Biology subjects

Jiang, J.

Publications and source records attributed to Jiang, J..

At least 325 records · Page 18Linked to original sources

bioRxiv2019

Active monomer RTR-1 derived from the root of Rhodomyrtus tomentosa induces apoptosis in gastric carcinoma cells by inducing ER stress and inhibiting the STAT3 signalling pathway

ObjectiveRhodomyrtus tomentosa, a flowering plant belonging to the Myrtaceae family, is considered an antitumour substance with versatile biological and pharmacological activities. And RTR-1 is an active monomer purified from the root of Rhodomyrtus tomentosa. However, the detail of the mechanisms of anti-cancer activity of RTR-1 remains to be elucidated and the effect on gastric cancer cells is unknown. MethodsCell proliferation was determined by MTT and clone formation assay. The effect of RTR-1 on cell cycle and apoptosis was analyzed utilizing flow cytometry, respectively. Moreover, western blotting was used to detect the expression of cell cycle- and apoptosis-related protein. ResultsBased on MTT and clone formation assay, we noticed that RTR-1 inhibited the proliferation of gastric carcinoma (BGC823 and SGC7901) cells in a dose- and time-dependent manner. Furthermore, the results of flow cytometry and western blotting showed that RTR-1 induced cell cycle arrest in the G2/M phase through the ATM-Chk2-p53-p21 signalling pathway and induced cell apoptosis by inhibiting the signal transducers and activators of transcription 3 (STAT3) pathway and activating the endoplasmic reticulum stress (ER stress) pathway. ConclusionTaken together, these results demonstrate that RTR-1 induces cell cycle arrest and promotes apoptosis in gastric carcinoma, indicating its potential application for gastric cancer therapy.

cancer biology↗

bioRxiv2019

Prevalence of beta-lactam drug-resistance genes in commensal Escherichia coli contaminating ready-to-eat lettuce

The objective of this study was to evaluate the prevalence of antibiotic resistance and beta-lactam drug resistance genes in Escherichia coli isolated from ready-to-eat lettuce, obtained from local supermarkets in Northern California. Bags of lettuce were purchased from 4 chain supermarkets during three different periods--Oct 2018-Jan 2019, Feb 2019-Apr 2019 and May 2019-July 2019. From 91 packages of lettuce, we recovered 34 E. coli isolates from 22 (24%) lettuce samples. All E. coli isolates were genotyped by multilocus sequence typing (MLST), and we found 15 distinct sequence types (STs). Five of these genotypes (ST2819, ST4600, ST2432, ST1198 and ST5143) have been reported to cause infection in humans. Twenty (59%) E. coli isolates were found resistant to at least one of the antibacterial drugs. They included resistance to ampicillin (AMP, 85%) and ampicillin/sulbactam (SAM, 50%), cefoxitin (FOX, 40%) and cefuroxime (CXM, 35%). We found 8 (40%) of 20 beta-lactam resistant E. coli isolates to carry blaCTX-M; 5 (25%) tested positive for blaSHV, while only 4 (20%) tested positive for blaTEM. Additionally, we identified a class A broad-spectrum beta-lactamase SED-1 gene, blaSED, reported by others in Citrobacter sedlakii isolated from bile of a patient. This study found that a large proportion of fresh lettuce carry beta-lactam drug-resistant E. coli, which could serve as a reservoir for drug resistance genes that could potentially enter pathogens to cause human infections.

