Jessica M.V. Pereira , Fernanda C. Ferreira , Marcos I. Marcondes
<div><div>Dairy herds have adopted sexed semen (SS) and beef semen (BS) to control heifer inventory and increase calf sales revenue. Beef in vitro–produced embryo transfer (beef IVP-ET) may be an alternative to increase calf sales revenue. Additionally, raising those Jersey-beef crossbred or pure beef animals in a dairy system may be a new source of revenue. We aimed to evaluate the effects of breed strategies combining dairy conventional semen (CS), SS, BS, and beef IVP-ET on herd dynamics and profitability with strategies of marketing those animals at 1 d old or raising them to a weight of 180 kg. A Markov chain model was developed to maximize the profitability of Jersey herds by changing the number of dairy heifers sold at birth and the culling rate of cows in their third parity or greater. The model presents inputs on the reproductive and productive performance of heifers and cows over time. The last year's data (year 10, steady state) was used to calculate accrual operational cost and revenue per cow per year. We varied the breeding strategy by breeding order and parities, the embryo transfer cost ($85 or $170), the pure beef calf market price ($200 or $300), and the marketing strategy. A total of 8 scenarios plus a default scenario were simulated. Overall, the proportion of SS use was 47.3 ± 0.6% (mean ± SD). For the scenarios replacing all CS breedings with BS breedings, the percentage of BS used was 52.3 ± 0.6%. When beef IVP-ET was used, the percentages of BS and beef IVP-ET used were 22.4 ± 0.1% and 31.0 ± 0.1%, respectively. We observed that when we compared the combination of BS and dairy SS with the default scenario, the production of purebred Jersey male calves was reduced by 83.5%, and profit per cow per year was increased from $113.50 to $203.30. When a beef IVP-ET cost of $85 per transfer was used (scenarios 2 and 3), profit per cow per year was $145.50 and $176.20 for pure beef calf prices of $200 and $300, respectively. In scenario 4, with a beef IVP-ET cost of $170, the lowest profit ($52.90 per cow per year) was found when marketing 1-d-old pure beef calves at $200. The highest profit was achieved for the scenario of raising the Jersey-beef crossbred animals to 180 kg ($232.90, scenario 6), followed by scenario 7 ($222.90, using the combination of BS, dairy SS, and beef IVP-ET) with an embryo transfer cost of $85. Under the current market conditions, combining SS and BS in the reproductive program was a feasible economic opportunity for Jersey herds, yielding the highest net return. The adoption of beef IVP-ET in a reproductive program can potentially increase profit per cow per year, but its profitability will depend on the beef IVP-ET pregnancy cost, the pure beef market price, calf performance, and herd reproductive performance. In conclusion, raising the Jersey-beef crossbred calves may be a profitable strategy, and dairy producers need to evaluate the best option to invest in, as it will take extra risk to produce high-q
{"title":"Effects of beef semen and beef embryo strategies on profitability: Economics of using beef semen and beef in vitro–produced embryo transfer in Jersey herds","authors":"Jessica M.V. Pereira , Fernanda C. Ferreira , Marcos I. Marcondes","doi":"10.3168/jds.2023-24530","DOIUrl":"10.3168/jds.2023-24530","url":null,"abstract":"<div><div>Dairy herds have adopted sexed semen (SS) and beef semen (BS) to control heifer inventory and increase calf sales revenue. Beef in vitro–produced embryo transfer (beef IVP-ET) may be an alternative to increase calf sales revenue. Additionally, raising those Jersey-beef crossbred or pure beef animals in a dairy system may be a new source of revenue. We aimed to evaluate the effects of breed strategies combining dairy conventional semen (CS), SS, BS, and beef IVP-ET on herd dynamics and profitability with strategies of marketing those animals at 1 d old or raising them to a weight of 180 kg. A Markov chain model was developed to maximize the profitability of Jersey herds by changing the number of dairy heifers sold at birth and the culling rate of cows in their third parity or greater. The model presents inputs on the reproductive and productive performance of heifers and cows over time. The last year's data (year 10, steady state) was used to calculate accrual operational cost and revenue per cow per year. We varied the breeding strategy by breeding order and parities, the embryo transfer cost ($85 or $170), the pure beef calf market price ($200 or $300), and the marketing strategy. A total of 8 scenarios plus a default scenario were simulated. Overall, the proportion of SS use was 47.3 ± 0.6% (mean ± SD). For the scenarios replacing all CS breedings with BS breedings, the percentage of BS used was 52.3 ± 0.6%. When beef IVP-ET was used, the percentages of BS and beef IVP-ET used were 22.4 ± 0.1% and 31.0 ± 0.1%, respectively. We observed that when we compared the combination of BS and dairy SS with the default scenario, the production of purebred Jersey male calves was reduced by 83.5%, and profit per cow per year was increased from $113.50 to $203.30. When a beef IVP-ET cost of $85 per transfer was used (scenarios 2 and 3), profit per cow per year was $145.50 and $176.20 for pure beef calf prices of $200 and $300, respectively. In scenario 4, with a beef IVP-ET cost of $170, the lowest profit ($52.90 per cow per year) was found when marketing 1-d-old pure beef calves at $200. The highest profit was achieved for the scenario of raising the Jersey-beef crossbred animals to 180 kg ($232.90, scenario 6), followed by scenario 7 ($222.90, using the combination of BS, dairy SS, and beef IVP-ET) with an embryo transfer cost of $85. Under the current market conditions, combining SS and BS in the reproductive program was a feasible economic opportunity for Jersey herds, yielding the highest net return. The adoption of beef IVP-ET in a reproductive program can potentially increase profit per cow per year, but its profitability will depend on the beef IVP-ET pregnancy cost, the pure beef market price, calf performance, and herd reproductive performance. In conclusion, raising the Jersey-beef crossbred calves may be a profitable strategy, and dairy producers need to evaluate the best option to invest in, as it will take extra risk to produce high-q","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":"107 11","pages":"Pages 9491-9503"},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141465133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Raul Rivera-Chacon , Cátia Pacífico , Sara Ricci , Renee M. Petri , Nicole Reisinger , Qendrim Zebeli , Ezequias Castillo-Lopez
