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The Caohai Wetland is located in a region of karst within the Yunnan-Guizhou Plateau, and serves as an important nature reserve for migratory birds. It is therefore of considerable ecological value in China. The presence and concentration of per- and polyfluoroalkyl substances (PFASs) in the wetland were unknown prior to this investigation. This study documents the occurrence, distribution, and ecological risks of 16 PFASs in the Caohai Wetland. The analysis showed that 11 PFASs were widely present in the Caohai Wetland; total concentrations (defined as the concentration of the total of all studied PFASs, ΣPFASs) ranged from 1.78 ng/L to 112.21 ng/L (mean 19.43 ng/L). Perfluorobutanoic acid (PFBA), perfluorooctanoic acid (PFOA) and potassium perfluorobutanesulfonate (PFBS) were the dominant forms in surface water, contributing 48.12%, 14.61%, and 11.59% to the total PFASs burden, respectively. Chlorinated polyfluoroalkyl ether sulfonic acid (F-53B) was also detected frequently and occurred at relatively high concentrations (0.14–1.48 ng/L, mean 0.48 ng/L). In the absence of point sources, high PFASs concentrations occurred inside a nearby town, resulting from anthropogenic activities. Risk assessment revealed that both individual and combined PFASs pose a relatively low risk to aquatic organisms at the present time. However, long-term monitoring of PFASs in the Caohai Wetland is needed given the potential of PFASs to be biomagnified and the extremely important ecological value of the Caohai Wetland.

Domestication and breeding have reshaped the genomic architecture of chicken, but the retention and loss of genomic elements during these evolutionary processes remain unclear. We present the first chicken pan-genome constructed using 664 individuals, which identified an additional approximately 66.5-Mb sequences that are absent from the reference genome (GRCg6a). The constructed pan-genome encoded 20,491 predicated protein-coding genes, of which higher expression levels are observed in conserved genes relative to dispensable genes. Presence/absence variation (PAV) analyses demonstrated that gene PAV in chicken was shaped by selection, genetic drift, and hybridization. PAV-based genome-wide association studies identified numerous candidate mutations related to growth, carcass composition, meat quality, or physiological traits. Among them, a deletion in the promoter region of IGF2BP1 affecting chicken body size is reported, which is supported by functional studies and extra samples. This is the first time to report the causal variant of chicken body size quantitative trait locus located at chromosome 27 which was repeatedly reported. Therefore, the chicken pan-genome is a useful resource for biological discovery and breeding. It improves our understanding of chicken genome diversity and provides materials to unveil the evolution history of chicken domestication.

Background: An increasing number of studies have explored disease and growth traits through quantitative trait locus (QTLs) in chickens. Nevertheless, the pathogenic genes underlying the QTL effects remain poorly understood. Alkaline phosphatase (ALP) is a marker of osteoblast maturation and an important indicator of bone metabolism. The change of ALP can reflect the bone metabolism and growth traits of animals to a certain extent. Results: In this study, we identified a SNP site at ST3GAL4 that found by genome-wide association studies (GWAS) in previous studies, and found another 8 SNPs by DNA sequencing. Interestingly, there are 4 SNPs rs475471G>A, rs475533C>T, rs475621A>G, rs475647C>A were completely linked by haplotype analysis, and selected a tag SNP rs475471G>A to analyze the correlation between this SNP and ALP level in Hubbard leg disease population and an F2 chicken resource population produced by Anka and Gushi chickens, and carried out population genetic analysis in 18 chicken breeds. Association analysis showed that this QTL within ST3GAL4 were highly correlated with ALP level, the mutant individuals with genotype AA had the highest ALP level, followed by GA and GG genotypes. The mutant individuals with genotype AA and GA genotype had higher values for body weight (BW), chest width (CW), body slanting length (BSL), pelvis width (PW) at 4-week, the semi-evisceration weight (SEW), evisceration weight (EW) and Leg weight (LW) of AA and GA genotype also higher. The amplification and typing of 4,852 DNA samples from 18 different breeds and the result shown GG genotype mainly existed in egg-type chickens and dual-type chickens, while AA genotype mainly distributed in commercial broilers and F2 resource population. The individuals of AA genotype had the highest ALP and showed better growth performance. This is the first time to report the causal variant of ST3GAL4 gene that located at chromosome 24 related to chicken serum ALP level. Besides, tissue expression analysis used Cobb broiler showed that there were significant differences between different genotypes in spleen and duodenum.Conclusions: This study the first time to determine 9 SNPs within ST3GAL4 were related to ALP in chickens, 4 of them were complete linkage sequence variants, which provide useful information on the mutation of ST3GAL4 and could predict the serum ALP level of chicken early and effectively as a potential molecular breeding marker.

