Emerging issues in genomic selection

Genomic selection (GS) is now practiced successfully across many species. However, many questions remain, such as long-term effects, estimations of genomic parameters, robustness of genome-wide association study (GWAS) with small and large datasets, and stability of genomic predictions. This study summarizes presentations from the authors at the 2020 American Society of Animal Science (ASAS) symposium. The focus of many studies until now is on linkage disequilibrium between two loci. Ignoring higher-level equilibrium may lead to phantom dominance and epistasis. The Bulmer effect leads to a reduction of the additive variance; however, the selection for increased recombination rate can release anew genetic variance. With genomic information, estimates of genetic parameters may be biased by genomic preselection, but costs of estimation can increase drastically due to the dense form of the genomic information. To make the computation of estimates feasible, genotypes could be retained only for the most important animals, and methods of estimation should use algorithms that can recognize dense blocks in sparse matrices. GWASs using small genomic datasets frequently find many marker-trait associations, whereas studies using much bigger datasets find only a few. Most of the current tools use very simple models for GWAS, possibly causing artifacts. These models are adequate for large datasets where pseudo-phenotypes such as deregressed proofs indirectly account for important effects for traits of interest. Artifacts arising in GWAS with small datasets can be minimized by using data from all animals (whether genotyped or not), realistic models, and methods that account for population structure. Recent developments permit the computation of P-values from genomic best linear unbiased prediction (GBLUP), where models can be arbitrarily complex but restricted to genotyped animals only, and single-step GBLUP that also uses phenotypes from ungenotyped animals. Stability was an important part of nongenomic evaluations, where genetic predictions were stable in the absence of new data even with low prediction accuracies. Unfortunately, genomic evaluations for such animals change because all animals with genotypes are connected. A top-ranked animal can easily drop in the next evaluation, causing a crisis of confidence in genomic evaluations. While correlations between consecutive genomic evaluations are high, outliers can have differences as high as 1 SD. A solution to fluctuating genomic evaluations is to base selection decisions on groups of animals. Although many issues in GS have been solved, many new issues that require additional research continue to surface.     

Comparative pharmacokinetics and pharmacokinetic/pharmacodynamic analysis by nonlinear mixed‐effects modeling of cefquinome in nonpregnant,pregnant, and lactating goats after intravenous and intramuscular administration

Cefquinome is a fourth‐generation cephalosporin that is used empirically in goats. Different physiologic factors like pregnancy or lactation could determine the pharmacokinetic behavior of drugs in the organism. The objectives of this study are to (a) compare the pharmacokinetics of cefquinome after intravenous and intramuscular administration in adult nonpregnant (n = 6), pregnant (n = 6), and lactating goats (n = 6), at a dose of 2 mg/kg, with rich sampling by nonlinear mixed‐effects modeling, (b) conduct a pharmacokinetic/pharmacodynamic analysis to evaluate the efficacy of the recommended posology in goats with different physiological states, and (c) determine the optimal posology that achieve a PTA value ≥ 90%, taking into account a T > MIC ≥ 60% of a MIC value ≤ 0.25 µg/ml, in the different subpopulations of goats for both routes. Gestation significantly increased Ka and V1, while reduced F0, Cl, and Q. On the other hand, lactation significantly increased V1 and reduced Tk0. Cefquinome concentrations achieved in placental cotyledon, amniotic fluid, and fetal serum indicate a minimal penetration across the placental barrier. Moreover, milk penetration of cefquinome was minimal. The total body clearance of cefquinome for goats was 0.29 L kg^?1 hr^?1, that is apparently higher than the reported for cows (0.13 L kg^?1 hr^?1) and pigs (0.16 L kg^?1 hr^?1). So, the optimal dose regimen for cefquinome after intravenous and intramuscular administration required higher dose and frequency of administration compared with recommendations for cows or pigs. Therefore, 2 mg kg^?1 8 hr^?1 and 5 mg kg^?1 12 hr^?1 could be used for IV and IM routes, respectively, for the treatment of respiratory infections caused by P. multocida and M. haemolytica, but only 5 mg kg^?1 12 hr^?1 by both routes should be recommended for Escherichia coli infections.     

番鸭产蛋各期肝脂肪酸组成及AMPK信号通路基因表达研究

旨在探究产蛋各期番鸭肝腺苷酸活化蛋白激酶（AMPK）信号通路基因表达和肝脂肪酸组成,为番鸭肝脂质代谢应答产蛋提供机理研究。本研究选取开产前22周龄、产蛋初期30周龄、产蛋中期40周龄和产蛋末期60周龄母番鸭各15羽,全自动生化仪测定血脂水平,苏木精-伊红（HE）染色和油红O染色观察肝组织学结构,实时荧光定量PCR （qRT-PCR）检测肝AMPK通路基因表达,气相色谱-质谱联用法（GC-MS）检测产蛋各期肝脂肪酸组成。结果表明,总胆固醇（TC）、低密度脂蛋白胆固醇（LDL-C）、甘油三酯（TG）和极低密度脂蛋白胆固醇（VLDL-C）水平在40周龄显著高于22、30和60周龄（P<0.05）;高密度脂蛋白胆固醇（HDL-C）水平在30和40周龄显著低于22和60周龄（P<0.05）。肝HE和油红O染色切片显示,肝在22周龄呈实质状,至产蛋40和60周龄,肝脂滴沉积明显（P<0.05）。AMPKα1在22、30、40和60周龄呈本底低水平表达,并显著低于产蛋各期肉碱脂酰转移酶1（CPT1）和脂肪酸合成酶（FAS）的表达量（P<0.05）,FAS在22、40和60周龄均呈高水平表达（P<0.05）;羟甲基戊二酰辅酶A还原酶（HMGR）、肝细胞核因子4α（HNF4α）、乙酰辅酶A羧化酶1（ACC1）和固醇调控元件结合蛋白-1（SREBP1c）在40周龄表达量显著高于22和30周龄（P<0.05）。肝中饱和脂肪酸（SFA）、单不饱和脂肪酸（MUFA）和多不饱和脂肪酸（PUFA）主要由C16∶0、C18∶0、C18∶1和C20∶2 n-6构成,分别占总脂肪酸含量的32%、16%、30%和9%。C14∶0和C16∶0含量在40周龄显著高于22周龄（P<0.05）;C24∶0、C20∶2 n-6和PUFA含量在60周龄显著高于22和40周龄（P<0.05）。综上,番鸭产蛋期肝通过上调FAS等脂质合成基因表达,合成大量长链脂肪酸,沉积于肝,并增加血脂水平。     

