SNP Loci Research Articles

Development of a panel of SNP loci in the emblematic southern damselfly (Coenagrion mercuriale) using a hybrid method: pitfalls and recommendations for large-scale SNP genotyping in a non-model endangered species.

Genomic markers are essential tools for studying species of conservation concern, yet non-model species often lack a reference genome. Here we describe a methodology for identifying and genotyping thousands of SNP loci in the southern damselfly (Coenagrion mercuriale), a bioindicator of freshwater stream quality classified as near-threatened, with locally declining populations. We used a hybrid approach combining reduced representation sequencing and target enrichment. First, we identified putative SNP loci using ddRADseq and de novo assembly. Then, single primer enrichment technology targeted 6,000 of these SNPs across 1,920 individuals. Challenges encountered included sequence recapture failure, coverage depth discrepancies, and aberrant FIS values. We provide recommendations to address such issues. After multiple filtering steps, 2,092 SNPs were retained and used to analyse the genetic structure of 131 individuals belonging to 11 populations in France, comparing central and marginal populations. Genetic differentiation was lower among central populations, with no sign of inbreeding. As compared to microsatellite loci, SNPs exhibited greater resolution in detecting fine-scaled genetic structure, identifying putative hybrids in adjacent populations. In this study, we emphasise the difficulties of large-scale SNP genotyping in non-model species via a hybrid method that ultimately did not offer the expected cost and time saving compared to classical ddRAD approaches. However, SNPs showed greater power than previously available markers in identifying conservation units or admixture events, and the panel of reusable probes we describe here offers the potential to improve conservation efforts through future diachronic studies or finer estimations of key parameters like effective population size.

Genetic Diversity Analysis and Identification of Candidate Genes for Growth Traits in Chengkou Mountain Chicken.

Growth traits constitute critical factors in the breeding program of broiler chickens. The Chengkou mountain chicken A-lineage (CMC-A) represents a breed specifically bred for meat production. To further explore the growth performance of the CMC-A population, this study conducted whole-genome sequencing on 464 CMC-A roosters to systematically evaluate their genetic diversity. Additionally, runs of homozygosity (ROH) islands and genome-wide association studies (GWASs) were employed to identify the loci and functional genes influencing the growth traits in Chengkou mountain chickens. The results revealed a high level of genetic diversity and low levels of inbreeding in Chengkou mountain chickens. Several genes associated with stress resistance, muscle growth, and fat deposition were pinpointed through ROH island identification. Moreover, 52 SNP loci were detected, along with 71 candidate genes. These findings enhance our understanding of the genetic architecture underlying the growth traits in Chengkou mountain chickens and provide a theoretical foundation for subsequent breeding endeavors.

Mapping an avirulence gene in the sunflower parasitic weed Orobanche cumana and characterization of host selection based on virulence alleles

BackgroundSunflower broomrape (Orobanche cumana Wallr.) is a holoparasitic plant that jeopardizes sunflower production in most areas of Europe and Asia. Recently, populations with increased virulence, classified as race GGV, have been identified in Southern Spain’s Guadalquivir Valley gene pool. These populations overcome resistance genes in hybrids resistant to the predominant race FGV. This study aimed to (i) determine the inheritance and map the avirulence trait segregating in a cross between O. cumana individuals from populations EK23 (FGV) and IN201 (GGV), and (ii) characterize the host effect on the IN201 parental population allelic diversity.ResultsA segregating population consisting of 144 F2:3 families was evaluated for virulence using a differential sunflower genotype (Hybrid 1, resistant to race FGV and susceptible to race GGV) and genotyped with SNP markers. The ratio of avirulent to virulent F2:3 families was not significantly different to 1:3 (χ2 = 0.93; P = 0.34), indicating monogenic control of the avirulence/virulence trait. The AvrG−GV locus was mapped on the upper end of O. cumana chromosome 2, 9.2 cM distal from the SNP markers OS04791 and OS02805. Secretome analysis in the AvrG−GV region revealed a cysteine-rich CAP superfamily- and a glucan 1,3-beta-glucosidase family 3-encoding genes as possible candidates for AvrG−GV. SNP allelic analysis on the IN201 population parasitizing a highly susceptible genotype or the differential genotype Hybrid 1 showed that (i) IN201 structure was shaped towards virulent alleles at SNP loci linked to AvrG−GV (ii) there were significant allelic frequency differences associated with the host genotype at AvrG−GV–linked loci.ConclusionsThis study mapped for the first time an avirulence gene in parasitic plants using a classical genetic approach, confirmed a gene-for-gene model in the O.cumana –sunflower system, and showed the implication of this single avirulence gene in determining the structure of broomrape populations subjected to selection pressure posed by a resistant genotype. The results will contribute to a better understanding of the interaction between crops and weedy parasitic plants, and to effectively manage evolution of virulence by sustainable control strategies based on host genetic resistance.

