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Abstract Background Milk samples from 10,641 dairy cattle were screened by a mass spectrometry method for extreme concentrations of the A or B isoforms of the whey protein, β-lactoglobulin (BLG), to identify causative genetic variation driving changes in BLG concentration. Results A cohort of cows, from a single sire family, was identified that produced milk containing a low concentration of the BLG B protein isoform. A genome-wide association study (GWAS) of BLG B protein isoform concentration in milk from AB heterozygous cows, detected a group of highly significant single nucleotide polymorphisms (SNPs) within or close to the BLG gene. Among these was a synonymous G/A variation at position + 78 bp in exon 1 of the BLG gene (chr11:103256256G > A). The effect of the A allele of this SNP (which we named B’) on BLG expression was evaluated in a luciferase reporter assay in transfected CHO-K1 and MCF-7 cells. In both cell types, the presence of the B’ allele in a plasmid containing the bovine BLG gene from -922 to + 898 bp (relative to the transcription initiation site) resulted in a 60% relative reduction in mRNA expression, compared to the plasmid containing the wild-type B sequence allele. Examination of a mammary RNAseq dataset (n = 391) identified 14 heterozygous carriers of the B’ allele which were homozygous for the BLG B protein isoform (BB’). The level of expression of the BLG B’ allele was 41.9 ± 1.0% of that of the wild-type BLG B allele. Milk samples from three cows, homozygous for the A allele at chr11:103,256,256 (B’B’), were analysed (HPLC) and showed BLG concentrations of 1.04, 1.26 and 1.83 g/L relative to a mean of 4.84 g/L in milk from 16 herd contemporaries of mixed (A and B) BLG genotypes. The mechanism by which B’ downregulates milk BLG concentration remains to be determined. Conclusions High-throughput screening and identification of outliers, enabled the discovery of a synonymous G > A mutation in exon 1 of the B allele of the BLG gene (B’), which reduced the milk concentration of β-lactoglobulin B protein isoform, by more than 50%. Milk from cows carrying the B’ allele is expected to have improved processing characteristics, particularly for cheese-making.

[beta]-Carotene biochemistry is a fundamental process in mammalian biology. Aberrations either through malnutrition or potentially through genetic variation may lead to vitamin A deficiency, which is a substantial public health burden. In addition, understanding the genetic regulation of this process may enable bovine improvement. While many bovine QTL have been reported, few of the causative genes and mutations have been identified. We discovered a QTL for milk [beta]-carotene and subsequently identified a premature stop codon in bovine [beta]-carotene oxygenase 2 (BCO2), which also affects serum [beta]-carotene content. The BCO2 enzyme is thereby identified as a key regulator of [beta]-carotene metabolism. DOI: 10.1534/genetics.109.101741

The article presents a study that aims to determine the quantitative trait loci (QTL) that affects the concentration of β-lactoglobulin in milk and examines the effect of the genetic variants of β-lactoglobulin on fat, protein and casein concentration in bovine milk. The study measured the concentration of fat, protein and casein in milk during peak, middle and late lactation. Results indicate that high QTL was found in same position of the β-lactoglobulin gene on bovine.

Simple Summary: The genetic mechanisms underlying the growth phenotypic variation in the Haimen goat have not been fully revealed. This study uncovered the genetic structure and genome-wide selection signatures of Haimen goats, with a sequencing depth of 20×. Through selective sweep analysis, we identified the PNLIPRP1 gene that determines the growth traits of goats. Our study not only benefits the conservation of Haimen goats but also provides valuable insights into potential breeding strategies for this important goat breed. Understanding the genetic characteristics of indigenous goat breeds is vital for their conservation and breeding. Haimen goats, native to China's Yangtze River Delta, possess distinctive traits such as white hair, moderate growth rate, high-quality meat, and small body size. However, knowledge regarding the genetic structure and germplasm characteristics of Haimen goats remains limited. In this study, we performed 20× whole-genome resequencing of 90 goats (60 Haimen goats and 30 Boer goats) to identify single-nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) associated with growth traits. Here, we analyzed population genetic structure and genome-wide selection signatures between the Haimen and Boer goats based on whole-genome resequencing data. The principal component analysis (PCA) and neighbor-joining (N-J) tree results demonstrated significant genetic differentiation between the Haimen and Boer goats. The nucleotide diversity (Pi) and linkage disequilibrium (LD) decay results indicated higher genomic diversity in the Haimen goat population. Furthermore, selective sweep analysis identified candidate genes associated with growth traits. These genes exhibited strong selection signatures and were related to body size (DONSON, BMPR1B, and EPHA5), muscle development (GART, VGLL3, MYH15), and fat metabolism (ADAMTS5, LRP6, XDH, CPT1A, and GPD1). We also identified growth-related candidate genes (NCOR1, DPP6, NOTCH2, and FGGY) specific to Haimen goats. Among these genes, pancreatic lipase-related protein 1 (PNLIPRP1) emerged as the primary candidate gene influencing growth phenotypes. Further analysis revealed that a 26 bp Indel in PNLIPRP1 increased its gene expression, suggesting that this Indel could serve as a molecular marker for early marker-assisted selection, potentially enhancing early growth in goats. These findings provide valuable molecular markers and candidate genes for improving growth traits in Haimen goat breeding. [ABSTRACT FROM AUTHOR]

