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Genomic characterization of the Brazilian Crioulo Lageano: Insights for conservation of a Brazilian local bovine breed 巴西 Crioulo Lageano 的基因组特征:保护巴西地方牛种的启示。
IF 1.8 3区 农林科学 Q1 Veterinary Pub Date : 2024-05-08 DOI: 10.1016/j.livsci.2024.105481
Daiza Orth , Alexandre Floriani Ramos , Geraldo Magela Cortes Carvalho , Lucas Macedo Santos Basílio , Alexandre Rodrigues Caetano , Patrícia Ianella

Crioulo Lageano (CLAG) is a Brazilian taurine breed traditionally raised in the native fields of mountainous regions in the states of Santa Catarina and Paraná, located in the southern region from Brazil. The present study aimed to analyze the genetic diversity and structure of the breed to provide the basis for the development of strategies for its conservation. Samples from semen and DNA previously stored in the Brazilian Animal Gene Bank (BAGB), and samples collected from eight different farms registered in the Brazilian Association of Crioulo Lageano Cattle Breeders (ABCCL), were genotyped with different panels of SNP markers containing between 50 K and 777 K markers. Obtained estimates of average expected (HE = 0.373) and observed (HO = 0.382) heterozygosities suggest the presence of high levels of genetic variability in the breed. Molecular analysis of variance (AMOVA) revealed that only 2.11 % of the observed genetic variation could be attributed to differences between analyzed populations. Obtained pairwise FST estimates varied between 0.002 and 0.056, corroborating that the degree of differentiation between populations is low. Population structure analyses showed substructures between the studied populations, which could be related to the presence/absence of horns in the animals, in addition to other factors. The estimates obtained for the effective population size (Ne) considering bulls with semen stored in BGAB and the set of samples from the eight studied farms were 6 and 22, respectively, revealing that the Ne of the breed is far below that recommended by FAO for conservation of domestic animal populations. Population structure and admixture analyses comparing CLAG with six other taurine and zebu cattle breeds routinely raised in the region revealed evidence of possible unknown introgressions from animals of indicine origin. Obtained results provide solid insights into the diversity and genetic structure of the Brazilian CLGA breed and offer strategic information for the establishment of effective genetic management strategies for production herds, for the enrichment of the BAGB by collecting germoplasm and for the long-term conservation of this breed.

Crioulo Lageano(CLAG)是巴西的一个金牛品种,传统上在位于巴西南部地区的圣卡塔琳娜州和巴拉那州的山区原生地饲养。本研究旨在分析该品种的遗传多样性和结构,为制定保护策略提供依据。研究人员对之前储存在巴西动物基因库(BAGB)中的精液和 DNA 样本,以及从巴西克鲁罗-拉加诺牛饲养者协会(ABCCL)注册的 8 个不同农场收集的样本,使用不同的 SNP 标记组(包含 50 K 至 777 K 标记)进行了基因分型。获得的平均预期(HE = 0.373)和观察(HO = 0.382)杂合性估计值表明,该品种存在较高的遗传变异性。分子方差分析(AMOVA)显示,只有 2.11% 的观察到的遗传变异可归因于分析种群之间的差异。获得的成对 FST 估计值介于 0.002 和 0.056 之间,证实了种群之间的分化程度较低。种群结构分析表明,研究种群之间存在亚结构,除其他因素外,这可能与动物是否有角有关。考虑到精液储存在 BGAB 的公牛和来自 8 个研究农场的样本集,有效种群规模(Ne)的估计值分别为 6 和 22,这表明该品种的 Ne 远远低于联合国粮农组织为保护家畜种群而建议的数值。通过对 CLAG 与该地区常规饲养的其他六个牛种和斑马牛种进行种群结构和混杂分析,发现了可能存在来自籼牛的未知引种的证据。所获得的结果为了解巴西 CLGA 品种的多样性和遗传结构提供了可靠的信息,并为制定有效的生产牛群遗传管理策略、通过收集种质丰富 BAGB 以及长期保护该品种提供了战略信息。
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引用次数: 0
Genomic variability of the MHC region: Empirical evidence from five horse breeds MHC 区域的基因组变异:五个马种的经验证据
IF 1.8 3区 农林科学 Q1 Veterinary Pub Date : 2024-05-08 DOI: 10.1016/j.livsci.2024.105480
Nina Moravčíková , Radovan Kasarda , Hana Vostra Vydrova , Lubos Vostry , Barbora Karásková , Juraj Candrák , Marko Halo