Comprehensive Morphological and Molecular Insights into Drought Tolerance Variation at Germination Stage in Brassica napus Accessions.

Drought constitutes a noteworthy abiotic stressor, detrimentally impacting seed germination, plant development, and agricultural yield. In response to the threats imposed by climate change and water paucity, this study examined the morphological divergence and genetic governance of drought resilience traits at the germination stage in 196 rapeseed (Brassica napus L.) lines under both normal (0 MPa) and drought-induced stress (-0.8 MPa) scenarios. Our study showed that the composite drought tolerance D value is a reliable index for identifying drought resilience. Through a genome-wide association study (GWAS), we uncovered 37 significant SNP loci and 136 putative genes linked to drought tolerance based on the D value. A key discovery included the gene BnaA01g29390D (BnNCED3), encoding 9-cis-epoxycarotenoid dioxygenase, which exhibited significantly heightened expression levels in drought-resistant accessions (p < 0.01), underscoring its potential as a positive drought stress regulator and a suitable candidate for genetically enhancing drought resilience. Moreover, we pinpointed four stress-reactive transcription factors (BnaA07g26740D, BnaA07g26870D, BnaA07g26910D, and BnaA07g26980D), two E3 ubiquitin-protein ligases (BnaA05g22900D and BnaC06g28950D), two enzymes (BnaA01g29390D and BnaA03g48550D), and two photosystem-associated proteins (BnaA05g22950D and BnaC06g28840D) as vital components in drought response mechanisms. The construction of a regulatory network reveals an ABA-dependent pathway (NCED3/RGLG5/IDD14) that contributes to drought tolerance in rapeseed seedlings, alongside the involvement of a drought avoidance strategy (APRR6/PHYB). The SNPs and genes unveiled in this study offer a substantial theoretical foundation for subsequent investigations targeting genetic improvement for drought resilience during seed germination in rapeseed.

Screening of SNP Loci Related to Leg Length Trait in Leizhou Goats Based on Whole-Genome Resequencing.

Leizhou goats can be classified into tall and short types based on their size and habits. The tall Leizhou goats are well-suited for grazing management due to their robust physique, while the dwarf types are smaller, grow rapidly, and are more appropriate for feeding management systems. In this study, whole-genome resequencing was conducted to identify genomic variants in 15 Tall-legged (TL) and 15 Short-legged (SL) Leizhou goats, yielding 8,641,229 high-quality SNPs in the Leizhou goat genome. Phylogenetic tree and principal component analyses revealed obvious genetic differentiation between the two groups. Fst and θπ analyses identified 420 genes in the TL group and 804 genes in the SL group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that the phosphatidylinositol signaling system is associated with growth and development. Additionally, Genome-Wide Association Study (GWAS) analysis identified eight genes linked to leg length, including B4GALT7 and NR1D1. Notably, the NC_030818.1 (g.53666634T > C) variant was significantly associated with leg length traits, where the CC genotype was linked to shorter legs and the TT genotype to longer legs. This study identifies candidate genes and molecular markers, serving as a reference point for breeding and genetic improvement efforts in Leizhou goats and other goat breeds.

Abstract 4121042: Novel genetic risk loci of arterial stiffness in Asian ancestry individuals

Background: Arterial stiffness serves as an independent predictor of cardiovascular disease risk. Pulse-wave velocity (PWV) is a non-invasive measurement of arterial stiffness. However, the genetic risk variants associated with arterial stiffness in the Asian ancestry population remain largely unknown. This lack of knowledge hinders the development of targeted preventive and treatment strategies. Hypothesis: Arterial stiffness is associated with genotyped SNP loci that have genetic relationships with metabolic syndrome phenotypes. Methods: For PWV, we performed genome-wide association study and gene-based genetic association study in 912 individuals from the Tongji-BGI research cardiovascular health (TORCH) cohort. We then used linkage disequilibrium score regression to estimate pairwise genetic correlations between arterial stiffness, blood pressure, lipids, and diabetes. Results: Eleven risk loci associated with arterial stiffness were discovered at genome-wide significance ( P &lt; 5 × 10 −8 ), including three in intronic (rs978453410 mapping to PPP2R5E; rs146270927 mapping to ECI1; rs189517402 mapping to CNN2 ). UBE2U and ECI1 were identified as the PWV-associated genes by gene-based analysis. Genetic correlation analyses revealed inter-related of PWV with systolic blood pressure, mean arterial pressure, total cholesterol and diabetes. Conclusions: This research firstly identified eleven novel genetic variants associated with arterial stiffness in Asian ancestry individuals. Further research aimed at reducing arterial stiffness may benefit from the identification of SNPs and genes like ECI1, which is related to the oxidation of unsaturated fatty acids in the mitochondria.

