Identification of genetic effects and potential causal polymorphisms of CPM gene impacting milk fatty acid traits in Chinese Holstein

Our previous GWAS revealed 83 significant SNPs and 20 promising candidate genes associated with milk fatty acid traits in dairy cattle. Out of them, the carboxypeptidase M (CPM) gene contains a genome-wide significant SNP, Hapmap49848-BTA-106779, which is strongly associated with myristic acid (C14:0; P = 0.0064). Herein, we aimed to confirm the genetic effects of CPM on milk fatty acids in Chinese Holstein. Seven SNPs were detected by re-sequencing the sequences of entire exons and 3000 bp of up-/downstream flanking regions of the CPM gene, of which three were in 5' flanking region, one in the 3' UTR and three were in the 3' flanking region. Using the Haploview 4.1, we estimated the LD among the identified SNPs and found two haplotype blocks. With the animal model, we performed the SNP- and haplotype-based association analyses, and observed that these SNPs and haplotype blocks mainly had strong genetic associations with medium-chain saturated fatty acids (caproic acid, C6:0; caprylic acid, C8:0; capric acid, C10:0; and lauric acid, C12:0) (P < 0.0001-0.0257). In addition, using the Genomatix software, we predicted that three SNPs in the 5' flanking region of CPM (g.45079507A>G, g.45080228C>A and g.45080335C>G) changed the transcription factor binding sites for PREF (progesterone receptor biding site), ZBRK1 (transcription factor with eight central zinc fingers and an N-terminal KRAB domain), SOX9 (sex-determining region Y-box 9, dimeric binding sites), SOX6 (sex-determining region Y-box 6) and FOXP1-ES (alternative splicing variant of FOXP1, activated in ESCs). Further, the dual-luciferase reporter assay showed these three SNPs altered the transcriptional activity of CPM gene (P ≤ 0.0006). In summary, using the post-GWAS strategy, we first confirmed the significant genetic effects of CPM with milk fatty acids in dairy cattle, and identified three potential causal mutations.

Detection of Hole Pockets in the Candidate Type-II Weyl Semimetal MoTe_{2} from Shubnikov-de Haas Quantum Oscillations

The bulk electronic structure of T_{d}-MoTe_{2} features large hole Fermi pockets at the Brillouin zone center (Γ) and two electron Fermi surfaces along the Γ-X direction. However, the large hole pockets, whose existence has important implications for the Weyl physics of T_{d}-MoTe_{2}, has never been conclusively detected in quantum oscillations. This raises doubt about the realizability of Majorana states in T_{d}-MoTe_{2}, because these exotic states rely on the existence of Weyl points, which originated from the same band structure predicted by density functional theory (DFT). Here, we report an unambiguous detection of these elusive hole pockets via Shubnikov-de Haas (SdH) quantum oscillations. At ambient pressure, the quantum oscillation frequencies for these pockets are 988 and 1513 T, when the magnetic field is applied along the c axis. The quasiparticle effective masses m^{*} associated with these frequencies are 1.50 and 2.77 m_{e}, respectively, indicating the importance of Coulomb interactions in this system. We further measure the SdH oscillations under pressure. At 13 kbar, we detected a peak at 1798 T with m^{*}=2.86m_{e}. Relative to the oscillation data at a lower pressure, the amplitude of this peak experienced an enhancement, which can be attributed to the reduced curvature of the hole pockets under pressure. Combining our experimental data with DFT+U calculations, where U is the Hubbard parameter, our results shed light on why these important hole pockets have not been detected until now.