The aims of this research were to evaluate how prolonged feeding of a high-concentrate diet affects the ruminal degradation kinetics of fiber and starch, and to evaluate the effects of the high-concentrate diet on apparent total-tract nutrient digestibility in dairy cows. We also investigated the dysbiotic effects and the remodeling of the hindgut microbiome with prolonged high-concentrate feeding. Nine Holstein cows were used in 2 experimental periods; in each period, cows were first fed a 100% forage diet for 1 wk, followed by stepwise adaptation during one week to a high-concentrate (HC) diet (65% concentrate), which was then fed for 4 consecutive weeks. The kinetics of in situ ruminal degradability of grass silage (DM and NDF), corn grain and wheat grain (DM and starch), as well as the apparent total-tract nutrient digestibility were evaluated in the forage feeding and in wk 4 on the HC diet. Whereas the hindgut microbiome and fermentation profile were evaluated on a weekly basis. Regarding the in situ ruminal degradability due to grain type, the rate of degradation of the potentially degradable fraction and the effective rumen degradability of wheat grain were greater compared with corn grain. The in situ ruminal degradability of NDF decreased with the HC diet. However, the apparent total-tract digestibility of CP, fat, starch, NDF, ADF, and NFC increased with the HC diet compared with forage feeding. In addition, the HC diet increased the concentration of short-chain fatty acids in the hindgut, lowering fecal pH by 0.6 units, which correlated positively with microbial α diversity. This resulted in lower α diversity with the HC diet; however, α diversity (number of amplicon sequence variants) showed recovery in wk 3 and 4 on HC; in addition, microbial β diversity did not change from wk 2 onward on the HC diet. Two microbial enterotypes were identified: one for the forage diet with abundance of Akkermansia and Anaerosporobacter, and another enterotype for the HC diet with enrichment in Bifidobacterium and Butyrivibrio. Overall, results show that major microbial shifts and hindgut dysbiosis occurred in wk 1 on the HC diet. However, the hindgut microbial diversity of cows adapted after 3 wk of consuming the starch-rich ration. Thus, feeding the HC diet impaired fiber degradation in the rumen, but increased apparent total-tract nutrient digestibility. Likely, the forage diet contained less digestible NDF than the HC diet due to greater inclusion of forages with lower NDF digestibility and lower inclusion of more digestible nonforage NDF. Results also suggest that the adaptation of the hindgut microbial diversity of cows observed 3 weeks after the diet transition likely contributed to enhance total-tract nutrient digestibility.
这项研究的目的是评估长期饲喂高浓缩日粮如何影响纤维和淀粉的瘤胃降解动力学，并评估高浓缩日粮对奶牛表观总道养分消化率的影响。我们还研究了长期饲喂高浓缩饲料对后肠微生物群的菌群失调影响和重塑。九头荷斯坦奶牛被分成两个实验阶段；在每个阶段中，奶牛先饲喂 100%饲草日粮（Forage）一周，然后在一周内逐步适应高精料日粮（HC；65% 精料），并连续饲喂四周。在饲喂青贮饲料和饲喂高浓缩饲料的第 4 周，对青贮草（DM 和 NDF）、玉米粒和小麦粒（DM 和淀粉）的瘤胃原位降解动力学以及表观总养分消化率进行了评估。而后肠微生物群和发酵情况则每周评估一次。关于谷物类型引起的瘤胃原位降解率，小麦谷物潜在可降解部分的降解率和有效瘤胃降解率均高于玉米谷物。NDF的瘤胃原位降解率随着HC日粮的添加而降低。但是，与饲喂饲料相比，HC 日粮的粗蛋白、脂肪、淀粉、NDF、ADF 和 NFC 的表观总消化率增加了。此外，HC 日粮增加了后肠中短链脂肪酸的浓度，使粪便 pH 值降低了 0.6 个单位，这与微生物 α 多样性呈正相关。这导致 HC 导致α多样性降低；然而，α多样性（ASV 数量）在使用 HC 的第 3 和第 4 周出现恢复；此外，从使用 HC 的第 2 周起，微生物 β 多样性没有变化。确定了两种微生物肠型：一种用于饲粮，富含 Akkermansia 和 Anaerosporobacter；另一种用于 HC 饲粮，富含双歧杆菌和 Butyrivibrio。总之，结果表明，在饲喂 HC 的第 1 周，出现了重大的微生物转变和后肠菌群失调。然而，奶牛在食用富含淀粉的日粮 3 周后，其后肠微生物多样性得到了适应。因此，饲喂 HC 日粮影响了纤维在瘤胃中的降解，但增加了表观总养分消化率。饲粮中可消化的 NDF 可能少于 HC 日粮，这是因为饲粮中含有较多 NDF 消化率较低的饲草，而可消化的非饲草 NDF 含量较低。结果还表明，日粮转换 3 周后观察到的奶牛后肠微生物多样性的适应性可能有助于提高总茎秆营养物质的消化率。
{"title":"Prolonged feeding of high-concentrate diet remodels the hindgut microbiome and modulates nutrient degradation in the rumen and the total gastrointestinal tract of cows","authors":"Raul Rivera-Chacon , Cátia Pacífico , Sara Ricci , Renee M. Petri , Nicole Reisinger , Qendrim Zebeli , Ezequias Castillo-Lopez","doi":"10.3168/jds.2024-24919","DOIUrl":"10.3168/jds.2024-24919","url":null,"abstract":"<div><div>The aims of this research were to evaluate how prolonged feeding of a high-concentrate diet affects the ruminal degradation kinetics of fiber and starch, and to evaluate the effects of the high-concentrate diet on apparent total-tract nutrient digestibility in dairy cows. We also investigated the dysbiotic effects and the remodeling of the hindgut microbiome with prolonged high-concentrate feeding. Nine Holstein cows were used in 2 experimental periods; in each period, cows were first fed a 100% forage diet for 1 wk, followed by stepwise adaptation during one week to a high-concentrate (HC) diet (65% concentrate), which was then fed for 4 consecutive weeks. The kinetics of in situ ruminal degradability of grass silage (DM and NDF), corn grain and wheat grain (DM and starch), as well as the apparent total-tract nutrient digestibility were evaluated in the forage feeding and in wk 4 on the HC diet. Whereas the hindgut microbiome and fermentation profile were evaluated on a weekly basis. Regarding the in situ ruminal degradability due to grain type, the rate of degradation of the potentially degradable fraction and the effective rumen degradability of wheat grain were greater compared with corn grain. The in situ ruminal degradability of NDF decreased with the HC diet. However, the apparent total-tract digestibility of CP, fat, starch, NDF, ADF, and NFC increased with the HC diet compared with forage feeding. In addition, the HC diet increased the concentration of short-chain fatty acids in the hindgut, lowering fecal pH by 0.6 units, which correlated positively with microbial α diversity. This resulted in lower α diversity with the HC diet; however, α diversity (number of amplicon sequence variants) showed recovery in wk 3 and 4 on HC; in addition, microbial β diversity did not change from wk 2 onward on the HC diet. Two microbial enterotypes were identified: one for the forage diet with abundance of <em>Akkermansia</em> and <em>Anaerosporobacter</em>, and another enterotype for the HC diet with enrichment in <em>Bifidobacterium</em> and <em>Butyrivibrio</em>. Overall, results show that major microbial shifts and hindgut dysbiosis occurred in wk 1 on the HC diet. However, the hindgut microbial diversity of cows adapted after 3 wk of consuming the starch-rich ration. Thus, feeding the HC diet impaired fiber degradation in the rumen, but increased apparent total-tract nutrient digestibility. Likely, the forage diet contained less digestible NDF than the HC diet due to greater inclusion of forages with lower NDF digestibility and lower inclusion of more digestible nonforage NDF. Results also suggest that the adaptation of the hindgut microbial diversity of cows observed 3 weeks after the diet transition likely contributed to enhance total-tract nutrient digestibility.</div></div>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":"107 11","pages":"Pages 9235-9250"},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141465157","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M.M. Passamonti , M. Milanesi , L. Cattaneo , J. Ramirez-Diaz , A. Stella , M. Barbato , C.U. Braz , R. Negrini , D. Giannuzzi , S. Pegolo , A. Cecchinato , E. Trevisi , J.L. Williams , P. Ajmone Marsan