The purpose of this study was to analyse the level of variability in the autosomal genome, especially in the equine major histocompatibility complex region, in five horse breeds and identify heterozygosity-rich regions and potential footprints of balancing selection. Depending on data quality control, the dataset consisted of 51,168 or 53,874 single nucleotide polymorphism markers, available for 514 individuals (89 Lipizzan, 238 Old Kladruber, 47 Shagya Arabian, 61 Czech Warmblood and 81 Slovak Warmblood horses). Genomic variability within and between breeds was examined based on levels of heterozygosity (observed and expected), genomic inbreeding, Wright's FIS index and linkage disequilibrium. Subsequently, the screening of heterozygosity-rich regions and balancing selection signals derived from Tajima's D positive values was performed. As expected, due to the polymorphic nature of the major histocompatibility complex, the genomic variability level was generally higher when analysing only markers located in this area (mainly around genes belonging to class I). The Slovak and Czech Warmblood horses, as breeds with open herdbook, showed higher average values of heterozygosity indices than Lipizzan, Old Kladruber or Shagya Arabian breeds. Concerning only markers in the major histocompatibility complex region in complete or very high linkage disequilibrium, common patterns were found close to EQMHCB2, MHCB3 and EQMHCC1 genes belonging to class I and DQA1, DRB2, DRB3 and HLA-DOB genes from class II. Genome-wide, the number of heterozygosity-rich regions per animal ranged from 345.25 (Old Kladruber) to 603.33 (Czech Warmblood). Across all breeds, 254 heterozygosity-rich regions were detected directly in the major histocompatibility complex region (194 in class I and 60 in class II). Among them, the highest overlap showed regions found in the genomes of historically connected Czech and Slovak Warmblood breeds. The results suggested that the frequency of markers in heterozygosity-rich regions increased in Lipizzan, Old Kladruber and Shagya Arabian breeds in the genomic region of EQMCE1 gene (class I) and in Czech and Slovak Warmblood horses in DQB1, DQA2, DQB2, DQA3 and DRB2 genes (class II). Although the identified heterozygosity-rich regions formed 330 islands across the genomes of tested breeds, these islands were outside the major histocompatibility complex region. On the other hand, four of 425 balancing selection signals detected across breeds were located directly in the major histocompatibility complex region, close to DRA, DRB1, DQA1, DQB1 and DQB2 genes (class II). Shared islands and balancing selection footprints among breeds were found mainly on chromosomes 7 and 11.

本研究的目的是分析五个马品种常染色体基因组的变异水平,尤其是马主要组织相容性复合区的变异水平,并确定杂合度丰富的区域和潜在的平衡选择足迹。根据数据质量控制的不同,数据集由 51,168 或 53,874 个单核苷酸多态性标记组成,可用于 514 个个体(89 匹利比赞马、238 匹老克拉德鲁伯马、47 匹沙加阿拉伯马、61 匹捷克温血马和 81 匹斯洛伐克温血马)。根据杂合度(观察到的和预期的)、基因组近交、赖特 FIS 指数和连锁不平衡水平,对品种内和品种间的基因组变异性进行了研究。随后,对杂合度丰富的区域进行了筛选,并根据田岛 D 阳性值平衡了选择信号。不出所料,由于主要组织相容性复合体的多态性,仅分析位于该区域的标记物(主要围绕属于 I 类的基因)时,基因组变异水平普遍较高。斯洛伐克和捷克温血马作为开放群系的马种,其杂合指数的平均值高于利皮赞马、老克拉德鲁伯马或沙加阿拉伯马。仅就主要组织相容性复合体区域中完全或高度连锁不平衡的标记而言,在属于I类的EQMHCB2、MHCB3和EQMHCC1基因以及II类的DQA1、DRB2、DRB3和HLA-DOB基因附近发现了共同模式。在全基因组范围内,每只动物的杂合度富集区数量从 345.25(老克拉德鲁伯)到 603.33(捷克温血马)不等。在所有品种中,主要组织相容性复合体区域直接检测到 254 个杂合度丰富区域(I 类 194 个,II 类 60 个)。其中,重合度最高的区域出现在有历史渊源的捷克和斯洛伐克温血马品种的基因组中。研究结果表明,在利皮赞马、老克拉德鲁伯马和沙迦阿拉伯马品种的 EQMCE1 基因组区域(Ⅰ类)以及捷克和斯洛伐克温血马的 DQB1、DQA2、DQB2、DQA3 和 DRB2 基因组区域(Ⅱ类)中,杂合度丰富区域的标记频率有所增加。虽然已确定的富含杂合性的区域在受测品种的基因组中形成了 330 个岛屿,但这些岛屿都在主要组织相容性复合体区域之外。另一方面,在各品种检测到的 425 个平衡选择信号中,有 4 个直接位于主要组织相容性复合体区域,靠近 DRA、DRB1、DQA1、DQB1 和 DQB2 基因(II 类)。不同品种之间的共享岛和平衡选择足迹主要出现在 7 号和 11 号染色体上。
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引用次数: 0
Milk somatic cell count affects feed efficiency through increased heat production of lactating dairy cows 牛奶体细胞数通过增加泌乳奶牛的产热影响饲料效率
IF 1.8 3区 农林科学 Q1 Veterinary Pub Date : 2024-05-06 DOI: 10.1016/j.livsci.2024.105479
Pekka Huhtanen, Ali-Reza Bayat

The objective was to evaluate the relationships between somatic cell count (SCC) and feed efficiency using the data from two respiration chamber studies using Nordic Red cows (n = 136). The cows were fed ad libitum a total mixed ration (forage: concentrate 45:55 on dry matter (DM) basis) containing 162 and 379 g crude protein and neutral detergent fibre in kg DM, respectively. Average (± SD) DM intake and energy corrected milk (ECM) yield were 23.6 ± 3.4 and 37.7 ± 6.1 kg/d, respectively. Blood samples were collected in one of the studies (n = 86). Feed efficiency was expressed as ECM/DM intake, residual feed intake (RFI) and residual ECM yield (RECM). Feed efficiency decreased significantly with increased SCC irrespective of how the efficiency was expressed. Data from energy metabolism indicated that conversion of dietary gross energy to metabolizable energy (ME) was not influenced by SCC, but the efficiency of ME utilization decreased as a result of increased heat production. Increased heat production might be associated with the greater energy demand for immune function. Blood haptoglobin increased with SCC also indicating the role of immune function in increased heat production. Methane intensity increased by 1.0 g/kg ECM above cut-off value of 47 000 cells/mL. It is concluded that in addition to economic losses and animal welfare issues, increased milk SCC has negative environmental impact.

