Molecular cloning of the HGD gene and association of SNPs with meat quality traits in Chinese red cattle

Lactobacillus melliventris promotes hive productivity and immune functionality in Bombus terrestris performance in the greenhouse

Bumblebees are important pollinators in agricultural ecosystems, but their abundance is declining globally. There is an urgent need to protect bumblebee health and their pollination services. Bumblebees possess specialized gut microbiota with potential to be used as probiotics to help defend at-risk bumblebee populations. However, evidence for probiotic benefits on bumblebees is lacking. Here, we evaluated how supplementation with Lactobacillus melliventris isolated from bumblebee gut affected the colony development of Bombus terrestris. This native strain colonized robustly and persisted long-term in bumblebees, leading to a significantly higher quality of offspring. Subsequently, the tyrosine pathway was upregulated in the brain and fat body, while the Wnt and mTOR pathways of the gut were downregulated. Notably, the field experiment in the greenhouse revealed the supplementation of L. melliventris led to a 2.5-fold increase in the bumblebee survival rate and a more than 10% increase in the number of flowers visited, indicating a better health condition and pollination ability in field conditions. Our study represents a first screening for the potential use of the native gut member, L. melliventris, as probiotic strains in hive supplement for bumblebee breeding, which may be a practical approach to improve immunity and hive health.

Metabolic profiling of serum and urine in lactating dairy cows affected by subclinical ketosis using proton nuclear magnetic resonance spectroscopy

Ketosis is associated with high milk yield during lactating or insufficient feed intake in lactating dairy cows. However, few studies have been conducted on the metabolomics of ketosis in Korean lactating dairy cows. The present study aimed to investigate the serum and urine metabolites profiling of lactating dairy cows through proton nuclear magnetic resonance (¹H-NMR) spectroscopy and comparing those between healthy (CON) and subclinical ketosis (SCK) groups. Six lactating dairy cows were categorized into CON and SCK groups. All experimental Holstein cows were fed total mixed ration. Serum and urine samples were collected from the jugular vein of the neck and by hand sweeping the perineum, respectively. The metabolites in the serum and urine were determined using ¹H-NMR spectroscopy. Identification and quantification of metabolites was performed by Chenomx NMR Suite 8.4 software. Metabolites statistical analysis was performed by Metaboanalyst version 5.0 program. In the serum, the acetoacetate level was significantly (p < 0.05) higher in the SCK group than in the CON group, and whereas acetate, galactose and pyruvate levels tended to be higher. CON group had significantly (p < 0.05) higher levels of 5-aminolevulinate and betaine. Indole-3-acetate, theophylline, p-cresol, 3-hydroxymandelate, gentisate, N-acetylglucosamine, N-nitrosodimethylamine, xanthine and pyridoxine levels were significantly (p < 0.05) higher in the urine of the SCK group than that in the CON group, which had higher levels of homogentisate, ribose, gluconate, ethylene glycol, maltose, 3-methyl-2-oxovalerate and glycocholate. Some significantly (p < 0.05) different metabolites in the serum and urine were associated with ketosis diseases, inflammation, energy balance and body weight. This study will be contributed useful a future ketosis metabolomics studies in Korea.

Muricauda aurea sp. nov. and Muricauda profundi sp. nov., two marine bacteria isolated from deep sea sediment of Pacific Ocean