Breeding animals able to effectively respond to stress could be a long-term, sustainable, and affordable strategy to improve resilience and welfare in livestock systems. In the present study, the concentrations of 29 plasma biomarkers were used as candidate endophenotypes for metabolic stress response in single-SNP, gene- and haplotype-based GWAS using 739 healthy lactating Italian Holstein cows and 88,271 variants. Significant genetic associations were found in all the 3 GWAS approaches for plasma γ-glutamyl transferase concentration on BTA17, for paraoxonase on BTA4, and for alkaline phosphatase and zinc on BTA2. On these chromosomes, single-SNP and gene-based chromosome-wide association studies were performed, confirming GWAS findings. The signals identified for paraoxonase, γ-glutamyl transferase, and alkaline phosphatase were in proximity to the genes coding for them. The heritability of these 4 biomarkers ranged from moderate to high (from 0.39 to 0.54). Plasma biomarkers are known to undergo large changes in concentration during metabolic stress in the transition period, with an interindividual variability in the rate of change and recovery time. Genetics may account in part for these differences. To assess this, we studied a subset of 139 periparturient cows homozygous at 3 SNPs known to be respectively associated with concentration of plasma ceruloplasmin, paraoxonase, and γ-glutamyl transferase. We compared the immune-metabolic profile measured in plasma at −7, +5, and +30 d relative to calving between groups of opposite homozygotes. A significant effect of the genotype was found on paraoxonase and γ-glutamyl transferase plasma concentration at all the 3 time points. No evidence for genotype effect was detected for ceruloplasmin. Understanding the genetic control underlying metabolic stress response may suggest new approaches to foster resilience in dairy cows.
{"title":"Unraveling metabolic stress response in dairy cows: Genetic control of plasma biomarkers throughout lactation and the transition period","authors":"M.M. Passamonti , M. Milanesi , L. Cattaneo , J. Ramirez-Diaz , A. Stella , M. Barbato , C.U. Braz , R. Negrini , D. Giannuzzi , S. Pegolo , A. Cecchinato , E. Trevisi , J.L. Williams , P. Ajmone Marsan","doi":"10.3168/jds.2023-24630","DOIUrl":"10.3168/jds.2023-24630","url":null,"abstract":"<div><div>Breeding animals able to effectively respond to stress could be a long-term, sustainable, and affordable strategy to improve resilience and welfare in livestock systems. In the present study, the concentrations of 29 plasma biomarkers were used as candidate endophenotypes for metabolic stress response in single-SNP, gene- and haplotype-based GWAS using 739 healthy lactating Italian Holstein cows and 88,271 variants. Significant genetic associations were found in all the 3 GWAS approaches for plasma γ-glutamyl transferase concentration on BTA17, for paraoxonase on BTA4, and for alkaline phosphatase and zinc on BTA2. On these chromosomes, single-SNP and gene-based chromosome-wide association studies were performed, confirming GWAS findings. The signals identified for paraoxonase, γ-glutamyl transferase, and alkaline phosphatase were in proximity to the genes coding for them. The heritability of these 4 biomarkers ranged from moderate to high (from 0.39 to 0.54). Plasma biomarkers are known to undergo large changes in concentration during metabolic stress in the transition period, with an interindividual variability in the rate of change and recovery time. Genetics may account in part for these differences. To assess this, we studied a subset of 139 periparturient cows homozygous at 3 SNPs known to be respectively associated with concentration of plasma ceruloplasmin, paraoxonase, and γ-glutamyl transferase. We compared the immune-metabolic profile measured in plasma at −7, +5, and +30 d relative to calving between groups of opposite homozygotes. A significant effect of the genotype was found on paraoxonase and γ-glutamyl transferase plasma concentration at all the 3 time points. No evidence for genotype effect was detected for ceruloplasmin. Understanding the genetic control underlying metabolic stress response may suggest new approaches to foster resilience in dairy cows.</div></div>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":"107 11","pages":"Pages 9602-9614"},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141465160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Milk and dairy products are important in the human diet not only for the macronutrients, such as proteins and fats, that they provide, but also for the supply of essential micronutrients, such as minerals. Minerals are present in milk in soluble form in the aqueous phase and in colloidal form associated with the macronutrients of the milk. These 2 forms affect the nutritional functions of the minerals and their contribution to the technological properties of milk during cheese making. The aim of the present work was to study and compare the detailed mineral profiles of dairy foods (milk, whey, and cheese) obtained from cows, buffaloes, goats, ewes and dromedary camels, and to analyze the recovery in the curd of the individual minerals according to a model cheese-making procedure applied to the milk of these 5 dairy species. The detailed mineral profile of the milk samples was obtained by inductively coupled plasma–optical emission spectroscopy. We divided the 21 minerals identified in the 3 different matrices into essential macro- and microminerals, and environmental microminerals, and calculated the recovery of the individual minerals in the cheeses. The complete mineral profiles and the recoveries in the cheeses were then analyzed using a linear mixed model with Species, Food, and their interaction included as fixed effects, and Sample within Species as a random effect. The mineral profiles of each food matrix were then analyzed separately with a general linear model in which only the fixed effect of Species was included. The results showed that the species could be divided into 2 groups: those producing a more diluted milk characterized by a higher content of soluble minerals (in particular, K), and those with a more concentrated milk with a higher colloidal mineral content in the skim of the milk (such as Ca and P). The recoveries of the minerals in the curd were in line with the initial content in the milk, and also highlighted the fact that the influence of the brine was not limited to the Na content but to its whole mineral makeup. These results provide valuable information for the evaluation of the nutritional and technological properties of milk, and for the uses made of the byproducts of cheese making from the milk of different species.