microbiology↗

bioRxiv2019

GWAS and Fine-Mapping of Livability and Six Disease Traits in Holstein Cattle

BackgroundHealth traits are of significant economic importance to the dairy industry due to their effects on milk production and associated treatment costs. Genome-wide association studies (GWAS) provide a means to identify associated genomic variants and thus reveal insights into the genetic architecture of complex traits and diseases. The objective of this study is to investigate the genetic basis of seven health traits in dairy cattle and to identify potential candidate genes associated with cattle health using GWAS, fine mapping, and analyses of multitissue transcriptome data.\n\nResultsWe studied cow livability and six direct disease traits, mastitis, ketosis, hypocalcemia, displaced abomasum, metritis, and retained placenta, using de-regressed breeding values and more than three million imputed DNA sequence variants. After data edits and filtering on reliability, phenotypes for 11,880 to 24,699 Holstein bulls were included in the analyses of the seven traits. GWAS was performed using a mixed-model association test, and a Bayesian fine-mapping procedure was conducted to calculate a posterior probability of causality to each variant and gene in the candidate regions. The GWAS results detected a total of eight genome-wide significant associations for three traits, cow livability, ketosis, and hypocalcemia, including the bovine MHC region associated with livability. Our fine-mapping of associated regions reported 20 candidate genes with the highest posterior probabilities of causality for cattle health. Combined with transcriptome data across multiple tissues in cattle, we further exploited these candidate genes to identify specific expression patterns in disease-related tissues and relevant biological explanations such as the expression of GC in the liver and association with mastitis as well as the CCDC88C expression in CD8 cells and association with cow livability.\n\nConclusionsCollectively, our analyses report six significant associations and 20 candidate genes of cattle health. With the integration of multi-tissue transcriptome data, our results provide useful information for future functional studies and better understanding of the biological relationship between genetics and disease susceptibility in cattle.

genetics↗

bioRxiv2019

Evolutionary changes of phosphoenolpyruvate transporter (PPT) during the emergence of C4 photosynthesis

C4 photosynthesis is a complex trait, which evolved from its ancestral C3 photosynthesis by recruiting pre-existing genes. The evolutionary history of enzymes involved in the C4 shuttle has been extensively studied. Here we analyze the evolutionary changes of phosphoenolpyruvate (PEP) transporter (PPT) during its recruitment from C3 to C4 photosynthesis. Our analysis shows that 1) among the two PPT paralogs, i.e. PPT1 and PPT2, PPT1 is an ancestral copy while PPT2 is a derived copy; 2) during C4 evolution, PPT1 shifted its expression from predominantly in root to in leaf, and from bundle sheath cell to mesophyll cell, supporting that PPT1 was recruited into C4 photosynthesis; 3) PPT1 gained increased transcript abundance, gained more rapid and long-lasting responses to light during C3 to C4 evolution, while PPT2 lost its responsiveness to light; 4) PPT1 gained a number of new cis-elements during C4 evolution; 5) C4 PPT1 can complement the phenotype of Arabidopsis PPT1 loss-of-function mutant, suggesting that it is a bidirectional transporter and its transport direction did not alter during C4 evolution. We finally discuss mechanistic linkages between these observed changes in PPT1 and C4 photosynthesis evolution.\n\nHigh lightDuring the process of C4 photosynthesis evolution, PPT not only experienced changes in its expression location and transcript abundance, but also acquired new cis-elements in its promoter region and accumulated protein variations.

evolutionary biology↗

bioRxiv2019

Transient uterine hypercontractility causes oxidative stress in the fetal brain, sex-dependent mitochondrial abnormalities, and altered social behavior of adolescent male rat offspring

The impact of transient ischemic-hypoxemic insults on the developing fetal brain is poorly understood despite evidence suggesting an association with neurodevelopmental disorders such as schizophrenia and autism. To address this, we designed an aberrant uterine hypercontractility paradigm with oxytocin to better assess the consequences of acute, but transient, placental ischemia-hypoxemia in term pregnant rats. Using MRI imaging, we confirmed that oxytocin-induced aberrant uterine hypercontractility significantly compromised uteroplacental perfusion. This was supported by the observation of oxidative stress and increased lactate concentration in the fetal brain. Genes related to oxidative stress pathways were significantly upregulated in male, but not female, offspring 1 h after oxytocin-induced placental ischemia-hypoxemia. Persistent upregulation of select mitochondrial electron transport chain complex proteins in the anterior cingulate cortex of adolescent male offspring suggested that this sex-specific effect was enduring. Functionally, offspring exposed to oxytocin-induced uterine hypercontractility showed male-specific abnormalities in social behavior with associated region-specific changes in gene expression and functional cortical connectivity. Our findings, therefore, indicate that even transient but severe placental ischemia-hypoxemia could be detrimental to the developing brain and point to a possible mitochondrial link between intrauterine asphyxia and neurodevelopmental disorders.