A genome-wide association study of the racing performance traits in Yili horses based on Blink and FarmCPU models

Racing performance traits are the main indicators for evaluating the performance and value of sport horses. The aim of this study was to identify the key genes for racing performance traits in Yili horses by performing a genome-wide association study (GWAS). Breeding values for racing performance traits were calculated for Yili horses (n = 827) using an animal model. Genome-wide association analysis of racing performance traits in horses (n = 236) was carried out using the Blink, and FarmCPU models in GAPIT software, and genes within the significant regions were functionally annotated. The results of GWAS showed that a total of 24 significant SNP markers (P < 6.05 × 10− 9) and 22 suggestive SNP markers (P < 1.21 × 10− 7) were identified. Among them, the Blink associated 16 significant SNP loci and FarmCPU associated 12 significant SNP loci. A total of 127 candidate genes (50 significant) were annotated. Among these, CNTN6 (motor coordination), NIPA1 (neuronal development), and DCC (dopamine pathway maturation) may be the main candidate genes affecting speed traits. SHANK2 (neuronal synaptic regulation), ISCA1 (mitochondrial protein assembly), and KCNIP4 (neuronal excitability) may be the main candidate genes affecting ranking score traits. A common locus (ECA1: 22698579) was significantly associated with racing performance traits, and the function of the genes at this locus needs to be studied in depth. These findings will provide new insights into the detection and selection of genetic variants for racing performance and will help to accelerate the genetic improvement of Yili horses.

Parental Reconstruction from a Half-Sib Population of Stoneless Jujube Ziziphus jujuba Mill. Based on Individual Specific SNP Markers Using Multiplex PCR.

The selection of unique and individual-specific SNPs is important as compared with universal SNPs for individual identification. Therefore, the main significance of this research is the selection of specific SNPs in male parent and the identification of offspring with these specific SNPs in their genome by multiplex PCR, which is utilized for genotyping of 332 half-sib plants of Ziziphus jujuba.This cost-effective method makes as much as possible to utilize the same amount of each pair of various targeted loci primers. After PCR amplification of targeted genome parts, the mixed products can be directly used in a next-generation sequencing platform. We concomitantly amplified 10 unique SNP loci at 10 different chromosomes of male JingZao 39 plants in 332 half-sib plants and sequenced them on the Illumina Novaseq 6000 platform. Analysis of SNP genotyping accuracy of 332 half-sib plants showed that all 10 unique SNPs in all 332 plants were correctly amplified in this multiplex PCR method. Furthermore, based on Mendelian inheritance, we identified 124 full-sib plants that have 10 unique SNPs in their genomes. These results were further confirmed by whole genome resequencing of 82 randomly selected half-sib plants, and the identity-by-descent values of all full-sib plants were between 0.4399 to 0.5652. This study displayed a cost-effective multiplex PCR method and proper identification of pollen parent through specific SNPs in half-sib progenies and firstly obtained a full-sib population between 'Wuhezao' and 'JingZao 39', segregating for stone and stoneless fruit.

Human Impacts on Great Lakes Walleye Sander vitreus Structure, Diversity and Local Adaptation.

Artificial propagation and wild release may influence the genetic integrity of wild populations. This practice has been prevalent in fisheries for centuries and is often termed 'stocking'. In the Laurentian Great Lakes (Great Lakes here-on), walleye populations faced declines from the 1950s to the 1970s, prompting extensive stocking efforts for restoration. By the mid-2010s, walleye populations showed signs of recovery, but the genetic legacy of stocking on population structure at the genomic level remains unclear. Using a dataset of 45,600 genome-aligned SNP loci genotyped in 1075 walleye individuals, we investigated the genetic impacts of over 50 years of stocking across the Great Lakes. Population structure was associated with both natural geographic barriers and stocking from non-native sources. Admixture between Lake Erie walleye and walleye from the re-populated Tittabawassee River indicate that stocking may have re-distributed putatively adaptive alleles around the Great Lakes. Genome scans identified FST outliers and evidence of selective sweeps, indicating local adaptation of spawning populations is likely. Notably, one genomic region showed strong differentiation between Muskegon River and walleye from the Tittabawassee River, which was re-populated by Muskegon strain walleye, suggesting admixture and selection both impact the observed genetic diversity. Overall, our study underscores how artificial propagation and translocations can significantly alter the evolutionary trajectory of populations. The findings highlight the complex interplay between stocking practices and population genetic diversity, emphasising the need for careful management strategies to preserve the genetic integrity of wild populations amidst conservation efforts.

