Journal of Dairy Science最新文献

{"title":"Effects of feeding colostrum volume at 6%, 8%, 10%, or 12% of birth body weight on efficiency of IgG absorption, gastric emptying, and postfeeding behavior in Holstein calves.","authors":"G Frederick, M Wieland, A Singh, R Ewing, M A Steele, H Somula, S Mann","doi":"10.3168/jds.2025-27228","DOIUrl":"https://doi.org/10.3168/jds.2025-27228","url":null,"abstract":"<p><p>Our objective was to evaluate how feeding colostrum at different volumes at the first feeding affects IgG absorption, gastric emptying, and calf behavior. Female Holstein calves (n = 88) were enrolled in a randomized block design to receive a single colostrum volume corresponding to 6%, 8%, 10%, or 12% of birth body weight (BBW). A subset of animals in 8 blocks (n = 32 calves) also received a gastric emptying marker acetaminophen (Ac) at a dose of 150 mg/kg metabolic body weight (BBW^0.75). Colostrum was administered within 2 h of birth via esophageal tube feeder. Blood samples were collected before (0 h) and 24 h after feeding. For the calves receiving Ac, plasma samples were also collected at 2, 4, 6, 8, 10, and 48 h after feeding. Colostrum and 24-h serum IgG concentrations were measured using radial immunodiffusion. Apparent efficiency of absorption (AEA) was calculated from 24-h serum IgG concentrations. Plasma Ac concentration was determined using an enzymatic colorimetric assay, and the proportion of Ac remaining in the stomach (Ac_s) at 8 h was modeled. Audio and video recordings of calf behavior during the first 2 h after feeding were analyzed with a custom ethogram. Data analysis was performed using mixed models or Fisher's exact tests as appropriate. Results are reported as LSM with 95% CI unless otherwise specified. The mean (range) BBW of calves was 40 (31.8-49.1) kg. Pooled colostrum had a median (range) Brix value of 24.2% (21.2%-29.6%) and IgG concentrations of 86.7 g/L (73.2-121.1 g/L). Calves in the 6%, 8%, 10%, and 12% groups were fed median (range) colostrum volumes (L) of 2.3 (2.0-2.8), 3.1 (2.5-3.9), 4.0 (3.5-4.5), and 4.8 (4.2-5.6), respectively. The 24-h serum IgG concentrations (g/L) were lowest in the 6% group (28.8 [25.8-31.8]), increased to 37.4 (34.4-40.4) in the 8% group, and were highest in the 10% and 12% groups (41.1 [38.1-44.1] and 43.4 [40.4-46.4], respectively). Group differences were observed for AEA (%), which gradually declined with an increasing feeding rate and was highest in the 6% and 8% groups (47.8 [44.9-50.7] and 46.2 [43.3-49.0], respectively), declined to 41.0 (38.1-43.9) in the 10% group, and was lowest at 36.3 (33.5-39.2) in the 12% group. At 8 h, Ac_s (%) was 50.4 (43.8-57.0), 55.3 (49.2-61.5), 57.9 (51.8-64.0), and 65.5 (59.2-71.8) of the original dose in the 6%, 8%, 10%, and 12% groups, respectively. Group differences in behavior were identified for kicking, a colic-like behavior, which was observed only in the 10% (n = 21 kicks total) and 12% (n = 40 kicks total) groups. Feeding a single colostrum meal equivalent to 8% or 10% of BBW within 2 h after birth offers a compromise in terms of IgG absorption, gastric emptying, and calf behavior. A larger volume (12% BBW) resulted in marginal improvement in serum IgG concentration, reduced AEA and gastric emptying, and was associated with increased colic-like behaviors.</p>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145181749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Invited review: A systematic review of the effects of pair housing on dairy calf welfare and productivity.","authors":"Katarína Bučková, Ágnes Moravcsíková, Radka Šárová","doi":"10.3168/jds.2024-26251","DOIUrl":"https://doi.org/10.3168/jds.2024-26251","url":null,"abstract":"<p><p>Individual housing of dairy calves has received criticism due to animal welfare concerns. Therefore, it is important to provide researchers and practitioners with accurate and reliable scientific knowledge on alternative housing systems for dairy calves. Our objective was to critically evaluate the scientific knowledge on pair-housed dairy calves. The outcomes investigated were the performance, behavior, reactivity to stress, health, learning abilities, and emotional states of pair-housed calves. Primary research articles were found through targeted Web of