Simple Summary: Milk production and its composition are important for the economy, and they depend on complex biological processes. By finding the key genes and causal mutations linked to milk yield, we can improve breeding strategies for dairy animals. Thanks to advanced bioinformatics tools, it is now easier to find the genetic factors that affect milk traits. In our study, we used these methods to explore the genetics of milk traits in Murciano-Granadina goats. Although we found distinct genes associated with each trait, the regulatory proteins showed shared-yet-dynamic roles in controlling gene activity across different traits. This helped us understand how genes work together in the mammary gland, which affects milk production and udder health. The Murciano-Granadina goat (MUG) is a renowned dairy breed, known for its adaptability and resilience, as well as for its exceptional milk traits characterized by high protein and fat content, along with low somatic cell counts. These traits are governed by complex biological processes, crucial in shaping phenotypic diversity. Thus, it is imperative to explore the factors regulating milk production and lactation for this breed. In this study, we investigated the genetic architecture of seven milk traits in MUGs, employing a two-step computational analysis to examine genotype–phenotype associations. Initially, a random forest algorithm identified the relative importance of each single-nucleotide polymorphism (SNP) in determining the traits of interest. The second step applied an information theory-based approach to exploring the complex genetic architecture of quantitative milk traits, focusing on epistatic interactions that may have been overlooked in the first step. These approaches allowed us to identify an almost distinct set of candidate genes for each trait. In contrast, by analyzing the promoter regions of these genes, we revealed common regulatory networks among the milk traits under study. These findings are crucial for understanding the molecular mechanisms underlying gene regulation, and they highlight the pivotal role of transcription factors (TFs) and their preferential interactions in the development of these traits. Notably, TFs such as DBP, HAND1E47, HOXA4, PPARA, and THAP1 were consistently identified for all traits, highlighting their important roles in immunity within the mammary gland and milk production during lactation. [ABSTRACT FROM AUTHOR]

Simple Summary: Fourier Transform Infrared Spectroscopy (FT-MIRS) is widely used in milk quality detection, dairy herd improvement (DHI), and other fields. It is an economical, fast, accurate, and nondestructive batch tool for determining production performance phenotypes of dairy cows. Milk is one of the most important ways to provide the human body with the fatty acids it needs. There are a huge number of dairy cows in China. Therefore, it is possible to control fatty acid production in the milk source through targeted husbandry and breeding on large pastures to improve the quality of milk production. However, this work has not yet officially begun in China. In summary, our work uses FT-MIRS for the first time to study the phenotypic properties of milk fatty acid content and the genetic mechanism of its formation and to estimate genetic parameters. At the same time, SNPs significantly related to fatty acid content were discovered and the genes or adjacent genes had critical regulatory effects on milk fat synthesis, milk protein synthesis, adipocyte differentiation, mammary gland development, milk synthesis, and growth and development in dairy cows, thus providing a new perspective for cow genetic selection in China. Fourier Transform Mid-Infrared Spectroscopy (FT-MIRS) can be used for quantitative detection of milk components. Here, milk samples of 458 Chinese Holstein cows from 11 provinces in China were collected and we established a total of 22 quantitative prediction models in milk fatty acids by FT-MIRS. The coefficient of determination of the validation set ranged from 0.59 (C18:0) to 0.76 (C4:0). The models were adopted to predict the milk fatty acids from 2138 cows and a new high-throughput computing software HiBLUP was employed to construct a multi-trait model to estimate and analyze genetic parameters in dairy cows. Finally, genome-wide association analysis was performed and seven novel SNPs significantly associated with fatty acid content were selected, investigated, and verified with the FarmCPU method, which stands for "Fixed and random model Circulating Probability Unification". The findings of this study lay a foundation and offer technical support for the study of fatty acid trait breeding and the screening and grouping of characteristic dairy cows in China with rich, high-quality fatty acids. It is hoped that in the future, the method established in this study will be able to screen milk sources rich in high-quality fatty acids. [ABSTRACT FROM AUTHOR]