Genome-wide association study integrated with transcriptome analysis to identify boron efficiency-related candidate genes and favorable haplotypes in Brassica napus L.

Rapeseed (Brassica napus L.) is a major oil crop worldwide that is vigorously promoted for cultivation in China. Boron (B) is an essential micronutrient for plant growth and development. However, agricultural soils in rapeseed planting areas often show either B deficiency or severe B deficiency. Increasing the resistance to B deficiency is a pivotal goal in the breeding of rapeseed, yet the genetic basis for variations in B efficiency-related traits remains unclear. In this study, a natural population with 391 rapeseed accessions was used to investigate B efficiency-related traits through a nutrient solution system, including relative root length (RRL), shoot dry weight (SDW), root dry weight (RDW), and B efficiency coefficient (BEC), which exhibited extensive phenotypic variations under B deficiency. Through a genome-wide association study (GWAS) of B efficiency-related traits using high-density SNP markers obtained from whole-genome resequencing, we identified 106 significantly associated SNPs by employing both the general linear model and the mixed linear model. Among these SNP loci, two prominent SNP clusters were detected on chrA03:14087835–14764672 and chrC03:20110319–22135492 at low B level across three repeated experiments of multiple traits. Integrated with the transcriptome analysis, four genes, BnaA03g29020D, BnaA03g29440D, BnaC03g33010D, and BnaC03g34490D, exhibiting higher differentially expressed fold-change along with favorable haplotypes within the promoter or coding region were identified as candidate genes that could potentially be involved in B efficient utilization, and their favorable haplotypes improved seedling growth and productivity under B deficiency. In view of the lack of B mineral resources in China, rapid and accurate identification of more B-efficient alleles and the study of the genetic mechanism underlying crops in response to B deficiency have important theoretical and practical significance for cultivating B-efficient varieties and maintaining green, sustainable agriculture quickly and accurately.1

Causal Effects of Rheumatoid Arthritis, Ankylosing Spondylitis, Juvenile Idiopathic Arthritis on Psoriasis: A Mendelian Randomization Study.

It is well-documented that rheumatoid arthritis (RA), ankylosing spondylitis (AS), and juvenile idiopathic arthritis (JIA) often exhibit skin manifestations, with psoriasis typically occurring around the time of diagnosis. Thus, it is essential to investigate the potential causal relationship between these forms of arthritis and psoriasis. The OpenGWAS provided traitIDs for exposure factors (RA (bbj-A-74), AS (ebi-A-GCST005529), and JIA (finn-b-JUVEN-ARTHR)) and outcome (psoriasis, finn-b-L12-PSORIASIS). bbj-A-74had 19,190 samples (9,739,303 SNPs), ebi-A-GCST005529had 22,647 samples (99,962 SNPs), finn-b-JUVEN-ARTHR had 173,622 samples (16,380,296 SNPs), and psoriasis had 216,752 samples (16,380,464 SNPs). Initially, 57 RA SNPs, 25 AS SNPs, and 5 JIA SNPs were acquired. Causal links were explored via univariate Mendelian Randomization (UVMR) analysis, with sensitivity analyses ensuring reliability. Additionally, multivariate MR (MVMR) analysis was conducted to further estimate the effect of each exposure factor on psoriasis. Significant causal links (P < 0.05, OR > 1) were found between bbj-A-74, ebi-A-GCST005529, finn-b-JUVEN-ARTHR, and finn-b-L12-PSORIASIS, indicating associations of RA, AS, and JIA with psoriasis. Sensitivity analyses ensured the reliability of these finding, showing no heterogeneity, horizontal pleiotropy, or SNP locus oversensitivity in UVMR results. Furthermore, MVMR analysis revealed AS and JIA as psoriasis risk factors, while RA showed non-significant protective effects. This suggests AS and JIA may contribute to psoriasis onset or exacerbation when coexisting. MR analyses were conducted to investigate the causal links between RA, AS, JIA, and psoriasis, enhancing our grasp of the underlying mechanisms of psoriasis.

