Haploview: analysis and visualization of LD and haplotype maps

Multidimensional insights into the biodiversity of Streptomyces in soils of China: a pilot study

Streptomyces, a diverse group of filamentous bacteria found predominantly in soil, play a crucial role in nutrient cycling and produce many valuable secondary metabolites for the pharmaceutical industry. In this pilot study, we collected 19 soil samples from 14 provinces in China to preliminarily investigate the biodiversity and genetic structure of Streptomyces in soils of China from different dimensions, using recently developed cost-efficient amplicon and whole-genome library preparation methods. Amplicon analysis showed that Actinobacteria were among the most abundant bacteria, with 0.3% of amplicon sequence variants (ASVs) belonging to Streptomyces. Meanwhile, we successfully isolated 136 Streptomyces natural strains and assembled their genomes, including 26 previously unreported species, underscoring the need for further exploration of soil Streptomyces in China. Population genetics analysis revealed that homologous recombination may primarily drive the extensive genetic diversity observed in Streptomyces, as well as a complex population structure. Complementing this, pan-genome analysis shed light on gene diversity within Streptomyces and led to the discovery of rare genes, further emphasizing the vast genetic diversity of this genus. Additionally, multiple metabolic gene clusters were found in these Streptomyces strains, as well as some potentially unique or uncommon ones were found. These findings not only highlight the biological and metabolic diversity of Streptomyces but also provide a technical framework for future studies on the global biodiversity and evolution of this genus.

IMPORTANCE

Streptomyces, a prominent group of Actinobacteria, holds significant importance in ecosystems and biotechnology due to their diverse array of metabolic products. However, research on the biodiversity of soil Streptomyces across extensive geographical scales in China has been limited, and their genetic diversity has rarely been evaluated using modern population genetics principles. This pilot study successfully addresses these gaps by conducting a preliminary exploration on the biodiversity of Streptomyces in Chinese soils from multiple perspectives, providing valuable insights for a deeper understanding of their biodiversity and a novel technical framework for future large-scale explorations of its diversity.

Extended Typing of Common Erythrocyte Antigens in Tunisian Blood Donors and Its Usefulness in Transfusion Immunology

Extended RBC antigens typing is very valuable in transfusion immunology since it is highly recommended to ensure better transfusion practices and avoid transfusion-related complications and to establish registries for rare blood donors as recommended by the International Society of Blood Transfusion and World Health Organization. A group of 236 Tunisian blood donors were genotyped for 19 common blood loci using the Sequence-specific primers polymerase chain reaction (SSP-PCR) method. The statistical analysis was done using the HaploView Software. The study showed the dominance of the loci: RHCE*e, KEL*02, FY*02 and CO*01; and the absence of the homozygous state of the CO*02 allele. Furthermore, two complete linkage disequilibrium leading to the absence of the two alleles RHCE*C-RHCE*E (C-E) and FY*01N.01 (FY*Anull) were detected. Additionally, it appeared that approximately 91% of these blood donors are positive for the RHD gene; and all subjects who lacked the RHD exon 10 are homozygous for the RHCE*c and RHCE*e variants. The study also revealed that the RH1 negative blood cannot be universal to the Rh system because almost all RH1 negative donated blood is RH:-2,4,-3,5 (ccee), which may constitute a risk in some recipients carrying the anti-RH4 and/or anti-RH5 antibodies. Considering that some donated RBC units may contain blood with very immunogenic phenotypes, great caution is required when transfusing some subjects, especially in emergency situations because it can be a step towards subsequent complex or multiple alloimmunization.

Genome-Wide Association Analyses Identify Hydrogen Peroxide-Responsive Loci in Wheat Diversity

Hydrogen peroxide (H2O2) is a signaling molecule that plays a crucial role in plant growth and development against different abiotic stresses. Identifying genetic factors associated with H2O2 regulation and homeostasis can provide valuable insights for improving stress tolerance. Here, we explored genetic diversity of root and shoot traits mediated by H2O2 using a global diversity panel of 150 bread wheat cultivars. The H2O2 treatment significantly reduced root and shoot growth. We calculated relative values and stress tolerance index (STI) of root and shoot traits and performed genome-wide association studies (GWAS). This led to identification of 108 marker-trait associations including the topmost associations on chromosomes 3B, 2A, 5A, 3B, 5D, 5A, 6B, 4B, and 3B for relative root length, STI root length, relative shoot length, STI shoot length, relative root fresh weight, relative shoot fresh weight, STI shoot fresh weight, and relative and STI root-shoot ratio, respectively. Linkage disequilibrium analysis revealed that major alleles of significant markers were linked with high relative values and STIs for all traits except for relative root length and relative root-shoot ratio. The selected candidate genes were involved mostly in metal ion binding, transmembrane transport, oxidation-reduction process, protein phosphorylation, DNA, and ADP binding processes. These findings provide a fundamental basis for functional analysis of putative candidate genes linked to H2O2-mediated root-shoot growth of wheat. The result will also help to construct genetic map for H2O2-mediated root-shoot growth variation.

Therapeutic efficacy of artemether-lumefantrine in North-Eastern states of India and prevalence of drug resistance-associated molecular markers

BACKGROUND

Plasmodium falciparum is the main cause of malaria in North-Eastern (NE) states of India. Artemether-lumefantrine (AL) was introduced as first-line therapy against uncomplicated P. falciparum cases in 2013 after the emergence of resistance to sulfadoxine-pyrimethamine. The aim of the study was to assess the therapeutic efficacy of AL and status of molecular markers in the circulating parasites.

METHODS

Therapeutic efficacy of AL was assessed in NE states as per World Health Organization guidelines. Patients with P. falciparum positive peripheral blood smear were enrolled and treated with AL and clinical and parasitological parameters were monitored over a 28-day follow-up period. Furthermore, the pfmdr1, pfdhfr, pfdhps and pfk13 genes were amplified and sequenced for mutation analysis.

RESULTS

A total of 231 cases were enrolled and therapeutic efficacy was determined in 215 (93.1%) patients who completed their 28 days' follow-up while 10 patients withdrew and 6 were lost to follow up during study. Overall 99.5% and 98.6% of adequate clinical and parasitological response was observed with and without PCR correction, respectively. Only three cases (1.4%) of late parasitological failure were observed in Mizoram site. One case of recrudescence and two cases of reinfection were detected by msp1 and msp2 genotyping. Mutation analysis showed the 15.8%, 100%, 90.5% mutants in pfmdr1, pfdhfr and pfdhps gene respectively and three non-synonymous mutations were also found in pfk13gene.

CONCLUSIONS

This study reports that AL is efficacious against uncomplicated P. falciparum cases in NE states of India. However, prevalence of mutations in molecular marker associated with anti-malarial resistance (pfmdr1, pfdhfr, pfdhps and pfk13) gene indicate possible emergence of drug resistance. This is to underline the fact that the drug is efficacious for now, but rising mutations indicate that continuous monitoring is essential for effective treatment regime.

Three FGFR4 gene polymorphisms contribute to the susceptibility of urethral cancer in the middle and south of Iraq population

BACKGROUND

Urothelial cell carcinoma is quite prevalent, making up close to 90 % of all cases. Men are more likely to suffer from it than women, and it mostly affects the elderly. Fibroblast growth factor receptor 4 (FGFR4) plays an important role in cell proliferation and cancer progression.

AIM

this study was conducted to assess the association between FGFR4 gene polymorphism and the risk of Urothelial Cell Carcinoma in Iraq.

METHODS

genomic DNA samples were extracted from a total 200 samples of blood. Three primers were designed to enhance three commonly observed genetic variation, rs2011077, rs351855, and rs1966265. The single strand conformation polymorphisms technique (SSCP) was genotyped and confirmed by further sequencing protocols.

RESULTS

The results of this study show that cases with the G/A variant of the rs351855 genotype have a marked increase in risk to Urothelial Cell Carcinoma (P = 0.001, OR 0.32, 95 % CI 0.20 to 0.94). Cases with genotype rs2011077: T\C has also associated with the increased the risk of UCC (P = 0.001, OR= 0.50, 95 % CI = 0.33 to 0.76). The Linkage Disequilibrium revealed a significant relationship between the T allele of the rs2011077 locus and the A allele of the rs351855 locus, leading to the formation of the T\A haplotype in cases diagnosed with the UCC. Our results show that FGFR4 gene polymorphisms (rs351855 and rs2011077) have significant associations with increased risk of Urothelial Cell Carcinoma.

CONCLUSION

current study indicates that the specific polymorphisms have proven to be promising as a major genetic marker for identifying cases who may be more susceptible to diagnosis and recurrence Urothelial Cell Carcinoma.

Evaluation of SIRT1 Protein Levels and SIRT1/rs7895833 Distributions in Turkish Patients With Obstructive Sleep Apnea

OBJECTIVE

Obstructive Sleep Apnea (OSA) is a common heterogeneous sleep disorder that significantly impacts the sleep quality of individuals and leads to severe complications. Patients with OSA often experience disrupted circadian rhythm, hyperactive hypoxia response, and endothelial dysfunction, yet the underlying molecular mechanism remains poorly known. Recent research suggests promising evidence of the potential role of SIRT1 in the etiology of OSA, warranting further investigation.

METHODS

We investigated the associations of the SIRT1 promoter variant (rs7895833A > G) with OSA severity in 199 individuals who underwent an overnight polysomnography at the sleep clinic.