Enteral nutrition (EN) and foods for special medical purposes (FSMPs) can be used to meet the specific nutritional needs of patients. There are multiple types of EN products and nutritionally complete FSMPs on the market. The peptides in these products are important nutritional components, while their presence in different products remains unclear. To provide better clinical guidelines, we analyzed and compared the molecular weight (MW) distribution, types, and quantities of peptides and bioactive peptides of two EN products (liquid products) and two FSMPs with nutritionally complete formulas (powder products). Our results showed that each product had a unique peptide profile. The two liquid products and one powder product (Samples 1–3) had a higher content of peptides. Sample 1 contained 75.60% peptides with an MW less than 375 Da and contained 95.21% peptides with an MW less than 1000 Da, being rich in short peptides. Sample 2 and 3 had high levels of peptides with MW values between 180 Da and 2000 Da. Additionally, Sample 4 contained high levels of proteins, containing 69.18% peptides with MW values larger than 10,000 Da. Further, Sample 1 had more bioactive dipeptides and Sample 2 had more long bioactive peptides. Our results suggest that peptides in different EN and FSMP products are very different and should be evaluated in more detail. This will provide valuable information for clinical medical professionals, help them to guide patients with different physiological conditions better, and ultimately benefit patients. [ABSTRACT FROM AUTHOR]

Carotenoids are essential nutrients for humans and animals, and carotenoid coloration represents an important meat quality parameter for many farmed animals. Increasingly, studies have demonstrated that vertebrate carotenoid cleavage oxygenases (CCOs) are essential enzymes in carotenoid metabolism and are therefore potential candidate genes for improving carotenoid deposition. However, our understanding of carotenoid bioavailability and CCOs functions in invertebrates, particularly marine species, is currently quite limited. We previously identified that a CCO homolog, PyBCO-like 1, was the causal gene for carotenoid coloration in the 'Haida golden scallop', a variety of Yesso scallop (Patinopecten yessoensis) characterized by carotenoid enrichment. Here, we found that another CCO-encoding gene named PyBCO2 (β-carotene oxygenase 2) was widely expressed in P. yessoensis organs/tissues, with the highest expression in striated muscle. Inhibiting BCO2 expression in P. yessoensis through RNA interference led to increased carotenoid (pectenolone and pectenoxanthin) deposition in the striated muscle, and the color of the striated muscle changed from white to light orange. Our results indicate that PyBCO2 might be a candidate gene used for improving carotenoid content in normal Yesso scallops, and also in 'Haida golden scallops'. [ABSTRACT FROM AUTHOR]

In the animal kingdom, sexually dimorphic color variation is a widespread phenomenon that significantly influences survival and reproductive success. However, the genetic underpinnings of this variation remain inadequately understood. Our investigation into sexually dimorphic color variation in the desert-dwelling Guinan population of the toad-headed agamid lizard (Phrynocephalus putjatai) utilized a multidisciplinary approach, encompassing phenotypic, ultrastructural, biochemical, genomic analyses, and behavioral experiments. Our findings unveil the association between distinct skin colorations and varying levels of carotenoid and pteridine pigments. The red coloration in males is determined by a genomic region on chromosome 14, housing four pigmentation genes: BCO2 and three 6-pyruvoyltetrahydropterin synthases. A Guinan population-specific nonsynonymous single nucleotide polymorphism in BCO2 is predicted to alter the electrostatic potential within the binding domain of the BCO2-β-carotene complex, influencing their interaction. Additionally, the gene MAP7 on chromosome 2 emerges as a potential contributor to the blue coloration in subadults and adult females. Sex-specific expression patterns point to steroid hormone-associated genes (SULT2B1 and SRD5A2) as potential upstream regulators influencing sexually dimorphic coloration. Visual modeling and field experiments support the potential selective advantages of vibrant coloration in desert environments. This implies that natural selection, potentially coupled with assortative mating, might have played a role in fixing color alleles, contributing to prevalence in the local desert habitat. This study provides novel insights into the genetic basis of carotenoid and pteridine-based color variation, shedding light on the evolution of sexually dimorphic coloration in animals. Moreover, it advances our understanding of the driving forces behind such intricate coloration patterns. [ABSTRACT FROM AUTHOR]

Milk production is one of the most important economic utility of goats. Guanzhong dairy goat is a local dairy goat in Shaanxi Province of China and has high milk yield and quality. However, there are relatively few studies on molecular markers of milk production traits in Guanzhong dairy goats. In this study, we sequenced the whole genomes of 20 Guanzhong dairy goats, 10 of which had high milk yield (HM) and 10 of which had low milk yield (LM). We detected candidate signatures of selection in HM goats using Fst and π‐ratio statistics and identified several candidate genes including ANPEP, ADRA1A and PRKG1 associated with milk production. Our results provide the basis for molecular breeding of milk production traits in Guanzhong dairy goats. [ABSTRACT FROM AUTHOR]