Science, ScienceDirect, PubMed, and Agricola searches. Studies were included if peer-reviewed, published in English, based upon original data, and pair-housed calves were compared with individually housed calves. After applying the inclusion criteria, 48 articles were left. Most articles did not report differences in behavior of individually and pair-housed calves. Few exceptions included social behavior, behavioral reaction to husbandry procedures, and behavior in the human approach test. Social behavior tended to be better developed in pair-housed calves, which also showed more flexible behavioral reactions to several husbandry procedures. However, pair-housed calves interacted less with a human in the human approach test. We found no consistent evidence of impaired health or improved productivity, learning abilities, and emotional states in pair-housed calves. In conclusion, pair housing provides calves with more benefits than individual housing and improves or does not affect variables of a high value to the producer. We encourage research on longer-term effects of pair housing, such as social behavior or productivity of dairy cows, because the number of long-term studies is limited.</p>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145181764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prevalence of Listeria monocytogenes in mozzarella cheese: A systematic review and meta-analysis.","authors":"Roberto Condoleo, Maria Concetta Campagna, Aya Zarea, Pina Briganti, Linda D'Amici, Maria Francesca Iulietto","doi":"10.3168/jds.2025-26815","DOIUrl":"https://doi.org/10.3168/jds.2025-26815","url":null,"abstract":"<p><p>Listeria monocytogenes is a human pathogen responsible for listeriosis, a sporadic but serious disease that poses significant health risks, particularly to vulnerable populations such as pregnant women, the elderly, and immunocompromised individuals. Mozzarella cheese, a widely consumed fresh dairy product, may represent as a potential vehicle for this pathogen, primarily due to the risk of post-processing contamination. This study presents a systematic review and meta-analysis aimed at estimating the prevalence of L. monocytogenes in mozzarella cheese at the end of the manufacturing process. The literature search identified 13 studies that met the predefined inclusion criteria from international citation databases. Additionally, 10 years of data were retrieved from an Italian laboratory database, covering mozzarella samples tested in Italy and 2 studies from gray literature. In total, 16 studies were analyzed using random-effects meta-analysis, and the pooled prevalence of L. monocytogenes in mozzarella was estimated at 1.2% (95% CI: 0.0-4.2) although a high heterogeneity among studies was observed (I² = 78%). Despite the detection of the pathogen in some studies, the concentration levels were below the limit of quantification, implying low levels of contamination. The results confirm that L. monocytogenes can occur in mozzarella, typically due to post-stretching cross-contamination. The findings underline the importance of implementing effective hygiene practices and highlight the need for further predictive microbiology models tailored to mozzarella's unique properties to better assess the consumer exposure.</p>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145181698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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 comparative analysis of dairy production systems: Milk production tiers and their impact on dairy calf and heifer cost of production in Brazil.","authors":"L H R Silva, A L Silva, M I Marcondes, C S Bittencourt, J V C Rodrigues, W P F Amorim, E P Lima Netto, T E Silva, J H C Costa, P P Rotta","doi":"10.3168/jds.2025-26579","DOIUrl":"https://doi.org/10.3168/jds.2025-26579","url":null,"abstract":"<p><p>The objective of this study was to estimate the costs associated with raising dairy calves and heifers in Brazil during 2021. Additionally, it sought to determine the average number of lactations that heifers should remain in the herd to cover their production costs, analyzing data from 311 dairy farms in Minas Gerais. These farms were categorized into 3 milk productive tiers based on daily milk production per cow: lower production