[Clinical phenotypes of epilepsy associated with GABRA1 gene variants]

Objective: To summarize the clinical phenotypes of epilepsy in patients with GABRA1 gene variants. Methods: A total of 11 epileptic patients (4 boys and 7 girls) who were treated in the Department of Pediatrics, Peking University First Hospital from March 2016 to July 2019 and detected with GABRA1 gene heterozygous pathogenic variants by targeted next-generation sequencing were enrolled. The features of clinical manifestations, electroencephalogram (EEG), and neuroimaging were analyzed retrospectively. Results: A total of 11 epileptic patients carried GABRA1 gene pathogenic variants, of whom 10 were de novo variants and the other one was inherited from the patient's mother. Two patients had the same variants. Six variants were novel. Ages at seizure onset ranged from 3 to 14 months, and the median age was 8 months. The seizure was first observed within 1 year in 10 patients and beyond 1 year of age in 1 patient. Multiple seizure types were observed, including focal seizures in 10 patients, generalized tonic clonic seizures (GTCS) in 3 patients, myoclonic seizures in 3 patients, and epileptic spasm in 2 patients. There were 5 patients with multiple seizure types. Sensitivity to fever was observed in 9 patients, among whom 6 patients had a history of status epilepticus. Two patients had photoparoxysmal response. Five patients had abnormal EEG background, and 6 patients had abnormal discharges in EEG during interictal phase. Brain magnetic resonance imaging (MRI) was normal in all patients. Developmental delay in various degrees was present in 9 patients. Among the 11 patients, Dravet syndrome was diagnosed in 5 patients, West syndrome in 2 patients, undiagnosed early-onset epileptic encephalopathy in 1 patient, and focal epilepsy in the other 3 patients. The ages at the last follow-up ranged from 8 months to 12 years. During follow-up, 8 patients were seizure-free for 6 months to 8 years, and 1 patient had discontinuation of medication. Conclusions: In epilepsy associated with GABRA1 gene variants, de novo pathogenic variants are more common than inherited. Most epilepsy caused by GABRA1 gene variants occurs in infancy. Most patients have multiple seizures and focal seizures are common. Most patients have a comparatively favorable prognosis, but they may still have varied degrees of developmental delay.

Retirement planning: the perceptions of pre-retirement nurses within different hospitals in China

AIM

This study explored the perceptions of senior Chinese nurses working in different hospital types, about retirement planning; and compared the results from two hospitals.

BACKGROUND

A recent review indicates that nurses with inadequate retirement planning could be faced with a retirement crisis. In China, hospitals are classified into different levels, and salaries, job satisfaction and the turnover of nurses varies among these levels. These factors may also influence nurses' perceptions of retirement planning.

METHODS

In a descriptive, qualitative design, 27 semi-structured individual interviews were conducted with nurses who were between 50 and 60 years old and recruited from two hospitals in China from April to September 2018. The interviews were transcribed and analysed thematically.

FINDINGS

Four main themes emerged from the interviews, namely, the understanding of pre-retirement nurses of retirement planning, the attitudes of pre-retirement nurses towards retirement planning, factors influencing nurses' retirement planning and the retirement planning activity of nurses. Most nurses participating in this study did not know much about retirement planning, but they all agreed on its importance. We identified the influencing factors of retirement planning and several differences regarding the perceptions of nurses about retirement planning in different hospitals.

CONCLUSION

In this cohort of nurses, planning for a good retirement was thought to be important; however, their readiness for retirement and the influences around planning for retirement were varied in type and scope.

IMPLICATIONS FOR POLICY

Governments and employing hospitals should develop reasonable measures and policies to support nurses in their understanding of the benefits of retirement planning and help them to prepare for retirement. Information about retirement planning should be made available and options for planning explained. Any systematic hurdles to retirement planning should be mitigated or eliminated.

Combining multi-population datasets for joint genome-wide association and meta-analyses: The case of bovine milk fat composition traits