Simple Summary: pH was one of the main factors affecting meat storage/shelf life, and was also directly related to meat freshness, taste and overall quality. To extend storage/shelf life, pH-related candidate genes were mined to provide new opportunities for genetic improvement. We obtained candidate genes related to pH through a genome-wide association analysis to provide research directions for extending meat storage/shelf life. pH was one of the important meat quality traits, which was an important factor affecting the storage/shelf life and quality of meat in meat production. In order to find a way to extend the storage/shelf life, the pH values (pH45min, pH24h, pH48h and pH72h) of the longissimus dorsi muscles in F2 individuals of 462 Texel sheep × Altay sheep were determined, genotyping was performed using Illumina Ovine SNP 600 K BeadChip and whole genome resequencing technology, a genome-wide association analysis (GWAS) was used to screen the candidate genes and molecular markers for pH values related to the quality traits of mutton, and the effects of population stratification were detected by Q–Q plots. The results showed that the pH population stratification analysis did not find significant systemic bias, and there was no obvious population stratification effect. The results of the association analysis showed that 28 SNPs significantly associated with pH reached the level of genomic significance. The candidate gene associated with pH45min was identified as the CCDC92 gene by gene annotation and a search of the literature. Candidate genes related to pH24h were KDM4C, TGFB2 and GOT2 genes. The candidate genes related to pH48h were MMP12 and MMP13 genes. The candidate genes related to pH72h were HILPDA and FAT1 genes. Further bioinformatics analyses showed 24 gene ontology terms and five signaling pathways that were significantly enriched (p ≤ 0.05). Many terms and pathways were related to cellular components, processes of protein modification, the activity of protein dimerization and hydrolase activity. These identified SNPs and genes could provide useful information about meat and the storage/shelf life of meat, thereby extending the storage/shelf life and quality of meat. [ABSTRACT FROM AUTHOR]

Simple Summary: The deposition of carotenoids in chicken skin makes the skin color turn from white into yellow. The enzyme β-carotene oxygenase 2 (BCO2) plays a key role during the degradation process of carotenoids in chicken skin. Hence, the concentration of carotenoids in chicken skin was measured, and significant differences in BCO2 gene expression in the back skin between yellow and white skin and one SNP c.890A>G in BCO2 were found to be potentially associated with the chicken skin color. The results of this study showed that the c.890A>G may be used as a genetic marker in breeding for yellow skin in Chinese indigenous chicken. Carotenoid consumption decreases the risk of cancer, osteoporosis, or neurodegenerative diseases through interrupting the formation of free radicals. The deposition of carotenoids in chicken skin makes the skin color turn from white into yellow. The enzyme β-carotene oxygenase 2 (BCO2) plays a key role during the degradation process of carotenoids in skin. How the BCO2 affects the skin color of the chicken and whether it is the key factor that results in the phenotypic difference between yellow- and white-skin chickens are still unclear. In this research, the measurement of the concentration of carotenoids in chicken skin by HPLC showed that the carotenoid concentration in chickens with a yellow skin was significantly higher than that in white-skin chickens. Moreover, there were significant differences in BCO2 gene expression in the back skin between yellow- and white-skin chickens. Scanning the SNPs in BCO2 gene revealed a G/A mutation in exon 6 of the BCO2 gene in white and yellow skin chicken. Generally, one SNP c.890A>G was found to be associated with the chicken skin color and may be used as a genetic marker in breeding for yellow skin in Chinese indigenous chickens. [ABSTRACT FROM AUTHOR]

Simple Summary: Milk and other dairy products are commonly consumed in many parts of the world. Dairy cattle, having millions of milk trait records, make excellent model species for understanding the genetics controlling the production of milk. This manuscript gives a summary of the current understanding of the genetic signals for milk production, in terms of the biological pathways they are involved with, and highlights a number of methods that can be used to identify the genes and variants underlying these signals. Knowledge of these variants will improve the ability of farmers and animal breeding companies to increase the rate of genetic gain for milk traits and enable the use of technologies such as gene editing. Milk is a complex liquid, and the concentrations of many of its components are under genetic control. Many genes and pathways are known to regulate milk composition, and the purpose of this review is to highlight how the discoveries of quantitative trait loci (QTL) for milk phenotypes can elucidate these pathways. The main body of this review focuses primarily on QTL discovered in cattle (Bos taurus) as a model species for the biology of lactation, and there are occasional references to sheep genetics. The following section describes a range of techniques that can be used to help identify the causative genes underlying QTL when the underlying mechanism involves the regulation of gene expression. As genotype and phenotype databases continue to grow and diversify, new QTL will continue to be discovered, and although proving the causality of underlying genes and variants remains difficult, these new data sets will further enhance our understanding of the biology of lactation. [ABSTRACT FROM AUTHOR]