neuroscience↗

bioRxiv2019

Common genetic variation indicates separate etiologies for periventricular and deep white matter hyperintensities

We conducted a genome-wide association meta-analysis of two ischemic white matter disease subtypes in the brain, periventricular and deep white matter hyperintensities (PVWMH and DWMH). In 26,654 participants, we found 10 independent genome-wide significant loci only associated with PVWMH, four of which have not been described previously for total WMH burden (16q24.2, 17q21.31, 10q23.1, 7q36.1). Additionally, in both PVWMH and DWMH we observed the previous association of the 17q25.1 locus with total WMH. We found that both phenotypes have shared but also distinct genetic architectures, consistent with both different underlying and related pathophysiology. PVWMH had more extensive genetic overlap with small vessel ischemic stroke, and unique associations with several loci implicated in ischemic stroke. DWMH were characterized by associations with loci previously implicated in vascular as well as astrocytic and neuronal function. Our study confirms the utility of these phenotypes and identifies new candidate genes associated only with PVWMH.

neuroscience↗

bioRxiv2019

Targeting the Cx43 Carboxyl Terminal H2 Domain Preserves Left Ventricular Function Following Ischemia-Reperfusion Injury

BackgroundCT1 is a 25 amino acid therapeutic peptide incorporating the Zonula Occludens-1 (ZO-1)-binding domain of connexin43 (Cx43) that is currently in Phase III clinical testing for healing chronic skin wounds. In preclinical studies in mice, we reported that CT1 reduces arrhythmias and improves ventricular function following cardiac injury, effects that were accompanied by increases in PKC{varepsilon} phosphorylation of Cx43 at serine 368 (pS368). In this study, we undertake a systematic characterization of the molecular mode-of-action of CT1 in mitigating the effects of ischemia reperfusion injury on ventricular contractile function.\n\nMethods and ResultsTo determine the basis of CT1-mediated increases in pS368 we undertook tandem mass spectrometry of reactants in an in vitro assay of PKC{varepsilon} phosphorylation, identifying an interaction between negatively charged amino acids in the CT1 Asp-Asp-Leu-Glu-Iso sequence and positively charged lysines (Lys345, Lys346) in a short -helical sequence (H2) within the Cx43 CT domain. In silico modeling provided further support of the specificity of this interaction, leading us to conclude that CT1 has potential to directly interact with both Cx43 and ZO-1. Using surface plasmon resonance, thermal shift and phosphorylation assays, we characterized a series of CT1 variant peptides, identifying sequences competent to interact with either ZO-1 PDZ2 or the Cx43 CT, but with limited or no ability to bind both polypeptides. Based on this analysis, it was found that only those peptides competent to interact with Cx43, but not ZO-1 alone, resulted in increased pS368 phosphorylation in vitro and in vivo. Moreover, in a mouse model of global ischemia reperfusion injury we determined that pre-ischemic infusion only with those peptides competent to bind Cx43 preserved left ventricular (LV) contractile function following injury. Interestingly, a short 9 amino acid (MW=1110) Cx43-binding variant of the original 25 amino acid CT1 sequence demonstrated potent LV-protecting effects when infused either before or after ischemic injury.\n\nConclusionsInteraction of CT1 with the Cx43 CT, but not ZO-1 PDZ2, explains cardioprotection mediated by this therapeutic peptide. Pharmacophores targeting the Cx43 carboxyl terminus could provide a novel translational approach to preservation of ventricular function following ischemic injury.