In genome-wide association studies (GWAS), sample size is the most important factor affecting statistical power that is under control of the investigator, posing a major challenge in understanding the genetics underlying difficult-to-measure traits. Combining data sets available from different populations for joint or meta-analysis is a promising alternative to increasing sample sizes available for GWAS. Simulation studies indicate statistical advantages from combining raw data or GWAS summaries in enhancing quantitative trait loci (QTL) detection power. However, the complexity of genetics underlying most quantitative traits, which itself is not fully understood, is difficult to fully capture in simulated data sets. In this study, population-specific and combined-population GWAS as well as a meta-analysis of the population-specific GWAS summaries were carried out with the objective of assessing the advantages and challenges of different data-combining strategies in enhancing detection power of GWAS using milk fatty acid (FA) traits as examples. Gas chromatography (GC) quantified milk FA samples and high-density (HD) genotypes were available from 1,566 Dutch, 614 Danish, and 700 Chinese Holstein Friesian cows. Using the joint GWAS, 28 additional genomic regions were detected, with significant associations to at least 1 FA, compared with the population-specific analyses. Some of these additional regions were also detected using the implemented meta-analysis. Furthermore, using the frequently reported variants of the diacylglycerol acyltransferase 1 (DGAT1) and stearoyl-CoA desaturase (SCD1) genes, we show that significant associations were established with more FA traits in the joint GWAS than the remaining scenarios. However, there were few regions detected in the population-specific analyses that were not detected using the joint GWAS or the meta-analyses. Our results show that combining multi-population data set can be a powerful tool to enhance detection power in GWAS for seldom-recorded traits. Detection of a higher number of regions using the meta-analysis, compared with any of the population-specific analyses also emphasizes the utility of these methods in the absence of raw multi-population data sets to undertake joint GWAS.

Identification of genetic associations of ECHS1 gene with milk fatty acid traits in dairy cattle

Our previous genome-wide association study identified 83 genome-wide significant SNPs and 20 novel promising candidate genes for milk fatty acids in Chinese Holstein. Among them, the enoyl-CoA hydratase, short chain 1 (ECHS1) and enoyl-CoA hydratase and 3-hydroxyacyl CoA dehydrogenase (EHHADH) genes were located near two SNPs and one SNP respectively, and they play important roles in fatty acid metabolism pathways. We herein validated whether the two genes have genetic effects on milk fatty acid traits in dairy cattle. By re-sequencing the full-length coding region, partially adjacent introns and 3000 bp up/downstream flanking sequences, we identified 12 SNPs in ECHS1: two in exons, four in the 3' flanking region and six in introns. The g.25858322C>T SNP results in an amino acid replacement from leucine to phenylalanine and changes the secondary structure of the ECHS1 protein, and single-locus association analysis showed that it was significantly associated with three milk fatty acids (P = 0.0002-0.0013). The remaining 11 SNPs were found to be significantly associated with at least one milk fatty acid (P = <0.0001-0.0040). Also, we found that two haplotype blocks, consisting of nine and two SNPs respectively, were significantly associated with eight milk fatty acids (P = <0.0001-0.0125). However, none of polymorphisms was observed in the EHHADH gene. In conclusion, our findings are the first to indicate that the ECHS1 gene has a significant genetic impact on long-chain unsaturated and medium-chain saturated fatty acid traits in dairy cattle, although the biological mechanism is still undetermined and requires further in-depth validation.

Head and Neck Cancer Immunotherapy beyond the Checkpoint Blockade

The success of immune checkpoint receptor blockade has brought exciting promises for the treatment of head and neck squamous cell carcinoma (HNSCC). While patients who respond to checkpoint inhibitors tend to develop a durable response, <15% of patients with HNSCC respond to immune checkpoint inhibitors, underscoring the critical need to alleviate cancer resistance to immunotherapy. Major advances have been made to elucidate the intrinsic and adaptive resistance mechanisms to immunotherapy. Central genomic events in HNSCC have been found to possess previously unknown roles in suppressing immune sensing. Such inhibitory function affects both the innate and adaptive arms of tumor-specific immunity. While checkpoint blockade effectively reinvigorates adaptive T-cell responses, additional targeting of the oncogenic inhibitors of innate immune sensing likely informs a novel and potent strategy for immune priming. This review discusses the recent advances on the identification of key HNSCC oncogenes that impair antitumor immunity and emerging immune-priming approaches that sensitize poorly immunogenic HNSCCs to checkpoint blockade. These approaches include but are not limited to cancer vaccine systems utilizing novel type I interferon agonists as immune adjuvants, radiation, DNA damage-inducing agents, and metabolic reprogramming. The goal of these multipronged approaches is to expand tumor-specific effector T-cells, break checkpoint receptor-mediated tolerance, and metabolically support sustained T-cell activation. The translation of therapeutics that reverses oncogenic inhibition of immune sensing requires thorough characterization of the HNSCC regulators of innate immune sensors, development of additional immunocompetent HNSCC mouse models, as well as engineering of more robust immune adjuvant delivery systems. Built on the success of checkpoint blockade, validation of novel immune-priming approaches holds key promises to expand the pool of responders to immunotherapy.