Milk yield and composition phenotypes are systematically recorded across several lactations in goats, but the majority of genome-wide association studies (GWAS) performed so far have rather ignored the longitudinal nature of such data. Here, we have used two different GWAS approaches to analyse data from three lactations recorded in Murciano-Granadina goats. In Analysis 1, independent GWAS have been carried out for each trait and lactation, while a single longitudinal GWAS, jointly considering all data, has been performed in Analysis 2. In both analyses, genome-wide significant QTL for lactose percentage on chromosome 2 (129.77-131.01 Mb) and for milk protein percentage on the chromosome 6 (74.8-94.6 Mb) casein gene cluster region were detected. In Analysis 1, several QTL were not replicated in all three lactations, possibly due to the existence of lactation-specific genetic determinants. In Analysis 2, we identified several genome-wide significant QTL related to milk yield and protein content that were not uncovered in Analysis 1. The increased number of QTL identified in Analysis 2 suggests that the longitudinal GWAS is particularly well suited for the genetic analysis of dairy traits. Moreover, our data confirm that variability within or close to the casein complex is the main genetic determinant of milk protein percentage in Murciano-Granadina goats., (© 2023 Stichting International Foundation for Animal Genetics.)

Aralkylamine N-acetyltransferase (AANAT) and acetylserotonin O-methyltransferase (ASMT), the two rate-limiting enzymes for melatonin synthesis, regulate melatonin production in mammals. Through analysis of the milk melatonin level and dairy herd improvement (DHI) index, it was found that the melatonin concentration in milk was significantly negatively correlated with the 305 day milk yield (305M) and peak milk yield (PeakM) (p < 0.05), while it was significantly positively correlated with the serum melatonin concentration (p < 0.05). The full-length of AANAT and ASMT were sequenced and genotyped in 122 cows. Three SNPs in AANAT and four SNPs in ASMT were significantly related to MT levels in the milk and serum (p < 0.05). The SNPs in AANAT were temporarily denoted as N-SNP1 (g.55290169 T>C), N-SNP2 (g.55289357 T>C), and N-SNP3 (g.55289409 C>T). The SNPs in ASMT were temporarily denoted as M-SNP1 (g.158407305 G>A), M-SNP2 (g.158407477 A>G), M-SNP3 (g.158407874 G>A), and M-SNP4 (g.158415342 T>C). The M-SNP1, M-SNP2, and M-SNP3 conformed to the Hardy−Weinberg equilibrium (p > 0.05), while other SNPs deviated from the Hardy−Weinberg equilibrium (p < 0.05). The potential association of MT production and each SNP was statistically analyzed using the method of linkage disequilibrium (LD). The results showed that N-SNP2 and N-SNP3 had some degree of LD (D′ = 0.27), but M-SNP1 and M-SNP2 had a strong LD (D′ = 0.98). Thus, the DHI index could serve as a prediction of the milk MT level. The SNPs in AANAT and ASMT could be used as potential molecular markers for screening cows to produce high melatonin milk. [ABSTRACT FROM AUTHOR]

Background: Production, marketability and consumer preference of red tilapia often depends upon the intensity of coloration. Hence, new approaches to develop coloration are now geared to improve market acceptability and profit. This study evaluated the effects of carotenoid-rich diets on the phenotypic coloration, carotenoid level, weight gain and expression of coloration-linked genes in skin, fin and muscle tissues. Carotenoids were extracted from dried Daucus carota peel, Ipomoea aquatica leaves, and Moringa oleifera leaves. Eighty (80) size-14 fish were fed with carotenoid-rich treatments twice a day for 120 days. The phenotypic effect of the carotenoid extracts was measured through a color chart. Skin carotenoid level was measured through UV-vis spectrophotometer. csf1ra, Bcdo2 and StAR expression analysis was done using qRT-PCR. Results: Treatments with carotenoid extracts yielded higher overall scores on phenotypic coloration and tissue carotenoid levels. Differential expression of carotenoid-linked genes such as the elevated expression in csf1ra and lower expression in Bcdo2b following supplementation of the enhanced diet supports the phenotypic redness and increased carotenoid values in red tilapia fed with D. carota peel and I. aquatica leaves. Conclusions: Overall improvement in the redness of the tilapia was achieved through the supplementation of carotenoid-rich diet derived from readily available plants. Differential expression of coloration-linked genes supports the increase in the intensity of phenotypic coloration and level of carotenoids in the tissues. The study emphasizes the importance of carotenoids in the commercial tilapia industry and highlights the potential of the plant extracts for integration and development of feeds for color enhancement in red tilapia. [ABSTRACT FROM AUTHOR]