tier (LOW) 12.0 L/cow per day (7.4-14.5 L/cow per day); intermediate production tier (INT) 18.0 L/cow per day (14.6-22.5 L/cow per day), and upper production tier (UPP) 26.7 L/cow per day (22.6-32.0 L/cow per day). Mean comparisons were performed using the GLIMMIX procedure of SAS. The main cost factors were feed, labor, and machinery, which together accounted for 83.0%, 85.0%, and 83.0% of the total costs for LOW, INT, and UPP tiers, respectively. The cost of raising a heifer from birth to calving tended to be lower for INT tier ($1,821.40 ± $44.35) and higher for LOW tier ($2,006.40 ± $62.52), whereas UPP tier had a cost of $1,884.60 ± $62.52, which was similar to both LOW and INT tiers. To cover their production costs, the average number of lactations that cows should remain in the herd was 3.98 (1.33-9.33) lactations for the LOW tier, 2.64 (1.33-6.33) lactations for the INT tier, and 1.64 (0.66-3.66) lactations for the UPP tier. Dairy farms with lower production have higher costs for rearing calves and heifers due to prolonged development and delayed age at first calving, largely due to less efficient growth, feeding and reproduction methods. Feed was the main cost, followed by labor and machinery. Improving genetics and management or purchasing better genetic animals can reduce costs and increase productivity, especially on farms with limited resources.</p>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145181768","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Describing the decision-making process of Ontario dairy farmers when managing down dairy cattle: A qualitative focus group study.","authors":"John E Brindle, Michael W Brunt, David L Renaud, Derek B Haley, Todd F Duffield, Charlotte B Winder","doi":"10.3168/jds.2025-26939","DOIUrl":"https://doi.org/10.3168/jds.2025-26939","url":null,"abstract":"<p><p>The objective of this study was to investigate Ontario dairy farmers' attitudes and perceptions toward down dairy cows, and the barriers and motivators influencing the use of best management practices. Four focus groups were conducted in southwestern Ontario in 2024, with a total of 21 dairy producers participating. Producers were asked about current practices, thoughts on best management practices, challenges to adopting best practices, and facilities and equipment for down cow care. The focus groups were audio recorded, transcribed, and analyzed using applied thematic analysis. Five themes were identified from the data: adaptive and flexible management strategies; farm resources and facilities; veterinary relationships and communication; producer experience and emotional impact; and animal-centered decision-making. Producers emphasized a balance between proactive, long-term strategies, such as prevention, record-keeping, and research-driven improvements, and the need for flexible, real-time decision-making to address the unpredictable nature of down cows. Facility design, labor availability, financial constraints, and veterinary collaboration played important roles in the care they provided to down cows. Further, producers highlighted the emotional burden of making euthanasia decisions and discussed the balance of animal welfare and economic sustainability. Producers also expressed a need for more research, better diagnostic tools, and practical on-farm solutions to improve down cow management. Addressing these challenges requires coordinated efforts that integrate practical tools, infrastructure improvements, producer education, and veterinary support systems. The interplay of these factors underscores the need for a holistic approach to support producers in navigating the multifaceted challenges they face in their daily work. This study contributes to understanding the multidimensional factors influencing dairy producers' management practices in caring for down dairy cows.