目的是利用北欧红牛(n = 136)的两项呼吸室研究数据,评估体细胞数(SCC)与饲料效率之间的关系。奶牛自由采食混合日粮(按干物质(DM)计算,饲草与精料的比例为 45:55),其中粗蛋白和中性洗涤纤维的含量分别为 162 克和 379 克(以千克 DM 计)。平均(± SD)DM 摄入量和能量校正奶(ECM)产量分别为 23.6 ± 3.4 kg/d 和 37.7 ± 6.1 kg/d。其中一项研究采集了血液样本(n = 86)。饲料效率用 ECM/DM摄入量、剩余饲料摄入量 (RFI) 和剩余 ECM 产量 (RECM) 表示。无论效率如何表示,饲料效率都随着 SCC 的增加而明显下降。能量代谢数据表明,日粮毛能转化为代谢能(ME)不受 SCC 的影响,但由于产热量增加,ME 的利用效率降低。产热增加可能与免疫功能需要更多能量有关。血液隐血红蛋白随 SCC 的增加而增加,这也表明免疫功能在产热增加中的作用。甲烷强度比 47 000 cells/mL 临界值高 1.0 g/kg ECM。结论是,除了经济损失和动物福利问题外,牛奶 SCC 的增加还会对环境造成负面影响。
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引用次数: 0
Effect of genetic and sex effect on genomic prediction for horn development in Nellore cattle 遗传和性别效应对内洛尔牛角发育基因组预测的影响
IF 1.8 3区 农林科学 Q1 Veterinary Pub Date : 2024-05-03 DOI: 10.1016/j.livsci.2024.105478
Larissa Bordin Temp , Ludmilla Costa Brunes , Letícia Silva Pereira , Sabrina Thaise Amorim , Cláudio Ulhôa Magnabosco , Raysildo Barbosa Lobo , Ovidio Carlos de Brito , Ricardo Viacava , Fernando Baldi

This study aimed to evaluate the influence of phenotypic classification of horn development, animal sex effect, and non-autosomal SNP (single nucleotide polymorphism) markers on the genetic parameters and genomic prediction ability for horn development in Nellore cattle using the single-step genomic best linear unbiased prediction method. The polled phenotype was evaluated in two (presence and absence of horns), three (scurs and polled offspring from a horned parent, and the polled and horned animals), and four (absence of horn, polled born to a parent with horn, scurs, and presence of horn) phenotypic categories. A total of 12 statistical models were evaluated. The variance components were estimated using the THRGIBBS1F90 software, and a threshold animal model was used for genomic prediction analyses with the single-step genomic BLUP (ssGBLUP) procedure. Accuracy, bias, and dispersion parameters were evaluated based on the linear regression (LR) method. The highest heritability (0.84) was obtained when the polled character was evaluated as a binary trait. The lowest heritability estimates (0.44 to 0.45) for horn development were obtained when the phenotype was classified into three categories. For the same horn development classification method, the heritability estimates were similar regardless of the genomic evaluated models and fixed effects included in the model. For models considering four and three phenotypic categories for horn development, the inclusion of the sex effect as a fixed effect within the CG did not improve the accuracy, bias, and dispersion of genomic predictions for horn development. Analyzing the trait with binary expression, the highest prediction accuracy was observed when the effect of sex was not included in the CG and without the SNPs in the sex chromosomes. These models displayed the highest dispersion, pointing out the low robustness of genomic prediction. In addition, models that use less than four categories to classify the horn development phenotype, with no discrimination between polled and homozygous polled displayed lower prediction ability. The inclusion of non-autosomal SNPs in the analyses for the models considering four phenotypic categories leads to an improvement in prediction accuracy in 5,26 %, bias, and dispersion reduction, 37 % and 4,55 %, respectively, compared with models that only considered autosomal SNPs. The selection using genomic information for the polled trait is feasible, and it is an alternative to obtaining polled Nellore animals. The binary coding of horn development is an unsuitable oversimplification of polled phenotype, and probably, the genetic background of horn development is more complex than previously proposed. The most adequate prediction model to evaluate the horn development in Nellore cattle was considering four phenotypic categories and including non-autosomal SNP in the analyses for genomic prediction purposes of naturally genetically polled animals. Genetic dehor