Background: The accumulation of carotenoids in adipose tissue leading to yellow fat is, in sheep, a heritable recessive trait that can be attributed to a nonsense mutation in the beta-carotene oxygenase 2 (BCO2) gene. However, not all sheep breeds suffering from yellow fat have this nonsense mutation, meaning that other functional mechanisms must exist. We investigated one such breed, the Norwegian spælsau. Results: In spælsau we detected an aberration in BCO2 mRNA. Nanopore sequencing of genomic DNA revealed the insertion of a 7.9 kb endogenous Jaagsiekte Sheep Retrovirus (enJSRV) sequence in the first intron of the BCO2 gene. Close examination of its cDNA revealed that the BCO2 genes first exon was spliced together with enJSRV-sequence immediately downstream of a potential -AG splice acceptor site at enJSRV position 415. The hybrid protein product consists of 29 amino acids coded by the BCO2 exon 1, one amino acid coded by the junction sequence, followed by 28 amino acids arbitrary coded for by the enJSRV-sequence, before a translation stop codon is reached. Conclusions: Considering that the functional BCO2 protein consists of 575 amino acids, it is unlikely that the 58 amino acid BCO2/enJSRV hybrid protein can display any enzymatic function. The existence of this novel BCO2 allele represents an alternative functional mechanism accounting for BCO2 inactivation and is a perfect example of the potential benefits for searching for structural variants using long-read sequencing data. [ABSTRACT FROM AUTHOR]

Background: The DGAT1 gene encodes an enzyme responsible for catalysing the terminal reaction in mammary triglyceride synthesis, and underpins a well-known pleiotropic quantitative trait locus (QTL) with a large influence on milk composition phenotypes. Since first described over 15 years ago, a protein-coding variant K232A has been assumed as the causative variant underlying these effects, following in-vitro studies that demonstrated differing levels of triglyceride synthesis between the two protein isoforms. Results: We used a large RNAseq dataset to re-examine the underlying mechanisms of this large milk production QTL, and hereby report novel expression-based functions of the chr14 g.1802265AA > GC variant that encodes the DGAT1 K232A substitution. Using expression QTL (eQTL) mapping, we demonstrate a highly-significant mammary eQTL for DGAT1, where the K232A mutation appears as one of the top associated variants for this effect. By conducting in vitro expression and splicing experiments in bovine mammary cell culture, we further show modulation of splicing efficiency by this mutation, likely through disruption of an exon splice enhancer as a consequence of the allele encoding the 232A variant. Conclusions: The relative contributions of the enzymatic and transcription-based mechanisms now attributed to K232A remain unclear; however, these results suggest that transcriptional impacts contribute to the diversity of lactation effects observed at the DGAT1 locus. [ABSTRACT FROM AUTHOR]

Background: Within the last few years a large amount of genomic information has become available in cattle. Densities of genomic information vary from a few thousand variants up to whole genome sequence information. In order to combine genomic information from different sources and infer genotypes for a common set of variants, genotype imputation is required. Results: In this study we evaluated the accuracy of imputation from high density chips to whole genome sequence data in Brown Swiss cattle. Using four popular imputation programs (Beagle, FImpute, Impute2, Minimac) and various compositions of reference panels, the accuracy of the imputed sequence variant genotypes was high and differences between the programs and scenarios were small. We imputed sequence variant genotypes for more than 1600 Brown Swiss bulls and performed genome-wide association studies for milk fat percentage at two stages of lactation. We found one and three quantitative trait loci for early and late lactation fat content, respectively. Known causal variants that were imputed from the sequenced reference panel were among the most significantly associated variants of the genome-wide association study. Conclusions: Our study demonstrates that whole-genome sequence information can be imputed at high accuracy in cattle populations. Using imputed sequence variant genotypes in genome-wide association studies may facilitate causal variant detection. [ABSTRACT FROM AUTHOR]