</p>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145181742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimizing early lactation performance in dairy cows through co-supplementation of rumen-protected methionine and omega-3-enriched calcium salts.","authors":"T L France, K S Juarez-Leon, A Javaid, M G Vogellus, D C Reyes, J W McFadden","doi":"10.3168/jds.2025-27297","DOIUrl":"https://doi.org/10.3168/jds.2025-27297","url":null,"abstract":"<p><p>Supplementing rumen-protected Met (RP-Met) during the transition period has been shown to improve DMI and increase milk production in dairy cows. Omega-3 fatty acids (FA), particularly eicosapentaenoic acid (EPA; C20:5) and docosahexaenoic acid (DHA; C22:6), are known to support immune function in nonruminants, but their effects in dairy cows remain less defined. We aimed to investigate the combined effects of RP-Met and calcium salts (CS) of FA enriched with EPA and DHA on lactation performance in periparturient Holstein cows. Seventy-nine multiparous cows were enrolled in a randomized complete block design and assigned to 1 of 4 dietary treatments (n = 18 to 19 per treatment) from 3 wk before (-21 ± 3 d) to 3 wk after calving as follows: (1) no RP-Met and CS without n-3 FA (-Met/-n3FA; CS contained 56.0% saturated FA, 35.2% oleic acid, and 8.10% linoleic acid), (2) RP-Met with CS without n-3 FA (+Met/-n3FA), (3) no RP-Met with CS enriched in n-3 FA (-Met/+n3FA; CS contained 64.5% SFA, 25.4% oleic acid, 5.10% linoleic acid, 0.60% linolenic acid, 2.60% EPA and 1.40% DHA), or 4) RP-Met and CS enriched in n-3 FA (+Met/+n3FA). All cows were fed a corn silage-based TMR pre- and postpartum. Diets were formulated to provide either ≤0.96 g Met/Mcal of ME (-Met) or ≥1.13 g Met/Mcal of ME (+Met). Calcium salts were included at 1.5% of dietary DM across all diets. Prepartum DMI, BW, and BCS were unaffected by treatment. The main effect of treatment (supplemental Met and n-3 FA) increased postpartum DMI, Met (25.2 vs. 20.1 g/d Met prepartum and 59.9 vs. 35.9 g/d Met postpartum for +Met and -Met diets, respectively) and n-3 FA intakes (1.36 vs. 0 g/d EPA and DHA prepartum and 6.61 vs. 0 g/d EPA and DHA postpartum for +n3FA and -n3FA diets, respectively). Co-supplementation increased ECM, and FCM yields, and milk fat and true protein yields, and tended to increase milk yield, relative to diets containing only RP-Met or only n-3 FA. Cows co-supplemented with RP-Met and CS enriched in n-3 FA had marginally higher plasma glucose and lower plasma triglyceride concentrations at calving, and reduced plasma total and nonessential AA concentrations during lactation. Nutrient-specific responses included increased plasma Met in cows fed +Met diets and elevated milk lactose contents and yields, along with higher n-3 FA and PUFA contents and yields in cows fed CS enriched in n-3 FA. The additive effects of co-supplementation suggest potential synergy when cows are fed Met, EPA, and DHA. Although the underlying mechanisms were not fully elucidated, the observed improvements may be linked to enhanced mammary de novo FA synthesis, altered AA utilization, and increased hepatic gluconeogenesis, collectively supporting improved metabolic function and lactation performance in early lactation dairy cows.</p>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145181733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High Fischer ratio oligopeptide-fortified goat milk: A dual efficacy study on enhancing protein nutritional value and improving functional characteristics.","authors":"Junnan Wan, Xiaoxue Fan, Haiying Tao, Kaisheng Zhang, Cunfang Wang, Yanbo Luo","doi":"10.3168/jds.2025-27291","DOIUrl":"https://doi.org/10.3168/jds.2025-27291","url":null,"abstract":"<p><p>Functional dairy products represent a substantial area of interest, but the market offers a limited variety of products enriched with oligopeptides. This study focused on the incorporation of high Fischer ratio oligopeptide (HFO) derived from whey protein into goat milk using ultrasonic-assisted pasteurization. A comprehensive examination was conducted to assess the impact of the oligopeptide on the physicochemical properties, stability, and functional characteristics of goat milk. This analysis encompassed the evaluation of protein composition and content, antioxidant capacity, and various other functional attributes. The results revealed that HFO addition significantly increased both protein and whey protein content, enhancing nutritional value. Moreover, HFO fortification notably improved antioxidant activity, foamability, and emulsification properties. Although HFO incorporation elevated viscosity and particle size and reduced the absolute zeta potential, it minimally affected the distribution of fat globules. Storage stability studies indicated that HFO supplementation contributed to extending the shelf life of pasteurized milk. This study demonstrates the dual functionality of HFO in enhancing the nutritional profile and improving the techno-functional properties of goat milk. These findings offer valuable insights for advancing the production of functional goat milk products using oligopeptides as bioactive ingredients or specialized foods for medical purposes.