Functional Allele Research Articles

The E3 ligase TaE3V-B1 ubiquitinates proteins encoded by the vernalization gene TaVRN1 and regulates developmental processes in wheat

Abstract In wheat (Triticum aestivum), early maturity is desired to avoid the hot and dry summer season, especially in view of climate change. Here, we report that TaE3V1, a C3H2C3 RING-type E3 ligase that interacts with TaVRN1, is associated with early development. Aside from its RING domain, TaE3V1 does not harbor any domains that are conserved in other RING-type or other E3 ligase proteins. TaE3V-B1b, encoded by the functional TaE3V1 allele, interacts with and ubiquitinates TaVRN1. In contrast, TaE3V-B1a, encoded by a natural nonfunctional TaE3V1 allele, neither interacts with TaVRN1 nor has E3 ligase activity. TaE3V-B1b activity decreases with plant age under warmer temperatures, but not under the low temperatures required for vernalization. We employed a gene editing method to simultaneously inactivate the three homoeologous TaE3V1 genes to validate their functions. Overall, our results suggest that the naturally mutated and edited TaE3V1 alleles can accelerate wheat development and aid adaptation to warming climates.

Abstract B006: Rescuing expression of a tumor suppressor gene – restoring FH in Hereditary leiomyomatosis and renal cell carcinoma

Abstract Hereditary leiomyomatosis and renal cell carcinoma (HLRCC) is a disorder characterized by the loss of fumarate hydratase (FH) activity, leading to the development of cutaneous leiomyomas, uterine leiomyomas, and aggressive early-onset type 2 papillary renal cell carcinoma. In HLRCC, the disease is driven by the somatic loss of the remaining functional FH allele in individuals carrying a germline pathogenic variant in one copy of the FH gene. The complete loss of FH activity disrupts the tricarboxylic acid (TCA) cycle, resulting in the accumulation of fumarate, which disrupts signaling pathways and contributes to the oncogenic phenotype. We recently identified a single nucleotide polymorphism (SNP) in an intronic region of the fumarate hydratase (FH) gene that leads to the loss of FH activity (Crooks et al., 2023). This SNP introduces a novel splice-acceptor site, resulting in the inclusion of an aberrant exon between wild-type exons 9 and 10. This ‘poison-like’ exon encodes a premature STOP codon, producing a nonfunctional truncated FH protein. Previous studies have shown that restoring FH activity can abrogate pathogenic behavior in patient-derived cells, highlighting the potential for therapeutic interventions targeting FH activity restoration. Our goal is to restore FH enzymatic activity by preventing the inclusion of this cryptic exon in carriers of this variant. To achieve this, we are exploring strategies to restore functional FH production by interfering with the inclusion of the pathogenic intron during splicing by removing the splice acceptor using CRISPR-Cas9 or base editing technologies. We tested these approaches by generating a reporter cell line that recapitulates the splicing pattern observed in patients, where expression of GFP depends on correct splicing between exon 9 and 10. We successfully identified antisense oligonucleotide (ASO) and single-guide RNA (sgRNA) sequences that restore GFP expression in our reporter cell lines. We are now evaluating the efficacy of these reagents in patient-derived cells. An alternative approach involves using synthetic RNA to restore FH expression. The expression of proteins from synthetic RNAs is a promising strategy for treating cancer and infectious diseases. We are currently investigating the efficiency of restoring FH activity through in-vitro transcribed (IVT) mRNA. This approach has the advantage of enabling FH function restoration in cells with mutations that are not amenable to antisense oligonucleotide (ASO) or gene editing techniques. This work serves as an avenue to investigate the application of nucleic acid therapies to restoring activity tumor suppressor genes in kidney cancer. Citation Format: Siddhardha S. Maligireddy, Mariana D. Mandler, Jodie C. Lunger, Christina M. Fitzsimmons, Daniel R. Crooks, Geetha M. Cawthon, Christopher J. Ricketts, Cathy D. Vocke, W. Marson Linehan, Pedro J. Batista. Rescuing expression of a tumor suppressor gene – restoring FH in Hereditary leiomyomatosis and renal cell carcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr B006.

Mouse models for pancreatic ductal adenocarcinoma are affected by the cre-driver used to promote KRASG12D activation.