本研究旨在利用单步基因组最佳线性无偏预测法,评估牛角发育的表型分类、动物性别效应和非常染色体 SNP(单核苷酸多态性)标记对内洛尔牛角发育的遗传参数和基因组预测能力的影响。对花粉表型进行了两类(有角和无角)、三类(有角亲本的后代有鳞和花粉,以及花粉和有角动物)和四类(无角、有角亲本所生的花粉、有鳞和有角)表型评估。共评估了 12 个统计模型。使用 THRGIBBS1F90 软件估算了方差分量,并使用单步基因组 BLUP(ssGBLUP)程序对阈值动物模型进行了基因组预测分析。根据线性回归(LR)方法评估了准确性、偏差和分散参数。当将花粉特征作为二元性状进行评估时,遗传率最高(0.84)。将表型分为三类时,牛角发育的遗传率估计值最低(0.44 至 0.45)。对于相同的角发育分类方法,无论基因组评估模型和模型中包含的固定效应如何,遗传力估计值都是相似的。对于角发育表型分为四类和三类的模型,将性别效应作为固定效应包含在基因组中并不能提高角发育基因组预测的准确性、偏差和分散性。在分析二元表达的性状时,如果在基因组中不包含性别效应,也不包含性染色体上的 SNPs,则预测准确率最高。这些模型的离散度最高,表明基因组预测的稳健性较低。此外,使用少于四个类别对牛角发育表型进行分类、不区分花粉和同卵花粉的模型预测能力较低。与只考虑常染色体 SNP 的模型相比,将非常染色体 SNP 纳入考虑四个表型类别的模型的分析中,预测准确率提高了 5.26%,偏差和离散度分别降低了 37% 和 4.55%。利用基因组信息对花粉性状进行选择是可行的,也是获得花粉内洛尔动物的一种替代方法。牛角发育的二元编码是对花粉表型的过度简化,可能牛角发育的遗传背景比之前提出的更为复杂。评估内洛尔牛角发育的最适当预测模型是考虑四个表型类别,并将非常染色体 SNP 纳入分析,以实现对天然遗传花粉牛的基因组预测。遗传去角法可作为一种低成本、非侵入性的方法大规模采用,利用基因组信息和交配策略提高无角动物的频率。
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引用次数: 0
Differential ovulation responses in nulliparous and multiparous rabbit females: A cannula-mediated study 无排卵和多排卵雌兔的排卵反应差异:插管介导的研究
IF 1.8 3区 农林科学 Q1 Veterinary Pub Date : 2024-05-01 DOI: 10.1016/j.livsci.2024.105475
María Pilar Viudes-de-Castro , Francisco Marco-Jiménez , José Salvador Vicente

In order to explore a less stressful and hormone-independent insemination method in rabbits, we aimed to evaluate the influence of a new insemination cannula on reproductive performance. Two assays were conducted. In the first, 136 nulliparous and multiparous females were treated with 12.5 IU of eCG to improve their receptivity and divided into four stimulation groups (aGnRHControl, Extender, Seminal and Sperm) to test ovulation frequency and rate. The control group received 1 µg of buserelin acetate intramuscularly to induce ovulation. The other groups used a 3D printed cannula to introduce 0.5 ml of extender, undiluted seminal plasma or resuspended sperm into the vagina. After six days, laparoscopy was performed to assess ovulation frequency and rate. Results showed that nulliparous does exhibited higher ovulation frequencies compared to multiparous does, regardless of the stimulation group.

In the second assay, reproductive performance (delivery rate and litter size at birth) of 109 females treated with 12.5 IU of eCG to improve their receptivity was studied after insemination with a seminal dose using the 3D printed cannula. Forty-nine of them were induced to ovulate with buserelin acetate as a control. The results confirmed previous findings, as cannula stimulation allowed better delivery rates in receptive nulliparous than multiparous does. Differential response to multiparous does to the physical stimulus of the cannula could be supported by the histological changes and loss of contractile response that occur after multiple births. Litter sizes at birth were similar between experimental groups.

In conclusion, the 3D designed cannula showed promising results in nulliparous does in ovulating frequency, and further refinement is needed to enhance its effectiveness, particularly in multiparous rabbits.

为了探索一种压力较小且不依赖激素的兔子人工授精方法,我们旨在评估一种新型人工授精插管对兔子繁殖性能的影响。我们进行了两项试验。在第一项试验中,136 只单胎和多胎雌兔接受了 12.5 IU eCG 治疗,以提高它们的受精能力,并被分为四个刺激组(aGnRHC 控制组、延长组、精液组和精子组),以测试排卵频率和排卵率。对照组肌肉注射 1 µg 醋酸丁螺环酮诱导排卵。其他组则使用 3D 打印插管将 0.5 毫升扩展剂、未稀释的精浆或重新悬浮的精子引入阴道。六天后,进行腹腔镜检查以评估排卵频率和排卵率。结果显示,与多胎雌性母猪相比,无论采用哪种刺激组,空怀母猪的排卵频率都更高。在第二项试验中,使用 12.5 IU eCG 治疗以提高雌性母猪接受能力的 109 只雌性母猪,在使用 3D 打印插管进行精液剂量授精后,其繁殖性能(分娩率和产仔数)得到了研究。作为对照组,其中 49 只使用醋酸丁螺环酮诱导排卵。结果证实了之前的研究结果,因为插管刺激可接受的无阴道雌鼠比多阴道雌鼠的分娩率更高。多胎雌鼠对插管物理刺激的反应不同,这可能是由于多胎雌鼠在分娩后会发生组织学变化并失去收缩反应。总之,三维设计插管在无产仔母兔的排卵频率方面显示出良好的效果,但仍需进一步改进以提高其有效性,尤其是在多产仔兔中。
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引用次数: 0
Effect of dulcitol on growth performance, antioxidant activity, immune function, and intestinal microflora of growing-finishing pigs 杜冷丁对生长育成猪的生长性能、抗氧化活性、免疫功能和肠道微生物区系的影响
IF 1.8 3区 农林科学 Q1 Veterinary Pub Date : 2024-05-01 DOI: 10.1016/j.livsci.2024.105476
Zhengqun Liu , Shiyue Liang , Diankui Wang , Zi Zheng , Ning Li , Chunhua Zhang , Jun Yan , Renmin Liu , Pei He , Qianjun Li , Shuqin Mu