{"title":"Detailed mineral profile of milk, whey, and cheese from cows, buffaloes, goats, ewes, and dromedary camels, and efficiency of recovery of minerals in their cheese","authors":"Nicolò Amalfitano , Nageshvar Patel , Mohamed-Laid Haddi , Hamida Benabid , Michele Pazzola , Giuseppe Massimo Vacca , Franco Tagliapietra , Stefano Schiavon , Giovanni Bittante","doi":"10.3168/jds.2023-24624","DOIUrl":"10.3168/jds.2023-24624","url":null,"abstract":"<div><div>Milk and dairy products are important in the human diet not only for the macronutrients, such as proteins and fats, that they provide, but also for the supply of essential micronutrients, such as minerals. Minerals are present in milk in soluble form in the aqueous phase and in colloidal form associated with the macronutrients of the milk. These 2 forms affect the nutritional functions of the minerals and their contribution to the technological properties of milk during cheese making. The aim of the present work was to study and compare the detailed mineral profiles of dairy foods (milk, whey, and cheese) obtained from cows, buffaloes, goats, ewes and dromedary camels, and to analyze the recovery in the curd of the individual minerals according to a model cheese-making procedure applied to the milk of these 5 dairy species. The detailed mineral profile of the milk samples was obtained by inductively coupled plasma–optical emission spectroscopy. We divided the 21 minerals identified in the 3 different matrices into essential macro- and microminerals, and environmental microminerals, and calculated the recovery of the individual minerals in the cheeses. The complete mineral profiles and the recoveries in the cheeses were then analyzed using a linear mixed model with Species, Food, and their interaction included as fixed effects, and Sample within Species as a random effect. The mineral profiles of each food matrix were then analyzed separately with a general linear model in which only the fixed effect of Species was included. The results showed that the species could be divided into 2 groups: those producing a more diluted milk characterized by a higher content of soluble minerals (in particular, K), and those with a more concentrated milk with a higher colloidal mineral content in the skim of the milk (such as Ca and P). The recoveries of the minerals in the curd were in line with the initial content in the milk, and also highlighted the fact that the influence of the brine was not limited to the Na content but to its whole mineral makeup. These results provide valuable information for the evaluation of the nutritional and technological properties of milk, and for the uses made of the byproducts of cheese making from the milk of different species.</div></div>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":"107 11","pages":"Pages 8887-8907"},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141537192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dairy cattle health traits are paramount from a welfare and economic viewpoint, and modern breeding programs therefore prioritize the genetic improvement of these traits. Estimated breeding values for health traits are published as the probability of animals staying healthy. They are obtained using threshold models, which assume that the observed binary phenotype (i.e., healthy or sick) is dictated by an underlying normally distributed liability exceeding or not exceeding a threshold. This methodology requires significant computing time and faces convergence challenges, as it implies a nonlinear system of equations. Linear models have more straightforward computations and provide a robust approximation to threshold models; thus, they could be used to overcome these challenges. However, linear models yield estimated breeding values on the observed scale, requiring an approximation to the liability scale analogous to that from threshold models to later obtain the estimated breeding values on the probability scale. In addition, the robustness of the approximation of linear to threshold models depends on the amount of information and the incidence of the trait, with extreme incidence (i.e., ≤5%) deviating from optimal approximation. Our objective was to test a transformation from the observed to the liability, and then to the probability scale, in the genetic evaluation of health traits with moderate and very low (extreme) incidence. Data comprised displaced abomasum (5.1 million), ketosis (3.6 million), lameness (5 million), and mastitis (6.3 million) records from a Holstein population with a pedigree of 6 million animals, of which 1.7 million were genotyped. Univariate threshold and linear models were performed to predict breeding values. The agreement between estimated breeding values on the probability scale derived from threshold and linear models was assessed using Spearman rank correlations and comparison of estimated breeding values distributions. Correlations were at least 0.95, and estimated breeding value distributions almost entirely overlapped for all the traits but displaced abomasum, the trait with the lowest incidence (2%). Computing time was ∼3 times longer for threshold than for linear models. In this Holstein population, the approximation was suboptimal for a trait with extreme incidence (2%). However, when the incidence was ≥6%, the approximation was robust, and its use is recommended along with linear models for analyzing categorical traits in large populations to ease the computational burden.