The fundamental biology of pancreatic ductal adenocarcinoma has been greatly impacted by the characterization of genetically engineered mouse models that allow temporal and spatial activation of oncogenic KRAS (KRASG12D). One of the most commonly used models involves targeted insertion of a cre-recombinase into the Ptf1a gene. However, this approach disrupts the Ptf1a gene, resulting in haploinsufficiency that likely affects sensitivity to oncogenic KRAS (KRASG12D). This study aims to determine if Ptf1a haploinsufficiency affected the acinar cell response to KRASG12D before and after induction of pancreatic injury. We performed morphological and molecular analysis of three genetically engineered mouse models that express a tamoxifen-inducible cre-recombinase to activate KrasG12D in acinar cells of the pancreas. The cre-recombinase was targeted to the acinar-specific transcription factor genes, Ptf1a or Mist1/Bhlha15, or expressed within a BAC-derived Elastase transgene. Histological and RNA-seq analyses were used to delineate differences between the models. Up to two months after tamoxifen induction of KRASG12D, morphological changes were negligible. However, induction of pancreatic injury by cerulein resulted in widespread PanIN lesions in Ptf1acreERT pancreata within seven days and maintained for at least five weeks post-injury, which was not seen in the models with two functional Ptf1a alleles. RNA-seq analysis prior to injury induction suggested Ptf1acreERT and Mist1creERT mice have unique profiles of gene expression that predict a differential response to injury. Multiplex analysis of pancreatic tissue confirmed different inflammatory responses between the models. These findings suggest Ptf1a haploinsufficiency in Ptf1acreERT mouse models promotes KRASG12D priming of genes for promotion of PDAC.

Genetic analysis of a blood donor with combined FUT1 and ABO dual blood group gene variants resulting in para-Bombay and A2 subtype blood types and a literature review

To investigate the serological and molecular genetic characteristics of a voluntary blood donor with combined FUT1 and ABO blood group gene variants causing para-Bombay and A2 subtype, and to review relevant literature on para-Bombay blood types carrying alleles such as FUT101W.37 and FUT101W.23. A blood donor with para-Bombay and A2 subtype who participated in voluntary blood donation at the Dongguan Blood Center in August 2023 was selected as the study subject. Serological tests were performed to identify the ABO blood group, Lewis blood group antigens, and unexpected serum antibodies in the donor. Adsorption-elution test was conducted to detect trace antibodies in the blood donor's plasma to trace the A, B and H antigens on the red blood cell surface. Sanger sequencing was carried out to analyze the sequences of the FUT1 and ABO genes. Using keywords such as "para-Bombay" "FUT1*01W.37" and "FUT1*01W.23" both in Chinese and English, relevant literature on para-Bombay blood type subjects carrying FUT1*01W.37 and FUT1*01W.23 alleles was retrieved from the CNKI, Wanfang Data Knowledge Service Platform, and PubMed databases, and the retrieval time was set as from the establishment of database to December 2022. This study has been approved by the Ethics Committee of Dongguan Blood Center (No. 2022005), and informed consent of blood donation was obtained from the blood donor. Serological testing of the blood donor revealed inconsistent results between forward and reverse ABO blood typing, negative H antigen on the red blood cell surface, Le(a-b+) secretor type for Lewis blood group, and unexpected anti-H antibodies in the plasma, indicating a suspected para-Bombay type. Absorption-elution test suggested the blood type of the blood donor to be para-Bombay and A subtype. Sanger sequencing showed that the donor has harbored homozygous FUT1*(c.35T+c.803A)/(c.35T+c.803A) variant, with the FUT1*(c.35T+c.803A) allele containing a dual nucleotide variant unrecorded by the International Society of Blood Transfusion (ISBT) FUT1 gene variant database, which was similar to the weakly functional allele of FUT101W. 37(c.803G>A) as recorded by the ISBT database. The ABO genotype was heterozygous ABOA2.05/O.01.02. Combining the results of serological and genetic testing, the blood type of the blood donor was determined to be para-Bombay and A2 subtypes. Literature review has identified a pregnant women from Qingdao carrying the FUT1*01W.37 allele and 2 individuals carrying a heterozygous FUT1*01W.23 allele. This study has discovered a blood donor with coexisting para-Bombay and ABO subtype blood groups. Based on the characteristics of red blood cell surface antigens, the FUT1*01W.37 as classified as an FUT1 null allele.

Natural variation of WBR7 confers rice high yield and quality by modulating sucrose supply in sink organs.