RESULTS

The minor allele frequency was observed as 0.309 in males (n = 149) and 0.310 in females (n = 50). No significant associations were observed between genotypes and apnea-hypopnea index (AHI) in the entire sample. However, we observed a significant association (p = 0.034) between the rs7895833-G and the severity of OSA in females stratified by AHI. Additionally, we found statistically significant inverse correlations between age and SIRT1 protein levels in the total sample (p = 0.013) and the male group (p = 0.018), suggesting a potential age-related expression of SIRT1. Our analysis also confirmed the published literature, showing correlations between the AHI and clinical parameters such as age, BMI, Epworth sleepiness scale, and neck circumference.

CONCLUSIONS

Overall, SIRT1 may indirectly affect OSA pathogenesis, which might be influenced by gender. Further detailed analysis involving large population-based biobanks, especially focusing on gender-based differences, will improve our understanding of the role and potential of SIRT1 in OSA management.

Genetic testing as a tool for diagnosis of congenital stationary night blindness (CSNB) in white spotted breeds in Poland

Congenital stationary night blindness (CSNB) has been connected to the leopard complex spotting phenotype (LP) in various horse breeds. CSNB associated with LP is thought to be caused by a 1378 bp insertion in TRPM1, with homozygotes being nightblind and having few to no spots of pigment in their white patterned area. This study aimed to assess the prevalence of CSNB alleles in tarant-colored horses in Poland through a three-primer system for an allele-specific Polymerase Chain Reaction (PCR). The TRPM1 gene insertion was genotyped in 221 horses belonging to Małopolska, Felin and Shetland Ponies. The chi-square (χ²) test indicates, that χ2 <5.991 suggesting that the population is in Hardy-Weinberg equilibrium. Of the horses carrying the LP allele, 7 % of Małopolska horses, 4,8 % of Felin ponies and 6.25 % of the Shetland ponies were homozygous for the TRMP1 insertion, indicating low-light vision issues, crucial for horses working in dim conditions. This study highlights the utility of genetic testing for accurate phenotype evaluation, and clinical and breeding management.

Association of GLP1R locus with mental ill-health endophenotypes and cardiometabolic traits: A trans-ancestry study in UK Biobank

AIMS

Glucagon-like peptide 1 receptor agonists (GLP1RA), used to treat type 2 diabetes and obesity, have been associated with off-target behavioural effects. We systematically assessed genetic variation in the GLP1R locus for impact on mental ill-health (MIH) and cardiometabolic phenotypes across diverse populations within UK Biobank.

MATERIALS AND METHODS

All genetic variants with minor allele frequency >1% in the GLP1R locus were investigated for associations with MIH phenotypes and cardiometabolic phenotypes. Linear or Logistic regression analyses (adjusted for age, sex, population structure and genotyping chip) were conducted separately in unrelated individuals of self-reported white British (N = 408 774), white European (N = 50 314), South Asian (N = 7667), multiple-ancestry groups (N = 10 437) or African-Caribbean (N = 7641) subsets. All ancestries were subsequently combined in an inverse variance-weighted fixed effects meta-analysis. Bonferroni correction for multiple testing was applied (for number of independent genetic variants).

RESULTS

Associations were identified between GLP1R variants and body mass index (BMI), blood pressure and type 2 diabetes in all ancestries. All ancestries except South Asian had significant MIH associations (mood instability: rs111265626-G, odds ratio [OR] 0.851 [confidence interval, CI 0.79-0.92], risk-taking behaviour: rs75408972-T, OR 1.05 [CI 1.03-1.08] or chronic pain: rs9296280-C, OR 0.645 [CI 0.54-0.78]). The trans-ancestry meta-analysis showed mainly consistent effect sizes and directions for metabolic traits, but discordant directions MIH associations. Only signals for chronic pain, stroke and BMI influenced expression of GLP1R.

CONCLUSIONS

GLP1R variants have consistent cardiometabolic effects across ancestries, but effects on MIH phenotypes are more varied. Any observed behavioural changes with GLP1RA are likely not acting directly through GLP1R.

Interaction of tissue inhibitor of metalloproteinase 3 gene polymorphism, blood cadmium and total urinary arsenic levels on clear cell renal cell carcinoma

In renal cell carcinoma (RCC), tissue inhibitor of metalloproteinase (TIMP) 3 expression is lost, suggesting that the TIMP3 gene may function as a tumor suppressor gene. Cadmium (Cd) and arsenic (As) exposure may affect the expression of TIMP3. Here we investigate the association of clear cell RCC with TIMP3 polymorphisms, and explore whether TIMP3 polymorphisms modify the relationship between blood Cd or total urinary As levels and clear cell RCC respectively. We recruited 281 clear cell RCC patients and 689 sex- and age-matched controls. The clear cell RCC was diagnosed by pathological evaluation after image-guided biopsy or surgical resection of the renal tumor. Concentrations of blood Cd and lead, and also total urinary As, were measured. We determined TIMP3 polymorphisms using the Agena Bioscience MassARRAY system. Odds ratio (OR) of clear cell RCC was significantly inversely correlated with TIMP3 rs9609643 GA/AA genotype, with OR = 0.63 (95% confidence interval, CI, 0.44-0.91). For TIMP3 rs715572 AA compared to the GG/GA genotype, the OR of clear cell RCC was 1.60 with 95% CI of 1.01-2.56. Individuals with high blood Cd concentrations and the TIMP3 rs9609643 GG genotype exhibited a higher OR of clear cell RCC than reference groups (OR = 4.48, 95% CI 2.09-9.60). This study presents a novel finding that the GA/AA genotype of TIMP3 rs9609643 significantly decreased the clear cell RCC risk, and AA genotype of TIMP3 rs715572 significantly increased the clear cell RCC risk. Furthermore, this study first identified that the TIMP3 rs9609643 risk genotypes appear to interact with high blood Cd levels to increase the OR of clear cell RCC.

Genomic Insights into Vector-Pathogen Adaptation in Haemaphysalis longicornis and Rhipicephalus microplus

As crucial vectors that transmit pathogens to humans and livestock, ticks pose substantial global health threats and economic burdens. We analyzed 328 tick genomes to explore the population's genetic structure and the adaptive evolution of H. longicornis and R. microplus, two tick species with distinct life cycle characteristics. We observed distinct genetic structures in H. longicornis and R. microplus. Gene flow estimation revealed a closer genetic connection in R. microplus than H. longicornis, which was facilitated by geographical proximity. Notably, we identified a set of candidate genes associated with possible adaptations. Specifically, the immune-related gene DUOX and the iron transport gene ACO1 showed significant signals of natural selection in R. microplus. Similarly, H. longicornis exhibited selection in pyridoxal-phosphate-dependent enzyme genes associated with heme synthesis. Moreover, we observed significant correlations between the abundance of pathogens, such as Rickettsia and Francisella, and specific tick genotypes, which highlights the role of R. microplus in maintaining these pathogens and its adaptations that influence immune responses and iron metabolism, suggesting potential coevolution between vectors and pathogens. Our study highlights the vital genes involved in tick blood feeding and immunity, and it provides insights into the coevolution of ticks and tick-borne pathogens.

Genome-Wide Mapping, Allelic Fingerprinting, and Haplotypes Validation Provide Insights Into the Genetic Control of Phenotypic Plasticity in Rice

Plant density significantly impacts photosynthesis, crop growth, and yield, thereby shaping the [CO2] fertilization effect and intricate physiological interactions in rice. An association panel of 171 rice genotypes was evaluated for physiological and yield-related traits, including the cumulative response index, under both normal planting density (NPD) and low planting density (LPD) conditions. LPD, serving as a proxy for elevated atmospheric [CO2], significantly increased all trait values, except for harvest index, compared to NPD. A genome-wide association study identified 172 QTNs, including 12 associated with multiple traits under NPD or LPD conditions. Candidate gene mining and network analysis within QTN regions identified potential candidates such as OsHAK1, RGA1, OsalphaCA3, OsalphaCA4, OsalphaCA5, OsCYP38, and OsPIN1, influencing various physiological and yield-related traits under LPD conditions. A significant relationship between the percentage of favorable alleles in genotypes and their performance under different conditions was observed. Potential haplotypes were validated using genotypes identified with contrasting [CO2] responses, grown under LPD and Free-Air [CO2] Enrichment facility. These findings can aid in selectively breeding genotypes with favorable alleles or haplotypes to enhance [CO2] responsiveness in rice. Incorporating greater phenotypic plasticity can help develop climate-smart rice varieties that increase grain yield and quality while mitigating losses from warming temperatures.

Interactive and evolutionary effect of CASZ1 gene variants on varicose veins susceptibility in South Asian Indians

BACKGROUND

Varicose veins (VV) are spectrum of common vascular diseases having complex genetic etiology. The Castor Zinc Finger 1 (CASZ1) gene has been involved in vascular development and its variant has shown association with VV in various ethnicities, but CASZ1 susceptibility to VV risk is unexplored in the South Asian Indian population. The objective of this study was to estimate the association of the CASZ1 gene variations and VV susceptibility in the South Asian Indians, and to examine the evolutionary patterns of these variants compared to other populations.

METHODOLOGY

Population based case control analysis was conducted on all CASZ1 variants present in the Global Screening Array, including the established VV variant rs11121615 with a focus on validating and identification of both novel and established genetic markers to capture a full spectrum of population-specific genetic markers unique to studied population group. Linkage disequilibrium patterns and cumulative variant effects were also analyzed, followed by selection pressure assessment using neutrality tests.