Dulcitol (DUL) has multiple biological functions such as anti-inflammatory, antioxidant, and anti-cancer. However, little is known about the DUL used in swine diets. This experiment investigated the effects of DUL on the growth performance, apparent digestibility of nutrient, blood profiles, and fecal microbiota of growing-finishing pigs. A total of 144 barrows (initial body weight (BW) of 30.1 ± 0.7 kg) were blocked based on BW and assigned to 4 dietary treatments in a 72-d trial, each treatment had 6 replicate pens and 6 pigs per pen. Dietary treatments included a control (CON) diet and 3 DUL diets with DUL supplementation at the concentration of 100 (DUL1), 500 (DUL2), and 1,000 (DUL3) mg/kg in the basal diet, respectively. Results showed that DUL supplementation increased the final BW, average daily gain, and average daily feed intake of pigs (p < 0.05). Additionally, DUL2 decreased the feed-to-gain ratio of the pigs and increased the apparent digestibility of gross energy, dry matter, crude protein, ash, and calcium compared to CON group (p < 0.05). The contents of IgG and IgM in serum increased linearly with an increased inclusion level of DUL, whereas the serum IL-1β and TNF-α contents were linearly decreased with the increased DUL levels (p < 0.05). Similarly, DUL addition linearly increased the activity of SOD, GSH-px, and CAT, but decreased the MDA contents in serum (p < 0.05). Microbial analysis showed that the DUL supplementation had no effects on the diversity of fecal microbiota. While LEfSe analysis showed that Rikenellaceae_RC9_gut_group was enriched in DUL1 group, while the Enterobacterales were enriched in DUL3 group. Spearman correlation analysis identified a correlation between the abundance of Lactobacillus and Prevotellaceae_NK3B31_group and the functions of antioxidants and immune (p < 0.05). Collectively, current study demonstrated that 500 mg/kg DUL supplementation could increase growth performance and nutrients digestibility, as well as promote serum immune and antioxidant indices of growing-finishing pigs.

杜冷丁(DUL)具有多种生物功能,如消炎、抗氧化和抗癌。然而,人们对猪日粮中使用的 DUL 却知之甚少。本实验研究了 DUL 对生长育成猪的生长性能、表观营养消化率、血液特征和粪便微生物群的影响。在一项为期 72 天的试验中,共有 144 头公猪(初始体重(BW)为 30.1 ± 0.7 千克)根据体重进行了分群,并被分配到 4 种日粮处理中,每种处理有 6 个重复栏,每栏 6 头猪。日粮处理包括对照(CON)日粮和 3 种 DUL 日粮,基础日粮中 DUL 的补充浓度分别为 100(DUL1)、500(DUL2)和 1000(DUL3)毫克/千克。结果表明,添加 DUL 能提高猪的最终体重、平均日增重和平均日采食量(p < 0.05)。此外,与 CON 组相比,DUL2 降低了猪的料增比,提高了总能、干物质、粗蛋白、灰分和钙的表观消化率(p < 0.05)。血清中 IgG 和 IgM 的含量随着 DUL 添加量的增加而线性增加,而血清中 IL-1β 和 TNF-α 的含量随着 DUL 添加量的增加而线性减少(p < 0.05)。同样,添加 DUL 可线性提高 SOD、GSH-px 和 CAT 的活性,但降低血清中 MDA 的含量(p < 0.05)。微生物分析表明,补充 DUL 对粪便微生物群的多样性没有影响。LEFSe分析表明,DUL1组富集了Rikenellaceae_RC9_gut_group,而DUL3组富集了Enterobacterales。斯皮尔曼相关分析表明,乳酸杆菌和Prevotellaceae_NK3B31_组的丰度与抗氧化和免疫功能之间存在相关性(p <0.05)。综上所述,本研究表明,补充 500 mg/kg DUL 可提高生长育成猪的生长性能和营养物质消化率,并促进其血清免疫和抗氧化指标的提高。
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引用次数: 0
Genome-wide single nucleotide polymorphisms reveal the genetic diversity and population structure of Creole goats from northern Peru 全基因组单核苷酸多态性揭示秘鲁北部克里奥尔山羊的遗传多样性和种群结构
IF 1.8 3区 农林科学 Q1 Veterinary Pub Date : 2024-05-01 DOI: 10.1016/j.livsci.2024.105473
Flor-Anita Corredor , Deyanira Figueroa , Richard Estrada , William Burgos-Paz , Wilian Salazar , Wilder Cruz , Roiser Lobato , Pedro Injante , David Godoy , Christian Barrantes , Jorge Ganoza , Juancarlos Cruz , Carlos I. Arbizu