Association of SPP1 and NCAPG genes with milk production traits in Chinese Holstein cows: polymorphism and functional validation analysis.

Milk production traits play an important role in dairy cattle breeding, and single nucleotide polymorphisms can be used as effective molecular markers for milk production trait marker-assisted breeding in dairy cattle. Based on the results of the preliminary GWAS, candidate genes SPP1 and NCAPG associated with milk production traits were screened. In this study, the aim was to screen and characterize the SNPs of SPP1 and NCAPG genes about milk production traits. Two SNPs and one haplotype block of the SPP1 gene and four SNPs and one haplotype block of the NCAPG gene were obtained by amplification, sequencing and association analysis, and all six SNPs were located in the exon region. Association analysis showed that all six SNPs were significantly associated with milk protein percentage. Linkage disequilibrium analysis showed that 2 SNPs of SPP1 (g. 36,700,265 C > T and g. 36,693,596 C > A) constituted a haplotype that correlated with milk protein percentage, and the dominant haplotype was H2H2, which was CCTT. 4 SNPs of NCAPG (g. 37,342,705 C > A, g. 37,343,379 G > T, g. 37,374,314 C > A and g. 37,377,857 G > A) constituted a haplotype associated with milk protein percentage, 305-days milk protein yield and 305 days milk yield. Tissue expression profiling results revealed that SPP1 and NCAPG had the highest expression in mammary tissue. Interference with SPP1 and NCAPG inhibited the proliferation of Bovine mammary epithelial cells. (BMECs), down-regulated the expression of PCNA, CDK2 and CCND1, up-regulated the expression of BAX and BAD, and promoted apoptosis. Reduced triglyceride synthesis in BMECs, down-regulated the expression of DGAT1, DGAT2, LPIN1, and AGPAT6.SPP1 and NCAPG are involved in the synthesis of milk proteins, and interfering with SPP1 and NCAPG decreased the secretion of β-casein, κ-casein, and αs1-casein, as well as up-regulated the CSN2 and CSN3 expression. The above results indicate that the SNP loci of SPP1 and NCAPG can be used as potential molecular markers to improve milk production traits in dairy cows, laying the foundation for marker-assisted selection. It also proves that SPP1 and NCAPG can be used as candidate key genes for milk production traits in dairy cows, providing new insights into the physiological mechanisms of lactation regulation in dairy cows.

Study on the relationship between KCNQ1 gene-environment interaction and abnormal glucose metabolism in the elderly in a county of Hechi City, Guangxi.

This study aimed to understand the potassium voltage-gated channel KQT-like subfamily, member 1 gene polymorphism in a rural elderly population in a county in Guangxi and to explore the possible relationship between its gene polymorphism and blood sugar. The 6 SNP loci of blood DNA samples from 4355 individuals were typed using the imLDRTM Multiple SNP Typing Kit from Shanghai Tianhao Biotechnology Co. The data combining epidemiological information (baseline questionnaire and physical examination results) and genotyping results were statistically analyzed using GMDR0.9 software and SPSS22.0 software. A total of 4355 elderly people aged 60 years and above were surveyed in this survey, and the total abnormal rate of glucose metabolism was 16·11 % (699/4355). Among them, male:female ratio was 1:1·48; the age group of 60-69 years old accounted for the highest proportion, with 2337 people, accounting for 53·66 % (2337/4355). The results of multivariate analysis showed that usually not doing farm work (OR 1·26; 95 % CI 1·06, 1·50), TAG ≥ 1·70 mmol/l (OR 1·19; 95 % CI 1·11, 1·27), hyperuricaemia (OR 1·034; 95 % CI 1·01, 1·66) and BMI ≥ 24 kg/m2 (OR 1·06; 95 % CI 1·03, 1·09) may be risk factors for abnormal glucose metabolism. Among all participants, rs151290 locus AA genotype, A allele carriers (AA+AC) were 0.70 times more likely (0.54 to 0.91) and 0.82 times more likely (0.70 to 0.97) to develop abnormal glucose metabolism than CC genotype carriers, respectively. Carriers of the T allele at the rs2237892 locus (CT+TT) were 0.85 times more likely to have abnormal glucose metabolism than carriers of the CC genotype (0.72 to 0.99); rs2237897 locus CT gene. The possibility of abnormal glucose metabolism in the carriers of CC genotype, TT genotype and T allele (CT + TT) is 0·79 times (0·67-0·94), 0·74 times (0·55-0·99) and 0·78 times (0·66, 0·92). The results of multifactor dimensionality reduction showed that the optimal interaction model was a three-factor model consisting of farm work, TAG and rs2237897. The best model dendrogram found that the interaction between TAG and rs2237897 had the strongest effect on fasting blood glucose in the elderly in rural areas, and they were mutually antagonistic. Environment-gene interaction is an important factor affecting abnormal glucose metabolism in the elderly of a county in Hechi City, Guangxi.