Grain chalkiness is an undesirable trait that negatively regulates grain yield and quality in rice. However, the regulatory mechanism underlying chalkiness is complex and remains unclear. We identified a positive regulator of white-belly rate (WBR). The WBR7 gene encodes sucrose synthase 3 (SUS3). A weak functional allele of WBR7 is beneficial in increasing grain yield and quality. During the domestication of indica rice, a functional G/A variation in the coding region of WBR7 resulted in an E541K amino acid substitution in the GT-4 glycosyltransferase domain, leading to a significant decrease in decomposition activity of WBR7A (allele in cultivar Jin23B) compared with WBR7G (allele in cultivar Beilu130). The NIL(J23B) and knockout line NIL(BL130)KO exhibited lower WBR7 decomposition activity than that of NIL(BL130) and NIL(J23B)COM, resulting in less sucrose decomposition and metabolism in the conducting organs. This caused more sucrose transportation to the endosperm, enhancing the synthesis of storage components in the endosperm and leading to decreased WBR. More sucrose was also transported to the anthers, providing sufficient substrate and energy supply for pollen maturation and germination, ultimately leading to an increase rate of seed setting and increased grain yield. Our findings elucidate a mechanism for enhancing rice yield and quality by modulating sucrose metabolism and allocation, and provides a valuable allele for improved rice quality.

Reinterpretation of genetic testing for Cardiomyopathies: Less is more

Abstract Background In the last years, the concept of reinterpretation of genetic testing has been considered as part of the diagnostic workflow. However, this process requires time, expert curators and new pieces of evidence to evaluate, as functional studies, segregation and allele frequency data. Last year, the European Society of Cardiology (ESC) published new guidelines for the management of cardiomyopathies. This document includes a precise list of genes associated with the different types of Cardiomyopathies and their level of contribution, according to ClinGen evaluation: definitive/strong, moderate, limited, and refuted/disputed. This document poses a real support in the reinterpretation of tests that report variants in genes not clearly correlated with these phenotypes. Purpose To evaluate the impact of the new ESC indications regarding genetic testing, we reconsidered all genetic results performed in our Clinic in patients with confirmed or suspicious Cardiomyopathy. Methods From 2017 to 2023 we analyzed 296 probands eligible for Cardiomyopathy genetic testing, in particular: 105 patients were tested for Arrhythmogenic Cardiomyopathy (ACM), 113 for Hypertrophic Cardiomyopathy (HCM) and 78 for Dilated Cardiomyopathy (DCM), using a custom sequencing panel including 44 genes (11 genes for ACM, 34 for DCM and 29 for HCM). Results Comparison analysis with the genes reported from the ESC guidelines, considering only the definitive, moderate, and strong genes, showed that 24 genes are not more associated with the phenotype and then not clinically actionable. In this scenario, we reconsidered 12 variants (8%), previously classified as VUS, changing the referral status of 8 patients, from uncertain to negative. Conclusions These results highlight the importance of variant reinterpretation as a fundamental step of genetic testing, posing the importance of the selection of the genes to analyze, in order to improve the management of the patients.

Thai pharmacogenomics database -2 (TPGxD-2) sequel to TPGxD-1, analyzing genetic variants in 26 non-VIPGx genes within the Thai population.

Next-generation sequencing (NGS) has transformed pharmacogenomics (PGx), enabling thorough profiling of pharmacogenes using computational methods and advancing personalized medicine. The Thai Pharmacogenomic Database-2 (TPGxD-2) analyzed 948 whole genome sequences, primarily from the Electricity Generating Authority of Thailand (EGAT) cohort. This study is an extension of the previous Thai Pharmacogenomic Database (TPGxD-1) and specifically focused on 26 non-very important pharmacogenes (VIPGx) genes. Variant calling was conducted using Sentieon (version 201808.08) following GATK's best workflow practices. We then annotated variant call format (VCF) files using Golden Helix VarSeq 2.5.0. Star allele analysis was performed with Stargazer v2.0.2, which called star alleles for 22 of 26 non-VIPGx genes. The variant analysis revealed a total of 14,529 variants in 26 non-VIPGx genes, with TBXAS1 had the highest number of variants (27%). Among the 14,529 variants, 2328 were novel (without rsID), with 87 identified as clinically relevant. We also found 56 known PGx variants among the known variants (n = 12,201), with UGT2B7 (19.64%), CYP1B1 (8.9%), SLCO2B1 (8.9%), and POR (8.9%) being the most common. We reported a high frequency of intermediate metabolizers (IMs) in CYP2F1 (34.6%) and CYP4A11 (8.6%), and a high frequency of decreased functional alleles in POR (53.9%) and SLCO1B3 (34.9%) genes. This study enhances our understanding of pharmacogenomic profiling of 26 non-VIPGx genes of notable clinical importance in the Thai population. However, further validation with additional computational and reference genotyping methods is necessary, and novel alleles identified in this study should undergo further orthogonal validation.