Two novel Gram-stain-negative, aerobic, rod-shaped, carotenoid-pigmented and non-flagellated bacteria, designated BC31-1-A7T and BC31-3-A3T, were isolated from polyethylene-terephthalate-degrading bacterial consortia enriched from deep-sea sediment collected in the Pacific Ocean. Optimal growth of both strains was observed at 28–32 °C, at pH 7.5 and in the presence of 3–4% (w/v) NaCl. The 16S rRNA gene sequence analysis revealed that strains BC31-1-A7T and BC31-3-A3T were closely related to Muricauda aquimarina JCM 11811T, Muricauda lutimaris KCTC 22173T, Muricauda ruestringensis DSM 13258T, Muricauda zhangzhouensis DSM 25030T, Muricauda oceani JCM 33902T and Muricauda oceanensis KCTC 72200T with 96.8–98.9% sequence similarity. The 16S rRNA gene sequence similarity between strains BC31-1-A7T and BC31-3-A3T was 97.5%. The genomic G+C contents of strains BC31-1-A7T and BC31-3-A3T were 42.1 and 41.6 mol%, respectively. The average nucleotide identity and digital DNA–DNA hybridization values between strain BC31-3-A3T, strain BC31-1-A7T and their six closely related type strains were 77.6–84.3% and 20.5–27.9%, respectively. Menaquinone-6 was detected as the major isoprenoid quinone in all strains. Their major fatty acids were iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH. The major polar lipids of strains BC31-1-A7T and BC31-3-A3T were identified as one phosphatidylethanolamine, some unidentified polar lipids and one aminolipid. Based on their distinct taxonomic characteristics, strains BC31-1-A7T and BC31-3-A3T represent two novel species in the genus Muricauda . The names proposed to accommodate these two strains are Muricauda aurea sp. nov. and Muricauda profundi sp. nov., and the type strains are BC31-1-A7T (=MCCC M23246T=KCTC 82569T) and BC31-3-A3T (=MCCC M23216T=KCTC 82302T), respectively.

The application of gene marker-assisted selection and proteomics for the best meat quality criteria and body measurements in Qinchuan cattle breed

In the past few decades, enhancement of animal productivity has been gaining increasing attention among decisions-makers, politicians, mangers, and breeders, because of the increasing of world population and shortage of natural resources. The selection of high productivity animals is the main goal, through the application of genetic improvement programs. The use of molecular genetics has conferred significant breeding advantages over conventional breeding techniques. In this regard, many economic characteristics are controlled by a small number of multiple gene loci, each of which is responsible for trait diversity and hence they are referred to as quantitative trait loci (QTL). Single-nucleotide polymorphisms (SNPs), which have recently been discovered through DNA sequencing, are considered one of the most useful types of genetic marker. SNPs are found where different nucleotides occur at the same position in the DNA sequence. They are found in both coding and noncoding regions of the genome and are present at one SNP in every 1000 b. Strategies for the identification and application of markers are based on reference to examples of loci that can control various traits. Furthermore, markers for growth, body measurements, and meat quality traits are preferred, because they can be used to predict the performance of animals, via blood samples, in the first few days of animal life. Marker-assisted selection using SNPs, such asSIRT1, SIRT2, LPL, CRTC2, SIX4, UCPs, and ZBTB38as selection criteria of body measurements and meat traits in beef cattle, will be beneficial in selection and breeding programs. The proteomic is a novel marker and a new approache of biotechnology which increases the understanding of the biological processes, besides being a remarkable biomarker that interrelated to growth and meat quality traits. Proteomics is a vigorous tool as usage for deduces molecular processes between quality traits and muscle proteins, which are helpful in analyzing the mechanisms of biochemistry that influence quality. So they could be potential biomarker for some meat quality traits. Among them, Actin, Myosin, Heat shock proteins are used a novel approaches in the field of biotechnology to understand the proteomics changes. This review article highlights the novel findings on the potential use of MAS and proteomics as biomarker for the selection for meat quality and carcass traits in Qinchuan cattle breed.

Transcriptomic Analysis of Ovaries from Pigs with High And Low Litter Size

Litter size is one of the most important economic traits for pig production as it is directly related to the production efficiency. Litter size is affected by interactions between multiple genes and the environment. While recent studies have identified some genes associated with prolificacy in pigs, transcriptomic studies of specific genes affecting litter size in porcine ovaries are rare. In order to identify candidate genes associated with litter size in swine, we assessed gene expression differences between the ovaries of Yorkshire pigs with extremely high and low litter sizes using the RNA-Seq method. A total of 1 243 differentially expressed genes were identified: 897 genes were upregulated and 346 genes were downregulated in high litter size ovary samples compared with low litter size ovary samples. A large number of these genes related to steroid hormone regulation in animal ovaries, including 59 Gene Ontology terms and 27 Kyoto Encyclopedia of Genes and Genomes pathways involved in steroid biosynthesis and ovarian steroidogenesis. From these differentially expressed genes, we identified a total of 11 genes using a bioinformatics screen that may be associated with high litter size in Yorkshire pigs. These results provide a list of new candidate genes for porcine litter size and prolificacy to be further investigated.