Clinical characteristics and treatments of patients with alpha-fetoprotein producing gastric carcinoma

Alpha-fetoprotein (AFP) is a well-known tumor marker of hepatic carcinoma and yolk sac tumor. Alpha-fetoprotein producing gastric carcinoma (AFPGC) is a rare type of gastric cancer with high malignancy and poor prognosis, which make it different from other types of gastric cancer. This rare gastric cancer patient subgroup is likely frequently misdiagnosed which may be related to lack of knowledge of the disease. The purpose of this article is to summarize the mechanism of AFP positive gastric cancer, classification, biological behavior and treatment, in order to assist clinical practitioners to detect AFPGC earlier and treat it better. Previous studies have showed that AFPGC has a complex pathophysiology mechanism. AFPGC is more aggressive and characterized by stronger proliferation, neovascularization, lymphatic invasion and distant metastasis. Furthermore, so far there has been no standard treatment for patients with AFPGC. Nevertheless, our present study summarizes some effective treatments based on previous research outcome. In conclusion, the present study demonstrates that the importance of detecting AFP routinely in serum and tissues in gastric cancer cases, which will greatly improve the diagnosis rate of AFPGC, and in regards to treatment, surgery, chemotherapy, targeted therapy and interventional treatment may have positive impacts on AFPGC treatment outcome. However, further study with a larger sample is required to confirm the reliability and validity of these methods.

Clinical and genetic characteristics of familial hypercholesterolemia patients with type 2 diabetes

PURPOSE

Though type 2 diabetes mellitus (T2DM) is an important and independent risk factor for coronary artery disease (CAD) in the general population, the impact of T2DM on CAD in patients with familial hypercholesterolemia (FH) is less understood. Thus, the current study aimed to examine the features of FH patients with T2DM and explore the effects of T2DM on CAD in FH.

METHODS

A total of 289 clinical heterozygous FH (HeFH) patients diagnosed with Dutch Lipid Clinic Criteria were consecutively recruited and divided into a T2DM group (n = 58) and non-T2DM group (n = 231). Clinical characteristics and laboratory findings were compared between the two groups. Target exome sequencing was used for gene mutation analysis.

RESULTS

HeFH patients with T2DM had significantly higher levels of triglycerides, body mass index and free fatty acids than did non-T2DM patients; moreover, patients with T2DM more frequently exhibited hypertension. However, the spectrum of FH-causing mutations was not significantly different (p = 0.061). Notably, patients with T2DM had higher prevalence of CAD (p = 0.012) and higher Gensini Score (p = 0.002). The regression analysis confirmed that HbA1c was an independent risk factor for both the presence and severity of CAD [OR 2.321 (1.098-4.904), p = 0.027; OR 1.349 (1.032-1.762), p = 0.028, respectively] in patients with HeFH.

CONCLUSIONS

Although there were not many differences in the clinical, lipid and genetic aspects of HeFH patients with and without T2DM, T2DM and HbA1c were associated with worse coronary lesions, suggesting that diabetes and the degree of blood glucose control are also important determinants of cardiovascular disease in these patients.