Methyltransferase 1 (OsMTS1) interacts with hydroxycinnamoyltransferase 1 (OsHCT1) and promotes heading by upregulating heading date 1 (Hd1)

Heading date determines the distribution and yield potentials of rice, and is an ideal target for crop improvement using CRISPR/Cas9 genome editing system. In this study, we reported the loss-of-function of Methyltransferase 1 (MTS1), which promotes heading in rice. Here, we constructed knockouts and overexpression transgenic plants of OsMTS1 in ZH8015 and Nipponbare (NIP) for the first time to validate its heading date function in rice subspecies Oryza sativa ssp. Indica and O. Sativa ssp. Japonica, respectively. The OsMTS1 knockouts in ZH8015 and NIP rice significantly promoted heading date under both natural short days (NSD) and natural long days (NLD) conditions, while the overexpression of OsMTS1 significantly delayed heading date in ZH8015 and NIP rice under both NSD and NLD conditions. Likewise, the complementation transgenic plants displayed late heading date phenotype. OsMTS1 repressed heading through up-regulating Heading date 1 (Hd1) and down-regulating Early heading date 1 (Ehd1) and Heading date 3a (Hd3a). The OsMTS1 protein interacted with OsHCT1 proteins using a yeast two-hybrid (Y2H) assay. The Y2H and overexpression confirmed that OsMTS1 interacted with OsHCT1, which delayed heading by 4.7 days under NLD. Taken together, CRISPR/Cas9, genetic complementation, and overexpression results validated that OsMTS1 represses heading in Indica and Japonica rice under both NLD and NSD conditions. These results demonstrated that OsMTS1 is a useful target for breeding early maturing rice varieties by CRISPR/Cas9 gene editing of the functional allele.

ASYNAPSIS3 has diverse dosage-dependent effects on meiotic crossover formation in Brassica napus.

Crossovers create genetic diversity and are required for equal chromosome segregation during meiosis. Crossover number and distribution are highly regulated by different mechanisms that are not yet fully understood, including crossover interference. The chromosome axis is crucial for crossover formation. Here, we explore the function of the axis protein ASYNAPSIS3. To this end, we use the allotetraploid species Brassica napus; due to its polyploid nature, this system allows a fine-grained dissection of the dosage of meiotic regulators. The simultaneous mutation of all 4 ASY3 alleles results in defective synapsis and drastic reduction of crossovers, which is largely rescued by the presence of only one functional ASY3 allele. Crucially, while the number of class I crossovers in mutants with 2 functional ASY3 alleles is comparable to that in wild type, this number is significantly increased in mutants with only one functional ASY3 allele, indicating that reducing ASY3 dosage increases crossover formation. Moreover, the class I crossovers on each bivalent in mutants with 1 functional ASY3 allele follow a random distribution, indicating compromised crossover interference. These results reveal the distinct dosage-dependent effects of ASY3 on crossover formation and provide insights into the role of the chromosome axis in patterning recombination.

Identification and development of functional markers for purple grain genes in durum wheat (Triticum durum Desf.).

Two allelic variants of Pp-A3 and Pp-B1 were identified in purple durum wheat. Molecular markers at both loci were developed and validated on an independent panel, offering a breakthrough for wheat improvement. Purple wheats are a class of cereals with pigmented kernels of particular interest for their antioxidant and anti-inflammatory properties. Although two complementary loci (Pp-B1 and Pp-A3), responsible for purple pericarp have been pinpointed in bread wheat (Triticum aestivum L.), in durum wheat (Triticum durum Desf.) the causative genes along with functional and non-functional alleles are still unknown. Here, using a quantitative trait loci (QTL) mapping approach on a RIL population derived from purple and non-purple durum wheat genotypes, we identified three major regions on chromosomes 2A, 3A, and 7B explaining the highest phenotypic variation (> 50%). Taking advantage of the Svevo genome, a MYB was reannotated on chromosome 7B and reported as a candidate for Pp-B1. An insertion of ~ 1.6kb within the first exon led to a non-functional allele (TdPpm1b), whereas the functional allele (TdPpm1a) was characterized and released for the first time in durum wheat. Pp-A3 was instead identified as a duplicated gene, of which only one was functional. The promoter sequencing of the functional allele (TdPpb1a) revealed six 261-bp tandem repeats in purple durum wheat, whereas one unit (TdPpb1b) was found in the yellow once. Functional molecular markers at both loci were developed to precisely discriminate purple and not purple genotypes, representing a valuable resource for selecting superior purple durum lines at early growth stages. Overall, our results expand the understanding of the function of MYB and bHLH activators in durum wheat, paving new ways to explore cis-regulatory elements at the promoter level.