Fine mapping of quantitative trait loci underlying sensory meat quality traits in three French beef cattle breeds

Improving the traits that underlie meat quality is a major challenge in the beef industry. The objective of this paper was to detect QTL linked to sensory meat quality traits in 3 French beef cattle breeds. We genotyped 1,059, 1,219, and 947 young bulls and their sires belonging to the Charolais, Limousin, and Blonde d'Aquitaine breeds, respectively, using the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). After estimating relevant genetic parameters using VCE software, we performed a linkage disequilibrium and linkage analysis on 4 meat traits: intramuscular fat content, muscle lightness, shear force, and tenderness score. Heritability coefficients largely ranged between 0.10 and 0.24; however, they reached a maximum of 0.44 and 0.50 for intramuscular fat content and tenderness score, respectively, in the Charolais breed. The 2 meat texture traits, shear force and tenderness score, were strongly genetically correlated (-0.91 in the Charolais and Limousin breed and -0.86 in the Blonde d'Aquitaine breed), indicating that they are 2 different measures of approximately the same trait. The genetic correlation between tenderness and intramuscular fat content differed across breeds. Using a significance threshold of 5 × 10(-4) for QTL detection, we found more than 200 significant positions across the 29 autosomal chromosomes for the 4 traits in the Charolais and Blonde d'Aquitaine breeds; in contrast, there were only 78 significant positions in the Limousin breed. Few QTL were common across breeds. We detected QTL for intramuscular fat content located near the myostatin gene in the Charolais and Blonde d'Aquitaine breeds. No mutation in this gene has been reported for the Blonde d'Aquitaine breed; therefore, it suggests that an unknown mutation could be segregating in this breed. We confirmed that, in certain breeds, markers in the calpastatin and calpain 1 gene regions affect tenderness. We also found new QTL as several QTL on chromosome 3 that are significantly associated with meat tenderness in the Blonde d'Aquitaine breed. Overall, these results greatly contribute to the goal of building a panel of markers that can be used to select animals of high meat quality.

Modeling tenderness for genetic and quantitative trait loci analyses

Tenderness is the one of the most important attributes of beef with regards to the intent of consumers to repurchase. Beef tenderness is frequently measured objectively as Warner-Bratzler shear force. However, to better understand the genetics underlying tenderness, better descriptors were derived herein. Two traits, adjusted shear force and aging rate, were calculated to incorporate measures of Warner-Bratzler shear force repeated over aging time of 2 muscles, longissimus dorsi (LD) and semitendinosus (ST). Analysis of these traits indicated that the shear forces of the 2 muscles are lowly correlated and aging rate, as calculated, was not correlated with adjusted shear force. Breed, SNP, and QTL effects were analyzed for the 4 traits (2 traits × 2 muscles). For adjusted shear force, the QTL were located on cattle chromosomes BTA 5, 18, 25, and 29. With the exception of the QTL on BTA 5, the adjusted shear force QTL were observed for either the LD or the ST but not both muscles. The QTL for aging rate were located on BTA 1, 4, 7, 11, 13, 19, and 20.

