Journal of animal science最新文献

{"title":"Omega-3 supplement alters water consumption and plasma fatty acid profile of beef heifers.","authors":"Kendal L Green,Madison R Kovarna,Ethan R Schlegel,Cody L Wright,Ana Clara B Menezes,Zachary K Smith,Jessica N Drum","doi":"10.1093/jas/skaf312","DOIUrl":"https://doi.org/10.1093/jas/skaf312","url":null,"abstract":"Flaxseed oil contains elevated levels of omega-3 fatty acids (n-3 FA), which have been shown to impact reproductive performance. This study aimed to determine the effects of a flaxseed oil-based supplement on reproductive parameters, feeding behavior, and lipid profile in beef heifers. Sixty Angus and Simmental × Angus heifers (14 months old ± 2 months), blocked by full body weight (BW; 396.79 ± 33.78 kg) ± SD and antral follicle count, were randomly assigned to one of two ad libitum supplementation treatments: a commercial loose mineral supplement (CON; n = 30) or flaxseed oil-based supplement (FLAX; n = 30) for 8 weeks. Heifers were individually fed by an automated feeding system where basal diet (TMR), a mix of corn silage, grass hay, and DDGS as offered ad libitum. Water and supplements were provided in separate feeders to measure intake and were compiled over 24 hours for each animal by the Insentec system. On week 5, heifers were enrolled in a fixed-time artificial insemination (FTAI) protocol. The presence of a corpus luteum (CL) was recorded weekly, as well as the largest follicle diameter (LFD) and CL presence on days of the FTAI protocol (D0, D7, and D9). Puberty attainment was determined when a CL could be visualized by ultrasound and/or the blood sample contained concentrations of P4 above the threshold level of 1 ng/mL. Pregnancy diagnosis [P/AI; % (n)] was performed at ∼30d and ∼60d following AI. Plasma samples were collected once weekly and on days 0, 7 and 9 of the FTAI protocol for circulating progesterone (P4), estradiol (E2), and fatty acid (FA) profiles. Water intake in kilograms per day (kg/d) was lower in FLAX while TMR intake (kg/d) tended (P = 0.08) to be greater in FLAX compared to CON. Additionally, puberty tended to be attained faster (P = 0.10), and P4 on D9 tended to be lower (P = 0.09) for FLAX heifers. Concentrations of α-linolenic (ALA), and linoleic (LA) acids was greater in FLAX (P < 0.03). In addition, eicosapentaenoic (EPA), arachidonic (AA), and total polyunsaturated fatty acids (PUFA) tended to be greater for heifers in the FLAX group (P > 0.07). In conclusion, supplementation of n-3 FA caused lower water intake, higher plasma FA, and a tendency for faster puberty attainment. In conjunction, these findings offer data to support the use of a flaxseed oil-based supplement as a positive supplementation strategy for beef heifers to induce an optimal endocrine environment and potentially anticipate puberty.","PeriodicalId":14895,"journal":{"name":"Journal of animal science","volume":"50 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145025855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Different sources and dosages of zinc oxide and copper influence growth performance and intestinal health of post-weaning piglets.","authors":"Clara Negrini,Hadhemi Baccouri,Alessandra Monteiro,Luca Lo Verso,Paolo Trevisi,Marie-Pierre Létourneau-Montminy,Frédéric Guay","doi":"10.1093/jas/skaf314","DOIUrl":"https://doi.org/10.1093/jas/skaf314","url":null,"abstract":"In pig production, weaning is a critical period where piglets face several environmental stressors. This transition leads to a significant growth reduction and can result in digestive disorders, including diarrhea. To formulate a feed that meets zinc (Zn) and copper (Cu) requirements during the weaning period while minimizing their release into the environment, it became evident that a more bioavailable micro-mineral supplement is necessary. This project aimed to evaluate two sources of Zn (standard oxides and potentiated oxide (ZnO)) and Cu (sulphate and monovalent Cu), on the growth performance, intestinal health (inflammation, barrier function, mucosal stress), and microbiota abundance and composition of weaned piglets. At weaning (21 days), 135 piglets were selected. The experimental diets were composed as follows: basal diet with the addition of: 1) Negative control (NC): 150 mg/kg ZnO and 150 mg/kg Cu (sulphate); 2) Positive control (PC): 2,600 mg/kg ZnO and 150 mg/kg Cu (sulphate); 3) SpEU: 150 mg/kg potentiated form of ZnO (HiZox®) and 150 mg/kg monovalent Cu oxide (CoRouge®); 4) SpCA: 300 mg/kg potentiated ZnO and 150 mg/kg monovalent Cu. The experimental diets were provided for 