RESULTS

Three CASZ1 variants rs72860191 (OR 1.58, 95% CI 1.07-2.32, p = 0.01), rs7519604 (OR 1.43, 95% CI 1.05-1.94, p = 0.01), and rs11121615 (OR 0.69, 95% CI 0.50-0.95, p = 0.02) were observed to be significantly associated with VV. Haplotype analysis identified unique haplotype structure of South Asian Indians compared to other global populations. Moreover, the cumulative OR was observed to be higher than the independently estimated values (OR = 2.41, 95% CI 1.48-3.94), indicating genotypic epistasis of VV associated variants. The neutrality tests revealed balancing selection within CASZ1 in the studied population compared to other populations, CONCLUSION: The present study identified CASZ1 variants and their epistatic interactions is associated with VV susceptibility supported with evidence of balancing selection, provides crucial insights into the genetic architecture of VV in studied group, highlighting the impact of evolutionary forces on disease susceptibility.

Polymorphisms in the calcium voltage-gated channel subunit Alpha1 D (CACNA1D) gene are associated with spontaneous preterm birth in Taiwanese women

PURPOSE

Calcium signaling is essential for immune function, myometrial contractions, and hormone secretion, all of which contribute to preterm birth. In this study, we investigated the associations of 3 single-nucleotide polymorphisms (SNPs) in CACNA1D gene, which encodes the Cav1.3 calcium channel, with the risk of spontaneous preterm birth (sPTB).

METHODS

A hospital-based case-control study was conducted with 112 women of sPTB and 1120 term control women. Three CACNA1D SNPs (rs9810888 T/G, rs1045958 C/T, and rs881883 G/A) were genotyped.

RESULTS

The T/G genotype of the CACNA1D rs9810888 SNP was associated with a reduced risk of sPTB (odds ratio: 0.61, 95 % confidence interval: 0.41-0.91, P = 0.01, Pc = 0.03). However, no significant associations were observed for the other 2 SNPs. Haplotype analysis revealed no significant differences between the case and control groups.

CONCLUSION

Our findings suggest that the intronic rs9810888 T/G variant of CACNA1D gene protects against sPTB in Taiwanese women.

SLAF-seq technology-based genome-wide association and population structure analyses of hot pepper and sweet pepper

BACKGROUND

Utilizing Single Nucleotide Polymorphism (SNP) marker technology, a phylogenetic and agronomic trait network analysis was conducted on the collected hot pepper and sweet pepper germplasm resources, providing a theoretical basis for parental selection and new varieties.

RESULTS

Specific-locus amplified fragment sequencing (SLAF-seq) technology was employed for a genome-wide association study (GWAS) on 197 hot pepper and sweet pepper germplasm resources, generating 1404.88 Mb clean reads data with an average Q30 of 91.5% and mean GC content of 37.96%. Through sequencing data analysis, a total of 639,815 SLAF tags were obtained with an average sequencing depth of 12.16x, among which 86,381 were polymorphic SLAF tags, leading to the development of 18,145,155 SNP markers. The identified SNP markers were used for cluster analysis of the genetic structure and phylogenetic relationships of hot pepper and sweet pepper germplasm resources, dividing the 197 hot pepper and sweet pepper germplasm resources into 9 clusters. Additionally, a genome-wide association analysis was conducted on 25 agronomic traits of the 197 hot pepper and sweet pepper materials, yielding a substantial number of significantly associated SNP loci with agronomic traits. A correlation network analysis diagram was drawn among the various agronomic traits, preliminarily determining the relationships between the 25 agronomic characteristics of hot pepper and sweet pepper and the positions of 15 agronomic traits (p < 1.707 × 10-8) on the chromosomes were annotated, forming multi-trait aggregation regions.

CONCLUSIONS

Our research reveals the genetic diversity, phylogenetic relationships, and population structure of 197 hot pepper and sweet pepper germplasm resources, providing a basis for germplasm identification, resource utilization, and breeding.

Genome-specific association study (GSAS) for exploration of variability in hemp (Cannabis sativa)

Hemp (Cannabis sativa L.) is a versatile crop with substantial potential for creating productive, sustainable, and resilient agricultural systems. However, in contrast to other crops such as cereals, hemp is highly heterozygous, resulting in both challenges and opportunities for agriculture, breeding, and research. Here, we utilise the heterozygosity of hemp to explore the genetic basis of phenotypic variability in a population generated from a single self-pollinated hemp plant. The S1 population shows extensive variability in plant growth, development, and reproductive patterns. Using reduced representation sequencing, selection of alleles heterozygous in the parent plant, and a model originally developed for genome-wide association studies (GWAS), we were able to identify statistically significant single nucleotide variants (SNVs) and haplotypes associated with phenotypic traits of interest, such as flowering time or biomass yield. This new approach, which we term genome-specific association study (GSAS), enables the mapping of traits in a single generation without the need for a large number of diverse cultivars or samples. GSAS might be applicable to other highly heterozygous vegetable and fruit crops, informing the breeding of new cultivars with enhanced uniformity and improved performance in traits relevant to various applications.

The integration of quantile regression with 3VmrMLM identifies more QTNs and QTN-by-environment interactions using SNP- and haplotype-based markers

Current methods used in genome-wide association studies frequently lack power owing to their inability to detect heterogeneous associations and rare and multiallelic variants. To address these issues, quantile regression is integrated with a three (compressed) variance component multi-locus random-SNP-effect mixed linear model (3VmrMLM) to propose q3VmrMLM for detecting heterogeneous quantitative trait nucleotides (QTNs) and QTN-by-environment interactions (QEIs), and then design haplotype-based q3VmrMLM (q3VmrMLM-Hap) for identifying multiallelic haplotypes and rare variants. In Monte Carlo simulation studies, q3VmrMLM had higher power than 3VmrMLM, sequence kernel association test (SKAT), and integrated quantile rank test (iQRAT). In a re-analysis of 10 traits in 1439 rice hybrids, 261 known genes were identified only by q3VmrMLM and q3VmrMLM-Hap, whereas 175 known genes were detected by both the new and existing methods. Of all the significant QTNs with known genes, q3VmrMLM (179: 140 variance heterogeneity and 157 quantile effect heterogeneity) found more heterogeneous QTNs than 3VmrMLM (123), SKAT (27), and iQRAT (29); q3VmrMLM-Hap (121) mapped more low-frequency (<0.05) QTNs than q3VmrMLM (51), 3VmrMLM (43), SKAT (11), and iQRAT (12); and q3VmrMLM-Hap (12), q3VmrMLM (16), and 3VmrMLM (12) had similar power in identifying gene-by-environment interactions. All significant and suggested QTNs achieved the highest predictive accuracy (r = 0.9045). In conclusion, this study describes a new and complementary approach to mining genes and unraveling the genetic architecture of complex traits in crops.

Association of the TGFB1 Gene Polymorphisms with Pain Symptoms and the Effectiveness of Platelet-Rich Plasma in the Treatment of Lateral Elbow Tendinopathy: A Prospective Cohort Study

The regenerative properties of platelet-rich plasma (PRP) result from the high concentration of growth factors, including transforming growth factor beta 1 (TGF-β1). Nevertheless, this form of therapy may not always be effective due to the variability in genetic factors. In this study, the association of TGFB1 gene polymorphisms with the effectiveness of lateral elbow tendinopathy (LET) treatment with PRP was investigated. The effectiveness of therapy was assessed using minimal clinically important difference (MCID) and patient-reported outcome measures (PROM), specifically visual analog scale (VAS), quick version of disabilities of the arm, shoulder, and hand score (QDASH), and patient-rated tennis elbow evaluation (PRTEE) for two years (in weeks 2, 4, 8, 12, 24, 52, and 104). The most effective therapy was noticed in CC rs2278422 genotype carriers, whereas carriers of AA, CC, and CC genotypes (rs12461895, rs4803455, rs2241717) showed more severe pain before therapy. Moreover, the analyses revealed an association of studied polymorphisms with such parameters of blood morphology as eosinophils (EOS), neutrophils (NEU), and monocytes (MONO). In conclusion, genotyping of rs2278422 variant may be a valuable diagnostic method for patient selection for PRP therapy, while genotyping of rs12461895, rs4803455, and rs2241717 polymorphisms may be used for prediction of increased risk of pain sensation.

A natural variant of COOL1 gene enhances cold tolerance for high-latitude adaptation in maize

Low temperature severely limits the growth, yield, and geographical distribution of maize (Zea mays L.). How maize adapts to cold climates remains largely unclear. Here, we identify a basic helix-loop-helix (bHLH) transcription factor, COLD-RESPONSIVE OPERATION LOCUS 1 (COOL1), as a crucial regulator of maize cold tolerance through genome-wide association studies. Natural variations in the COOL1 promoter affect the binding affinity of ELONGATED HYPOCOTYL5 (HY5), a transcriptional factor repressing COOL1 transcription. COOL1, in turn, negatively regulates downstream cold-responsive genes, thereby modulating cold tolerance. Moreover, calcium-dependent protein kinase CPK17 translocates to the nucleus and stabilizes COOL1 in response to cold stress. Intriguingly, the cold-tolerant allele of COOL1 is predominantly distributed in northern high latitudes with cold climates. This study defines a previously unknown pathway by which the COOL1-centered module regulates cold tolerance for high latitudinal adaptation in maize.

Family-based genetics identifies association of CUBN, IL1RL1 and PRKN variants with leprosy in Bangladesh

Previous studies have demonstrated the association between the occurrence of leprosy and several host genetic variants that can vary across different ethnic groups and populations. Since leprosy susceptibility genes have not been investigated in detail in the Bangladeshi population that still includes highly endemic areas, we here studied known associations between leprosy and 13 genetic markers located in 11 genes in a leprosy endemic area in Bangladesh for which an association with leprosy was previously found in an isolated former leprosy colony in the Brazilian Amazon. For this study, a family-based analysis using 60 parent-affected child trios was performed, followed by a case-control study of 210 leprosy patients and 189 healthy controls from the same area (endemic controls). Genotypes for 11 markers were determined by TaqMan SNP genotyping. In the family-based study, a significant association was found between leprosy and three single nucleotide polymorphisms, rs1801224, rs13001714, and rs1801582, located in the CUBN, IL1RL1, and PRKN genes, respectively. These findings were not replicated in the case-control sample. Variants in the CUBN, IL1RL1, and PRKN genes were associated with leprosy in Bangladesh, validating the initial Brazilian finding in a population sample of distinct ethnic background.