Using eDNA to Supplement Population Genetic Analyses for Cryptic Marine Species: Identifying Population Boundaries for Alaska Harbour Porpoises.

Isolation by distance and biogeographical boundaries define patterns of population genetic structure for harbour porpoise along the Pacific coast from California to British Columbia. Until recently, inadequate sample sizes in many regions constrained efforts to characterise population genetic structure throughout the coastal waters of Alaska. Here, tissue samples from beachcast strandings and fisheries bycatch were supplemented with targeted environmental DNA (eDNA) samples in key regions of Alaska coastal and inland waters. Using a geographically explicit, hierarchical approach, we examined the genetic structure of Alaska harbour porpoises, using both mitochondrial DNA (mtDNA) sequence data and multilocus SNP genotypes. Despite a lack of evidence of genetic differentiation from nuclear SNP loci, patterns of relatedness and genetic differentiation from mtDNA suggest natal philopatry at multiple geographic scales, with limited gene flow among sites possibly mediated by male dispersal. A priori clustering of sampled areas at an intermediate scale (eastern and western Bering Sea, Gulf of Alaska and Southeast Alaska) best explained the genetic variance (12.37%) among regions. In addition, mtDNA differentiation between the Gulf of Alaska and eastern Bering Sea, and among regions within the Gulf of Alaska, indicated significant genetic structuring of harbour porpoise populations in Southeast Alaska. The targeted collection of eDNA samples from strata within Southeast Alaska was key for elevating the statistical power of our mtDNA dataset, and findings indicate limited dispersal between neighbouring strata within coastal and inland waters. These results provide evidence supporting a population boundary within the currently recognised Southeast Alaska Stock. Together, these findings will prove useful for ongoing management efforts to reduce fisheries conflict and conserve genetic diversity in this iconic coastal species.

Correlation and regression analysis of FA2H and ELOVL3 functional genes for cashmere fineness with production performance in Liaoning cashmere goat

Liaoning cashmere goat (LCG) is characterized by the highest individual cashmere yield, but its cashmere fineness tends to be coarse. Therefore, our research primarily focuses on reducing cashmere fineness. Through lipidomics screening and identification, we identified the crucial functional genes FA2H and ELOVL3 associated with cashmere fineness. Subsequently, using PCR-seq, we conducted gene typing and SNP analysis on the experimental population DNA, In the FA2H gene, a SNP locus T42443G was detected in LCG buck, with the TT genotype showing advantageous traits in cashmere fineness, meat quality, and body size, while the TG genotype demonstrated advantages in slaughter performance,In LCG doe, the TG genotype shows advantageous traits in cashmere fineness, milk production, and meat quality, while the TT genotype exhibits advantages in slaughter performance, lambing, and body size. In the ELOVL3 gene, a SNP locus C2133A was identified in LCG buck, where the CC genotype was advantageous for cashmere fineness, Only CA genotype was found in slaughter and meat quality. Additionally, and the CA genotype showed superiority in body size. On LCG doe, The CC genotype was the advantageous genotype in terms of cashmere fineness, milk production, slaughter performance, and meat quality. The CA genotype was the advantageous genotype in terms of lambing and body size. The dominant genotypes identified to influence both doe cashmere fineness and slaughter performance were TT and CC. The identified dominant haplotype combination for cashmere production performance in LCG was CCTG. The dominant haplotype combination for doe slaughter performance was the CCTT haplotype combination. The dominant haplotype combination for buck slaughter performance was the CATG haplotype combination. Therefore, the TT genotype of the FA2H gene and the CC genotype of the ELOVL3 gene in LCG buck, and the TG genotype of the FA2H gene and the CC genotype of the ELOVL3 gene in doe can be used as molecular markers for assisted selection of cashmere fineness. CCTG haplotype combination was the superior haplotype combinations for cashmere production performance. To provide a theoretical basis for the breeding and expansion of fine-fiber type new strains of LCG.