Breeding wheat for organic farming: Can the high grain protein gene Gpc-B1 help to tackle challenges in view of end-use quality?

Organic farming contributes to sustain healthy ecosystems, but challenges such as lower crop yields and supply of the nitrogen needs of crops remain. Wheat is the most important organic arable crop in Europe and grain protein content is the main quality trait also for grading organic wheat despite that high baking quality can be also realized at lower protein contents. Hence, breeding of organic wheat varieties that realize a stable high grain protein content even at lower nitrogen availability is of utmost importance to guarantee income of organic wheat growers. A major QTL for high grain protein content was identified in wild emmer and transferred into bread wheat. We tested six different wheat genetic backgrounds varying for the presence/absence of the functional Gpc-B1 allele in multi-location trials in Central Europe for their performance under organic growing. The increase in grain protein content caused by the functional Gpc-B1 allele was present in almost all genetic backgrounds, however, was not consistent across all tested quality traits. None the less, the functional Gpc-B1 allele may play a major role to increase the stability of organic wheat to reach minimum requirements by traders and processors with respect to grain protein content.

Cell cycle arrest combined with CDK1 inhibition suppresses genome-wide mutations by activating alternative DNA repair genes during genome editing

Cells regularly repair numerous mutations. However, the effect of CRISPR/Cas9-induced dsDNA breaks on the repair processes of naturally occurring genome-wide mutations is unclear. In this study, we used TSCE5 cells with the heterozygous thymidine kinase genotype (TK+/-) to examine these effects. We strategically inserted the target sites for guide RNA (gRNA)/Cas9 and I-SceI into the functional allele and designed the experiment such that deletions of > 81bp or base substitutions within exon five disrupted the TK gene, resulting in a TK-/- genotype. TSCE5 cells in the resting state exhibited 16 genome-wide mutations that affected cellular functions. After gRNA/Cas9 editing, these cells produced 859 mutations, including 67 high-impact variants that severely affected cellular functions under standard culture conditions. Mutation profile analysis indicated a significant accumulation of C to A substitutions, underscoring the widespread induction of characteristic mutations by gRNA/Cas9. In contrast, gRNA/Cas9-edited cells under conditions of S∼G2/M arrest and cyclin-dependent kinase 1 inhibition showed only five mutations. Transcriptomic analysis revealed the downregulation of DNA replication genes and upregulation of alternative DNA repair genes, such as zinc finger protein 384 (ZNF384) and dual specificity phosphatase, under S∼G2/M conditions. Additionally, activation of nucleotide and base excision repair gene, including O-6-methylguanine-DNA methyltransferase and xeroderma pigmentosum complementation group C, was observed. This study highlights the profound impact of CRISPR/Cas9 editing on genome-wide mutation processes and underscores the emergence of novel DNA repair pathways. Finally, our findings provide significant insights into the maintenance of genome integrity during genome editing.

Significant interaction between root system architecture and stratified phosphorus availability for the initial growth of rice in a flooded soil culture