Variants in BMP15 Gene Affect Promoter Activity and Litter Size in Gobi Short Tail and Ujimqin Sheep

Reproductive performance in sheep plays a crucial role in determining the economic efficiency of the industry, with increasing litter size being a key focus for genetic improvement. The BMP15 gene is widely recognized as a major gene influencing sheep fertility. In this study, specific mutations in the BMP15 gene of Gobi short tail sheep were identified through direct sequencing, and these mutations were genotyped using the MassARRAY system. The g.54285159_54285161TTA indel was significantly associated with litter size in Gobi short tail sheep (p < 0.05). Three mutations, including g.54291460G>A, g.54288671C>T, and the g.54285159_54285161TTA indel, were significantly associated with litter size in Ujimqin sheep (p < 0.05). Furthermore, the promoter activity analysis demonstrated that the A allele exhibited significantly higher promoter activity compared to the G allele of the g.54291460G>A mutation. These findings highlight valuable genetic markers for improving sheep litter size and provide a robust theoretical foundation for further research on the BMP15 gene's role in reproduction.

RsWRKY40 coordinates the cold stress response by integrating RsSPS1-mediated sucrose accumulation and the CBF-dependent pathway in radish (Raphanus sativus L.)

Cold stress adversely affects crop growth and development. Radish is an important root vegetable crop, and its taproot formation is susceptible to low temperatures. However, the molecular basis of the cold stress response has not yet been fully dissected in radish. Here, a sucrose phosphate synthase gene (RsSPS1) was identified through a genome-wide association study and transcriptome analysis. RsSPS1 was responsible for sucrose synthesis, and sucrose was shown to be involved in taproot growth, cambium activity, and cold tolerance in radish. RsSPS1 regulated cambium activity and cold stress response by modulating sucrose content. Moreover, RsWRKY40 was identified as the upstream transcription activator of RsSPS1 by binding to its promoter. RsWRKY40 functioned in cambium activity and cold tolerance by modulating RsSPS1-mediated sucrose accumulation. Furthermore, RsWRKY40 promoted the RsCBF1 and RsCBF2 expression levels, resulting in elevated cold resilience. RsWRKY40 also enhanced its own transcription, forming a positive auto-regulatory loop to regulate cold stress response in radish. Together, a transcription module of RsWRKY40 orchestrated cold stress response by integrating sucrose accumulation and the CBF-dependent pathway was uncovered. These findings would provide novel insight into the molecular mechanism underlying cold-responsive sucrose accumulation and cambium activity and facilitate the genetic improvement of cold tolerance in radish breeding programs.

Association of IL10 gene SNVs rs1800896 (A>G), rs1800871 (C>T), rs1800872 (C>A) and haplotypes with COVID-19 severity and outcome in the Brazilian population

BACKGROUND

Elevated concentrations of IL-10 have been detected in coronavirus disease (COVID-19) patients and are a possible disease severity marker. Single nucleotide variants (SNVs) and their haplotypes can be associated with differences in IL-10 levels and with viral disease susceptibility.

AIM

Evaluate the associations of SNVs and their haplotypes in Brazilian patients with COVID-19 severity and outcome.

METHODS

In this cross-sectional and case-control study, the patients were selected from the University Hospital of State University of Londrina (HU-UEL) (n = 367) and were subdivided into mild (n = 165), moderate (n = 72) and severe (n = 130) groups. The DNA samples of the participants were subjected to real-time PCR for the detection of rs1800896 (A>G), rs1800871 (C>T) and rs1800872 (C>A) genotypes. The haplotypes were inferred with PHASE v2.1.1.

RESULTS

The severe cases of COVID-19 were independently associated with the GG genotype (rs1800896) (P = 0.038, OR 2.522, 95 % CI 1.053-6.038) as well as with the GCC haplotype in homozygosity (P = 0.037, OR 2.767, 95 % CI 1.065-7.191).

CONCLUSION

These results showed that the GG genotype of rs1800896 or the GCC haplotype are associated with COVID-19 severity in Brazilian patients.

Association between mitochondrial DNA copy number and production traits in pigs

Mitochondria are essential organelles in the regulation of cellular energetic metabolism. Mitochondrial DNA copy number (mtDNA_CN) can be used as a proxy for mitochondria number, size, and activity. The aims of our study are to evaluate the effect of mtDNA_CN and mitochondrial haploblocks on production traits in pigs, and to identify the genetic background of this cellular phenotype. We collected performance data of 234 pigs and extracted DNA from skeletal muscle. Whole-genome sequencing data was used to determine mtDNA_CN. We found positive correlations of muscle mtDNA_CN with backfat thickness at 207 d (+0.14; p-value = 0.07) and negative correlations with carcase loin thickness (-0.14; p-value = 0.03). Pigs with mtDNA_CN values below the lower quartile had greater loin thickness (+4.1 mm; p-value = 0.01) and lower backfat thickness (-1.1 mm; p-value = 0.08), which resulted in greater carcase lean percentage (+2.4%; p-value = 0.04), than pigs with mtDNA_CN values above the upper quartile. These results support the hypothesis that a reduction of mitochondrial activity is associated with greater feed efficiency. Higher mtDNA_CN was also positively correlated with higher meat ultimate pH (+0.19; p-value <0.01) but we did not observe significant difference for meat ultimate pH between the two groups with extreme mtDNA_CN. We found no association of the most frequent mitochondrial haploblocks with mtDNA_CN or the production traits, but several genomic regions that harbour potential candidate genes with functions related to mitochondrial biogenesis and homeostasis were associated with mtDNA_CN. These regions provide new insights into the genetic background of this cellular phenotype but it is still uncertain if such associations translate into noticeable effects on the production traits.

DNAJC13 influences responses of the extended reward system to conditioned stimuli: a genome-wide association study

Reward system dysfunction is implicated in the pathogenesis of major psychiatric disorders. We conducted a genome-wide association study (GWAS) to identify genes that influence activation strength of brain regions within the extended reward system in humans. A homogeneous sample of 214 participants was genotyped and underwent functional magnetic resonance imaging (fMRI). All subjects performed the 'desire-reason dilemma' (DRD) paradigm allowing systematic investigation of systems-level mechanisms of reward processing in humans. As a main finding, we identified the single nucleotide variant rs113408797 in the DnaJ Heat Shock Protein Family Member C13 gene [DNAJC13], alias Receptor-Mediated Endocytosis 8 [RME-8], that was associated with the activation strength of the ventral tegmental area (VTA; p = 2.50E-07) and the nucleus accumbens (NAcc; p = 5.31E-05) in response to conditioned reward stimuli. Moreover, haplotype analysis assessing the information across the entire DNAJC13 locus demonstrated an impact of a five-marker haplotype on VTA activation (p = 3.21E-07), which further corroborates a link between this gene and reward processing. The present findings provide first direct empirical evidence that genetic variation of DNAJC13 influences neural responses within the extended reward system to conditioned stimuli. Further studies are required to investigate the role of this gene in the pathogenesis and pathophysiology of neuropsychiatric disorders.

FLT1 and other candidate fetal haemoglobin modifying loci in sickle cell disease in African ancestries

Known fetal haemoglobin (HbF)-modulating loci explain 10-24% variation of HbF level in Africans with Sickle Cell Disease (SCD), compared to 50% among Europeans. Here, we report fourteen candidate loci from a genome-wide association study (GWAS) of HbF level in patients with SCD from Cameroon, Tanzania, and the United States of America. We present results of cell-based experiments for FLT1 candidate, demonstrating expression in early haematopoiesis and a possible involvement in hypoxia associated HbF induction. Our study employed genotyping arrays that capture a broad range of African and non-African genetic variation and replicated known loci (BCL11A and HBS1L-MYB). We estimated the heritability of HbF level in SCD at 94%, higher than estimated in unselected Europeans, and suggesting a robust capture of HbF-associated loci by these arrays. Our approach, which involved genotype imputation against six reference haplotype panels and association analysis with each of the panels, proved superior over selecting a best-performing panel, evidenced by a substantial proportion of panel-specific (up to 18%) and a low proportion of shared (28%) imputed variants across the panels.

Association of MSX1 gene polymorphisms and maxillary lateral incisor agenesis in Non-syndromic cleft lip and/or palate individuals

Background

To investigate the association between MSX1 gene polymorphisms and maxillary lateral incisor agenesis with and without Non Syndromic Cleft lip and palate (NSCL/P) in a South Indian population.

Methods

The study sample was divided into four groups: Group I: Twenty five Cleft lip and palate (NSCL/P) subjects with unilateral/bilateral congenitally missing maxillary lateral incisors, without agenesis of any other permanent teeth, Group II: Twenty five individuals with NSCL/P and a full complement of teeth, Group III: Twenty five non-cleft individuals with unilateral/bilateral congenitally missing maxillary lateral incisors and Control group: Twenty five healthy individuals with normal teeth development and without orofacial defects. MSX1 gene polymorphisms rs12532, rs1042484 and rs11726039 were genotyped by Sanger sequencing method with pre designed primer using ABI 3730 DNA sequencer. Associations were tested using Pearson Chi-square analysis.