14 days (phase 1) post-weaning. Subsequently, all piglets received the same diets for phase 2 (14-28 days) and phase 3 (28-42 days). Piglets were weighed at weaning and on days (d) 14, 28, and 42. At d7 and d14, blood was collected for intestinal health status marker analyses. At d14, fecal samples were collected to assess the effects on microbiota, calprotectin, and neopterin. In the first phase, average daily gain (ADG) and average daily feed intake (P = 0.001) resulted in higher outcomes in the PC group. Feed conversion was higher in the SpEU and SpCA groups (P = 0.002). For the overall performance, however, highest ADG were observed in both the PC and SpCA groups (P = 0.001). The citrulline was found to be higher in the NC group (P = 0.002). The diamine oxidase was higher in SpCA than PC group (P = 0.008). Zinc concentrations in feces and serum were higher for PC treatment (P = 0001, P = 0.037, respectively). From the results it was possible to confirm the positive effects of the administration of 300 mg/kg of the potentiated ZnO and 150 mg/kg monovalent copper oxide could be a valid substitute of pharmacological ZnO.","PeriodicalId":14895,"journal":{"name":"Journal of animal science","volume":"53 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145008863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Age-related evolution of serum biochemistry and intestinal fatty acid signaling, innate immune response and barrier function in suckling and newly weaned piglets.","authors":"Fitra Yosi,Kristina Hartinger,Frederike Lerch,Julia C Vötterl,Simone Koger,Suchitra Sharma,Doris Verhovsek,Barbara U Metzler-Zebeli","doi":"10.1093/jas/skaf313","DOIUrl":"https://doi.org/10.1093/jas/skaf313","url":null,"abstract":"It is helpful for diagnostic purposes to improve our current knowledge of gut development and serum biochemistry in young piglets. This study investigated serum biochemistry, and gut site-specific patterns of short-chain fatty acids (SCFA) and expression of genes related to barrier function, innate immune response, antioxidative status and sensing of fatty and bile acids in suckling and newly weaned piglets. The experiment consisted of two replicate batches with 10 litters each. Piglets could suckle freely and had access to creep feed from day of life (DoL) 3. Weaning occurred on DoL28. Blood, gastric, cecal, and colonic digesta, as well as jejunal and cecal tissue were collected on DoL3, 7, 14, 21, 28, 31, and 35 (n = 10/sex/DoL). Serum liver enzyme activities were high on DoL3 but decreased thereafter, reflecting the immature state of hepatocytes after birth (P < 0.05). Age-related fluctuations in serum glucose and lipids indicated changes in energy metabolism within the suckling period and lower feed intake after weaning. Short-chain fatty acids (SCFA) increased in cecal digesta from DoL3 to 28 (P < 0.05). After weaning, lower gastric and cecal SCFA on DoL31 and DoL35, respectively, versus DoL28 mirrored lower feed intake, whereas colonic SCFA increased after weaning (P < 0.05). Jejunal and cecal expression of free fatty acid receptors and monocarboxylate transporters changed with increasing age (P < 0.05). For some genes including FFAR2 and FFAR3 in the cecum, expression levels declined from DoL3 onwards (P < 0.05), indicating an inverse relationship with luminal SCFA availability. However, there was no unique jejunal and cecal expression pattern for fatty acid receptors and transporters, and pattern-recognition receptors (PRR), probably corresponding to the age-related changes in their ligands. Increasing expression of anti-inflammatory IL10 in jejunum and cecum from DoL3 to 28 may be indicative of a build-up of immune tolerance (P < 0.05). Postweaning expression of PRR was not increased, but reduced jejunal expression of antioxidative enzymes and increased cecal expression of proinflammatory TNFA combined with lower expression of MUC2, OCLN, and ZO1 compared to the suckling phase indicated compromised gut homeostasis (P < 0.05). Overall, the present results show study-specific age-related patterns of genes associated with mucosal metabolite sensing or defense mechanisms in the jejunum and cecum from birth to after weaning.","PeriodicalId":14895,"journal":{"name":"Journal of animal science","volume":"12 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145008861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The serum levels of triacylglycerols, non-esterified fatty acids and beta-hydroxybutyrate as markers of reproductive capability of primiparous dairy cows.","authors":"Tereza Toralová,Jaromír Ducháček,Matúš