cell biology↗

bioRxiv2019

Clinical manifestations and phenotypic analysis of new ANK1 gene mutations in 12 Chinese children with hereditary spherocytosis

ObjectiveTo summarize the clinical features and laboratory examination of ANK1 gene in 12 children with hereditary spherocytosis in China, and to determine the genetic mutations in those children.\n\nMethodsThe clinical data of children and their parents were collected and analyzed. The sequence of related genes was analyzed by second-generation sequencing technology. The suspected pathogenic mutations were detected by Sanger sequencing\n\nResultsNew mutations in the coding region of ANK1 was detected in 12 patients, which caused amino acid changes in the gene encoding, causing structural changes or loss of function.\n\nConclusionANK1 (c.1914_c.1918delTTTG), ANK1 (c.399T>G), ANK1 (c.1564delC), ANK1 (c.4439dupA ), ANK1 (c.4510_4513del), ANK1 (c.2961delC), ANK1 (c.2142dupT), ANK1 (c.2858+1G>C), ANK1 (c.3235delG), ANK1 (c.4739A>G), ANK1 (c.2638-2 A>G), ANK1 (c. 4739A>G) mutations in the coding region of the gene are the cause of suspicious disease in these 12 Chinese children. At the same time, second-generation gene sequencing technology is an effective means of confirming HS. Different types of mutations (P=0.388)and different mutation areas (P=0.660)had no significant effect on the severity of anemia. The 12 gene mutation sites in this study have not been included in the human genome database, dbSNP (v138) and ExAC databases. The new ANK1 gene mutations found in HS children can provide further exploration of the genetic etiology of HS in Chinese population.

genetics↗

bioRxiv2019

Cell cycle inhibitor Whi5 records environmental information to coordinate growth and division in yeast

Proliferating cells need to evaluate the environment to determine the optimal timing for cell cycle entry, which is essential for coordinating cell division and growth. In the budding yeast Saccharomyces cerevisiae, the commitment to the next round of division is made in G1 at the Start, triggered by the inactivation of the inhibitor Whi5 through multiple mechanisms. However, how a cell reads environmental condition and uses this information to regulate Start is poorly understood. Here, we show that Whi5 is a key environmental indicator and plays a crucial role in coordinating cell growth and division. We found that under a variety of nutrient and stress conditions, the concentration of Whi5 in G1 is proportional to the doubling time in the environment. Thus, under a poorer condition a longer doubling time results in a higher Whi5 concentration, which in turn delays the next cell cycle entry to ensure sufficient cell growth. In addition, the coordination between division and the environment is further fine-tuned in G1 by environmentally dependent G1 cyclin-Cdk1 contribution and Whi5 threshold at Start. Our results show that Whi5 serves as an environmental memory and that the cell adopts a simple and elegant mechanism to achieve an adaptive cellular decision making.

systems biology↗

bioRxiv2019

Changes in the Physicochemical Properties and Microbial Communities of Rhizospheric Soil after Cassava/Peanut Intercropping

Cassava/peanut intercropping is a popular cultivation method in southern China and has the advantages of apparently increased yield and economic efficiency compared with monoculture, however, the ecological benefits of this method are poorly understood. This study aimed to investigate the effects of intercropping on the physicochemical properties and microbial community structures of soil. Field trials were performed to determine the effects of cassava/peanut intercropping on rhizospheric soil nutrient content, enzyme activities, microbial quantity and microbial community structure. The microbial community was characterized by 16S rRNA tag-based high-throughput sequencing on the Illumina MiSeq platform. Results showed that cassava/peanut intercropping could improve the physicochemical properties of rhizospheric soil by increasing the available nutrient content, pH, bacterial quantity, and some enzyme activities and by altering the microbial community structure. 16S rRNA gene sequencing demonstrated that the microbial community structure varied between the intercropping and monoculture systems. Nitrospirae, Verrucomicrobia and Gemmatimonadetes were more abundant in the intercropping system than in the monocultures. Redundancy analysis (RDA) revealed that the abundances of DA101, Pilimelia and Ramlibacter were positively correlated with environmental parameters such as available nitrogen and pH, and these were dominant genera in the rhizospheric soil of the intercropped peanut plants.