SAT-LB056 Is AIP a Tumor Suppressor or an Oncogene? AIP as a Novel Regulator of the Oncogene BCL6 in Diffuse Large B Cell Lymphoma

Background: Heterozygous germline loss-of-function mutations in the aryl hydrocarbon receptor interacting protein (AIP) gene are usually associated with acromegaly or gigantism due to a young-onset somatotropinoma. AIP functions as a tumor suppressor gene in the pituitary, while its role in other tumours is unknown. AIP is highly expressed in patients with Diffuse Large B Cell Lymphoma (DLBCL) compared to any other tumor type. DLBCL arises from germinal centre B cells which characteristically express the transcriptional repressor B cell lymphoma-6 (BCL6), key for germinal centre formation. Increased expression of BCL6 can lead to the development of DLBCL. Despite the obvious importance of BCL6 expression in GC B cells, the mechanisms by which it is regulated are still poorly understood. Aim: The aim of this study was to investigate the relationship of the high AIP expression, BCL6 and the pathobiology of DLBCL. Methods: We generated mice carrying a conditional homozygous deletion of Aip in T and B cells (Aip^fl/fl;Rag1^Cre/+). Co-localization of AIP and members of the BCL6 ubiquitination/proteasome pathway by immunofluorescence analysis. Ubiquitin-mediated proteasomal degradation study was done by immuno-precipitation (IP). Results: Our study found that AIP is highly expressed in DLBCL. Genetic deletion of Aip revealed that AIP supported BCL6 expression in mice. The ubiquitin E3 ligase FBXO11 has been previously shown to add ubiquitin to BCL6. We found that AIP could bind to the deubiquitinase UCHL1 and that UCHL1 could remove ubiquitin from BCL6 thereby supporting BCL6 expression by preventing FBXO11 mediated degradation of BCL6 recapitulating what we observed in Aip deficient B cells. Conclusions: The data presented here reveal AIP to be a novel positive regulator of BCL6 protein expression which is commonly up-regulated in DLBCL and prevents FBXO11 degradation of BCL6 by enabling the UCHL1 to remove ubiquitin from BCL6. Therefore, AIP is a potential novel therapeutic target to treat DLBCL. It appears that AIP function as a tumor suppressor in the pituitary and as an oncogene to the pathobiology of DLBCL. Unless otherwise noted, all abstracts presented at ENDO are embargoed until the date and time of presentation. For oral presentations, the abstracts are embargoed until the session begins. Abstracts presented at a news conference are embargoed until the date and time of the news conference. The Endocrine Society reserves the right to lift the embargo on specific abstracts that are selected for promotion prior to or during ENDO.

[Application of dental floss traction-assisted endoscopic submucosa dissection to rectal neuroendocrine neoplasm]

Objective: To evaluate the safety and efficacy of dental floss traction-assisted endoscopic submucosal dissection (DFS-ESD) for rectal neuroendocrine neoplasm (NEN). Methods: A retrospective cohort study was performed. Clinical data of rectal NEN patients undergoing ESD at Endoscopy Center of Zhongshan Hospital, Fudan University from January 2016 to December 2017 were retrospectively analyzed. Inclusion criteria: 1) age of 18 to 80 years old; 2) maximal diameter of lesions <1.5 cm; 3) tumor locating in the submucosa without invasion into the muscularis propria; 4) no enlarged lymph nodes around bowel and in abdominal cavity; 5) ESD requested actively by patients. A total of 37 patients were enrolled, including 23 male and 14 female cases with mean age of (56.0±11.3) years. All the lesions were single tumor of stage T1, and the mean size was 0.8±0.2(0.5-1.2) cm. Postoperative pathology revealed all samples as neuroendocrine tumors (NET). Seventeen patients received DFS-ESD treatment (DFS-ESD group) and 20 patient received conventional ESD treatment (conventional ESD group). In DFS-ESD group, after the mucosa was partly incised along the marker dots, the endoscopy was extracted, and the dental floss was tied to one arm of the metallic clip. When the endoscope was reinserted, the hemoclip was attached onto the incised mucosa; another hemoclip was attached onto normal mucosa opposite to the lesion in the same way. The submucosa was clearly exposed with the traction of dental floss and the resection could proceed. The conventional ESD group received the traditional ESD operation procedure. The operation time, modified operation time (remaining time after excluding the assembly time of dental floss traction in DFS-ESD group), en bloc resection rate, R0 resection rate, morbidity of operative complication, recurrence and metastasis were compared between two groups. Results: The average tumor size was (0.8±0.2) cm in DFS-ESD group and (0.7±0.2) cm in conventional ESD group (t=0.425, P=0.673). According to postoperative pathological grading of rectal neuroendocrine neoplasm, 13 were G1 and 4 were G2 in DFS-ESD group, while 17 cases were G1 and 3 cases were G2 in conventional ESD group without significant difference (P=0.680). There were no significant differences in baseline data between in the two groups (all P>0.05). All the basal resection margins were negative, the en bloc resection rate was 100% and the R0 resection rate was 100%. Pathological results showed tumor tissue close to the burning margin in 5 cases of conventional ESD group and in 2 cases of DFS-ESD group (P=0.416). The operation time was (17.9±6.6) minutes in conventional ESD group and (14.7±3.3) minutes in DFS-ESD group (t=1.776, P=0.084). The modified operation time of DFS-ESD group was (11.9±2.8) minutes, which was significantly shorter than (17.9±6.6) minutes in conventional ESD group (t=3.425, P=0.002). The hospital stay was (2.3±0.6) days and (2.0±0.5) days in conventional ESD group and DFS-ESD group, respectively, without significant difference (t=1.436, P=0.160). No patient was transferred to surgery, and no delayed bleeding or perforation occurred in either group. There was no recurrence or primary tumor-related death, and all the patients recovered well during a follow-up period of 14(1-24) months. Conclusion: Dental floss traction-assisted ESD for rectal neuroendocrine neoplasm can simplify operation and ensure negative basal margin.

