, we aimed to investigate whether the presence of different GSTO1 and GSTO2 genetic variants, individually or combined, might represent determinants of risk for OC development. Genotyping was performed in 110 OC patients and 129 matched controls using a PCR-based assay for genotyping single nucleotide polymorphisms. The results of our study show that homozygous carriers of the GSTO2 variant G allele are at an increased risk of OC development in comparison to the carriers of the referent genotype (OR1 = 2.16, 95% CI: 0.88-5.26, p = 0.08; OR2 = 2.49, 95% CI: 0.93-6.61, p = 0.06). Furthermore, individuals with GST omega haplotype H2, meaning the concomitant presence of the GSTO1*A and GSTO2*G alleles, are more susceptible to OC development, while carriers of the H4 (*A*A) haplotype exhibited lower risk of OC when crude and adjusted haplotype analysis was performed (OR1 = 0.29; 95% CI: 0.12-0.70; p = 0.007 and OR2 = 0.27; 95% CI: 0.11-0.67; p = 0.0054). Overall, our results suggest that GSTO locus variants may confer OC risk.

Detection of MAPT polymorphisms and H1 haplotype in frontotemporal dementia (FTD) Greek patients

Detection of MAPT polymorphisms and H1 haplotype in frontotemporal dementia (FTD) Greek patients

Association of Pick's disease with the MAPT H2 haplotype

Association of Pick's disease with the MAPT H2 haplotype

MAPT H2 haplotype and risk of Pick's disease in the Pick's disease International Consortium: a genetic association study

Pick's disease is a rare and predominantly sporadic form of frontotemporal dementia that is classified as a primary tauopathy. Pick's disease is pathologically defined by the presence in the frontal and temporal lobes of Pick bodies, composed of hyperphosphorylated, three-repeat tau protein, encoded by the MAPT gene. MAPT has two distinct haplotypes, H1 and H2; the MAPT H1 haplotype is the major genetic risk factor for four-repeat tauopathies (eg, progressive supranuclear palsy and corticobasal degeneration), and the MAPT H2 haplotype is protective for these disorders. The primary aim of this study was to evaluate the association of MAPT H2 with Pick's disease risk, age at onset, and disease duration. In this genetic association study, we used data from the Pick's disease International Consortium, which we established to enable collection of data from individuals with pathologically confirmed Pick's disease worldwide. For this analysis, we collected brain samples from individuals with pathologically confirmed Pick's disease from 35 sites (brainbanks and hospitals) in North America, Europe, and Australia between Jan 1, 2020, and Jan 31, 2023. Neurologically healthy controls were recruited from the Mayo Clinic (FL, USA, or MN, USA between March 1, 1998, and Sept 1, 2019). For the primary analysis, individuals were directly genotyped for the MAPT H1-H2 haplotype-defining variant rs8070723. In a secondary analysis, we genotyped and constructed the six-variant-defined (rs1467967-rs242557-rs3785883-rs2471738-rs8070723-rs7521) MAPT H1 subhaplotypes. Associations of MAPT variants and MAPT haplotypes with Pick's disease risk, age at onset, and disease duration were examined using logistic and linear regression models; odds ratios (ORs) and β coefficients were estimated and correspond to each additional minor allele or each additional copy of the given haplotype. We obtained brain samples from 338 people with pathologically confirmed Pick's disease (205 [61%] male and 133 [39%] female; 338 [100%] White) and 1312 neurologically healthy controls (611 [47%] male and 701 [53%] female; 1312 [100%] White). The MAPT H2 haplotype was associated with increased risk of Pick's disease compared with the H1 haplotype (OR 1·35 [95% CI 1·12 to 1·64], p=0·0021). MAPT H2 was not associated with age at onset (β -0·54 [95% CI -1·94 to 0·87], p=0·45) or disease duration (β 0·05 [-0·06 to 0·16], p=0·35). Although not significant after correcting for multiple testing, associations were observed at p less than 0·05: with risk of Pick's disease for the H1f subhaplotype (OR 0·11 [0·01 to 0·99], p=0·049); with age at onset for H1b (β 2·66 [0·63 to 4·70], p=0·011), H1i (β -3·66 [-6·83 to -0·48], p=0·025), and H1u (β -5·25 [-10·42 to -0·07], p=0·048); and with disease duration for H1x (β -0·57 [-1·07 to -0·07], p=0·026). The Pick's disease International Consortium provides an opportunity to do large studies to enhance our understanding of the pathobiology of Pick's disease. This study shows that, in contrast to the decreased risk of four-repeat tauopathies, the MAPT H2 haplotype is associated with an increased risk of Pick's disease in people of European ancestry. This finding could inform development of isoform-related therapeutics for tauopathies. Wellcome Trust, Rotha Abraham Trust, Brain Research UK, the Dolby Fund, Dementia Research Institute (Medical Research Council), US National Institutes of Health, and the Mayo Clinic Foundation.