ecology↗

bioRxiv2019

Robust Hierarchical Density Estimation and Regression for Re-stained Histological Whole Slide Image Co-registration

For many disease conditions, tissue samples are colored with multiple dyes and stains to add contrast and location information for specific proteins to accurately identify and diagnose disease. This presents a computational challenge for digital pathology, as whole-slide images (WSIs) need to be properly overlaid (i.e. registered) to identify co-localized features. Traditional image registration methods sometimes fail due to the high variation of cell density and insufficient texture information in WSIs - particularly at high magnifications. In this paper, we proposed a robust image registration strategy to align re-stained WSIs precisely and efficiently. This method is applied to 30 pairs of immunohistochemical (IHC) stains and their hematoxylin and eosin (H&E) counterparts. Our approach advances the existing methods in three key ways. First, we introduce refinements to existing image registration methods. Second, we present an effective weighting strategy using kernel density estimation to mitigate registration errors. Third, we account for the linear relationship across WSI levels to improve accuracy. Our experiments show significant decreases in registration errors when on matching IHC and H&E pairs, enabling subcellular-level analysis on stained and re-stained histological images. We also provide a tool to allow users to develop their own registration benchmarking experiments.

bioinformatics↗

bioRxiv2019

A cellular census of healthy lung and asthmatic airway wall identifies novel cell states in health and disease

Human lungs enable efficient gas exchange, and form an interface with the environment which depends on mucosal immunity for protection against infectious agents. Tightly controlled interactions between structural and immune cells are required to maintain lung homeostasis. Here, we use single cell transcriptomics to chart the cellular landscape of upper and lower airways and lung parenchyma in health. We report location-dependent airway epithelial cell states, and a novel subset of tissue-resident memory T cells. In lower airways of asthma patients, mucous cell hyperplasia is shown to stem from a novel mucous ciliated cell state, as well as goblet cell hyperplasia. We report presence of pathogenic effector Th2 cells in asthma, and find evidence for type-2 cytokines in maintaining the altered epithelial cell states. Unbiased analysis of cell-cell interactions identify a shift from airway structural cell communication in health to a Th2-dominated interactome in asthma.

immunology↗

bioRxiv2018

A critical role of the T3SS effector EseJ in intracellular trafficking and replication of Edwardsiella piscicida in non-phagocytic cells

Edwardsiella piscicida (E. piscicida) is an intracellular pathogen within a broad spectrum of hosts. Essential to E. piscicida virulence is its ability to survive and replicate inside host cells, yet the underlying mechanisms and the nature of the replicative compartment remain unclear. Here, we characterized its intracellular lifestyle in non-phagocytic cells and showed that intracellular replication of E. piscicida in non-phagocytic cells is dependent on its type III secretion system. Following internalization, E. piscicida is contained in vacuoles that transiently mature into early endosomes, but subsequently bypasses the classical endosome pathway and fusion with lysosomes which depends on its T3SS. Following a rapid escape from the degradative pathway, E. piscicida was found to create a specialized replication-permissive niche characterized by endoplasmic reticulum (ER) markers. We also found that a T3SS effector EseJ is responsible for intracellular replication of E. piscicida by preventing endosome/lysosome fusion. Furthermore, in vivo experiments confirmed that EseJ is necessary for bacterial colonization of E. piscicida in both mice and zebrafish. Thus, this work elucidates the strategies used by E. piscicida to survive and proliferate within host non-phagocytic cells.\n\nAuthor summaryE. piscicida is a facultative intracellular bacterium associated with septicemia and fatal infections in many animals, including fish and humans. However, little is known about its intracellular life, which is important for successful invasion of the host. The present study is the first comprehensive characterization of E. piscicidas intracellular life-style in host cells. Upon internalization, E. piscicida is transiently contained in Rab5-positive vacuoles, but the pathogen prevents further endosome maturation and fusion with lysosomes by utilizing an T3SS effector EseJ. In addition, the bacterium creates an specialized replication niche for rapid growth via an interaction with the ER. Our study provides new insights into the strategies used by E. piscicida to successfully establishes an intracellular lifestyle that contributes to its survival and dissemination during infection.