Gašparík,Veronika Kinterová,Nikola Marešová,Radim Codl,Luděk Stádník","doi":"10.1093/jas/skaf276","DOIUrl":"https://doi.org/10.1093/jas/skaf276","url":null,"abstract":"Metabolic stress and negative energy balance (NEB) are typical undesirable accompanying phenomenon of the post-partum period in dairy cattle. They negatively affect not only milk production but also the reproductive abilities of the cow, and it is therefore desirable to recognize NEB early to prevent its development. Metabolic stress markers are traditionally total cholesterol (tChol), non-esterified fatty acids (NEFA), beta-hydroxybutyrate (BHB) and triacylglycerols (TAGs). The aim of this work was to determine whether the level of the aforementioned markers in the blood correlates with the ability of a primiparous dairy cow to conceive soon after the first calving. Therefore, oocytes were collected from the monitored cows shortly after calving using the ovum pick-up method, and their quality was subsequently determined. We observed cumulus cell expansion, oocytes quality, maturation rate and the amount and distribution of lipids within the oocyte. In addition to the mentioned markers, we also monitored the effect of the season in which aspiration was performed to assess its impact on the reproductive indicators of the monitored cows. We observed a negative correlation between higher TAGs and oocyte maturation rate, while the number of aspirated oocytes per cow and the fertilization capability were positively associated with TAGs. Additionally, higher BHB levels in blood were linked to enhanced fertilization capability. The higher levels of TAGs, BHB and NEFA in blood were associated with increased lipid intensity and higher lipid content was positively correlated with both the quality of cumulus cells and oocytes. In summary, we found that NEFA, BHB and TAGs are the most reliable markers of a cow's readiness to become pregnant after her first calving. The use of tChol, however, remains very controversial. Moreover, primiparous cows are more prepared for re-pregnancy in the warmer season.","PeriodicalId":14895,"journal":{"name":"Journal of animal science","volume":"34 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145018272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic prediction and genome-wide association study for liver abscesses in crossbred beef cattle.","authors":"H L Bradford,L A Kuehn,W M Snelling,B N Keel,S A Jones,R M Thallman,A K Lindholm-Perry","doi":"10.1093/jas/skaf275","DOIUrl":"https://doi.org/10.1093/jas/skaf275","url":null,"abstract":"Liver abscesses are a concern in feedlot cattle, and little is known about the role of genetics in their development. This study aimed to estimate genetic parameters and to identify single nucleotide polymorphisms (SNP) associated with liver abscesses. Crossbred cattle representing 18 breeds in the United States Meat Animal Research Center Germplasm Evaluation Program were phenotyped for liver abscesses at slaughter (n = 9,044). Seventeen percent of cattle had liver abscesses. These cattle had genotypes that were imputed to sequence variant genotypes. After filtering and quality control, 340,723 SNP were used in the analysis. Liver abscess prevalence was modeled with a single-step genomic best linear unbiased prediction (ssGBLUP) threshold model using a Bayesian framework. The model included contemporary group (sex, treatment group, and slaughter date), additive genomic, and residual effects. Genomic heritability was 0.039 (95% highest posterior density = 0.005, 0.081), which was very small. To assess prediction quality, a 5-fold random cross-validation structure was used. Method Linear Regression was used to assess accuracy, bias, and dispersion by comparing estimated breeding values (EBV) from full and reduced analyses. Cross-validation metrics showed EBV based on genotypes had 0.05 reliability (SD < 0.01) with no bias relative to EBV based on genotypes and phenotypes. For the genome-wide association study, SNP effects were back calculated from the EBV solutions from ssGBLUP. No SNP were associated with liver abscesses at a Benjamini-Hochberg adjusted 0.05 significance level. Although a large dataset was used, this result was because of the low genomic heritability and imprecise EBV used to calculate SNP effects. Based on these results, environmental factors contribute to most of the variation in liver abscesses. Genetic selection to reduce liver abscesses would be slow because of the low genomic heritability, measurement late in life, and inability to measure breeding animals. A faster