{"title":"Converting estimated breeding values from the observed to probability scale for health traits","authors":"Jorge Hidalgo , Shogo Tsuruta , Dianelys Gonzalez , Gerson de Oliveira , Miguel Sanchez , Asmita Kulkarni , Cory Przybyla , Giovana Vargas , Natascha Vukasinovic , Ignacy Misztal , Daniela Lourenco","doi":"10.3168/jds.2024-24767","DOIUrl":"10.3168/jds.2024-24767","url":null,"abstract":"<div><div>Dairy cattle health traits are paramount from a welfare and economic viewpoint, and modern breeding programs therefore prioritize the genetic improvement of these traits. Estimated breeding values for health traits are published as the probability of animals staying healthy. They are obtained using threshold models, which assume that the observed binary phenotype (i.e., healthy or sick) is dictated by an underlying normally distributed liability exceeding or not exceeding a threshold. This methodology requires significant computing time and faces convergence challenges, as it implies a nonlinear system of equations. Linear models have more straightforward computations and provide a robust approximation to threshold models; thus, they could be used to overcome these challenges. However, linear models yield estimated breeding values on the observed scale, requiring an approximation to the liability scale analogous to that from threshold models to later obtain the estimated breeding values on the probability scale. In addition, the robustness of the approximation of linear to threshold models depends on the amount of information and the incidence of the trait, with extreme incidence (i.e., ≤5%) deviating from optimal approximation. Our objective was to test a transformation from the observed to the liability, and then to the probability scale, in the genetic evaluation of health traits with moderate and very low (extreme) incidence. Data comprised displaced abomasum (5.1 million), ketosis (3.6 million), lameness (5 million), and mastitis (6.3 million) records from a Holstein population with a pedigree of 6 million animals, of which 1.7 million were genotyped. Univariate threshold and linear models were performed to predict breeding values. The agreement between estimated breeding values on the probability scale derived from threshold and linear models was assessed using Spearman rank correlations and comparison of estimated breeding values distributions. Correlations were at least 0.95, and estimated breeding value distributions almost entirely overlapped for all the traits but displaced abomasum, the trait with the lowest incidence (2%). Computing time was ∼3 times longer for threshold than for linear models. In this Holstein population, the approximation was suboptimal for a trait with extreme incidence (2%). However, when the incidence was ≥6%, the approximation was robust, and its use is recommended along with linear models for analyzing categorical traits in large populations to ease the computational burden.</div></div>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":"107 11","pages":"Pages 9628-9637"},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141615537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Q.Y. Hu , J.J. Man , J. Luo , F. Cheng , M. Yang , G. Lin , P. Wang
Enhancing gastrointestinal health, immunity, and digestion are key factors to support dairy goat kid performance. Several additives have been studied in relation to these actions. This study investigated the impact of mannan-rich fraction (MRF) inclusion in goat milk on the growth performance, gut health, rumen fermentation, and microbial profiles of Xinong Saanen dairy goat kids. A total of 80 kids aged 14 d and 4.72 ± 0.33 kg BW were randomly assigned into 2 groups: control and MRF (1 g/d MRF mixed into milk). Each group consisted of 40 kids with 10 kids per pen. All kids were given milk individually and fed a starter diet by pen, with the trial lasting 10 wk. Body weight and blood samples were collected on the seventh day at 2, 6, 10 and 12 wk of age, and feed intake was determined daily. From the first to seventh day at 12 wk of age, fecal samples were collected from 4 kids in each group to analyze nutrient digestibility. On the seventh day of 12 wk of age, 4 kids from each group were slaughtered for evaluation of rumen fermentation, rumen microbiota, and gut morphology. The results indicated that MRF supplementation led to greater overall BW, overall starter DMI, and overall ADG, along with a lower overall diarrhea rate. However, no difference in overall feed efficiency and apparent digestibility of nutrients was observed. Furthermore, MRF supplementation resulted in increased ileal villus height; higher RNA expression of claudin-1 and occludin in the duodenum; higher expression of ZO-1, JAM-2, and occludin in the jejunum; and higher expression of claudin-1, JAM-2, and occludin in the ileum. Additionally, the concentrations of overall IgA, overall IgM, and overall IgG were higher in the MRF group. The concentrations of ruminal acetate and total volatile fatty acid were higher with MRF supplementation (P < 0.05). Meanwhile, supplementation with MRF resulted in higher abundance of Bacteroidetes and Succinivibrio and lower abundance of Firmicutes and Succiniclasticum in the rumen. Overall, the growth performance, gut health, immunity, and ruminal microbial structure of dairy goat kids benefited from MRF supplementation.
{"title":"Early-life supplementation with mannan-rich fraction to regulate rumen microbiota, gut health, immunity, and growth performance in dairy goat kids","authors":"Q.Y. Hu , J.J. Man , J. Luo , F. Cheng , M. Yang , G. Lin , P. Wang","doi":"10.3168/jds.2024-24903","DOIUrl":"10.3168/jds.2024-24903","url":null,"abstract":"<div><div>Enhancing gastrointestinal health, immunity, and digestion are key factors to support dairy goat kid performance. Several additives have been studied in relation to these actions. This study investigated the impact of mannan-rich fraction (MRF) inclusion in goat milk on the growth performance, gut health, rumen fermentation, and microbial profiles of Xinong Saanen dairy goat kids. A total of 80 kids aged 14 d and 4.72 ± 0.33 kg BW were randomly assigned into 2 groups: control and MRF (1 g/d MRF mixed into milk). Each group consisted of 40 kids with 10 kids per pen. All kids were given milk individually and fed a starter diet by pen, with the trial lasting 10 wk. Body weight and blood samples were collected on the seventh day at 2, 6, 10 and 12 wk of age, and feed intake was determined daily. From the first to seventh day at 12 wk of age, fecal samples were collected from 4 kids in each group to analyze nutrient digestibility. On the seventh day of 12 wk of age, 4 kids from each group were slaughtered for evaluation of rumen fermentation, rumen microbiota, and gut morphology. The results indicated that MRF supplementation led to greater overall BW, overall starter DMI, and overall ADG, along with a lower overall diarrhea rate. However, no difference in overall feed efficiency and apparent digestibility of nutrients was observed. Furthermore, MRF supplementation resulted in increased ileal villus height; higher RNA expression of claudin-1 and occludin in the duodenum; higher expression of ZO-1, JAM-2, and occludin in the jejunum; and higher expression of claudin-1, JAM-2, and occludin in the ileum. Additionally, the concentrations of overall IgA, overall IgM, and overall IgG were higher in the MRF group. The concentrations of ruminal acetate and total volatile fatty acid were higher with MRF supplementation (<em>P</em> < 0.05). Meanwhile, supplementation with MRF resulted in higher abundance of <em>Bacteroidetes</em> and <em>Succinivibrio</em> and lower abundance of <em>Firmicutes</em> and <em>Succiniclasticum</em> in the rumen. Overall, the growth performance, gut health, immunity, and ruminal microbial structure of dairy goat kids benefited from MRF supplementation.</div></div>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":"107 11","pages":"Pages 9322-9333"},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141615539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