Goat farming constitutes a significant source of income for farmers in northern Peru. There is currently an absence of information about the genetics of Peruvian Creole goats that would enable us to understand their origins and genetic spread. The objective of this study was to estimate the genetic diversity of Creole goats from northern Peru using SNP markers. This study involved the collection of 192 male Creole goats from three key goat production geographical departments in northern Peru. These goat samples were genotyped using the GGPGoat70k SNP panel. To explore the genetic influence of other breeds on Peruvian Creole goats, our dataset was combined with previously published SNP genotypes. External data set includes multiple breeds genotypes sampled from Argentina, Brazil, Spain, and Alpine breed from Italy, France, and Switzerland. After quality control 52,832 autosomal SNPs were used to assess genetic diversity in the Peruvian goats. For the population structure analysis of the merged data 20,513 common SNPs were used. Estimations for expected heterozygosity (He), observed heterozygosity (Ho), and inbreeding coefficient (FIS) were computed for the Peruvian groups. AMOVA, principal component analysis and ADMIXTURE were conducted to evaluate the population structure in the two data sets, Peru and merged. The results revealed a considerable genetic diversity, with Ho values ranging from 0.40 to 0.41 for the Peruvian sampling groups, and inbreeding coefficient was notably low for Peruvian goat. The population structure analysis demonstrated a distinction (p < 0.05) from other breeds. These findings suggest a level of genetic differentiation of the Peruvian goat population among other breeds, although further research is needed considering samples from other Peruvian areas. We expect this study will contribute to define genetic management strategies to prevent the loss of genetic diversity in Peruvian goat populations and for upcoming advancements in this field.

山羊养殖是秘鲁北部农民的重要收入来源。目前缺乏有关秘鲁克里奥尔山羊遗传学的信息,因此我们无法了解其起源和遗传传播情况。本研究的目的是利用 SNP 标记评估秘鲁北部克里奥尔山羊的遗传多样性。这项研究从秘鲁北部三个主要的山羊生产地区收集了 192 只克里奥尔山羊。使用 GGPGoat70k SNP 面板对这些山羊样本进行了基因分型。为了探索其他品种对秘鲁克里奥尔山羊的遗传影响,我们的数据集与之前公布的 SNP 基因型相结合。外部数据集包括来自阿根廷、巴西、西班牙的多个品种基因型样本,以及来自意大利、法国和瑞士的阿尔卑斯品种基因型样本。经过质量控制后,52832 个常染色体 SNP 被用于评估秘鲁山羊的遗传多样性。在对合并数据进行种群结构分析时,使用了 20,513 个常见 SNPs。计算了秘鲁群体的预期杂合度(He)、观察杂合度(Ho)和近交系数(FIS)。通过AMOVA、主成分分析和ADMIXTURE,对秘鲁和合并的两组数据的种群结构进行了评估。结果显示,秘鲁采样组的遗传多样性相当高,Ho 值在 0.40 至 0.41 之间,秘鲁山羊的近交系数明显较低。种群结构分析表明,秘鲁山羊与其他品种存在差异(p < 0.05)。这些研究结果表明,秘鲁山羊种群与其他品种之间存在一定程度的遗传分化,但还需要进一步研究秘鲁其他地区的样本。我们希望这项研究将有助于确定遗传管理策略,以防止秘鲁山羊种群遗传多样性的丧失,并促进该领域未来的发展。
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引用次数: 0
Herbage allowances of native grasslands and cow genotype affect follicular and uterine parameters in beef cows 原生草地的草量和奶牛基因型对肉牛卵泡和子宫参数的影响
IF 1.8 3区 农林科学 Q1 Veterinary Pub Date : 2024-04-30 DOI: 10.1016/j.livsci.2024.105477
Rodrigo Vivián Paradizo , Mariana Carriquiry , Guillermo Martinez Boggio , Carolina Viñoles , Ana Meikle , Ana Laura Astessiano

Reproduction is crucial in the efficiency of grazing-based beef production systems. There are different ways to improve reproductive indices in cattle, such as through herd management, nutrition and/or genetics. It was shown that different levels of herbage allowance and the use of crossbred cows could improve the follicular and uterine characteristics that translate into higher cow fertility. Our study aimed to evaluate the follicle size, oocyte quality, and changes in follicular fluid composition and uterine gene expression in crossbred and purebred cycling beef cows grazing native pastures at two different levels of herbage allowance for three years. The experimental design was a complete randomized block with two replications. We allocated a total of 32 multiparous cows, with eight cows per block in a two-by-two factorial arrangement of herbage allowance (HA: High (HI) and Low (LO)) and cow genotype (CG: Purebred (PU) and Crossbred (CR)). Cows with at least two previous ovulations were slaughtered at 190 ± 15 days postpartum and uterine tissue and ovaries of the cycling cows were collected. We obtained that the preovulatory follicle size, progesterone, and insulin-like growth factor 1 (IGF1) were greater in cows with HI than with LO long-term herbage allowance. Furthermore, the non-esterified fatty acids (NEFA) concentration was lower in crossbred cows. It suggests a lower mobilization of energy reserves in crossbred than in purebred cows. For the gene expression in uterine tissues, we only observed a greater expression of IGFBP2 and IGFBP4 mRNA in cows under LO HA. These findings reveal an effect of the herbage allowance and cow genotype in follicular and uterine parameters that can be translated into better cow fertility.