Phosphorus (P) deficiency is a major limiting factor for rice production in the tropics. The root system architecture (RSA) may play a significant role to capture P efficiently in soils; however, its function is poorly understood in flooded and puddled soil cultures. Two near-isogenic lines (NILs) contrasting RSA—qsor1-NIL (nonfunctional allele of qSOR1; shallow RSA) and Dro1-NIL (functional allele of DRO1; deep RSA)—were repeatedly grown for approximately 6 weeks in pots with three stratified P treatments. The treatments simulated P deficient conditions in puddled and subsoil layers, P available in the puddled layer, and P available in puddled and subsoil layers, that is, −P−P: no P applied in either the top-half (0–14 cm) or bottom-half (14–28 cm) layers; +P−P: P applied only in the top-half layer; and +P + P: P applied in the top-half and bottom-half layers, respectively. A significant interaction was observed between genotype and P treatment. The Dro1-NIL had a greater root surface area in the bottom half layer, which was advantageous for capturing P in the subsoil layer and resulted in greater biomass and P uptake in the +P + P treatment. Contrarily, the qsor1-NIL had a greater root surface area and longer root hair, resulting in greater biomass and P uptake in the −P−P treatment. The mechanism is unclear; however, the pleiotropic effect of qsor1, namely enhancing root hair elongation, might be more advantageous to explore P with minimal carbon costs than elongating nodal and lateral roots when P is not available in deep soil layers. No genotype differences were observed in the +P−P treatment, implying no apparent topsoil P-foraging effect of the shallow RSA in the flooded soil culture. The roles of RSA and root hairs should attract further attention for the genotypic improvement of lowland rice under P deficiency conditions in the tropics.

Impact of rice GENERAL REGULATORY FACTOR14h (GF14h) on low-temperature seed germination and its application to breeding.

Direct seeding is employed to circumvent the labor-intensive process of rice (Oryza sativa) transplantation, but this approach requires varieties with vigorous low-temperature germination (LTG) when sown in cold climates. To investigate the genetic basis of LTG, we identified the quantitative trait locus (QTL) qLTG11 from rice variety Arroz da Terra, which shows rapid seed germination at lower temperatures, using QTL-seq. We delineated the candidate region to a 52-kb interval containing GENERAL REGULATORY FACTOR14h (GF14h) gene, which is expressed during seed germination. The Arroz da Terra GF14h allele encodes functional GF14h, whereas Japanese rice variety Hitomebore harbors a 4-bp deletion in the coding region. Knocking out functional GF14h in a near-isogenic line (NIL) carrying the Arroz da Terra allele decreased LTG, whereas overexpressing functional GF14h in Hitomebore increased LTG, indicating that GF14h is the causal gene behind qLTG11. Analysis of numerous Japanese rice accessions revealed that the functional GF14h allele was lost from popular varieties during modern breeding. We generated a NIL in the Hitomebore background carrying a 172-kb genomic fragment from Arroz da Terra including GF14h. The NIL showed superior LTG compared to Hitomebore, with otherwise comparable agronomic traits. The functional GF14h allele from Arroz da Terra represents a valuable resource for direct seeding in cold regions.

Benzoxazole-derivatives enhance progranulin expression and reverse the aberrant lysosomal proteome caused by GRN haploinsufficiency

Heterozygous loss-of-function mutations in the GRN gene are a major cause of hereditary frontotemporal dementia. The mechanisms linking frontotemporal dementia pathogenesis to progranulin deficiency are not well understood, and there is currently no treatment. Our strategy to prevent the onset and progression of frontotemporal dementia in patients with GRN mutations is to utilize small molecule positive regulators of GRN expression to boost progranulin levels from the remaining functional GRN allele, thus restoring progranulin levels back to normal within the brain. This work describes a series of blood-brain-barrier-penetrant small molecules which significantly increase progranulin protein levels in human cellular models, correct progranulin protein deficiency in Grn+/− mouse brains, and reverse lysosomal proteome aberrations, a phenotypic hallmark of frontotemporal dementia, more efficiently than the previously described small molecule suberoylanilide hydroxamic acid. These molecules will allow further elucidation of the cellular functions of progranulin and its role in frontotemporal dementia and will also serve as lead structures for further drug development.

The ACE1 secondary metabolite gene cluster is a pathogenicity factor of wheat blast fungus

Wheat blast caused by Pyricularia oryzae pathotype Triticum is now becoming a very serious threat to global food security. Here, we report an essential pathogenicity factor of the wheat blast fungus that is recognized and may be targeted by a rice resistance gene. Map-based cloning of Pwt2 showed that its functional allele is the ACE1 secondary metabolite gene cluster of the wheat blast fungus required for its efficient penetration of wheat cell walls. ACE1 is required for the strong aggressiveness of Triticum, Eleusine, and Lolium pathotypes on their respective hosts, but not for that of Oryza and Setaria pathotypes on rice and foxtail millet, respectively. All ACE1 alleles found in wheat blast population are recognized by a rice resistance gene, Pi33, when introduced into rice blast isolates. ACE1 mutations for evading the recognition by Pi33 do not affect the aggressiveness of the rice blast fungus on rice but inevitably impair the aggressiveness of the wheat blast fungus on wheat. These results suggest that a blast resistance gene already defeated in rice may be revived as a durable resistance gene in wheat by targeting an Achilles heel of the wheat blast fungus.