Genetic Diversity and Population Structure of Actinidia eriantha by ITS Sequences

Background: Actinidia eriantha Benth is a widely used natural product from Traditional Chinese Medicine in the Actinidiaceae family. However, its wild resources have been declining due to over-exploitation. It has become urgent to investigate the genetic diversity for the conservation of A. eriantha, to evaluate the current species and discover strategies for preservation. Methods: The internal transcribed spacer (ITS) was used to evaluate the genetic diversity among and within populations of this species. Dnasp, PERMUT and Arlequin 3.0 software were used to calculate the genetic diversity index, and MEGA 5.0 software was used to construct the neighbor-joining (NJ) tree. Results: A total of 27 haplotypes were obtained by ITS sequence analysis of 12 populations, and the most frequently haplotype observed was H1. AMOVA analysis revealed that the genetic variation rates were 10.91% (FST = 0.22290) and 77.71% (FSC = 0.12306) among and within populations, respectively, with high genetic diversity at the species level (Hd = 0.692). The genetic distance among populations ranged from 0 to 0.004. The results of Permut analysis showed that there was no significant correlation between genetic distance and geographic distance (NST &gt; GST). The NJ tree was divided into two Clades (Clade A and Clade B), Clade B has obvious geographical specificity, and haplotypes of this clade are all specific to the GX-ZY population. Four types were found according to ITS sequences of A. eriantha, haplotypes H1 and H5 were ancient haplotypes. Conclusion: Our findings indicated that genetic diversity within populations was higher than observed among populations. This study is significant for further research endeavors focused on the efficient collection and preservation of wild resources of A. eriantha.

MAPT Locus in Parkinson's Disease Patients of Ashkenazi Origin: A Stratified Analysis.

Introduction: MAPT locus is associated with Parkinson's disease (PD), which is located within a large inversion region of high linkage disequilibrium (LD). We aimed to determine whether the H2-haplotype protective effect and its effect size depends on the GBA1 or LRRK2 risk allele carrier status, and to further characterize genetic alterations that might contribute to its effect. Methods: LD analysis was performed using whole-genome sequencing data of 202 unrelated Ashkenazi Jewish (AJ) PDs. A haplotype-divergent variant was genotyped in a cohort of 1200 consecutively recruited AJ-PDs. The odd ratios were calculated using AJ-non-neuro cases from the gnomAD database as the controls in an un-stratified and a stratified manner according to the mutation carrier status, and the effect on the Age at Motor Symptom Onset (AMSO) was examined. Expression and splicing quantitative trait locus (eQTL and sQTL) analyses were carried out using brain tissues from a database. Results: The H2 haplotype exhibited significant association with PD protection, with a similar effect size in GBA1 carriers, LRRK2-G2019S carriers, and non-carriers (OR = 0.77, 0.69, and 0.82, respectively), and there was no effect on AMSO. The LD interval was narrowed to approximately 1.2 Mb. The H2 haplotype carried potential variants in candidate genes (MAPT and SPPL2C); structural deletions and segmental duplication (KANSL1); and variants affecting gene expression and intron excision ratio in brain tissues (LRRC37A/2). Conclusions: Our results demonstrate that H2 is associated with PD and its protective effect is not influenced by the GBA1/LRRK2 risk allele carrier status. This effect may be genetically complex, resulting from different levels of variations such as missense mutations in relevant genes, structural variations, epigenetic modifications, and RNA expression changes, which may operate independently or in synergy.