A Cyclin Gene OsCYCB1;5 Regulates Seed Callus Induction in Rice Revealed by Genome Wide Association Study

Plant tissue culture is extensively employed in plant functional genomics research and crop genetic improvement breeding. The callus induction ability is critical for utilizing Agrobacterium-mediated genetic transformation. In this study, we conducted a genome-wide association study (GWAS) utilizing 368 rice accessions to identify traits associated with callus induction rate (CIR), resulting in the identification of a total of 104 significant SNP loci. Integrated with gene function annotation and transcriptome analysis, 13 high-confidence candidate genes involved in auxin-related, CYC cyclins, and histone H3K9-specific methyltransferase were identified in significant loci. Furthermore, we also verified a candidate gene, Os05g0493500 (OsCycB1;5), and employed the CRISPR/Cas9 system to generate OsCycB1;5 knockout mutants in rice (Oryza sativa L.). The OscycB1;5 mutant displays significantly reduced callus induction and proliferation capacity, this result indicating OsCycB1;5 is required for the callus formation in rice. Overall, this study provides several reliable loci and high-confidence candidate genes that may significantly affect callus formation in rice. This information will offer valuable insights into the mechanisms underlying callus formation not only in rice but also in other plants.

Novel plasma protein biomarkers: A time-dependent predictive model for Alzheimer's disease

BackgroundThe accurate prediction of Alzheimer's disease (AD) is crucial for the efficient management of its progression. The objective of this research was to construct a new risk predictive model utilizing novel plasma protein biomarkers for predicting AD incidence in the future and analyze their potential biological correlation with AD incidence. MethodsA cohort of 440 participants aged 60 years and older from the Alzheimer's Disease Neuroimaging Initiative (ADNI) longitudinal cohort was utilized. The baseline plasma proteomics data was employed to conduct Cox regression, LASSO regression, and cross-validation to identify plasma protein signatures predictive of AD risk. Subsequently, a multivariable Cox proportional hazards model based on these signatures was constructed. The performance of the risk prediction model was evaluated using time-dependent receiver operating characteristic (t-ROC) curves and Kaplan-Meier curves. Additionally, we analyzed the correlations between protein signature expression in plasma and predicted AD risk, the time of AD onset, the expression of protein signatures in cerebrospinal fluid (CSF), the expression of CSF and plasma biomarkers, and APOE ε4 genotypes. Colocalization and Mendelian randomization analyses was conducted to investigate the association between protein features and AD risk. GEO database was utilized to analyze the differential expression of protein features in the blood and brain of AD patients. ResultsWe identified seven protein signatures (APOE, CGA, CRP, CCL26, CCL20, NRCAM, and PYY) that independently predicted AD incidence in the future. The risk prediction model demonstrated area under the ROC curve (AUC) values of 0.77, 0.76, and 0.77 for predicting AD incidence at 4, 6, and 8 years, respectively. Furthermore, the model remained stable in the range of the 3rd to the 12th year (ROC ≥ 0.74). The low-risk group, as defined by the model, exhibited a significantly later AD onset compared to the high-risk group (P < 0.0001). Moreover, all protein signatures exhibited significant correlations with AD risk (P < 0.001) and the time of AD onset (P < 0.01). There was no strong correlation between the protein expression levels in plasma and CSF, as well as AD CSF biomarkers. APOE, CGA, and CRP exhibited significantly lower expression levels in APOE ε4 positive individuals (P < 0.05). Additionally, colocalization analysis reveals a significant association between AD and SNP loci in APOE. Mendelian randomization analysis shows a negative correlation between NRCAM and AD risk. Transcriptomic analysis indicates a significant downregulation of NRCAM and PYY in the peripheral blood of AD patients (P < 0.01), while APOE, CGA, and NRCAM are significantly downregulated in the brains of AD patients (P < 0.0001). ConclusionOur research has successfully identified protein signatures in plasma as potential risk biomarkers that can independently predict AD onset in the future. Notably, this risk prediction model has demonstrated commendable predictive performance and stability over time. These findings underscore the promising utility of plasma protein signatures in dynamically predicting the risk of AD, thereby facilitating early screening and intervention strategies.

Genome-Wide Association Studies of Hair Whorl in Pigs.