approach would be finding additional environmental interventions that maintain animal performance.","PeriodicalId":14895,"journal":{"name":"Journal of animal science","volume":"24 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145018163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Green tea extract complex as a phytogenic supplement to reduce bile salt hydrolase activity and enhance growth performance in weaning pigs.","authors":"Sungbo Cho,Robie Vasquez,Ji Hoon Song,Kyu-Yeol Son,Hee Yeon Kim,Si-Nae Park,Jong Pyo Chae,Jun-Ok Moon,Dae-Kyung Kang,In Ho Kim","doi":"10.1093/jas/skaf242","DOIUrl":"https://doi.org/10.1093/jas/skaf242","url":null,"abstract":"The post-weaning period is stressful for pigs due to changes in their environment and diet. The occurrence of diarrhea at this stage is high. Growth promoters such as antibiotics and zinc oxide (ZnO) have been used to not only reduce post-weaning diarrhea but also improve growth performance of weaning pigs. It has also been shown that the growth performance of pigs is negatively associated with bile salt hydrolase (BSH) in the gut. Antibiotic growth promoters (AGP) and ZnO administration have demonstrated effective inhibition of BSH, which is linked to enhanced growth performance in pigs. Therefore, this study evaluated the effects of a plant-based supplement, green tea extract, with butyric acid, and vitamin K (GBK), on growth performance, nutrient digestibility, fecal score, blood profile, and BSH activity of the gut microbiota of weaning pigs. Here, 192 crossbred weaning pigs [(Yorkshire × Landrace) × Duroc], aged 21 days, were subjected to a four-week-long feeding experiment. Pigs were divided into six treatments (n = 32 per treatment, 8 pens per treatment). After feeding, the average daily gain (ADG) and gain-to-feed (G:F) ratio improved linearly with GBK supplementation. During the feeding period, diarrhea was not observed in the treatment groups, and the fecal scores of the weaned pigs were not affected. Supplementation had no negative impact on the blood profile parameters of weaned pigs, including white blood cell count, red blood cell count, lymphocyte percentage, and blood urea nitrogen. Moreover, supplementation of GBK decreased the TNF-α and IL-6 while immunoglobulins (IgA, IgG) increased. In addition, GBK reduced the abundance of gut microbiota with BSH activity, including Clostridium sensu stricto 6, the Clostridia vadinBB60 group, Marvinbryantia, Muribaculaceae, and Enterococcus. Correlation analysis revealed that gut microbiota function related to secondary bile acid biosynthesis had a strong negative correlation with ADG, ADFI, and G:F ratio of the pigs. The combination of green tea, butyric acid, and vitamin K is an effective alternative to AGP and ZnO for improving growth performance, feed efficiency, and diarrhea score of weaned pigs. In addition, this feeding strategy had a modulatory effect on the gut microbiome, altering BSH activity associated with improved growth performance in weaning pigs.","PeriodicalId":14895,"journal":{"name":"Journal of animal science","volume":"57 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145018144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of algal oil as an alternative to fish oil in feline foods on serum concentrations of eicosapentaenoic acid and docosahexaenoic acid.","authors":"Laura A Motsinger,Catherine R Kalmbach,John Brejda,Nasson Mwakatage,Leslie Hancock,Dale A Fritsch","doi":"10.1093/jas/skaf252","DOIUrl":"https://doi.org/10.1093/jas/skaf252","url":null,"abstract":"Fish oil is a source of the n-3 fatty acids eicosapentaenoic acid (EPA) and docosahexanoic acid (DHA) that confer several health benefits. To ensure continuity in the supply of n-3 fatty acids, alternative sources are being sought. Algal oil may serve as a promising alternative to fish oil for supplementing DHA in cat foods. The purpose of this study was to determine if inclusion of algal oil in place of fish oil in feline foods would result in similar serum DHA and EPA concentrations. Cats were first fed a control food for 5 weeks and then randomized into two groups and fed test foods containing either fish oil or algal oil in sequential increasing concentrations of DHA (0.2%, 0.4%, and 0.6%). Serum was analyzed at the beginning and end of each of these 5-week feeding periods. Oil type had no effect on body weight of cats consuming foods containing either algal oil or fish oil; only cats that consumed the algal oil food with 0.6% DHA had a significant decrease from baseline in food intake (P = 0.0011). Analysis of serum fatty