Carotenoids are lipid-soluble pigments and important for a variety of physiological functions. They are major dietary vitamin A precursors and act as lipophilic antioxidants in a variety of tissues and are associated with important health benefits in humans and animals. All animals must acquire carotenoids from their diet, but to our knowledge, there are no studies investigating the intestinal carotenoid absorption and their blood concentrations in New World camelids. The present study aimed to assess the serum concentrations of selected carotenoids in llamas ( n = 13) and alpacas ( n = 27). Serum carotenoids as well as retinol (vitamin A) and α-tocopherol (vitamin E) were determined by high-performance liquid chromatography coupled with mass spectrometry and these were unable to detect any carotenoids ( α- and β-carotene, α- and β-cryptoxanthin, lutein, zeaxanthin, lycopene) in the samples. The concentrations of retinol in alpacas (2.89 ± 1.13 μmol/l; mean ± SD) were higher (p = 0.024) than those found in llamas (2.05 ± 0.87 μmol/l); however, the concentrations of α-tocopherol were not significantly (p = 0.166) different (llamas: 3.98 ± 1.83 μmol/l; alpacas: 4.95 ± 2.14 μmol/l). The results show that both llamas and alpacas are not able to absorb intact carotenoids, but efficiently convert provitamin A carotenoids to retinol. [ABSTRACT FROM AUTHOR]

Bovine respiratory disease complex (BRDC) is the most expensive disease in beef cattle in the United States costing the industry at least US$1 billion annually. Bovine respiratory disease complex causes damage to lung tissue resulting in persistent lung lesions observable at slaughter. Severe lung lesions at harvest have been associated with decreased preharvest ADG and increased clinical BRDC in the feedlot. Our objective was to identify SNP that are associated with severe lung lesions observed at harvest in feedlot cattle. We conducted a genomewide association study (GWAS) using a case-control design for severe lung lesions in fed cattle at slaughter using the Illumina Bovine HD array (approximately 770,000 SNP) and sample pooling. Lung samples were collected from 11,520 young cattle, a portion of which had not been treated with antibiotics (participating in a "natural" marketing program), at a large, commercial beef processing plant in central Nebraska. Lung samples with lesions (cases) and healthy lungs (controls) were collected when both phenotypes were in close proximity on the viscera (offal) table. We constructed 60 case and 60 control pools with 96 animals per pool. Pools were constructed by sampling sequence to ensure that case and control pool pairs were matched by proximity on the processing line. The Bovine HD array (770,000 SNP) was run on all pools. Fourteen SNP on BTA 2, 3, 4, 9, 11, 14, 15, 22, 24, and 25 were significant at the genomewide experiment-wise error rate of 5% (P ≤ 1.49 × 10-7). Eighty-five SNP on 28 chromosomes achieved a false discovery rate of 5% (P ≤ 5.38 × 10-6). Significant SNP were near (±100 kb) genes involved in tissue repair and regeneration, tumor suppression, cell proliferation, apoptosis, control of organ size, and immunity. Based on 85 significantly associated SNP in or near a collection of genes with diverse function on 28 chromosomes, we conclude that the genomic footprint of lung lesions is complex. A complex genomic footprint (genes and regulatory elements that affect the trait) is consistent with what is known about the cause of the disease: complex interactions among multiple viral and bacterial pathogens along with several environmental factors including dust, commingling, transportation, and stress. Characterization of sequence variation near significant SNP will enable accurate and cost effective genome-enhanced genetic evaluations for BRDC resistance in AI bulls and seed stock populations. [ABSTRACT FROM AUTHOR]

The gene encoding human β-carotene-9′,10′-oxygenase, which cleaves the 9′,10′ double bond in β-carotene into β-apo-10′-carotenal, was cloned and expressed in Escherichia coli. Under aqueous conditions, the optimum organic solvent for the formation of detergent micelles was toluene. The optimum pH, temperature, detergent type, and the optimum concentrations of detergent, substrate, and enzyme for β-apo-10′-carotenal production were 8.0, 37°C, Tween 40, 2.4%, 300 mg β-carotene/l, and 0.25 U/ml, respectively. Under the optimum conditions, 43 mg β-apo-10′-carotenal/l was produced after 21 h with a conversion of 14%. This is the first report to describe the enzymatic production of β-apo-10′carotenal. [ABSTRACT FROM AUTHOR]

Lycopene is a non-provitamin A carotenoid that exhibits several health benefits. Epidemiological data support a correlation between lycopene intake and the attenuation of several chronic diseases, including certain types of cancers and cardiovascular diseases. It is currently unknown whether the beneficial effects are from the native structure of lycopene or its metabolic derivatives: lycopenals, lycopenols, and lycopenoic acids. This literature review focuses on the current research on lycopene digestion, absorption, metabolism, and excretion. This review primarily focuses on in vivo studies because of the labile nature and difficulty of studying carotenoids within in vitro experimental models. The studies presented address tissue accumulation of lycopene, the modification of bioavailability due to genetic and dietary factors, and lycopene cleavage by the enzymes ß-carotene oxygenase 1 (BCO1) and ß-carotene oxygenase 2 (BCO2). The current literature suggests that the majority of lycopene is cleaved eccentrically by BCO2, yet further research is needed to probe the enzymatic cleavage activity at the tissue level. Additionally, results indicate that single nucleotide polymorphisms and dietary fat influence lycopene absorption and thus modify its health effects. Further research exploring the metabolism of lycopene, the mechanisms related to its health benefits, and optimal diet composition to increase the bioavailability is required. [ABSTRACT FROM AUTHOR]