Flowering time regulator qFT13-3 involved in soybean adaptation to high latitudes.

Soybean is a short-day plant that typically flowers earlier when exposed to short-day conditions. However, the identification of genes associated with earlier flowering time but without a yield penalty is rare. In this study, we conducted genome-wide association studies (GWAS) using two re-sequencing datasets that included 113 wild soybeans (G. soja) and 1192 cultivated soybeans (G. max), respectively, and simultaneously identified a candidate flowering gene, qFT13-3, which encodes a protein homologous to the pseudo-response regulator (PRR) transcription factor. We identified four major haplotypes of qFT13-3 in the natural population, with haplotype H4 (qFT13-3H4) being lost during domestication, while qFT13-3H1 underwent natural and artificial selection, increasing in proportion from 4.5% in G. soja to 43.8% in landrace and to 81.9% in improve cultivars. Notably, most cultivars harbouring qFT13-3H1 were located in high-latitude regions. Knockout of qFT13-3 accelerated flowering and maturity time under long-day conditions, indicating that qFT13-3 functions as a flowering inhibitor. Our results also showed that qFT13-3 directly downregulates the expression of GmELF3b-2 which is a component of the circadian clock evening complex. Field trials revealed that the qft13-3 mutants shorten the maturity period by 11 days without a concomitant penalty on yield. Collectively, qFT13-3 can be utilized for the breeding of high-yield cultivars with a short maturity time suitable for high latitudes.

PSP/DEGESCO: A Progressive Supranuclear Palsy Genome‐Wide Association Study in the Spanish Population

AbstractBackgroundProgressive supranuclear palsy (PSP) is a rare neurodegenerative tauopathy. We genotyped all the available histopatologically confirmed PSP cases from the Spanish National Biobank Network and patients with a probable PSP diagnosis recruited from research groups linked to the Dementia Genetics Spanish Consortium (DEGESCO). Here, we present the results of the genome‐wide association study (GWAS) performed after the first stage of this project.MethodDNA samples were genotyped by the Centro Nacional de Genotipado (Santiago de Compostela, Spain) using the Affymetrix Axiom 815K Spanish biobank array. After quality control, we kept 156 histopathological (discovery) and 197 clinical (validation) PSP samples. Then, we selected 650 and 800 sex‐matched controls from GR@ACE/DEGESCO for stratified genome‐wide association of the discovery and validation sets, respectively (Table 1). We ran PC1‐4 adjusted logistic regressions with plink v2.00 and meta‐analyzed the discovery and validation sets using METAL. Finally, we meta‐analyzed our results with 36 previously reported SNPs1 reaching the largest PSP sample size to date (N = 3053).ResultWe found a strong genome‐wide significant (GWS) signal associated to the MAPT H1/H2 haplotype (rs8070723 G: OR = 3.40; 95%CI = 2.64‐4.39; p = 2.60·10−20, Figure 1) and identified a previously unreported signal in chromosome 7p13 (rs76827509 T: OR = 0.45; 95%CI = 0.35‐0.58; p = 3.09·10−10). We replicated, with nominal significance, 5 GWS SNPs reported in previous GWAS (Table 2) and found significant effects for NFASC and TOMM40. Because APOE and TOMM40 are in strong linkage disequilibrium, we also checked the effect of APOE variants. We found a protective effect (OR = 0.66; 95%CI = 0.48‐0.90; p = 9.75·10−3) of the rs429358 C allele (APOE ε4) in our dataset.ConclusionThe strong GWS signal of the H1 haplotype confirms the validity of our GWAS results2. We were able to replicate several PSP loci (Table 1). The NFASC variant reached borderline GWS significance after meta‐analysis and is a good PSP risk factor candidate. Finally, the APOE ε4 allele was protective for PSP in our cohort. The second stage of PSP/DEGESCO genotyped 218 additional PSP samples. 1 Sanchez‐Contreras, M. Y. et al. Mol. Neurodegener. (2018) 2 Höglinger, G. U. et al. in Nature Genetics (2011)