pathology↗

bioRxiv2018

A simple method to co-purify genomic DNA, RNA, and proteins for functional studies

Understanding the regulation of gene expression, from the epigenetic modifications on genomes to posttranscriptional and translational controls, are critical for elucidating molecular mechanisms underlying distinct phenotypes in biology. With the rapid development of Multi-Omics analyses, it is desirable to minimize sample variations by using DNA, RNA, and proteins co-purified from the same samples. Currently, most of the co-purification protocols rely on Tri Reagent (Trizol as a common representative) and require protein precipitation and dissolving steps, which render difficulties in experimental handling and high-throughput analyses. Here, we established a simple and robust method to minimize the precipitation steps and yield ready-to-use RNA and protein in solutions. This method can be applied to samples in small quantity, such as protoplasts. We demonstrated that the protoplast system equipped with this method may facilitate studies on viroid biogenesis. Given the ease and the robustness of this new method, it will have broad applications for plant research and other disciplines in molecular biology.

plant biology↗

bioRxiv2018

Epigenome-wide meta-analysis of blood DNA methylation and its association with subcortical volumes: findings from the ENIGMA Epigenetics Working Group

DNA methylation, which is modulated by both genetic factors and environmental exposures, may offer a unique opportunity to discover novel biomarkers of disease-related brain phenotypes, even when measured in other tissues than brain, such as blood. A few studies of small sample sizes have revealed associations between blood DNA methylation and neuropsychopathology, however, large-scale epigenome-wide association studies (EWAS) are needed to investigate the utility of DNA methylation profiling as a peripheral marker for the brain. Here, in an analysis of eleven international cohorts, totalling 3,337 individuals, we report epigenome-wide meta-analyses of blood DNA methylation with volumes of the hippocampus, thalamus and nucleus accumbens (NAcc) -three subcortical regions selected for their associations with disease and heritability and volumetric variability. Analyses of individual CpGs revealed genome-wide significant associations with hippocampal volume at two loci. No significant associations were found for analyses of thalamus and nucleus accumbens volumes. CpG sites associated with hippocampus volume were significantly enriched within cancer-related genes and within regulatory elements containing the transcriptionally repressive histone H3K27 tri-methylation mark that is vital for stem cell fate specification. Cluster-based analyses revealed additional differentially methylated regions (DMRs) associated with hippocampal volume. DNA methylation at these loci affected expression of proximal genes involved in in learning and memory, stem cell maintenance and differentiation, fatty acid metabolism and type-2 diabetes. These DNA methylation marks, their interaction with genetic variants and their impact on gene expression offer new insights into the relationship between epigenetic variation and brain structure and may provide the basis for biomarker discovery in neurodegeneration and neuropsychiatric conditions.

genomics↗

bioRxiv2018

Wolbachia pipientis occurs in Aedes aegypti populations in New Mexico and Florida, USA