Genome scan for meat quality traits in Nelore beef cattle

Meat quality traits are economically important because they affect consumers' acceptance, which, in turn, influences the demand for beef. However, selection to improve meat quality is limited by the small numbers of animals on which meat tenderness can be evaluated due to the cost of performing shear force analysis and the resultant damage to the carcass. Genome wide-association studies for Warner-Bratzler shear force measured at different times of meat aging, backfat thickness, ribeye muscle area, scanning parameters [lightness, redness (a*), and yellowness] to ascertain color characteristics of meat and fat, water-holding capacity, cooking loss (CL), and muscle pH were conducted using genotype data from the Illumina BovineHD BeadChip array to identify quantitative trait loci (QTL) in all phenotyped Nelore cattle. Phenotype count for these animals ranged from 430 to 536 across traits. Meat quality traits in Nelore are controlled by numerous QTL of small effect, except for a small number of large-effect QTL identified for a*fat, CL, and pH. Genomic regions harboring these QTL and the pathways in which the genes from these regions act appear to differ from those identified in taurine cattle for meat quality traits. These results will guide future QTL mapping studies and the development of models for the prediction of genetic merit to implement genomic selection for meat quality in Nelore cattle.

BRCA1: a new candidate gene for bovine mastitis and its association analysis between single nucleotide polymorphisms and milk somatic cell score

Bovine mastitis is a very complex and common disease of dairy cattle and a major source of economic losses to the dairy industry worldwide. In this study, the bovine breast cancer 1, early onset gene (BRCA1) was taken as a candidate gene for mastitis resistance. The main object of this study was to investigate whether the BRCA1 gene was associated with mastitis in cattle. Through DNA sequencing, Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) and Created Restriction Site PCR (CRS-PCR) methods, three SNPs (G22231T, T25025A, and C28300A) were detected and twenty-four combinations of these SNPs were observed. The single SNP and their genetic effects on somatic cell score (SCS) were evaluated and a significant association with SCS was found in C28300A. The mean of genotype EE was significantly lower than those of genotypes EF and FF. The results of combined genotypes analysis of three SNPs showed that BBDDFF genotype with the highest SCS were easily for the mastitis susceptibility, whereas AACCEE genotype with the lowest SCS were favorable for the mastitis resistance. The information provided in the present study will be very useful for improving mastitis resistance in dairy cattle by marker-assisted selection.

Formula feeding alters hepatic gene expression signature, iron and cholesterol homeostasis in the neonatal pig

In the U.S. formula feeding remains more popular than breast-feeding. In the current study, neonatal piglets were breast fed and compared with those fed commercially available milk-based formula (milk) or soy-based formula (soy) from postnatal day 2 (PND2) until death at PND21 (the usual age of weaning). Liver weights were greater in formula-fed piglets ( P < 0.05) than in breast-fed piglets ( P < 0.05). Affymetrix array analysis revealed significant differences in hepatic gene expression signatures between piglets fed breast milk or formula, as well as between piglets fed milk or soy. In males, expression of 346 hepatic genes differed between formula-fed and breast-fed piglets, and soy-fed differed from milk-fed piglets in 277 genes. Furthermore, gene expression profiles of males differed from females, even when the same diet was consumed. Serum cholesterol was lower in piglets fed formula relative to breast-fed piglets ( P < 0.05), and this was associated with elevations in mRNA encoding cholesterol 7α-hydroxylase (CYP7A1). Consistent with the human literature, breast-fed piglets had lower hepatic iron accumulation than formula-fed piglets. Hepcidin, a major regulator of hepatic iron trafficking, was elevated in piglets fed formula relative to breast-fed piglets ( P < 0.05). Female piglets fed soy formula had increased expression of CYP3A enzymes ( P < 0.05), and soy formula feeding decreased expression of several hepatic genes considered estrogen inducible. These data suggest that: 1) gene expression profiles in neonates differ significantly depending on the diet consumed, 2) hepatic iron storage and cholesterol metabolism clearly differ between breast and formula feeding in piglets, 3) there is no evidence that soy is estrogenic in neonatal pig liver.