</p>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145102588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of voluntary waiting period length on milk yield, fertility, and culling in high-yielding, second-parity cows.","authors":"A Hansson, K Holtenius, R Båge, M Lindberg, C Kronqvist","doi":"10.3168/jds.2025-26348","DOIUrl":"https://doi.org/10.3168/jds.2025-26348","url":null,"abstract":"<p><p>The substantial increase in milk yield capacity in modern dairy herds has led to growing interest in extending the voluntary waiting period, the time from calving to first insemination, as a strategy to prolong the calving interval. However, the effects of an extended voluntary waiting period on fertility and milk production vary, particularly between primiparous and multiparous cows. This study evaluated the effect of an extended voluntary waiting period, compared with a conventional one, on fertility, milk production, and culling in second-parity cows from 12 high-yielding commercial herds. Cows were distributed, based on odd or even ear tag numbers, and allocated into either a 50- or 140-d voluntary waiting period. Data including calving records, fertility metrics, monthly milk yields, and culling rates were collected from the Swedish official milk recording scheme. Out of 819 cows enrolled, 590 completed a third calving. The protocol extended the interval from calving to first insemination by 60 d, which resulted in a 46-d increase in the calving interval (12.5 mo vs. 14.0 mo). Daily milk yields did not differ between groups and averaged 34 kg ECM per day between 2 consecutive calvings and 40 kg ECM per lactating day. Although average milk yield at the last test milking before dry-off tended to be lower in cows with an extended voluntary waiting period compared with those on a conventional one (LSM 32.5 ± 0.96 kg ECM vs. 33.7 ± 1.01 kg ECM), dry period length remained unaffected. Total milk yield in the first 100 d of the third lactation did not differ between treatments. Fertility outcomes were improved in the extended voluntary waiting period group compared with the conventional group, as indicated by a higher pregnancy proportion at first service (LSM 0.62 ± 0.050 vs. 0.46 ± 0.046), fewer inseminations per born calf (LSM 1.61 ± 0.131 vs. 2.02 ± 0.137), and shorter insemination period (LSM 20.8 ± 4.8 d vs. 35.6 ± 4.3 d). The voluntary waiting period did not influence culling rates. These findings indicate that a voluntary waiting period of 140 d may be a viable alternative to the conventional 50-d duration, without compromising milk production and fertility in second-parity cows from high-yielding herds.</p>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145102619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Social housing for dairy calves: Farmer acceptance of Canadian industry-led requirements","authors":"Katherine E. Koralesky,&nbsp;Taylor Dyck,&nbsp;Christine Kuo,&nbsp;Marina A.G. von Keyserlingk,&nbsp;Daniel M. Weary","doi":"10.3168/jds.2025-26881","DOIUrl":"10.3168/jds.2025-26881","url":null,"abstract":"<div><div>Research suggests that housing milk-fed calves in pairs or small groups from a young age can provide welfare benefits, leading some policymakers to encourage dairy farmers to adopt this practice. For example, Canada's industry-led Code of Practice for the Care and Handling of Dairy Cattle requires social housing for indoor-housed calves, starting in 2031. We assessed acceptance of social housing and this new Code requirement by conducting 23 interviews with 13 farmers in Alberta and British Columbia, Canada. Interview questions were designed to evaluate 8 constructs (affective attitude, burden, ethicality, opportunity costs, perceived effectiveness, self-efficacy, and