繁殖对于以放牧为基础的牛肉生产系统的效率至关重要。提高牛的繁殖指数有多种方法,如牛群管理、营养和/或遗传学。研究表明,不同水平的牧草补贴和杂交牛的使用可改善卵泡和子宫特性,从而提高牛的繁殖力。我们的研究旨在评估杂交和纯种循环饲养肉牛的卵泡大小、卵母细胞质量,以及卵泡液成分和子宫基因表达的变化。实验设计为两个重复的完全随机区组。我们共分配了 32 头多胎奶牛,每个区组 8 头奶牛,按牧草量(HA:高(HI)和低(LO))和奶牛基因型(CG:纯种(PU)和杂交(CR))的二乘二因子排列。在产后 190 ± 15 天屠宰至少有两次排卵的奶牛,并收集周期奶牛的子宫组织和卵巢。我们发现,长期食用HI草料的奶牛排卵前卵泡大小、孕酮和胰岛素样生长因子1(IGF1)均高于长期食用LO草料的奶牛。此外,杂交奶牛的非酯化脂肪酸(NEFA)浓度较低。这表明,与纯种奶牛相比,杂交奶牛的能量储备动员率更低。在子宫组织的基因表达方面,我们只观察到在 LO HA 条件下,奶牛的 IGFBP2 和 IGFBP4 mRNA 表达量更高。这些发现揭示了草料配给量和奶牛基因型对卵泡和子宫参数的影响,这种影响可转化为更好的奶牛繁殖力。
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引用次数: 0
Genetic parameters for mesenteric torsion in a pig maternal line 猪母系肠系膜扭转的遗传参数
IF 1.8 3区 农林科学 Q1 Veterinary Pub Date : 2024-04-16 DOI: 10.1016/j.livsci.2024.105474
Suelen Fernandes Padilha , Amauri Felipe Evangelista , Luis Orlando Duitama Carreño , Marcelo Silva Freitas , Jader Silva Lopes , Adriana Mércia Guaratini Ibelli , Jane de Oliveira Peixoto , Marcos Antônio Zanella Morés , Maurício Egídio Cantão , Mônica Corrêa Ledur , Rodrigo de Almeida Teixeira , Laila Talarico Dias

Mesenteric torsion (MT) is a condition characterized by the twisting of intestinal loops, leading to a disruption in blood flow and abdominal distension. Several factors can predispose animals to this condition, which primarily affects healthy, fast-growing pigs and often results in fatal outcomes. Given the absence of studies on the genetic factors associated with this condition, our research aimed to estimate the heritability coefficient for MT and explore the genetic correlations between MT and performance traits in pigs. Our dataset comprised of 43,384 records of pigs from a maternal line from a nucleus farm. These pigs were born between 2010 and 2022 and had recorded information regarding MT status (0 for healthy and 1 for affected animals), weaning weight (WW), as well as pedigree, genotypes, and genomic estimated breeding values (GEBVs) for the following traits: MT status, days to reach 110 kg (D110), feed conversion adjusted to 110 kg (FC110), and backfat thickness adjusted to 110 kg (BT110). In our statistical model, the effects of contemporary group (CG: sex, year, and week of weaning) and the linear covariate WW were considered fixed effects, while the direct additive genetic effect was accounted as random. On average, pigs affected by MT had an age of 104.35 ± 37.75 days, and the condition had an overall herd frequency of 2.46 %. Mesenteric torsion occurred more frequently in female pigs raised in collective pens compared to non-castrated males raised in individual pens. Heritability estimates for MT, using both pedigree (0.13 ± 0.02) and genomic (0.12 ± 0.02) data, were of low magnitude. This suggests that while there is genetic variability associated with MT, a significant portion of this variation is due to environmental variance. The correlation between MT and BT110 GEBVs was of low magnitude (0.05). In contrast, the correlations between GEBVs for MT and both D110 and FC110 were moderate in magnitude (0.22 for both traits). This implies that pigs taking longer to reach 110 kg and those with poorer feed conversion are more likely to develop MT. There is genetic variability for mesenteric torsion in pigs. Selection aimed at improving feed conversion and reducing the age at which pigs reach 110 kg could lead to a decrease in the occurrence of MT within pig populations.

肠系膜扭转(MT)是一种以肠环扭转为特征的疾病,会导致血流中断和腹胀。有几种因素会导致动物患上这种疾病,主要影响健康、快速生长的猪,并经常导致死亡。鉴于缺乏对这种病症相关遗传因素的研究,我们的研究旨在估算 MT 的遗传系数,并探索 MT 与猪的性能特征之间的遗传相关性。我们的数据集包括一个核心农场母系猪的 43384 条记录。这些猪出生在 2010 年至 2022 年之间,记录了 MT 状态(0 代表健康,1 代表患病)、断奶体重(WW)以及下列性状的血统、基因型和基因组估计育种值(GEBVs)等信息:MT状态、达到110千克的天数(D110)、调整到110千克的饲料转化率(FC110)和调整到110千克的背膘厚度(BT110)。在我们的统计模型中,当代组(CG:性别、年份和断奶周数)和线性协变量 WW 的效应被视为固定效应,而直接加性遗传效应被视为随机效应。受肠系膜扭转影响的猪的平均日龄为 104.35 ± 37.75 天,该病症在猪群中的总发生率为 2.46%。与单独圈养的非阉割公猪相比,集体圈养的母猪肠系膜扭转发生率更高。使用血统(0.13 ± 0.02)和基因组(0.12 ± 0.02)数据估计的肠系膜扭转遗传率较低。这表明,虽然 MT 存在遗传变异,但其中很大一部分是环境变异造成的。MT 与 BT110 GEBV 之间的相关性较低(0.05)。相比之下,MT 与 D110 和 FC110 的 GEBV 之间的相关性中等(两个性状均为 0.22)。这意味着,达到 110 千克需要更长时间的猪和饲料转化率较低的猪更有可能出现 MT。猪肠系膜扭转存在遗传变异。旨在提高饲料转化率和降低猪只体重达到 110 千克的日龄的选育可减少猪群中 MT 的发生。
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引用次数: 0
Modelling of on-farm greenhouse gas emissions from dual-purpose meat and wool sheep production in different geographical regions of Norway 挪威不同地理区域肉羊和毛羊两用生产的农场温室气体排放建模
IF 1.8 3区 农林科学 Q1 Veterinary Pub Date : 2024-04-09 DOI: 10.1016/j.livsci.2024.105472
B.A. Åby , S. Samsonstuen , K.A. Beauchemin , L. Aass