In pigs, a hair whorl refers to hairs that form a ring of growth around the direction of the hair follicle at the dorsal hip. In China, a hair whorl is considered a negative trait that affects marketing, and no studies have been conducted to demonstrate whether hair whorl affects pig performance and provide an explanation for its genetic basis. Performance-measured traits and slaughter-measured traits of hair whorl and non-hair whorl pigs were differentially analyzed, followed by genome-wide association analysis (GWAS) and copy number variation (CNV) methods to investigate the genetic basis of hair whorl in pigs. Differential analysis of 2625 pigs (171 hair whorl and 2454 non-hair whorl) for performance measures showed that hair whorl and non-hair whorl pigs differed significantly (p < 0.05) in traits such as live births, total litter size, and healthy litter size (p < 0.05), while differential analysis of carcass and meat quality traits showed a significant difference only in the 45 min pH (p = 0.0265). GWAS identified 4 SNP loci significantly associated with the hair whorl trait, 2 of which reached genome-significant levels, and 23 candidate genes were obtained by annotation with the Ensembl database. KEGG and GO enrichment analyses showed that these genes were mainly enriched in the ErbB signaling, endothelial apoptosis regulation, and cell proliferation pathways. In addition, CNV analysis identified 652 differential genes between hair whorl and non-hair whorl pigs, which were mainly involved in the signal transduction, transcription factor activity, and nuclear and cytoplasmic-related pathways. The candidate genes and copy number variation differences identified in this study provide a new theoretical basis for pig breeding efforts.

Genome-Wide Association Study Reveals Marker–Trait Associations for Heat-Stress Tolerance in Sweet Corn

Sweet corn (Zea mays var. rugosa Bonaf.) is a crop with a high economic benefit in tropical and subtropical regions. Heat tolerance analysis and heat-tolerant gene mining are of great significance for breeding heat-resistant varieties. By combining improved genotyping using targeted sequencing (GBTS) with liquid chip (LC) technology, a high-density marker array containing 40 K multiple single polynucleotide polymorphisms (mSNPs) was used to genotype 376 sweet corn inbred lines and their heat-stress tolerance was evaluated in the spring and summer of 2019. In general, plant height, ear height and the number of lateral branches at the first level of the male flowers were reduced by 24.0%, 36.3%, and 19.8%, respectively. High temperatures in the summer accelerated the growth process of the sweet corn, shortening the days to shedding pollen by an average of 21.6% compared to the spring. A genome-wide association study (GWAS) identified 85 significant SNPs distributed on 10 chromosomes. Phenotypes in the spring and summer were associated with the 21 and 15 loci, respectively, and significant phenotypic differences between the two seasons caused by the temperature change were associated with the 49 SNP loci. The seed setting rate (SSR) was more susceptible to heat stress. An annotation analysis identified six candidate genes, which are either heat shock transcription factors (Hsfs) or heat shock proteins (Hsps) in Arabidopsis and rice (Oryza sativa), and these candidate genes were directly and indirectly involved in the heat-resistant response in the sweet corn. The current findings provide genetic resources for improving the heat-stress tolerance of sweet corn by molecular breeding.

Exploring the impact of inflammatory cytokines on alcoholic liver disease: a Mendelian randomization study with bioinformatics insights into potential biological mechanisms

ABSTRACT Background: Alcoholic liver disease (ALD) significantly contributes to global morbidity and mortality. The role of inflammatory cytokines in alcohol-induced liver injury is pivotal yet not fully elucidated. Objectives: To establish a causal link between inflammatory cytokines and ALD using a Mendelian Randomization (MR) framework. Methods: This MR study utilized genome-wide significant variants as instrumental variables (IVs) for assessing the relationship between inflammatory cytokines and ALD risk, focusing on individuals of European descent. The approach was supported by comprehensive sensitivity analyses and augmented by bioinformatics tools including differential gene expression, protein-protein interactions (PPI), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and analysis of immune cell infiltration. Results: Our findings reveal that increased levels of stem cell growth factor beta (SCGF-β, beta = 0.141, p = .032) and interleukin-7 (IL-7, beta = 0.311, p = .002) are associated with heightened ALD risk, whereas higher levels of macrophage inflammatory protein-1α (MIP-1α, beta = -0.396, p = .004) and basic fibroblast growth factor (bFGF, beta = -0.628, p = .008) are linked to reduced risk. The sensitivity analyses support these robust causal relationships. Bioinformatics analyses around inflammatory cytokine-associated SNP loci suggest multiple pathways through which cytokines influence ALD. Conclusion: The genetic evidence from this study convincingly demonstrates that certain inflammatory cytokines play directional roles in ALD pathogenesis. These findings provide insights into the complex biological pathways involved and underscore the potential for developing targeted therapies that modulate these inflammatory responses, ultimately improving clinical outcomes for ALD patients.