Results

The three SNPs, rs12532, rs1042484 and rs11726039 of MSX1 gene exhibited polymorphism. rs12532 was associated with reduced risk of maxillary lateral incisor agenesis in NSCL/P subjects. rs1042484 had significant association with the NSCL/P without maxillary lateral incisor agenesis (full complement of teeth) subjects. rs11726039 showed significant association with NSCL/P with or without maxillary lateral incisor agenesis.

Conclusion

The present study on a South Indian population revealed a significant association between the MSX1 gene polymorphisms and tooth agenesis in NSCL/P subjects. Keywords: MSX1, non syndromic cleft lip and palate, lateral incisor agenesis.

Combining genome-wide association and genomic prediction to unravel the genetic architecture of carotenoid accumulation in carrot

Carrots (Daucus carota L.) are a rich source of provitamin A, namely, α- and β-carotene. Breeding programs prioritize increasing β-carotene content for improved color and nutrition. Understanding the genetic basis of carotenoid accumulation is crucial for implementing genomic-assisted selection to develop high-carotenoid lines. While previous studies identified loci (Y2, Y, Or, and REC) associated with carrot color and carotenoid content, this study employed genome-wide association (GWA) in a diverse panel of 738 carrot accessions. We discovered a novel locus with a candidate gene encoding phytoene synthase, a key enzyme in carotenoid biosynthesis. The Y2, Y, Or, and REC loci are mostly fixed in orange varieties, yet considerable variation in carotenoid concentration persists. This suggests a multigenic trait influenced by the environment. GWA of carotenoid concentration identified a quantitative trait locus for total carotenoids and α-carotene. We explored the accuracy of genomic prediction (GP) models to predict carotenoid concentration. We determined the optimal number of plants and plots required for accurate carotenoid phenotyping, finding ≥5 plants per plot and three plots per site as the minimum effective sample per accession. GP models achieved accuracies ranging from 0.06 to 0.40 depending on the carotenoid measured and environment the carrots were assayed. Additional studies in breeding programs will clarify the potential of genomic-assisted selection for high-carotenoid carrots.

The allelic mutation of NBS-LRR gene causes premature senescence in wheat

Premature senescence has a significant impact on the yield and quality of wheat crops. The process is controlled by multiple and intricate genetic pathways and regulatory elements, whereby the discovery of additional mutants provides important insights into the molecular basis of this important trait. Here, we developed a premature senescence wheat mutant je0874, its leaves started to show yellow before heading stage; with plant growth and development, the degree of yellowing worsened rapidly, and chlorophyll content in flag leaf was reduced by 93.8 % at 15 days after heading, all other leaves became dryness at the grain filling stage. In the mutant, the reactive oxygen species (ROS) and its metabolites increased up to 34.8-47.3 %, while activities of ROS scavenging enzymes were reduced by 62.7-96.7 %. Premature senescence resulted in a reduction of thousand grain weight by over 50 %. Genetic analysis showed the mutation of senescence was controlled by a single recessive gene, and target gene was finely mapped to a 338 kb region of the long arm of chromosome 2D. This region contained a total of 6 annotated genes, while only gene TraesFLD2D01G513900 carried a SNP mutation. The gene contained an NBS-LRR domain, we named it Taps1. Allelic mutants of Taps1 exhibited a lesion mimic phenotype, and the mutant allele resulted in cell death in tobacco, which represent a novel gene controlling wheat senescence. Two haplotypes were identified in 180 accessions, which did not lead to cell death. These results contribute to increase our understanding of the regulation of premature plant senescence.

TTN:c.12478del in proximal I-band of titin represents a common molecular cause of dilated cardiomyopathy in Slovenian patients

BACKGROUND

Titin truncating variants (TTNtv-s) are the most common genetic cause of dilated cardiomyopathy (DCM). Only rare TTNtv-s in the constitutively expressed exons of the A-band of the protein titin are associated with DCM according to the guidelines, however, studies in large cohorts of patients with DCM suggest that the region where TTNtv-s are associated with DCM is wider, extending at least into the I-band. The aim of this study was to describe the molecular pathology of TTNtv-s in Slovenian patients with cardiomyopathy and to clinically characterise the most recurrent TTNtv.

RESULTS

We collected all TTNtv-s identified in patients with cardiomyopathy using next-generation sequencing genetic testing between 2010 and July 2024, resulting in 42 unique variants identified in 54 patients. The TTN:c.12478del variant, affecting not the A-band but the proximal I-band, specifically the cardiac-specific N2Bus region, was found to be the most recurrent variant, present in seven (11.6%) probands with DCM. Genetic characterisation revealed a probable founder origin of the variant. Clinical characterisation of these probands revealed a phenotype consistent with DCM and severely reduced left ventricular ejection fraction in all probands. Three (43%) of the probands had atrial fibrillation and/or non-sustained ventricular tachycardia. Based on literature reports and evidence supporting the pathogenicity of the TTN:c.12478del variant affecting the proximal I-band, we classified all rare TTNtv-s in constitutively expressed exons of the I-band as (likely) pathogenic. Therefore, 33 (78.6%) TTNtv-s were classified as (likely) pathogenic (13 in the I-band, affecting 19 probands and 20 in the A-band affecting 25 probands), meaning that TTNtv-s were identified in 44 genotype-positive Slovenian probands with DCM, explaining 73.3% of the molecular pathology of DCM.

CONCLUSION

We report an almost threefold higher diagnostic yield of TTNtv-s in probands with DCM compared to previously reported findings in cohorts of patients with DCM from other populations. We also highlight the need for screening for rare TTNtv-s in the constitutively expressed exons of the I-band and for TTN:c.12478del in patients with DCM in this geographical region.

Causal relationship of sleep duration on risks for metabolic syndrome: a Mendelian randomization study

BACKGROUND

The cluster of cardiovascular risk factors, referred to as metabolic syndrome (MetS), represents a substantial risk factor for cardiovascular diseases and presents a significant public health challenge. However, previous epidemiological investigations exploring the link between sleep duration and MetS lack experimental evidence to establish a causal relationship. Hence, he objective of this study is to examine the association between sleep duration and MetS by employing the Mendelian randomization (MR) approach.

METHODS

A cross-sectional study was conducted utilizing the Taiwan Biobank database, which comprised 33,270 predominantly Han Chinese individuals aged 30-70 years with no history of cancer and enrolled between 2008 and 2020. This study was conducted using Taiwan Biobank database. In MR analysis, we constructed weighted and unweighted genetic risk scores by calculating the SNP alleles significantly associated with sleep duration. Two-stage regression analysis was used to estimate odds ratio (OR) and 95% confidence interval (CI).

RESULTS

In the observational epidemiologic study, after multivariate adjustment, the OR for sleep durations of < 5, 8-9 and > 9 h compared to those with a sleep duration of 7 h were 1.23 (95% CI: 1.07, 1.43), 1.15 (95% CI: 1.06, 1.24) and 1.84 (95% CI: 1.43, 2.36), respectively. In the MR analyses after multivariate adjustment, the ORs of MetS per 1 standard deviation increase in the estimated sleep duration and the probability of long and short sleep durations derived from weighted genetic risk scores were 0.64 (95% CI: 0.63, 0.66), 1.55 (95% CI: 1.51, 1.59), and 1.66 (95% CI: 1.62, 1.70), respectively.

CONCLUSIONS

Observational and MR analyses demonstrated that short and long sleep durations are potential causal risk factors for MetS. Therefore, long and short sleep durations should be considered as risk factors in MetS-prevention strategies.

Association of Genes TRH, PRL and PRLR with Milk Performance, Reproductive Traits and Heat Stress Response in Dairy Cattle

In our previous study, we found that changes in plasma prolactin (PRL) concentration were significantly associated with heat stress in dairy cows, and that PRL plays an important role in milk performance. Microarray sequencing revealed that thyrotropin releasing hormone (TRH) and prolactin receptor (PRLR), two genes important for PRL expression or function, may affect milk performance, reproduction, and heat stress response in dairy cattle. In this study, we further validated the genetic effects of the three genes in Chinese Holsteins. The potential variants within the three genes were first detected in 70 Chinese Holstein bulls and then screened in 1152 Chinese Holstein cows using the KASP (Kompetitive allele-specific PCR) method. In total, 42 variants were identified. Further, 13 SNPs were retained for KASP genotyping, including 8 in TRH, 3 in PRL, and 2 in PRLR. Using SNP-based association analyses, the multiple significant (p < 0.05) associations of these 13 SNPs with milk performance, reproduction, and heat stress response traits were found in the Holstein population. Furthermore, linkage disequilibrium analysis found a haplotype block in each of the TRH and PRL genes. Haplotype-based association analyses showed that haplotype blocks were also significantly (p < 0.05) associated with milk performance, reproduction, and heat stress response traits. Collectively, our results identified the genetic associations of TRH, PRL, and PRLR with milk performance, reproduction, and heat stress response traits in dairy cows, and found the important roles of SNP g.55888602A/C and g.55885455A/G in TRH in all traits, providing important molecular markers for genetic selection of high-yielding dairy cows.

Fine mapping and identification of causal alleles at the Ur-11 locus controlling rust resistance in common bean (Phaseolus vulgaris L.)