Acanthopanax senticosus polysaccharide suppressing proliferation and metastasis of the human non-small cell lung cancer NCI-H520 cells is associated with Wnt/β-catenin signaling

Lung cancer (LC) is the highest lethality in all tumors. Non-small cell lung cancer (NSCLC) accounts for about 80% of all LC. Acanthopanax senticosus polysaccharide (ASPS) is extracted from the root of Acanthopanax senticosus (AS). Herein, we examined the effect and molecular mechanism of ASPS on NSCLC. The proliferation, invasion and migration of NCI-H520 cells were detected by cell counting kit-8 (CCK-8), transwell assay and wound healing assay, respectively. The epithelial-mesenchymal transition (EMT) and Wnt/β-catenin pathway-related factors were evaluated using quantitative real-time PCR (QRT-PCR) and western blot assay. Our results observed that ASPS significantly decreased the proliferation of cells at 24 and 48 h. Moreover, ASPS markedly repressed the invasion and migration capacities of cells in a concentration-dependent manner. Besides, ASPS obviously down-regulated the levels of matrix metalloproteinase-2 (MMP-2), MMP-9, fibronectin 1 (FN1), vimentin, wnt3a, phosphorylated-glycogen synthase kinase 3β (p-GSK3β) and cyclin D1, whereas, up-regulating E-cadherin level. The level of GSK3β was not changed in the different groups. ASPS conspicuously inhibited the abilities of proliferation and metastasis in human non-small cell lung cancer cell line NCI-H520 possibly by suppressing Wnt/β-catenin pathway mediated-EMT.

Long-term hydrolytically stable bond formation for future membrane-based deep ocean microfluidic chemical sensors

Future ocean profiling of dissolved inorganic carbon and other analytes will require miniaturised chemical analysis systems based on sealed gas membranes between two fluid channels. However, for long-term deployment in the deep ocean at high pressure, the ability to seal incompatible materials represents an immense challenge. We demonstrate proof of principle high strength bond sealing. We show that polydimethylsiloxane (PDMS) is a preferred membrane material for rapid CO2 transfer, without ion leakage, and report long-term stable bonding of thin PDMS membrane films to inert thermoplastic poly(methyl methacrylate) (PMMA) patterned manifolds. Device channels were filled with 0.01 M NaOH and subjected to repeated tape pull and pressure - flow tests without failure for up to six weeks. Bond formation utilised a thin coating of the aminosilane bis-[3-trimethoxysilylpropyl]amine (BTMSPA) conformally coated onto PMMA channels and surfaces and cured. All surfaces were subsequently plasma treated and devices subject to thermocompressive bond annealing. Successful chemically resistant bonding of membrane materials to thermoplastics opens the possibility of remote environmental chemical analysis and offers a route to float-based depth profiling of dissolved inorganic carbon in the oceans.