Genome-wide Identification and Functional Analyses of the 5-O-Glucosyltransferase Family Reveal Its Potential Roles in Anthocyanidin Diglucosides Synthesis of Grape Skins with Vitis amurensis Pedigree

Vitis amurensis grape cultivars and hybrids are mainly used to make wines in Northeast Asia with a cold winter. Anthocyanidin glucosylation at 5-O position catalyzed by 5-O-glucosyltransferase (5GT) in grape skins is crucial for color stability of red wines. To study 5GT functions in anthocyanidin diglucosides synthesis of V. amurensis, 20 5GTs were preliminarily identified from a genome-wide characterization of the UDP-glycosyltransferase family according to the reported 5GTs, which were also performed phylogenetic and bioinformatics analysis. Two important 5GTs, Vitvi0900582.t01 and Vitvi05g01269.t01, were screened through analyses of anthocyanidin diglucosides accumulation and gene expression in berry skins of three representative grape cultivars with significant differences in anthocyanin glycosylation. Fourteen alleles of each of the 5GTs were cloned from 14 V. amurensis cultivars and hybrids as well as from V. vinifera ‘Cabernet Sauvignon’, and sequence analysis and functional prediction were performed. From three perspectives of phenotype, transcriptional level, and genotype, it has been found that the functional allele at the Vitvi0900582.t01 locus of Chr 9 played a decisive role in the synthesis of abundant anthocyanidin diglucosides in V. amurensis. In addition, the trace anthocyanidin diglucosides detected in V. vinifera ‘Cabernet Sauvignon’ were led by the functional allele at the Vitvi05g01269.t01 locus of Chr 5. This study provides preliminary data for further research on the regulatory mechanism of anthocyanidin diglucosides in the grapes with the V. amurensis pedigree to improve their wine quality in future breeding efforts.

Effect of Water Deficit Stress on Reproductive Stage of Durum Wheat Near Isogenic Lines Carrying the NAM-B1 Gene

Background In wheat, the NAC family plays a crucial role in conferring cellular responses to different abiotic stresses, particularly drought. The functional NAM-B1 allele in durum wheat accelerates senescence, while its homologous genes contribute to improved water deficit stress tolerance. Therefore, the main objective of this study was to investigate the role of the NAM-B1 gene in durum wheat subjected to water deficit stress at two reproductive stages. Materials and Methods Three Near-Isogenic Lines carrying a functional NAM-B1 allele and their recurrent parent, Langdon (LDN), were used in this study. The study assessed NILs and LDN performance under varied water conditions (well-watered, 60%, and 80% water deficit of pot capacity) during flag leaf and anthesis stages. The agronomic performance of the three NILs and LDN was assessed for 16 traits, including plant height, grain yield, and thousand kernel weight. Additionally, physiological measurements, including stomatal resistance, chlorophyll content (SPAD values), and chlorophyll fluorescence (Fv/Fm) were taken. Results Significant genotypic effects were observed on seven agronomic traits, while 15 traits were influenced by the water stress treatment. The NILs exhibited accelerated maturity and a shorter grain-filling period, which were particularly pronounced under stress conditions. Severe water deficit resulted in reduced grain weight and thousand-grain weight in tested genotypes. Interestingly NILs carrying functional NAM-B1 showed taller plants and had higher tiller and spike numbers when compared to LND. Significant genotypic effects were observed for seven traits, and water stress treatments affected 15 traits. The NILs exhibited accelerated maturity and reduced grain weight under severe water deficit. Physiological measurements showed genotype and water-deficit differences, with NIL #504 displaying higher SPAD values, particularly under stress conditions, and a significant genotype X treatment effect was observed for stomatal resistance at the anthesis stage. Discussion Limited treatment × genotype interactions for most traits highlight the complexity of drought tolerance in the tested lines, which might be attributed to its quantitative nature influenced by multiple genes. The study emphasizes the necessity for future research to explore the role of other NAM-related genes in response to water deficit stress and their interactive effects with the NAM-B1 gene at different growth stages in wheat plants subjected to diverse stress conditions. Conclusion In conclusion, this study reveals pronounced genotypic effects, particularly in agronomic traits, such as maturation rate and grain filling period, under severe water deficit stress. Future studies are needed to understand the genetic mechanisms mediated by NAM-B1 genes in accelerating maturity in response to stress.