The Middle American rust resistance gene Ur-11 present in common bean (Phaseolus vulgaris L.) confers resistance to all but one known race of the pathogen Uromyces appendiculatus (Pers.) Unger. Even though progress has been made in understanding the host-pathogen interactions between common bean and U. appendiculatus, the causal alleles of the majority of rust resistance loci, including Ur-11, remain unknown. A genome-wide association study (GWAS) was conducted to identify genomic regions associated with resistance to the U. appendiculatus race 31-22, which is avirulent to Ur-11 but virulent to other Middle American rust resistance genes. GWAS using genotypic data consisting of approximately 70,959 SNP markers and phenotypic data based on the median reaction type (1-9 scale) of a panel of 357 Middle American breeding lines and cultivars, plus 5 germplasm lines with the Ur-11 locus derived from PI 181996, located Ur-11 on chromosome Pv11. Twenty-seven SNP markers clustered in the 55.16-55.56 Mb region of the P. vulgaris UI111 reference. Multiple DNA sequence alignments detected a missense mutation [c.1,328A > G] in the PvUI111.11G202400 gene model that encodes a leucine-rich repeat-containing protein in response to race 31-22. A PCR allele competitive extension marker (PACE) was developed and tested across a panel of ~ 700 Middle American dry bean genotypes. No recombination event was observed for the PACE marker among the tested genotypes; suggesting that the polymorphism on which it is based is very close to or in the Ur-11 gene. This PACE marker will be a useful and reliable marker for marker-assisted selection of Ur-11-based resistance to bean rust.

Association of salivary mmp-8 gene polymorphism with its protein expression in oral submucous fibrosis patients

OSF (Oral submucous fibrosis) is a chronic disease characterized by inflammation and progressive fibrosis of the submucosal tissues with the potential to progress into OSCC (Oral squamous cell carcinoma). Matrix metalloproteinases (MMP) are endopeptidases that play a role in extracellular matrix remodeling and pathophysiology of various diseases. The study aims to evaluate the gene polymorphism and protein expression of MMP-8 and their association with the severity of OSF. The cross-sectional study design involves patients diagnosed with OSF. DNA was extracted from saliva samples by the CTAB method followed by PCR and Sanger sequencing. The sequences were examined for MMP-8 polymorphism on Mega X software. ELISA was performed to assess the MMP-8 protein expression. The results of genetic polymorphism showed the alleles AG (rs11225395), TT (rs1861602574), CC (rs562617158), TT (rs2133511737), AA (rs1307439859), and CC (rs2133511706) consistent with disease severity. MMP-8 protein levels decreased with disease progression. Meanwhile, the association between the two showed a noteworthy significance with the presence of specific genetic variants, namely rs1320632, rs2133511732, rs1307439859, and rs2133511737, rs1307439859, rs562617158, rs11225395 shows a robust association with changes in MMP-8 protein expression. This study suggests a strong association between genotype and the modification of MMP-8 protein expression. In conclusion, MMP-8 may serve as a diagnostic biomarker in OSF.

Genome-wide association study dissects the genetic architecture of progesterone content in Persian walnut leaves (Juglans regia L.)

Progesterone (P4) is an endogenous sex steroid hormone involved in the ovulatory cycle and pregnancy of animal species. In sheep and goats, P4 analogues are used to induce synchronized ovulations and oestrus behavior of the females. In humans, P4 from chemical synthesis is used to treat peri-menopausal disorders. However, such molecules are released into aquatic environment and can be a source of pollution, are prohibited in organic farms and go against the trend of "naturality" in animal production as well as in human health. A natural alternative may consist in the extraction and use of P4 in plants. Mammalian hormones were discovered in an increasing number of plant species, including walnut leaves that contain high levels of P4. We compared the content of P4 in leaves of 170 accessions of Juglans regia from the walnut germplasm collection of INRAE Prunus-Juglans Biological Resources Center previously genotyped using the Axiom™ J. regia 700 K SNP array. We conducted a genome-wide association study (GWAS) using multi-locus models. When collected in October, P4 content goes from 34,1 to 287,5 mg/kg dry weight of leaves. The two laciniate accessions have the largest P4 content. We identified seven significant marker-trait associations on chromosomes 1, 2, 3, 6, 7, 15 and 16, and a candidate gene involved in the metabolism of sterols, precursors of plant steroid hormones. Our results raise the huge variability of P4 content within J. regia and propose a candidate gene which may have a role in the control of this variability, opening the way to a potential use of walnut P4 by the pharmaceutical industry towards more natural source of chemical compounds.

Integration of Multiomics Data Reveals Selection Characteristics of ITGB1 That Are Associated with Size Differentiation in Pigs

Min pigs, a prominent local breed from Northeast China, have diverged into two distinct breeds, Ermin (EM) pigs and Hebao (HB) pigs, through prolonged natural and artificial selection. Although these two breeds exhibit distinct differences in body size, the genetic mechanisms underlying this variation remain poorly understood. In this study, we performed whole-genome resequencing and transcriptome analysis on EM and HB pigs to elucidate the genetic basis of body size variation in Min pigs through genome-wide selection signal analysis and the identification of differentially expressed genes (DEGs). The analysis of genetic diversity and population genetic structure across 14 pig breeds revealed that, compared with other breeds, Min pigs present relatively high genetic diversity and a unique genetic structure. Notably, EM pigs exhibited significant genetic differentiation from HB pigs. Integrated analysis of whole-genome resequencing and transcriptome data revealed candidate genes associated with body size variation in Min pigs, including ENPP1, ENPP3, SPP1, CLU, ITGA11, ITGB1, IQGAP2, BMP7, and F2RL2. These genes are enriched primarily in pathways related to ECM-receptor interactions; pantothenate and CoA biosynthesis; starch and sucrose metabolism; nicotinate and nicotinamide metabolism; pyrimidine metabolism; nucleotide metabolism; cellular responses to lipids; biomineral tissue development; biomineralization; and other pathways related to cell signaling, metabolic responses, lipid deposition, and skeletal development. Notably, ITGB1 on chromosome 10 showed strong positive selection in EM pigs, with an SNP locus exhibiting a significant G/A allele frequency difference between EM pigs (G = 52.94%, A = 47.06%) and HB pigs (G = 0%, A = 100%). Our findings suggest that Min pigs potentially modulate lipid metabolism efficiency in adipose tissue through variations in the expression of the ITGB1 gene, potentially contributing to body size differences. These results provide new insights into the genetic mechanisms underlying body size variation in domestic pigs and serve as a valuable reference for identifying and breeding pig breeds with distinct body sizes.

Influence of MHC on genetic diversity and testicular expression of linked olfactory receptor genes

BACKGROUND

Olfactory receptor (OR) genes are highly polymorphic and form extensive families that recognize a wide range of vertebrate odorants. To explore the genetic diversity of MHC-linked OR genes and their connection to MHC genes, we conducted a combined haplotype analysis of MHC-linked OR and MHC class I genes to determine the influence of MHC on OR diversity, which could be associated with MHC-based mate selection.

RESULTS

We selected nine MHC-linked OR genes based on their expression levels in pig testes and developed a sequence-based typing method for these genes. We then performed high-resolution typing of these OR genes, along with three major classical MHC class I genes (SLA-1, -2, and - 3), in 48 pigs across six breeds. We observed significantly higher allelic diversity (P < 0.01) in ORs with strong linkage disequilibrium (LD) to SLA compared to those with weak or no LD, and we identified 48 SLA class I-OR haplotypes using the expectation-maximization algorithm. The genetic diversity of SLA-linked ORs was positively correlated with their expression levels in the testis. Specifically, SLA-linked ORs with higher testicular expression (FPKM ≥ 0.1) exhibited an increase in the number of codons under mutually diversifying selection with SLA compared to those with lower expression (FPKM < 0.1).

CONCLUSIONS

The presence of evolutionary interactions between MHC and linked OR genes supports the potential involvement of MHC-linked ORs in MHC-based mate selection. The use of combined haplotype information for MHC and linked ORs could provide new insights into the reproductive biology of animals.

Genome-wide association analysis and KASP markers development for protein quality traits in winter wheat

BACKGROUND

Wheat (Triticum aestivum L.) is a significant cereal crop that plays a vital role in global food production. To expedite the breeding of wheat cultivars with high protein quality, it is necessary to genetically analyze the traits related to quality. A genome-wide association study (GWAS) was conducted to identify the genomic regions responsible for protein quality traits in winter wheat.

RESULTS

Six protein quality traits were evaluated across two locations and two years for a total of 341 wheat accessions. Utilizing the wheat 40 K SNP array, GWAS identified 97 significantly stable SNPs at 43 loci for five out of six protein quality traits using a linear mixed model. The 43 loci distribution was four for grain protein content, two for flour protein content, one for wet gluten content, four for gluten index, and thirty-two for Zeleny sedimentation value. The most significant associations were identified on chromosomes 1 A, 1B, and 1D. Haplotype analysis of loci associated with the gluten index in the 412-416 Mb interval on chromosome 1D identified three blocks. Accessions with superior haplotypes showed a significantly higher gluten index than those with inferior haplotypes. Six KASP markers were successfully developed for the gluten index, while five KASP markers were developed for the Zeleny sedimentation value. Additionally, eight candidate genes were identified that may affect protein accumulation during grain development.

CONCLUSIONS

Our study identified 97 SNPs significantly associated with protein quality traits; developed 6 KASP markers for gluten index, and 5 KASP markers for Zeleny sedimentation values; screened 8 candidate genes that may be related to protein quality during grain development. Thise research will offer valuable insights for wheat breeding programs in China and globally.

Relationship of Neurotropin-3 Gene Polymorphism with Cognitive Impairment in Bipolar Disorder

Background

Neurotropin-3 (NT-3), a marker of neural plasticity, is reported to be altered in bipolar disorder (BD). This study was designed to evaluate NT-3 gene polymorphism (rs 6489630, rs 6332, and rs 11063714) in BD and its association with disease severity and cognition.

Methods

The study included 176 BD cases and 176 controls. All the participants were tested for NT-3 polymorphism and plasma NT-3. ACE-III scores were used to analyze cognition.