Single nucleotide polymorphism of CACNA2D1 gene and its association with milk somatic cell score in cattle

The objective of the present study was to identify polymorphisms of the CACNA2D1 gene, and to analyze associations between these polymorphisms and mastitis in several cattle breeds. Through PCR-RFLP methods and DNA sequencing, an allelic variant corresponding to the A→G mutations and Aspartic (Asp) to Glycine (Gly) amino acid replacement at positions 526745 in the exon 25 of bovine CACNA2D1 gene could be detected. Two alleles, A and G, and three genotypes, AA, AG and GG were defined. Genetic character in the studied populations indicated that the A526745G loci of CACNA2D1 gene was moderate polymorphism and fitted with Hardy-Weinberg equilibrium (P > 0.05). The effects of CACNA2D1 polymorphisms on somatic cell score (SCS) were analyzed and significant association was found between A526745G and SCS. The mean of genotype GG was significantly lower than those of genotype AG and AA (P = 0.0469). Information provided in this research could be useful in further studies to determine the role of CACNA2D1 gene in the mastitis resistance.

Three novel SNPs in the coding region of PPARγ gene and their associations with meat quality traits in cattle

The peroxisome proliferator-activated receptor γ (PPARγ) is a nuclear hormone receptor that regulates adipogenesis and many other biological processes. In the present study, we carried out PCR-SSCP and DNA sequencing analyses to examine SNPs in coding region of the PPARγ gene. A total of 660 individuals from five Chinese cattle breeds were genotyped. We identified three SNPs and their associations with meat quality traits were analyzed in 108 Qinchuan cattle. Two missense mutations and one synonymous mutation were found: 200 A>G (genotypes AA, AB and BB) resulting in D7G change, the silent substitution 42895 C>T (genotypes JJ and JI) and 72472 G>T (genotypes CC, DC and DD) producing Q448H change, respectively. The frequencies of PPARγ-A allele were 0.86, 0.83, 0.80, 0.72 and 0.87 for Qinchuan, Nanyang, Jiaxian, Luxi and Xianan populations, respectively. The frequencies of PPARγ-J allele varied from 0.87 to 0.96 in the five populations. In the 72472 G>T locus, the frequencies of PPARγ-C allele were higher than PPARγ-D allele in the five populations, and ranged from 0.58 to 0.82. Least squares analysis revealed that in 42895 C>T locus, there was a significant effect on tenderness in 18-20 months Qinchuan cattle (P<0.01), and in the 72472 G>T locus, animals with the genotype DC had lower mean values than these with genotype CC (P<0.01) for back fat thickness in 18-20 months, and animals with the genotype DD had lower mean values than these with genotypes CC and DC (P<0.01) for water holding capacity in 21-24 months (P<0.01). The SNPs we have identified may contribute to establishing a more efficient selection program for improving of genetic characteristics in indigenous Chinese cattle.

Molecular characterization, polymorphism of bovine ZBTB38 gene and association with body measurement traits in native Chinese cattle breeds

Zinc finger and BTB domain containing 38 (ZBTB38), binding to and repressing methylated DNA, is an important candidate gene for selection of body measurement traits through marker-assisted selection (MAS). The expression of ZBTB38 is regulated in human and animal height as well as other stature indexes. Genomic structural analysis shows that bovine ZBTB38 shares much similarity with human ZBTB38. We discovered and evaluated the potential association of the single nucleotide polymorphism (SNP) of the bovine ZBTB38 gene with body measurement traits in 722 individuals. The latest findings demonstrate that the A841G SNP in exon 1 is significantly associated with Body Length (BL), Hip Height (HH) and Heart Girth (HG). Furthermore, the analysis of A841G SNP marker shows that there are significant effects on the BL (P = 0.0389) in 722 individuals, significant effects on the HH (P = 0.0173) and HG (P = 0.0147) in Qinchuan improvement steers (QI) population, as well as significant effects on the WH (P = 0.0094) in Xuelong (XL) population. These results clearly suggest that the ZBTB38 gene is among of target genes for body measurement traits in bovine reproduction and breeding, and thus provide data for establishment of an animal model using cattle to study big animal body type.