The objective of this study was to identify genomic regions associated with milk fat percentage (FP), crude protein percentage (CPP), urea concentration (MU) and efficiency of crude protein utilization (ECPU: ratio between crude protein yield in milk and dietary crude protein intake) using grazing, mixed-breed, dairy cows in New Zealand. Phenotypes from 634 Holstein Friesian, Jersey or crossbred cows were obtained from two herds at Massey University. A subset of 490 of these cows was genotyped using Bovine Illumina 50K SNP-chips. Two genome-wise association approaches were used, a single-locus model fitted to data from 490 cows and a single-step Bayes C model fitted to data from all 634 cows. The single-locus analysis was performed with the Efficient Mixed-Model Association eXpedited model as implemented in the SVS package. Single nucleotide polymorphisms (SNPs) with genome-wide association p-values ≤ 1.11 × 10−6 were considered as putative quantitative trait loci (QTL). The Bayes C analysis was performed with the JWAS package and 1-Mb genomic windows containing SNPs that explained > 0.37% of the genetic variance were considered as putative QTL. Candidate genes within 100 kb from the identified SNPs in single-locus GWAS or the 1-Mb windows were identified using gene ontology, as implemented in the Ensembl Genome Browser. The genes detected in association with FP (MGST1, DGAT1, CEBPD, SLC52A2, GPAT4, and ACOX3) and CPP (DGAT1, CSN1S1, GOSR2, HERC6, and IGF1R) were identified as candidates. Gene ontology revealed six novel candidate genes (GMDS, E2F7, SIAH1, SLC24A4, LGMN, and ASS1) significantly associated with MU whose functions were in protein catabolism, urea cycle, ion transportation and N excretion. One novel candidate gene was identified in association with ECPU (MAP3K1) that is involved in post-transcriptional modification of proteins. The findings should be validated using a larger population of New Zealand grazing dairy cows. [ABSTRACT FROM AUTHOR]

Exactly six-hundred (600) scientific articles that report milk and milk products' color results in scientific journals in the last couple of decades were reviewed. Thereof, the greatest part of the articles derived from Europe (36.3%) and Asia (29.5%). The greatest share of researchers used Minolta colorimeters (58.8%), while 26.3% of them used Hunter devices. Most reports were on cheese (31.0%) followed by fermented products (21.2%). Moreover, the highest number of papers reported color data of milk and milk products made from cow's milk (44.81%). As expected, goat's cheese was the brightest (L* = 87.1), while cow's cheese was the yellowest (b* = 17.4). Most importantly, it appeared that color research results reported were often impossible to replicate or to interpret properly because of incomplete description of the methodology. In some of the manuscripts reviewed, illuminant source (61.0%), aperture size (93.8%), observer angle, and number of readings (over 70% of all cases) were not reported. It is therefore critical to set rules regarding the description of the methodology for (milk) color research articles in order to ensure replicability and/or comparison of studies. [ABSTRACT FROM AUTHOR]

Background: Pseudo-phenotypes, such as 305-day yields, estimated breeding values or deregressed proofs, are usually used as response variables for genome-wide association studies (GWAS) of milk production traits in dairy cattle. Computational inefficiency challenges the direct use of test-day records for longitudinal GWAS with large datasets. Results: We propose a rapid longitudinal GWAS method that is based on a random regression model. Our method uses Eigen decomposition of the phenotypic covariance matrix to rotate the data, thereby transforming the complex mixed linear model into weighted least squares analysis. We performed a simulation study that showed that our method can control type I errors well and has higher power than a longitudinal GWAS method that does not include time-varied additive genetic effects. We also applied our method to the analysis of milk production traits in the first three parities of 6711 Chinese Holstein cows. The analysis for each trait was completed within 1 day with known variances. In total, we located 84 significant single nucleotide polymorphisms (SNPs) of which 65 were within previously reported quantitative trait loci (QTL) regions. Conclusions: Our rapid method can control type I errors in the analysis of longitudinal data and can be applied to other longitudinal traits. We detected QTL that were for the most part similar to those reported in a previous study in Chinese Holstein. Moreover, six additional SNPs for fat percentage and 13 SNPs for protein percentage were identified by our method. These additional 19 SNPs could be new candidate quantitative trait nucleotides for milk production traits in Chinese Holstein. [ABSTRACT FROM AUTHOR]