acid concentrations showed that serum DHA increased at similar rates when fish oil and algal oil levels were increased in the food. Although increasing levels of fish and algal oil both increased serum EPA concentrations, the higher concentrations of EPA in the fish oil foods resulted in higher circulating concentrations of EPA in those cats. Algal oil was included at levels 3.7-fold lower than fish oil due to the high DHA content of algal oil. Overall, these data indicate that algal oil may serve as a good alternative dietary source of DHA. Fatty acid profiles of algal oil should be considered when selecting a replacement for fish oil in feline foods.","PeriodicalId":14895,"journal":{"name":"Journal of animal science","volume":"57 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145018164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of isoflavone supplementation, via red clover hay, on the growth and postgraze physiological recovery of beef steers grazing endophyte-infected tall fescue pastures.","authors":"Brittany E Davis,Alayna A Jacobs,Michael D Flythe,Tracy A Hamilton,Huihua Ji,F Neal Schrick,Jack P Goodman","doi":"10.1093/jas/skaf304","DOIUrl":"https://doi.org/10.1093/jas/skaf304","url":null,"abstract":"Livestock grazing endophyte-infected (E+) tall fescue can exhibit persistent systemic vasoconstriction and fescue toxicosis. Isoflavones in legumes, most notably red clover (RC), are known hypotensive agents. The objective of the experiment was to evaluate the effect of isoflavone supplementation via RC hay, every day or every other day (QOD), on average daily gain (ADG) of steers grazing E+ tall fescue pastures and their physiological recovery after grazing when managed on a non-toxic diet (28-d). In Spring 2018 (62-d) and 2019 (65-d), 36 Angus× steers were blocked by initial body weight (BW) into pastures (n = 6 pastures year-1) assigned to one of three supplement treatments: Dried distillers' grain with solubles (DDGS) only (CON; pasture + DDGS), 7.5% RC hay daily (based on 300-kg steer consuming 2.5%-BW; 7.5%-RC; pasture + DDGS + RC hay), or 7.5% RC hay QOD (7.5%-RC QOD; daily rotation of either: CON or 7.5%-RC). All supplements were isonitrogenous, and shrunk BW was collected at the start and end of the grazing period for determination of ADG. Each year, immediately after the grazing period, three steers were randomly selected from each pasture and moved to outdoor partially covered pens where they were fed a non-toxic diet for a recovery period of 28-d. The caudal artery of each steer was imaged immediately after grazing and then every 7-d over the recovery period using Doppler ultrasonography to monitor artery luminal areas (CAA). Jugular blood samples were collected immediately after grazing and on d-28 of recovery for determination of serum prolactin. Data were analyzed using the Mixed procedure of SAS with repeated measures and significance was set at P ≤ 0.05. Steer ADG was greater with 7.5%-RC daily or QOD (7.5%-RC: 0.77 kg d-1; 7.5%-RC QOD: 0.83 kg d-1), compared to CON (0.55 kg d-1; P < 0.01). Isoflavone supplementation via RC hay during the grazing period resulted in 2.5× larger CAA and higher serum prolactin concentrations immediately after grazing and over the recovery period, respectfully, compared with CON steers (P < 0.05). Furthermore, steers supplemented with 7.5%-RC during the grazing period were never vasoconstricted over the recovery period, but CON steers did not exhibit CAA recovery until d-21 (P < 0.05). Supplementation of isoflavones via RC hay daily or QOD, is an effective management strategy to improve ADG in cattle grazing E+ tall fescue pastures and reducing the time required for physiological recovery post-grazing.","PeriodicalId":14895,"journal":{"name":"Journal of animal science","volume":"17 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145018162","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Vision of How Low-Coverage Sequence Data Should Contribute to Genetic Evaluation in the Future.","authors":"R Mark Thallman,J E Borgert,Bailey N Engle,John W Keele,Warren M Snelling,Cedric Gondro,Larry A Kuehn","doi":"10.1093/jas/skaf294","DOIUrl":"https://doi.org/10.1093/jas/skaf294","url":null,"abstract":"Low-coverage sequencing refers to sequencing DNA of individuals to a low depth of coverage (e.g., 0.5X) and imputing that sequence to genomic sequence based on reference haplotypes from individuals sequenced to high depth of coverage (e.g., ≥ 10X). It has been proposed as an alternative to genotyping by SNP arrays. At least one commercial product based on it is