Displacement of abomasum (DA) is one of the most common and important disorders in dairy cattle. The objective of the present study was to detect the quantitative trait loci (QTL) for DA in Chinese Holstein using single-step genomic BLUP methodology. A total of 60,556 producer-recorded DA event records from 32,190 cows, together with 2,336 genotyped animals with 40,054 SNP markers, were used for the analysis. Genomic data were incorporated into a threshold model for variance component estimation, and the estimated heritability of DA was 0.108 (SE = 0.086). Results of genome-wide association studies were reported as the proportion of genetic variance explained 20-SNP windows. Eight QTLs covering 129 genes on Bos taurus autosomes 2, 4, 7, 10, 14, 17, 20 showed associations with DA. Ten genes, namely BMP4, SOCS4, GCH1, DDHD1, ATG14, ACBP/DBI, SMO, AHCYL2, CYP7A1, and CACNA1A, involved in insulin metabolism and lipid metabolism pathways may be considered as candidate genes of DA in dairy. The identified QTLs, biological pathways, and associated genes underlying DA identified from the present study will contribute to the understanding of the genetic architecture of this complex disease.

In this study, the occurrence, distribution, and ecological risk of 40 commonly used antibiotics, including 15 sulfonamides (SAs), 9 fluoroquinolones (FQs), 7 macrolides (MCs), 3 tetracyclines (TCs), 2 chloramphenicols (CAPs), and 4 other categories, in the aquatic environment of the karst plateau wetland Caohai of the Yangtze River basin in southwestern China are reported. In total, 27 antibiotics were detected, with the detection rate ranging from 5% to 100%. The total concentration at each site ranged from 21.8 ng/L to 954 ng/L, with the average concentration being 189 ng/L. FQs and MCs were the most predominant categories, contributing 29.3% and 25.0% of the total antibiotic burden. The five most commonly detected antibiotics were ciprofloxacin (CIP), oxytetracycline (OTC), acetyl sulfamethoxazole (ASMZ), norfloxacin (NOR), and florfenicol (FF). The spatial distribution of the total concentration at each site demonstrated a decreasing trend from the southeastern area upstream adjoining the main counties to the northwestern area downstream, indicating that human activities have a great impact. Meanwhile, the natural attenuation rates of different types of antibiotics in the direction of flow ranged from 17.6% to 100%, which implied the natural purification potential of the wetland for antibiotics. The cluster analysis results indicated that domestic sewage and wastewater from agriculture and animal husbandry were the main sources of contamination in the surrounding wetland. Risk quotients (RQs) assessment showed that most of the individuals were at low to medium risk and that the adverse risks posed by mixtures of antibiotics were higher than those posed by the individual antibiotics.

Background Ketosis is a common metabolic disease during the transition period in dairy cattle, resulting in long-term economic loss to the dairy industry worldwide. While genetic selection of resistance to ketosis has been adopted by many countries, the genetic and biological basis underlying ketosis is poorly understood. Results We collected a total of 24 blood samples from 12 Holstein cows, including 4 healthy and 8 ketosis-diagnosed ones, before (2 weeks) and after (5 days) calving, respectively. We then generated RNA-Sequencing (RNA-Seq) data and seven blood biochemical indicators (bio-indicators) from leukocytes and plasma in each of these samples, respectively. By employing a weighted gene co-expression network analysis (WGCNA), we detected that 4 out of 16 gene-modules, which were significantly engaged in lipid metabolism and immune responses, were transcriptionally (FDR GRINA, MAF1, MAFA, C14H8orf82 and RECQL4. Our phenome-wide association analysis (Phe-WAS) demonstrated that human orthologues of these candidate genes were also significantly associated with many metabolic, endocrine, and immune traits in humans. For instance, MAFA, which is involved in insulin secretion, glucose response, and transcriptional regulation, showed a significantly higher association with metabolic and endocrine traits compared to other types of traits in humans. Conclusions In summary, our study provides novel insights into the molecular mechanism underlying ketosis in cattle, and highlights that an integrative analysis of omics data and cross-species mapping are promising for illustrating the genetic architecture underpinning complex traits.