The mosquitoes Aedes aegypti (L.) and Ae. albopictus Skuse are the major vectors of dengue, Zika, yellow fever and chikungunya viruses worldwide. Wolbachia, an endosymbiotic bacterium present in many insects, is being utilized in novel vector control strategies to manipulate mosquito life history and vector competence to curb virus transmission. Earlier studies have found that Wolbachia is commonly detected in Ae. albopictus but sporadically detected in Ae. aegypti. In this study, we used a two-step PCR assay to detect Wolbachia in wild-collected samples of Ae. aegypti. The PCR products were sequenced to validate amplicons and identify Wolbachia strains. A Loop-mediated isothermal amplification (LAMP) assay was developed and used for detecting Wolbachia in selected mosquito specimens as well. We found Wolbachia in 85/148 (57.4%) wild specimens of Ae. aegypti from various cities in New Mexico and in 2/46 (4.3%) wild specimens of Ae. aegypti from St. Augustine, Florida. We did not detect Wolbachia in 94 samples of Ae. aegypti from Deer Park, Harris County, Texas. Wolbachia detected in Ae. aegypti from both New Mexico and Florida was the wAlbB strain of Wolbachia pipientis. A Wolbachia positive colony of Ae. aegypti was established from pupae collected in Las Cruces, New Mexico in 2018.

ecology↗

bioRxiv2018

Comparative evidence for the independent evolution of hair and sweat gland traits in primates

Humans differ in many respects from other primates, but perhaps no derived human feature is more striking than our naked skin. Long purported to be adaptive, humans unique external appearance is characterized by changes in both the patterning of hair follicles and eccrine sweat glands, producing decreased hair cover and increased sweat gland density. Despite the conspicuousness of these features and their potential evolutionary importance, there is a lack of clarity regarding how they evolved within the primate lineage. We thus collected and quantified the density of hair follicles and eccrine sweat glands from five regions of the skin in three species of primates: macaque, chimpanzee and human. Although human hair cover is greatly attenuated relative to that of our close relatives, we find that humans have a chimpanzee-like hair density that is significantly lower than that of macaques. In contrast, eccrine gland density is on average 10-fold higher in humans compared to chimpanzees and macaques, whose density is strikingly similar. Our findings suggest that a decrease in hair density in the ancestors of humans and apes was followed by an increase in eccrine gland density and a reduction in fur cover in humans. This work answers longstanding questions about the traits that make human skin unique and substantiates a model in which the evolution of expanded eccrine gland density was exclusive to the human lineage.

evolutionary biology↗

bioRxiv2018

Fast Bayesian fine-mapping of 35 production, reproduction and body conformation traits with imputed sequences of 27K Holstein bulls

Imputation has been routinely used to infer sequence variants in large genotyped populations based on reference populations of sequenced individuals. With increasing numbers of animals sequenced and the implementation of the 1000 Bull Genomes Project, fine-mapping of causal variants for complex traits is becoming possible in cattle. Using 404 ancestor bull sequences as reference, we imputed over 3 million selected sequence variants to 27,214 Holstein bulls with highly reliable phenotypes (breeding values) for 35 production, reproduction, and body conformation traits. We first performed whole-genome single-marker scans for each of the 35 traits using a mixed-model association test. The single-trait association statistics were then merged into multi-trait tests of 3 trait groups: production, reproduction, and body conformation. Both single- and multi-trait GWAS results were used to identify 282 candidate QTL regions for fine-mapping in the cattle genome. To facilitate fast and powerful fine-mapping analyses, we developed a Bayesian Fine-MAPping approach (BFMAP) to integrate fine-mapping with functional enrichment analysis. Our fine-mapping results identified 69 promising candidate genes for dairy traits, including ABCC9, VPS13B, MGST1, SCD, MKL1, and CSN1S1 for production traits; CHEK2, GC, and KALRN for reproduction traits; and TMTC2, ARRDC3, ZNF613, CCND2, and FGF6 for body conformation traits. Based on existing functional annotation data for cattle, we revealed biologically meaningful enrichment in our fine-mapped variants that can be readily tested in functional validation studies. In summary, these results demonstrated the utility of a fast Bayesian approach for fine-mapping and functional enrichment analysis, identified candidate causative genes and variants, and enhanced our understanding of the genetic basis of complex traits in dairy cattle.

genetics↗