G. Ahmad , J.R. Daddam , E. Trevisi , M. Mezzetti , G. Lovotti , E. Puda , K. Gallagher , I. Bernstein , M. Vandehaar , Z. Zhou
Reduced liver function, increased oxidative stress, and inflammation in early lactation negatively affect lactation performance and health of fresh cows. Previous findings from our group demonstrated that branched-chain AA (BCAA) infusion improved lactation performance and branched-chain keto-acids (BCKA) infusion decreased liver triglyceride (TG) in fresh cows. The objectives of this study were to determine the effect of BCAA and BCKA on blood and liver biomarkers of liver function, oxidative stress, and inflammation as well as expression of genes regulating inflammation and antioxidant metabolism in the liver. Thirty multiparous Holstein cows were used in a randomized block design receiving continuous abomasal infusion for 21 d after parturition. Treatments (10 cows each) were control (CON), cows abomasally infused with 0.9% saline; cows abomasally infused with BCAA (67 g valine, 50 g leucine, and 34 g isoleucine; BCA); and cows abomasally infused with BCKA (77 g keto-valine, 57 g keto-leucine, and 39 g keto-isoleucine; BCK). All cows were randomly assigned to treatments after parturition and received the same diet throughout the experimental period. Blood was collected at 3, 7, 14, and 21 d postpartum for liver function, oxidative stress, and inflammation biomarker profiling. Liver was also harvested on 7, 14, and 21 d postpartum for quantification of glutathione, protein carbonylation, and expression of genes. ANOVA was conducted for all data using PROC GLIMMIX in SAS. No treatment differences were observed for liver function biomarkers (bilirubin, gamma-glutamyl transferase, and aspartate aminotransferase). Cows receiving BCAA had lower blood NO2− and NO3− concentrations compared with CON. A tendency for lower advanced oxidized protein products was also observed in BCA cows compared with CON. Additionally, on d 7, BCA cows had lower protein carbonylation in the liver compared with CON. In contrast, BCK cows had higher plasma thiol and albumin, as well as liver reduced and total glutathione compared with CON cows. Compared with CON, BCK cows had higher expression glutathione reductase in the liver. Overall, these results suggest favorable alterations in oxidative stress and inflammation status in fresh cows receiving BCAA or BCKA infusion during the first 3 wk of lactation, which likely contributed to previously-observed changes in lactation performance and liver TG concentrations. Future work is required to evaluate the interrelated metabolism of BCAA and BCKA to better understand their effects on oxidative and immune metabolism.
{"title":"Effects of abomasal infusion of branched-chain amino acids or branched-chain keto-acids on liver function, inflammation, and oxidative stress in multiparous fresh cows","authors":"G. Ahmad , J.R. Daddam , E. Trevisi , M. Mezzetti , G. Lovotti , E. Puda , K. Gallagher , I. Bernstein , M. Vandehaar , Z. Zhou","doi":"10.3168/jds.2024-24914","DOIUrl":"10.3168/jds.2024-24914","url":null,"abstract":"<div><div>Reduced liver function, increased oxidative stress, and inflammation in early lactation negatively affect lactation performance and health of fresh cows. Previous findings from our group demonstrated that branched-chain AA (BCAA) infusion improved lactation performance and branched-chain keto-acids (BCKA) infusion decreased liver triglyceride (TG) in fresh cows. The objectives of this study were to determine the effect of BCAA and BCKA on blood and liver biomarkers of liver function, oxidative stress, and inflammation as well as expression of genes regulating inflammation and antioxidant metabolism in the liver. Thirty multiparous Holstein cows were used in a randomized block design receiving continuous abomasal infusion for 21 d after parturition. Treatments (10 cows each) were control (CON), cows abomasally infused with 0.9% saline; cows abomasally infused with BCAA (67 g valine, 50 g leucine, and 34 g isoleucine; BCA); and cows abomasally infused with BCKA (77 g keto-valine, 57 g keto-leucine, and 39 g keto-isoleucine; BCK). All cows were randomly assigned to treatments after parturition and received the same diet throughout the experimental period. Blood was collected at 3, 7, 14, and 21 d postpartum for liver function, oxidative stress, and inflammation biomarker profiling. Liver was also harvested on 7, 14, and 21 d postpartum for quantification of glutathione, protein carbonylation, and expression of genes. ANOVA was conducted for all data using PROC GLIMMIX in SAS. No treatment differences were observed for liver function biomarkers (bilirubin, gamma-glutamyl transferase, and aspartate aminotransferase). Cows receiving BCAA had lower blood NO<sub>2</sub><sup>−</sup> and NO<sub>3</sub><sup>−</sup> concentrations compared with CON. A tendency for lower advanced oxidized protein products was also observed in BCA cows compared with CON. Additionally, on d 7, BCA cows had lower protein carbonylation in the liver compared with CON. In contrast, BCK cows had higher plasma thiol and albumin, as well as liver reduced and total glutathione compared with CON cows. Compared with CON, BCK cows had higher expression <em>glutathione reductase</em> in the liver. Overall, these results suggest favorable alterations in oxidative stress and inflammation status in fresh cows receiving BCAA or BCKA infusion during the first 3 wk of lactation, which likely contributed to previously-observed changes in lactation performance and liver TG concentrations. Future work is required to evaluate the interrelated metabolism of BCAA and BCKA to better understand their effects on oxidative and immune metabolism.</div></div>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":"107 11","pages":"Pages 9309-9321"},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141615540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Presently, there is a gap in the knowledge of the structure-activity relationship of immunomodulatory peptides. In this study, PFPEVFG was selected as a peptide with immunomodulatory activity from casein hydrolysate by virtual screening, and its immunomodulatory activity was verified by the phagocytosis, proliferation, and expression of cytokines (IL-6, IL-1β, TNF-α) and chemokines (CXCL1, CXCL2) in RAW 264.7 macrophages. Next, molecular docking and double-stranded small interfering RNA mutually verified that the immunomodulatory activity of PFPEVFG was mediated by TLR2 and TLR4. Furthermore, the highest occupied molecular orbital (HOMO) analysis showed that the C19=O20 site with a HOMO contribution of 32.22988% was its active site, and the phenylalanine, where the C19=O20 site was located, was its active amino acid. Finally, the combination of pathway inhibitors and western blot revealed that PFPEVFG activated macrophages through the nuclear factor-κB signaling pathway. In summary, this study provided a new perspective on deeply understanding the structure-activity relationship of casein-derived immunomodulatory peptides, as well as a further theoretical and technological basis for the application of immunomodulatory peptides.