A Sin-QuEChERS, coupled to UHPLC Q-Exactive Orbitrap MS, was used for nontargeted high-throughput rapid screening and quantitative analysis of residual pesticides and metabolites in green teas. The sample was extracted with 0.1% formic acid in acetonitrile with shaking, salted out and centrifuged, and purified with Sin-QuEChERS Nano solid phase extraction column; with Full MS/ddMS2 as the data collection mode, the database containing 384 pesticides combined with Trace Finder 3.0 software, In the absence of standard products, rapid screening and confirmation of potential pesticide residues in tea samples with accurate mass, isotope abundance ratio, secondary fragment ions, etc. 20 pesticides were used as quality controls to verify the screening method, and the linearity of these pesticides was between 1 and 200 μg/L, and the correlation coefficients were all greater than 0.9922. Moreover, the LOQ was between 0.002 and 0.01 mg/kg. The average recoveries of spiked tea samples were 74%–111%. Efficiency and reliability of this method were investigated by the analysis of 38 Chinese green tea samples. 18 potential residual pesticides were detected by non-targeted screening. The researchers then conducted a quantitative analysis of the 18 potential residual pesticides.

Specific DNA mutations underlying several genetic defects associated with embryo loss or reduced calf survivability have been identified in dairy cattle, and a convenient and cost-effective platform is required for their routine screening. We developed Kompetitive allele-specific PCR (KASP) assays for discrimination of the wild-type alleles from the associated defective alleles at each of 8 common genetic defects in Holstein cattle, involving 5 SNP [HH1, HH3, HH4, bovine leukocyte adhesion deficiency (BLAD), and complex vertebral malformation (CVM)] and 3 insertion or deletion mutations [HH5, haplotype for cholesterol deficiency (HCD), and brachyspina (BS)]. A total of 390 cows from a Chinese Holstein herd were genotyped and the carriers identified at 7 of these 8 loci (except HH4), with the highest carrier frequencies found for CVM (10.5%) and HH1 (10.0%), followed by HH3 (2.6%), BS (2.1%), HCD (1.3%), HH5 (0.8%), and BLAD (0.5%). Surprisingly, 102 cows (26.2%) carried at least 1 of the 7 defective alleles. Our results demonstrate that these KASP assays are simple, rapid, and reliable for the detection of multiple genetic defects. The high carrier frequency of these genetic defects indicates an urgent need for routine molecular testing to eliminate the deleterious alleles from Chinese Holstein cattle.

An autosomal recessive genetic defect termed JH1 has been associated with early embryonic loss in the Jersey cattle breed. The genetic basis has been identified as a cytosine to thymine mutation in the CWC15 gene that changes an amino acid from arginine to a stop code. To screen for JH1 carriers in an imported Jersey population in China, a method based on a polymerase chain reaction amplification followed by a restriction fragment length polymorphism assay (PCR-RFLP) was developed for the accurate diagnosis of the JH1 allele. A total of 449 randomly chosen cows were examined with the PCR-RFLP assay, and 31 were identified as JH1 carriers, corresponding to a carrier frequency of 6.9%. The PCR-RFLP method was validated by DNA sequencing of 8 positive and 13 negative samples, with all 21 samples giving the expected DNA sequence. In addition, 3 negative and 3 positive samples were confirmed by a commercial microarray-based single nucleotide polymorphism assay. Finally, samples from 9 bulls in the United States of known status were correctly identified as carriers (5 bulls) or noncarriers (4 bulls). As the JH1 defect has most likely spread worldwide, implementing routine screening is necessary to avoid the risk of carrier-to-carrier matings and to gradually eradicate the deleterious gene.