Results

The NT-3 polymorphism (rs 6489630) was associated with cognitive impairment in BD (P = .010). The attention score was found to be decreased in the CT genotype (P = .028) when compared to the CC and TT genotypes of the rs6489630 variant. The visuospatial ability score was decreased in the GG genotype (P = .044) compared to the AG genotype of the rs11063714 variant. BD patients with the maniac episode showed a decrease in levels of Neurotrophin-3 in comparison to both the control group (P = .045) and the remission group (P = .017). Plasma NT-3 was associated with the YMRS (r = -0.221, P = .003), HDRS (r = 0.209, P = .005) and visuospatial ability score (r = 0.180, P = .017) in patients with BD.

Conclusion

Single nucleotide polymorphisms of NT-3 are associated with cognitive dysfunction in BD.

Genome-wide association mapping and genomic prediction analyses reveal the genetic architecture of grain yield and agronomic traits under drought and optimum conditions in maize

BACKGROUND

Drought is a major abiotic stress in sub-Saharan Africa, impacting maize growth and development leading to severe yield loss. Drought tolerance is a complex trait regulated by multiple genes, making direct grain yield selection ineffective. To dissect the genetic architecture of grain yield and flowering traits under drought stress, a genome-wide association study (GWAS) was conducted on a panel of 236 maize lines testcrossed and evaluated under managed drought and optimal growing conditions in multiple environments using seven multi-locus GWAS models (mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB, ISIS EM-BLASSO, and FARMCPU) from mrMLM and GAPIT R packages. Genomic prediction with RR-BLUP model was applied on BLUEs across locations under optimum and drought conditions.

RESULTS

A total of 172 stable and reliable quantitative trait nucleotides (QTNs) were identified, of which 77 are associated with GY, AD, SD, ASI, PH, EH, EPO and EPP under drought and 95 are linked to GY, AD, SD, ASI, PH, EH, EPO and EPP under optimal conditions. Among these QTNs, 17 QTNs explained over 10% of the phenotypic variation (R2 ≥ 10%). Furthermore, 43 candidate genes were discovered and annotated. Two major candidate genes, Zm00001eb041070 closely associated with grain yield near peak QTN, qGY_DS1.1 (S1_216149215) and Zm00001eb364110 closely related to anthesis-silking interval near peak QTN, qASI_DS8.2 (S8_167256316) were identified, encoding AP2-EREBP transcription factor 60 and TCP-transcription factor 20, respectively under drought stress. Haplo-pheno analysis identified superior haplotypes for qGY_DS1.1 (S1_216149215) associated with the higher grain yield under drought stress. Genomic prediction revealed moderate to high prediction accuracies under optimum and drought conditions.

CONCLUSION

The lines carrying superior haplotypes can be used as potential donors in improving grain yield under drought stress. Integration of genomic selection with GWAS results leads not only to an increase in the prediction accuracy but also to validate the function of the identified candidate genes as well increase in the accumulation of favorable alleles with minor and major effects in elite breeding lines. This study provides valuable insight into the genetic architecture of grain yield and secondary traits under drought stress.

Development and application of a cGPS 20K liquid-phase SNP microarray in Jiaji ducks

In order to provide a low-cost, high efficient, and highly accurate tool for molecular breeding of Jiaji ducks, we constructed a cGPS(Genotyping by Pinpoint Sequencing of captured targets) 20 K liquid-phase microarray using resequencing data from this valuable poultry breed for the first time. The microarray contains 20,327 high-quality snp loci, mainly from the 30 Jiaji duck resequencing samples collected in this study, and some loci were supplemented from the 135 duck resequencing data from KUNMING INSTITUTE OF ZOOLOGY.CAS. This microarray showed excellent performance in two production tests. The microarray was used to genotype a population of 236 Jiaji ducks, and the genotyping data were then used for population structure analysis and genome-wide association studies (GWAS) of plumage color phenotypes. According to the population structure analysis, the population of Jiaji ducks could be divided into four subpopulations using genetic distance matrices. Using GWAS analysis, 38 significant SNP loci were identified within a region on chromosome 14 that contained 30 genes. Among them, EDNRB2 and VAMP7 were identified as strong candidate genes for the regulation of plumage color in Jiaji ducks. Two mutations upstream of EDNRB2 were identified as tightly linked to the colorless phenotype. In addition, two KASP markers were designed for the SNP loci associated with EDNRB2 (HIC_SCAFFOLD_14_14984620, HIC_SCAFFOLD_14_15016766). The KASP genotyping results showed strong correlations between different genotypes on the SNP locus HIC_SCAFFOLD_14_15016766 and the plumage phenotype. In conclusion, this independently designed microarray will be useful for large-scale genotyping and can lay the foundation for future screening of mutation loci and functional genes.

The role of SELE gene polymorphism in ST-elevation myocardial infarction

Ischemic heart disease (IHD) is an important medical and social problem. ST-elevation myocardial infarction (STEMI) is the most severe form of IHD, affecting all layers of the heart muscle. One of the diagnostic criteria for endothelial dysfunction in myocardial infarction is the level of sE-selectin, a cell adhesion molecule that recruits neutrophils and induces neutrophil inflammation. The aim of this study is to investigate intronic polymorphisms rs5353, rs3917412 and rs1534904 of the E-selectin coding gene SELE in patients with STEMI. We have analyzed a group of patients with STEMI (n = 74) and a population sample of Tomsk (n = 136) as the control group. The frequencies of the rs5353 genotypes in the SELE gene have shown statistically significant differences between patients and the control sample (p = 0.004). The CC genotype is a predisposing factor to STEMI (OR = 6.93, CI:95 % (1.84-26.04), χ2 = 8.69, p = 0.002). The analyzed markers were not studied previously in cardiovascular diseases (CVDs) and were rarely involved in association studies at all; there is no information on these SNPs in the leading databases. At the same time, all three variants, according to the RegulomeDB classification, belong to the functional class 1f, and are highly likely to have regulatory potential relative not only to the SELE gene, but also to other genes in the nearby region. The analysis of the functional significance of the studied markers has shown the presence of a region more extensive than one gene, which is co-regulated by the studied nucleotide substitutions. The association of rs5353 with STEMI identified in this study once again confirms the involvement of the SELE gene in the pathogenesis of CVDs. It is possible that this entire region of the genome may be involved indirectly in the pathogenesis of CVD through the systems of inflammation, immune response and DNA repair.

Ovalbumin gene polymorphism: Implications for hatchability and egg quality changes during storage in Japanese quail

The aim of the study was to identify polymorphisms in the ovalbumin gene - SERPINB14 gene and evaluate their effect on hatchability traits and egg quality changes during storage in two strains of Japanese quails: meat-type (F33) and laying-type (S22). To individually determine hatchability traits for each female, eggs were collected and incubated. To determine egg quality traits, 10 eggs were collected from each female and stored for 14 weeks. Egg quality was analyzed 10 times during storage. All exons and the 3'UTR of the SERPINB14 gene were sequenced. A total of 17 SNPs were identified in both strains: 4 in exons, 5 in the 3'UTR, and 8 in intron regions. Association analysis showed significant effects of SNP14 and SNP16 on the percentage of late died embryos. Fresh egg weight in F33 females was influenced by eight SNPs: SNP6, SNP7, SNP9, SNP11, SNP14, SNP15, SNP16, and SNP17, with significant diplotype effects observed. Individuals with H3H3 and H7H7 diplotypes showed the highest egg weight. SNPs 6, 7, and 11 influenced eggshell thickness on the laying day and at 2, 4, and 14 weeks of storage. The effects of haplotypes on this trait were also observed. Significant SNP effects were also found on albumen weight and albumen percentage at different storage times. Moreover, diplotypes from block 1 influenced albumen traits during storage. These studies provide new information on the SERPINB14 gene polymorphism in Japanese quail, and some of the markers merit further validation as useful tools for selection to improve hatchability and egg quality in poultry breeding programs.

Functional analysis of key members affecting egg production in the transglutaminase gene family in chickens

The transglutaminase (TGMs) family plays a crucial role in regulating mammalian reproduction, yet its impact on poultry reproductive traits has not been extensively studied. In this study, we identified eight members of the TGMs family in chickens and examined the contributions of genetic variations of coagulation factor XIII A chain (F13A1), transglutaminase 4 (TGM4), and LOC101749664 to selective breeding in commercial layers through genetic variation response pattern analysis. Transcriptome data from various tissues of high- and low-egg-yielding Gushi chickens revealed significant positive correlations between the mRNA expression levels of TGM4 and F13A1 genes and egg production (P < 0.05). Genotype-phenotype correlation analysis showed that 26 single nucleotide polymorphisms (SNPs) within genomic sequences of TGM4 and F13A1 genes exhibited significant associations with egg production traits across different laying periods. Additionally, spatiotemporal expression patterns of TGM4 in ovarian follicles between high- and low-laying chicken breeds determined by RT-qPCR highlighted the pivotal role of TGM4 in follicle development. Functionally, the gain-of-function assay demonstrated that TGM4 promoted granulosa cell proliferation, inhibited apoptosis, and enhanced progesterone synthesis. In conclusion, this is the first study to elucidate the role of the TGMs gene family in regulating egg production in chickens, offering new insights for the selective breeding of layers with improved egg-laying traits.