目前，人们对免疫调节肽的结构-活性关系的认识仍是空白。本研究通过虚拟筛选从酪蛋白水解物中筛选出具有免疫调节活性的多肽 PFPEVFG，并通过对 RAW 264.7 巨噬细胞的吞噬、增殖、细胞因子（IL-6、IL-1β、TNF-α）和趋化因子（CXCL1、CXCL2）的表达来验证其免疫调节活性。接着，分子对接和双链小干扰 RNA（siRNA）相互验证了 PFPEVFG 的免疫调节活性是由 TLR2/4 介导的。此外，最高占据分子轨道（HOMO）分析表明，HOMO贡献率为32.22988%的C19 = O20位点是其活性位点，而C19 = O20位点所在的苯丙氨酸是其活性氨基酸。最后，结合通路抑制剂和 Western blot 发现，PFPEVFG 是通过核因子-κB（NF-κB）信号通路激活巨噬细胞的。总之，这项研究为深入理解酪蛋白衍生免疫调节肽的结构-活性关系提供了一个新的视角，也为免疫调节肽的应用提供了进一步的理论和技术基础。
{"title":"Novel casein-derived immunomodulatory peptide PFPEVFG: Activity assessment, molecular docking, activity site, and mechanism of action","authors":"Siyi Li, Yutong Jiang, Zhiqi Cao, Yanfeng Tuo, Guangqing Mu, Shujuan Jiang","doi":"10.3168/jds.2024-25173","DOIUrl":"10.3168/jds.2024-25173","url":null,"abstract":"<div><div>Presently, there is a gap in the knowledge of the structure-activity relationship of immunomodulatory peptides. In this study, PFPEVFG was selected as a peptide with immunomodulatory activity from casein hydrolysate by virtual screening, and its immunomodulatory activity was verified by the phagocytosis, proliferation, and expression of cytokines (IL-6, IL-1β, TNF-α) and chemokines (CXCL1, CXCL2) in RAW 264.7 macrophages. Next, molecular docking and double-stranded small interfering RNA mutually verified that the immunomodulatory activity of PFPEVFG was mediated by TLR2 and TLR4. Furthermore, the highest occupied molecular orbital (HOMO) analysis showed that the C<sub>19</sub>=O<sub>20</sub> site with a HOMO contribution of 32.22988% was its active site, and the phenylalanine, where the C<sub>19</sub>=O<sub>20</sub> site was located, was its active amino acid. Finally, the combination of pathway inhibitors and western blot revealed that PFPEVFG activated macrophages through the nuclear factor-κB signaling pathway. In summary, this study provided a new perspective on deeply understanding the structure-activity relationship of casein-derived immunomodulatory peptides, as well as a further theoretical and technological basis for the application of immunomodulatory peptides.</div></div>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":"107 11","pages":"Pages 8852-8864"},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141733095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Wang , S. Li , R. Peng , S.E. Räisänen , A.M. Serviento , X. Sun , K. Wang , F. Yu , M. Niu
Respiratory rate (RR) is an important indicator of the health and welfare status of dairy cows. In recent years, progress has been made in monitoring the RR of dairy cows using video data and learning methods. However, existing approaches often involve multiple processing modules, such as region of interest (ROI) detection and tracking, which can introduce errors that propagate through successive steps. The objective of this study was to develop an end-to-end computer vision method to predict RR of dairy cows continuously and automatically. The method leverages the capabilities of a state-of-the-art Transformer model, VideoMAE, which divides video frames into patches as input tokens, enabling the automated selection and featurization of relevant regions, such as a cow's abdomen, for predicting RR. The original encoder of VideoMAE was retained, and a classification head was added on top of it. Further, the weights of the first 11 layers of the pre-trained model were kept, whereas the weights of the final layer and classifier were fine-tuned using video data collected in a tiestall barn from 6 dairy cows. Respiratory rates measured using a respiratory belt for individual cows were serving as the ground truth (GT). The evaluation of the developed model was conducted using multiple metrics, including mean absolute error (MAE) of 2.58 breaths per minute (bpm), root mean squared error (RMSE) of 3.52 bpm, root mean squared prediction error (RMSPE; as a proportion of observed mean) of 15.03%, and Pearson r of 0.86. Compared with a conventional method involving multiple processing modules, the end-to-end approach performed better in terms of MAE, RMSE, and RMSPE. These results suggest the potential to implement the developed computer vision method for an end-to-end solution, for monitoring RR of dairy cows automatically in a tiestall setting. Future research on integrating this method with other behavioral detection and animal identification algorithms for animal monitoring in a freestall dairy barn can be beneficial for a broader application.