The whole-farm model, HolosNorSheep, was developed to estimate net greenhouse gas emissions from dual purpose sheep production in Norway. The model adopted a cradle-to-farm gate system boundary and is based on the International Panel on Climate Change methodology and includes direct emissions from enteric and manure methane (CH4; GWP100=27), direct and indirect nitrous oxide (N2O; GWP100=273) from manure and soils, direct carbon dioxide (CO2) emissions from energy use and indirect CO2 emissions from the production of input factors. Soil carbon balance is calculated using the ICBM-model. Emission intensities (CO2-eq/kg product) for sheep carcass and greasy wool, was estimated for five geographical regions of Norway (East, West, South, Mid and North). The geographical regions varied considerably in climate, feed resources, days on pasture and herd/farm management. Estimated emission intensities per kg carcass and greasy wool varied from 23.5 to 19.9 (Mid region) to 26.8 and 22.8 kg CO2-eq (North region) respectively. The difference between the Mid and North region was mainly due to higher CO2 and N2O emissions from use of fuel and N-fertilizer in the North, where a short growth season, and thus reduced grass yields, are compensated by using greater land area. Based on the distribution of sheep in the regions, and the emission intensities in each region, weighted average emission intensities per kg carcass and greasy wool were estimated as 25.1 and 23.3 kg CO2-eq, respectively. Five alternative methods for the allocation of the co-products were compared with the amounts allocated to greasy wool ranging from 0 % when using no allocation (i.e., all emissions allocated to the sheep carcass), 11 % for economic allocation, 12 % for mass allocation, 19 % for biophysical allocation based on energy requirement up to 31 % for allocation based on protein mass. The emission intensity for wool was highly sensitive to the allocation method used (range from 0 to 61 kg CO2-eq per kg greasy wool), while the effect on sheep carcass was lower (range 19 to 28 kg CO2-eq per kg carcass). For production systems where meat is the main product, as in Norway, allocation should be based on biophysical allocation based on energy requirement.

HolosNorSheep 是一个全农场模型,用于估算挪威两用羊生产的温室气体净排放量。该模型采用了 "从摇篮到牧场 "的系统边界,以国际气候变化专门委员会的方法为基础,包括肠道和粪便甲烷(CH4;GWP100=27)的直接排放、粪便和土壤的直接和间接氧化亚氮(N2O;GWP100=273)、能源使用的直接二氧化碳(CO2)排放以及投入要素生产的间接二氧化碳排放。土壤碳平衡采用 ICBM 模型计算。对挪威五个地理区域(东部、西部、南部、中部和北部)的绵羊胴体和油脂羊毛的排放强度(二氧化碳当量/千克产品)进行了估算。这些地理区域在气候、饲料资源、牧场日数和牧群/农场管理方面差异很大。每千克胴体和油脂羊毛的估计排放强度分别从23.5千克二氧化碳当量到19.9千克二氧化碳当量(中部地区)到26.8千克二氧化碳当量和22.8千克二氧化碳当量(北部地区)不等。中部地区和北部地区之间的差异主要是由于北部地区使用燃料和氮肥产生的二氧化碳和一氧化二氮排放量较高,而北部地区的生长季节较短,因此草产量减少,但使用的土地面积更大,从而弥补了这一不足。根据绵羊在各地区的分布以及各地区的排放强度,每千克胴体和每千克油脂羊毛的加权平均排放强度分别估计为 25.1 千克二氧化碳当量和 23.3 千克二氧化碳当量。比较了五种分配副产品的替代方法,分配给油脂羊毛的数量从不计分配时的 0%(即所有排放分配给绵羊胴体)、经济分配时的 11%、质量分配时的 12%、基于能量需求的生物物理分配时的 19%到基于蛋白质质量分配时的 31%不等。羊毛的排放强度对所使用的分配方法高度敏感(范围为每千克油脂羊毛 0 至 61 千克二氧化碳当量),而对绵羊胴体的影响较小(范围为每千克胴体 19 至 28 千克二氧化碳当量)。对于像挪威这样以肉类为主要产品的生产系统,分配应基于能量需求的生物物理分配。
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Livestock Science
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