LncRNA CDKN2B-AS1 regulates collagen expression

The long noncoding RNA CDKN2B-AS1 harbors a major coronary artery disease risk haplotype, which is also associated with progressive forms of the oral inflammatory disease periodontitis as well as myocardial infarction (MI). Despite extensive research, there is currently no broad consensus on the function of CDKN2B-AS1 that would explain a common molecular role of this lncRNA in these diseases. Our aim was to investigate the role of CDKN2B-AS1 in gingival cells to better understand the molecular mechanisms underlying the increased risk of progressive periodontitis. We downregulated CDKN2B-AS1 transcript levels in primary gingival fibroblasts with LNA GapmeRs. Following RNA-sequencing, we performed differential expression, gene set enrichment analyses and Western Blotting. Putative causal alleles were searched by analyzing associated DNA sequence variants for changes of predicted transcription factor binding sites. We functionally characterized putative functional alleles using luciferase-reporter and antibody electrophoretic mobility shift assays in gingival fibroblasts and HeLa cells. Of all gene sets analysed, collagen biosynthesis was most significantly upregulated (Padj=9.7 × 10− 5 (AUC > 0.65) with the CAD and MI risk gene COL4A1 showing strongest upregulation of the enriched gene sets (Fold change = 12.13, Padj = 4.9 × 10− 25). The inflammatory “TNFA signaling via NFKB” gene set was downregulated the most (Padj=1 × 10− 5 (AUC = 0.60). On the single gene level, CAPNS2, involved in extracellular matrix organization, was the top upregulated protein coding gene (Fold change = 48.5, P < 9 × 10− 24). The risk variant rs10757278 altered a binding site of the pathogen responsive transcription factor STAT1 (P = 5.8 × 10− 6). rs10757278-G allele reduced STAT1 binding 14.4% and rs10757278-A decreased luciferase activity in gingival fibroblasts 41.2% (P = 0.0056), corresponding with GTEx data. CDKN2B-AS1 represses collagen gene expression in gingival fibroblasts. Dysregulated collagen biosynthesis through allele-specific CDKN2B-AS1 expression in response to inflammatory factors may affect collagen synthesis, and in consequence tissue barrier and atherosclerotic plaque stability.

A comprehensive Thai pharmacogenomics database (TPGxD-1): Phenotype prediction and variants identification in 942 whole-genome sequencing data.

Computational methods analyze genomic data to identify genetic variants linked to drug responses, thereby guiding personalized medicine. This study analyzed 942 whole-genome sequences from the Electricity Generating Authority of Thailand (EGAT) cohort to establish a population-specific pharmacogenomic database (TPGxD-1) in the Thai population. Sentieon (version 201808.08) implemented the GATK best workflow practice for variant calling. We then annotated variant call format (VCF) files using Golden Helix VarSeq 2.5.0 and employed Stargazer v2.0.2 for star allele analysis. The analysis of 63 very important pharmacogenes (VIPGx) reveals 85,566 variants, including 13,532 novel discoveries. Notably, we identified 464 known PGx variants and 275 clinically relevant novel variants. The phenotypic prediction of 15 VIPGx demonstrated a varied metabolic profile for the Thai population. Genes like CYP2C9 (9%), CYP3A5 (45.2%), CYP2B6 (9.4%), NUDT15 (15%), CYP2D6 (47%) and CYP2C19 (43%) showed a high number of intermediate metabolizers; CYP3A5 (41%), and CYP2C19 (9.9%) showed more poor metabolizers. CYP1A2 (52.7%) and CYP2B6 (7.6%) were found to have a higher number of ultra-metabolizers. The functional prediction of the remaining 10 VIPGx genes reveals a high frequency of decreased functional alleles in SULT1A1 (12%), NAT2 (84%), and G6PD (12%). SLCO1B1 reports 20% poor functional alleles, while PTGIS (42%), SLCO1B1 (4%), and TPMT (5.96%) showed increased functional alleles. This study discovered new variants and alleles in the 63 VIPGx genes among the Thai population, offering insights into advancing clinical pharmacogenomics (PGx). However, further validation is needed using other computational and genotyping methods.