trust in the Canadian Dairy Code development process) derived from the “Theoretical Framework of Acceptance.” Participant acceptance varied, with some appreciating the benefits of social housing, and others citing concerns about the need for the requirement. Farmers generally thought they would be able to adopt social housing. Most participants prioritized concerns about calf health, but also considered calf socialization beneficial. However, some farmers also expressed frustration with the new Canadian Dairy Code requirement and did not feel their interests were represented in the Code development process. These findings highlight the need to address farmer concerns with new policies and practices, for example, through events that support farmers and their advisers to share successful approaches to implementation. Further research is required to better understand farmer views on representation in the development of policies that govern on-farm practices.</div></div>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":"108 11","pages":"Pages 12438-12449"},"PeriodicalIF":4.4,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145102561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genotype imputation accuracy of X chromosome variants in Holstein cattle based on different software and imputation strategies.","authors":"Tatiana C de Souza, Luis F B Pinto, Valdecy A R da Cruz, Tatiane S Chud, Victor B Pedrosa, Gerson A O Junior, Hinayah R de Oliveira, Henrique A Mulim, Filippo Miglior, Flávio S Schenkel, Luiz F Brito","doi":"10.3168/jds.2025-26715","DOIUrl":"https://doi.org/10.3168/jds.2025-26715","url":null,"abstract":"<p><p>The X chromosome is one of the largest in the cattle genome, but little is known about the imputation of X chromosome variants. Thus, the main objective of this study was to assess the imputation accuracy of SNPs located in the X chromosome based on different strategies. Data from 2,505 Holstein cattle were used, and the imputation was carried out in 2 steps. Step 1 consisted of imputation from 5 medium-density (MD) SNP panels to a consolidated MD SNP panel, and step 2 was based on imputation from this consolidated MD SNP panel to a high-density (HD) SNP panel. Six scenarios (S1-S6) were evaluated for imputing autosomal SNPs (S1^A, S2^A, S3^A, S4^A, S5^A, S6^A), as well as the entire X chromosome (S1^X, S2^X, S3^X, S4^X, S5^X, S6^X) and the pseudoautosomal region (PAR; S1^PAR, S2^PAR, S3^PAR, S4^PAR, S5^PAR, S6^PAR) and non-PAR (S1^non-PAR, S2^non-PAR, S3^non-PAR, S4^non-PAR, S5^non-PAR, S6^non-PAR) segments of the X chromosome. The validation population in all these scenarios had 169 females and zero (S1, S2, and S3) or 583 (S4, S5, and S6) males, whereas the reference population had 169 (S2, S5) or 392 (S1, S3, S4, S6) females and zero (S1, S4), 196 (S2, S5), or 1,361 (S3, S6) males. Two imputation software tools (Minimac and FindHap) were compared across scenarios. Step 1 provided a consolidated MD SNP panel containing 2,132 and 63,259 SNPs located on the X and autosomal chromosomes, respectively, and step 2 resulted in an HD SNP panel with 5,921 and 294,865 SNPs located on the X and autosomal chromosomes, respectively. In step 1, the lowest average allelic correlation (R) was 0.93 (S4^PAR) with Minimac and 0.79 (S4^PAR) with FindHap, whereas the lowest genotypic concordance rate (CR) was 95.0 (S4^PAR) with Minimac and 85.0 (S4^PAR) when using FindHap. In step 2, the lowest R was 0.93 (S4^PAR and S4^non-PAR) with Minimac and 0.66 (S4^X) with FindHap, whereas the lowest CR was 96.2 (S4^PAR) with Minimac and 80.3 (S4^X) with FindHap. In general, all the scenarios had high imputation accuracy of the X chromosome SNPs when using the Minimac software, whereas FindHap showed better accuracy with scenarios S3 and S6. Including both males and females in the reference and validation populations increased the imputation accuracy of X chromosome variants. These findings highlight the importance of the choice of the imputation software and the need for enlarging the reference populations to increase genotype imputation accuracy of the X chromosome variants in Holstein cattle.</p>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145102580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}