The link between the ANPEP gene and type 2 diabetes mellitus may be mediated by the disruption of glutathione metabolism and redox homeostasis

Aminopeptidase N (ANPEP), a membrane-associated ectoenzyme, has been identified as a susceptibility gene for type 2 diabetes (T2D) by genome-wide association and transcriptome studies; however, the mechanisms by which this gene contributes to disease pathogenesis remain unclear. The aim of this study was to determine the comprehensive contribution of ANPEP polymorphisms to T2D risk and annotate the underlying mechanisms. A total of 3206 unrelated individuals including 1579 T2D patients and 1627 controls were recruited for the study. Twenty-three common functional single nucleotide polymorphisms (SNP) of ANPEP were genotyped by the MassArray-4 system. Six polymorphisms, rs11073891, rs12898828, rs12148357, rs9920421, rs7111, and rs25653, were found to be associated with type 2 diabetes (Pperm ≤ 0.05). Common haplotype rs9920421G-rs4932143G-rs7111T was strongly associated with increased risk of T2D (Pperm = 5.9 × 10-12), whereas two rare haplotypes such as rs9920421G-rs4932143C-rs7111T (Pperm = 6.5 × 10-40) and rs12442778A-rs12898828A-rs6496608T-rs11073891C (Pperm = 1.0 × 10-7) possessed strong protection against disease. We identified 38 and 109 diplotypes associated with T2D risk in males and females, respectively (FDR ≤ 0.05). ANPEP polymorphisms showed associations with plasma levels of fasting blood glucose, aspartate aminotransferase, total protein and glutathione (P < 0.05), and several haplotypes were strongly associated with the levels of reactive oxygen species and uric acid (P < 0.0001). A deep literature analysis has facilitated the formulation of a hypothesis proposing that increased plasma levels of ANPEP as well as liver enzymes such as aspartate aminotransferase, alanine aminotransferase and gammaglutamyltransferase serve as an adaptive response directed towards the restoration of glutathione deficiency in diabetics by stimulating the production of amino acid precursors for glutathione biosynthesis.

Lipidomics-based association study reveals genomic signatures of anti-cancer qualities of pigmented rice sprouts

Introduction

The genetic wealth present in pigmented rice varieties offer abundant variation in different sources of antioxidants to meet nutritional security targets among rice-consuming communities. There is limited knowledge of the dynamic changes in the lipidome of rice during germination and the corresponding genes associated with the antioxidant and anti-cancerous properties of lipophilic fractions of pigmented rice sprouts (PRS).

Methods

In this study, we profiled the lipidome of diverse pigmented rice collections of germinated sprouts. Further, we employed Genome-wide association studies (GWAS), gene-set analysis, and targeted association analysis to identify the candidate genes linked to these lipids.

Results

The genetic analyses revealed 72 candidate genes involved in the regulation of these accumulating lipids in PRS. Marker trait associations (MTA) analysis shown that the combination GGTAAC/ACAAGCTGGGCCC was associated with increased levels of unsaturated lipids and carotenoids, which likely underlie these beneficial effects. This superior MTA combination exhibited potent inhibitory activity against HCT116 and A549 cell lines, with average 1/IC50 values of 0.03 and 0.02 (mL/μg), respectively, compared to the inferior MTAs.

Discussion

Collectively, our findings demonstrate that MTAs linked to selected GDSL esterase/lipase (GELP) genes, OsACP1, and lecithin-cholesterol acyltransferase significantly enhance antioxidant and anti-cancer properties, potentially through the mobilization of unsaturated lipids and carotenoids during germination. This study offers valuable insights into the health-promoting potential of germinated rice sprouts as a rich dietary source of antioxidants beneficial to human health.

Novel candidate genes and genetic basis analysis of kernel starch content in tropical maize

BACKGROUND

Starch is the most abundant carbohydrate in maize grains, serving as a primary energy source for both humans and animals, and playing a crucial role in various industrial applications. Increasing the starch content of maize grains is beneficial for improving the grain yield and quality. To gain insight into the genetic basis of starch content in maize kernels, a multiparent population (MPP) was constructed and evaluated for starch content in three different environments.

RESULTS

The integration of QTL mapping and genome-wide association analysis (GWAS) identified two SNPs, 8_166371888 and 8_178656036, which overlapped the QTL interval of qSC8-1, identified in the tropical maize line YML46. The phenotypic variance explained (PVE) by the QTL qSC8-1 was12.17%, while the SNPs 8_166371888 and 8_178656036 explained 10.19% and 5.72% of the phenotypic variance. Combined GWAS and QTL analyses led to the identification of two candidate genes, Zm00001d012005 and Zm00001d012687 located on chromosome 8.

CONCLUSIONS

The candidate gene Zm00001d012005 encodes histidine kinase, which is known to play a role in starch accumulation in rice spikes. Related histidine kinases, such as AHK1, are involved in endosperm transfer cell development in barley, which affects grain quality. Zm00001d012687 encodes triacylglycerol lipase, which reduces seed oil content. Since oil content in cereal kernels is negatively correlated with starch content, this gene is likely involved in regulating the starch content in maize kernels. These findings provide insights into the genetic mechanisms underlying kernel starch content and establish a theoretical basis for breeding maize varieties with high starch content.

Deciphering of Genomic Loci Associated with Alkaline Tolerance in Soybean [Glycine max (L.) Merr.] by Genome-Wide Association Study

Alkaline stress is one of the major abiotic constraints that limits plant growth and development. However, the genetic basis underlying alkaline tolerance in soybean [Glycine max (L.) Merr.] remains largely unexplored. In this study, an integrated genomic analysis approach was employed to elucidate the genetic architecture of alkaline tolerance in a diverse panel of 326 soybean cultivars. Through association mapping, we detected 28 single nucleotide polymorphisms (SNPs) significantly associated with alkaline tolerance. By examining the genomic distances around these significant SNPs, five genomic regions were characterized as stable quantitative trait loci (QTLs), which were designated as qAT1, qAT4, qAT14, qAT18, and qAT20. These QTLs are reported here for the first time in soybean. Seventeen putative candidate genes were identified within the physical intervals of these QTLs. Haplotype analysis indicated that four of these candidate genes exhibited significant allele variation associated with alkaline tolerance-related traits, and the haplotype alleles for these four genes varied in number from two to four. The findings of this study may have important implications for soybean breeding programs aimed at enhancing alkaline tolerance.

Functionally-informed fine-mapping identifies genetic variants linking increased CHD1L expression and HIV restriction in monocytes

Human Immunodeficiency Virus Type 1 (HIV) set-point viral load is a strong predictor of disease progression and transmission risk. A recent genome-wide association study in individuals of African ancestries identified a region on chromosome 1 significantly associated with decreased HIV set-point viral load. Knockout of the closest gene, CHD1L, enhanced HIV replication in vitro in myeloid cells. However, it remains unclear if HIV spVL associated variants are associated with CHD1L gene expression changes. Here we apply a heuristic fine-mapping approach to prioritize combinations of variants that explain the majority of set-point viral load variance and identify variants likely driving the association. We assess the combined impact of these variants on CHD1L regulation using publicly available sequencing studies, and test the relationship between CHD1L expression and set-point viral load using imputed CHD1L expression from monocytes. Taken together, this work characterizes genetically regulated CHD1L expression and further expands our knowledge of CHD1L-mediated HIV restriction in monocytes.

Effect of FABP4 Gene Polymorphisms on Fatty Acid Composition, Chemical Composition, and Carcass Traits in Sonid Sheep

Fatty acids (FAs) are a group of organic compounds that are regulated by polygenic and environmental factors and affect the taste, nutritional value, and quality of meat. Lamb meat is rich in FAs required by the human body, which has directed more attention to sheep research and meat production. The fatty acid-binding protein 4 (FABP4) gene is considered a candidate gene that can affect FA composition in livestock. Therefore, the aim of this study was to screen for genetic polymorphisms of FABP4 and confirm the association between these polymorphisms and FAs, chemical composition, and carcass traits in Sonid lambs. The results of the association study showed that g.57764667T>C, g.57764436T>G, g.57764242G>A, and g.57757988A>G were associated with the composition of certain long-chain FAs, and g.57764242G>A, g.57764436T>G, and g.57758026G>A were associated with free amino acid levels. In addition, g.57764667T>C and g.57757988A>G were associated with carcass weight and live weight in Sonid lambs. Therefore, the polymorphisms of the FABP4 gene are expected to be a genetic selection marker for superior traits in Sonid sheep breeding, which also provides new insights into how the ovine FABP4 gene affects traits of lamb quality.

GWAS analysis revealed genomic loci and candidate genes associated with the 100-seed weight in high-latitude-adapted soybean germplasm

KEY MESSAGE

In the present study, we identified 22 significant SNPs, eight stable QTLs and 17 potential candidate genes associated with 100-seed weight in soybean. Soybean is an economically important crop that is rich in seed oil and protein. The 100-seed weight (HSW) is a crucial yield contributing trait. This trait exhibits complex inheritance regulated by many genes and is highly sensitive to environmental factors. In this study, an integrated strategy of association mapping, QTL analysis, candidate gene and haplotype analysis was utilized to elucidate the complex genetic architecture of HSW in a panel of diverse soybean cultivars. Our study revealed 22 SNPs significantly associated with HSW through association mapping using five GWAS models across multiple environments plus a combined environment. By considering the detection of SNPs in multiple environments and GWAS models, the genomic regions of eight consistent SNPs within the ± 213.5 kb were depicted as stable QTLs. Among the eight QTLs, four, viz. qGW1.1, qGW1.2, qGW9 and qGW16, are reported here for the first time, and the other four, viz. qGW4, qGW8, qGW17 and qGW19, have been reported in previous studies. Thirty-two genes were detected as putative candidates within physical intervals of eight QTLs by in silico analysis. Twelve genes (out of total 32) showed significant differential expression patterns among the soybean accessions with contrasting HSW. Moreover, different haplotype alleles of 10 candidate genes are associated with different phenotypes of HSW. The outcome of the current investigation can be used in soybean breeding programs for producing cultivars with higher yields.