available for agricultural species. Concerns limiting adoption in its current form are: 1) the cost of storing the huge volume of data it generates and 2) whether that additional data will result in improved accuracy of genetic evaluation. This work envisions future implementation of low-coverage sequencing to reduce storage costs and enhance genetic evaluations by leveraging the additional information in the full sequence of the pangenome to account for more genetic variation. We propose addressing the storage issue by representing genomic sequence of an individual in a pair of haplotype arrays with each element pointing to an enumerated haplotype of the sequence within one of approximately 50,000 defined genome segments. Assuming 60 million genomic variants, the infrastructure required to translate the identifier of any enumerated haplotype into its genomic sequence would require less than 10 gigabytes of binary storage. Each haplotype array element would require 2 bytes, so the marginal binary storage required to represent the genomic sequence of an individual would be about 200 kilobytes (KB), similar to the genotypes from a SNP array with 200,000 markers. This assumes no pedigree and no ambiguity of the imputation, though the latter is unrealistic. Strategies to minimize, and when necessary, to manage and efficiently represent ambiguity are proposed. The genomic sequence of an individual could be stored in about 1 KB (binary) if both parents have unambiguous sequence stored as described above. The proposed system for representing the pangenome includes algorithms for read mapping and imputation intended to leverage all known genetic variation in the target population. It is also designed to use sequencing reads generated for imputing genomic sequence of new individuals to identify unrecognized mutations, crossovers, and structural variants, thus continuously improving the genome representation, especially if widespread use of low-coverage sequencing in livestock industries is realized. This could make improved genetic merit and management of livestock feasible without computational burden.","PeriodicalId":14895,"journal":{"name":"Journal of animal science","volume":"64 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145018161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fitting and diversity of lactation curves in Saanen dairy goats","authors":"Zhicheng He, Yongqiang Lv, Xiaochen Qin, Chengming Han, Xiaolong Wang, Ping Wang, Jun Luo, Juan J Loor, Cong Li","doi":"10.1093/jas/skaf309","DOIUrl":"https://doi.org/10.1093/jas/skaf309","url":null,"abstract":"The shapes of lactation curves are affected by genetic and environmental factors, and flexible models are required to fit such curves. This study aimed to compare the effects of the Gaussian process regression model (Gaussian model) for fitting lactation curves Saanen dairy goats versus the parametric Wood’s model. In addition, we investigated effects of environmental factors on the shape of lactation curves. Principal component analysis (PCA) detected 3 (541 lactations fitted using the Wood’s model [WDS]), 5 (raw data from the WDS fitted using the Gaussian model [GWDS]), and 6 (1,032 lactation datasets fitted using the Gaussian model [GDS]) principal components (PCs). The interpretation of PC1 and PC2 in the three datasets was consistent, with PC1 accounting for total milk production, PC2 accounting for persistency (reflecting the difference between early and late lactation), PC3 accounting for milk yield in early lactation (WDS) and relative milk yield in mid-lactation (GWDS and GDS), and PC4 to 6 being associated with fluctuations throughout lactation. The lactation curves of three datasets were clustered into 2 (WDS), 2 (GWDS), and 3 (GDS) clusters based on their PC scores, and mainly differed in total milk production and persistency. The total milk production increased from the first to third parities, but the mid-term relative milk production was highest in first-parity goats. Compared with kidding in spring, kidding in winter led to higher total milk production and persistency, and lower mid-term relative milk production. Low persistency was detected when the number of kids was ≥2. The Gaussian model is suitable for fitting daily milk yield records, with main sources of variance in the lactation curves of Saanen goats in China being total milk yield and persistency.","PeriodicalId":14895,"journal":{"name":"Journal of animal science","volume":"28 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144930712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}