Multi-population GWAS and enrichment analyses reveal novel genomic regions and promising candidate genes underlying bovine milk fatty acid composition

Background

The power of genome-wide association studies (GWAS) is often limited by the sample size available for the analysis. Milk fatty acid (FA) traits are scarcely recorded due to expensive and time-consuming analytical techniques. Combining multi-population datasets can enhance the power of GWAS enabling detection of genomic region explaining medium to low proportions of the genetic variation. GWAS often detect broader genomic regions containing several positional candidate genes making it difficult to untangle the causative candidates. Post-GWAS analyses with data on pathways, ontology and tissue-specific gene expression status might allow prioritization among positional candidate genes.

Results

Multi-population GWAS for 16 FA traits quantified using gas chromatography (GC) in sample populations of the Chinese, Danish and Dutch Holstein with high-density (HD) genotypes detects 56 genomic regions significantly associated to at least one of the studied FAs; some of which have not been previously reported. Pathways and gene ontology (GO) analyses suggest promising candidate genes on the novel regions including OSBPL6 and AGPS on Bos taurus autosome (BTA) 2, PRLH on BTA 3, SLC51B on BTA 10, ABCG5/8 on BTA 11 and ALG5 on BTA 12. Novel genes in previously known regions, such as FABP4 on BTA 14, APOA1/5/7 on BTA 15 and MGST2 on BTA 17, are also linked to important FA metabolic processes.

Conclusion

Integration of multi-population GWAS and enrichment analyses enabled detection of several novel genomic regions, explaining relatively smaller fractions of the genetic variation, and revealed highly likely candidate genes underlying the effects. Detection of such regions and candidate genes will be crucial in understanding the complex genetic control of FA metabolism. The findings can also be used to augment genomic prediction models with regions collectively capturing most of the genetic variation in the milk FA traits.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5573-9) contains supplementary material, which is available to authorized users.

Genetic association of DDIT3, RPL23A, SESN2 and NR4A1 genes with milk yield and composition in dairy cattle

Previously, we identified by RNA sequencing that DDIT3, RPL23A, SESN2 and NR4A1 genes were significantly differentially expressed between the mammary glands of lactating Holstein cows with extremely high and low milk protein and fat percentages; thus, these four genes are considered as promising candidates potentially affecting milk yield and composition traits in dairy cattle. In the present study, we further verified whether these genes have genetic effects on milk traits in a Chinese Holstein population. By re-sequencing part of the non-coding and the entire coding regions of the DDIT3, RPL23A, SESN2 and NR4A1 genes, a total of 35 SNPs and three insertions/deletions were identified, of which three were found in DDIT3, 12 in RPL23A, 16 in SESN2 and seven in NR4A1. Moreover, two of the insertions/deletions-g.125714860_125714872del and g.125714806delinsCCCC in SESN2-were novel and have not been reported previously. Subsequent single SNP analyses revealed multiple significant association with all 35 SNPs and three indels regressed against the dairy production traits (P-value = <0.0001-0.0493). In addition, with a linkage disequilibrium analysis, we found one, one, three, and one haplotype blocks in the DDIT3, RPL23A, SESN2 and NR4A1 genes respectively. Haplotype-based association analyses revealed that some haplotypes were also significantly associated with milk production traits (P-value = <0.0001-0.0461). We also found that 12 SNPs and two indels (two in DDIT3, two in RPL23A, nine in SESN2 and one in NR4A1) altered the specific transcription factor binding sites in the promoter, thereby regulating promoter activity, suggesting that they might be promising potential functional variants for milk traits. In summary, our findings first determined the genetic associations of DDIT3, RPL23A, SESN2 and NR4A1 with milk yield and composition traits in dairy cattle and also suggested potentially causal variants, which require in-depth validation.