{"title":"Learning end-to-end respiratory rate prediction of dairy cows from red, green, and blue videos","authors":"M. Wang , S. Li , R. Peng , S.E. Räisänen , A.M. Serviento , X. Sun , K. Wang , F. Yu , M. Niu","doi":"10.3168/jds.2023-24601","DOIUrl":"10.3168/jds.2023-24601","url":null,"abstract":"<div><div>Respiratory rate (RR) is an important indicator of the health and welfare status of dairy cows. In recent years, progress has been made in monitoring the RR of dairy cows using video data and learning methods. However, existing approaches often involve multiple processing modules, such as region of interest (ROI) detection and tracking, which can introduce errors that propagate through successive steps. The objective of this study was to develop an end-to-end computer vision method to predict RR of dairy cows continuously and automatically. The method leverages the capabilities of a state-of-the-art Transformer model, VideoMAE, which divides video frames into patches as input tokens, enabling the automated selection and featurization of relevant regions, such as a cow's abdomen, for predicting RR. The original encoder of VideoMAE was retained, and a classification head was added on top of it. Further, the weights of the first 11 layers of the pre-trained model were kept, whereas the weights of the final layer and classifier were fine-tuned using video data collected in a tiestall barn from 6 dairy cows. Respiratory rates measured using a respiratory belt for individual cows were serving as the ground truth (GT). The evaluation of the developed model was conducted using multiple metrics, including mean absolute error (MAE) of 2.58 breaths per minute (bpm), root mean squared error (RMSE) of 3.52 bpm, root mean squared prediction error (RMSPE; as a proportion of observed mean) of 15.03%, and Pearson r of 0.86. Compared with a conventional method involving multiple processing modules, the end-to-end approach performed better in terms of MAE, RMSE, and RMSPE. These results suggest the potential to implement the developed computer vision method for an end-to-end solution, for monitoring RR of dairy cows automatically in a tiestall setting. Future research on integrating this method with other behavioral detection and animal identification algorithms for animal monitoring in a freestall dairy barn can be beneficial for a broader application.</div></div>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":"107 11","pages":"Pages 9862-9874"},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141786863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This research introduces a systematic framework for calculating sample size in studies focusing on enteric methane (CH4, g/kg of DMI) yield reduction in dairy cows. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we conducted a comprehensive search across the Web of Science, Scopus, and PubMed Central databases for studies published from 2012 to 2023. The inclusion criteria were as follows: studies reporting CH4 yield and its variability in dairy cows, employing specific experimental designs (Latin square design [LSqD], crossover design, randomized complete block design [RCBD], and repeated measures design) and measurement methods (open-circuit respirometry chambers [RC], the GreenFeed system, and the sulfur hexafluoride tracer technique), conducted in Canada, the United States, and Europe. A total of 150 studies, comprising 177 reports, met our criteria and were included in the database. Our methodology for using the database for sample size calculations began by defining 6 CH4 yield reduction levels (5%, 10%, 15%, 20%, 30%, and 50%). Using an adjusted Cohen's f formula and conducting power analysis, we calculated the sample sizes required for these reductions in balanced LSqD and RCBD reports from studies involving 3 or 4 treatments. The results indicate that within-subject studies (i.e., LSqD) require smaller sample sizes to detect CH4 yield reductions compared with between-subject studies (i.e., RCBD). Although experiments using RC typically require fewer individuals due to their higher accuracy, our results demonstrate that this expected advantage is not evident in reports from RCBD studies with 4 treatments. A key innovation of this research is the development of a web-based tool that simplifies the process of sample size calculation (https://samplesizecalculator.ucdavis.edu/). Developed using Python, this tool leverages the extensive database to provide tailored sample size recommendations for specific experimental scenarios. It ensures that experiments are adequately powered to detect meaningful differences in CH4 emissions, thereby contributing to the scientific rigor of studies in this critical area of environmental and agricultural research. With its user-friendly interface and robust back-end calculations, this tool represents an important advancement in the methodology for planning and executing CH4 emission studies in dairy cows, aligning with global efforts toward sustainable agricultural practices and environmental conservation.
{"title":"Systematic review for optimizing sample size in dairy cow methane emission studies in temperate regions: A comprehensive methodological approach","authors":"J.F. Ramirez-Agudelo, E. Kebreab","doi":"10.3168/jds.2023-24529","DOIUrl":"10.3168/jds.2023-24529","url":null,"abstract":"<div><div>This research introduces a systematic framework for calculating sample size in studies focusing on enteric methane (CH<sub>4</sub>, g/kg of DMI) yield reduction in dairy cows. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we conducted a comprehensive search across the Web of Science, Scopus, and PubMed Central databases for studies published from 2012 to 2023. The inclusion criteria were as follows: studies reporting CH<sub>4</sub> yield and its variability in dairy cows, employing specific experimental designs (Latin square design [LSqD], crossover design, randomized complete block design [RCBD], and repeated measures design) and measurement methods (open-circuit respirometry chambers [RC], the GreenFeed system, and the sulfur hexafluoride tracer technique), conducted in Canada, the United States, and Europe. A total of 150 studies, comprising 177 reports, met our criteria and were included in the database. Our methodology for using the database for sample size calculations began by defining 6 CH<sub>4</sub> yield reduction levels (5%, 10%, 15%, 20%, 30%, and 50%). Using an adjusted Cohen's <em>f</em> formula and conducting power analysis, we calculated the sample sizes required for these reductions in balanced LSqD and RCBD reports from studies involving 3 or 4 treatments. The results indicate that within-subject studies (i.e., LSqD) require smaller sample sizes to detect CH<sub>4</sub> yield reductions compared with between-subject studies (i.e., RCBD). Although experiments using RC typically require fewer individuals due to their higher accuracy, our results demonstrate that this expected advantage is not evident in reports from RCBD studies with 4 treatments. A key innovation of this research is the development of a web-based tool that simplifies the process of sample size calculation (<span><span>https://samplesizecalculator.ucdavis.edu/</span><svg><path></path></svg></span>). Developed using Python, this tool leverages the extensive database to provide tailored sample size recommendations for specific experimental scenarios. It ensures that experiments are adequately powered to detect meaningful differences in CH<sub>4</sub> emissions, thereby contributing to the scientific rigor of studies in this critical area of environmental and agricultural research. With its user-friendly interface and robust back-end calculations, this tool represents an important advancement in the methodology for planning and executing CH<sub>4</sub> emission studies in dairy cows, aligning with global efforts toward sustainable agricultural practices and environmental conservation.</div></div>","PeriodicalId":354,"journal":{"name":"Journal of Dairy Science","volume":"107 11","pages":"Pages 9442-9458"},"PeriodicalIF":3.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141320330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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