Sperm production and quality in European eel (Anguilla anguilla) in relation to hormonal treatment

Aquaculture production relies on controlled management of gametogenesis, especially in species where assisted reproduction is needed for obtaining gametes in captivity. The present study used human chorionic gonadotropin (hCG) treatments to induce and sustain spermatogenesis in European eel (Anguilla anguilla). The aim was to evaluate effects of strip-spawning timing (12 vs. 24 hr) after weekly administration of hCG and the necessity of a primer dose (in addition to weekly hormonal treatment) prior to strip spawning (primer vs. no-primer) on sperm quality parameters. Sperm parameters included milt production (weight), density and sperm kinematics at Week 9, 11 and 13 after onset of treatment. Spermiation commenced in 11.5% of males in Week 5 and by Week 9, and all males produced milt. Male weight, milt production, sperm density and spermatocrit did not differ among hormonal treatments during the experimental period. Overall, male weight decreased from 106.3 to 93.0 g, milt weight increased from 3.5 to 5.4 g, sperm density counts decreased from 11.7 × 10⁹ to 10.5 × 10⁹ cells/ml, and spermatocrit decreased from 46.5% to 40.5%. Furthermore, spermatocrit was positively related to haemocytometer counts (R² = .86, p < .001), providing a reliable indicator of sperm density. Differences in sperm kinematics were observed depending on strip-spawning timing after hormonal injection (12 vs. 24 hr) but with no consistent pattern. These sperm quality parameters also did not consistently differ between the no-primer and primer treatments. Considering that each male may be stripped 4–5 times over the 2–3 months spawning season, omitting the primer would reduce animal handling, material costs and labour intensity, while sustaining high-quality sperm production.     

丁酸梭菌在家禽生产中应用的研究进展

丁酸梭菌作为一种益生菌,存在于人和动物的肠道中,不易受到胃酸、消化酶和胆汁酸等因素的影响,不仅可以通过把营养物质降解成丁酸为动物提供营养与能量,而且可以保护肠道健康,促进营养物质的吸收和动物的生长,以及增强免疫功能等,因此丁酸梭菌可以作为饲料添加剂用于畜禽生产。本文对丁酸梭菌对家禽生理、生产性能的影响及其机制进行综述,以便为丁酸梭菌在家禽生产中的应用提供参考。     

2020年底各地新玉米霉菌毒素风险分析

为了解呕吐毒素（DON）、玉米赤霉烯酮（ZEN）和黄曲霉毒素B1（AFB1）在2020年底新玉米中的污染情况,指导饲料生产企业和养殖场（户）开展霉菌毒素防控,降低霉菌毒素对饲料质量安全及养殖动物的影响,避免经济受损的风险。2020年12月在市场上采集新玉米样本225份,采用胶体金免疫层析法或上转发光免疫分析法对其霉菌毒素污染情况进行检测,依据安佑集团相关企业标准标和GB 13078-2017《饲料卫生标准》进行判定分析。结果表明：新玉米中霉菌毒素检出率为96.0%,其中DON、ZEN和AFB1的检出率分别为85.8%、87.1%和86.7%|DON、ZEN和AFB1在新玉米中的污染状况差别较大,按《饲料卫生标准》判定的超标率分别为0.0%、0.4%和11.6%|最大检测值分别为2500、534 μg/kg和＞100 μg/kg。就产地而言,山西、内蒙古、东北、安徽、山东、河南、云南、陕西等地霉菌毒素污染较重。综上,与2019年及2020年玉米霉菌毒素污染调查数据相比,2020年底新玉米污染程度较重。 [关键词] 玉米|霉菌毒素|胶体金免疫层析法|上转发光免疫分析法|污染规律     

应用液态悬浮芯片技术建立17种大肠杆菌耐药基因多重快速检测方法

为建立一种快速、高通量的多重耐药基因检测方法,利用Luminex液态芯片平台,建立了可同时检测17种耐药基因的液态芯片检测方法。该方法对大肠杆菌常见的七大类抗菌药物所对应的17种耐药基因（blaSHV、blaCMY-1、Aph3-IIa-1、aac(6)-Ib-cr、aadA-1、cmlA-1、gyrA、mcr-1、NDM-1、parC、qnrS-1、sul-1、sul-2、sul-3、tetA、tetB、tetX）进行序列分析,随后依次对其设计多重PCR特异性引物,构建特异的阳性质粒作为阳性参比品进行液态芯片检测条件优化,从而进行多重耐药基因液态芯片检测方法的研发。结果显示：成功构建了17种耐药基因的阳性质粒,并建立了两套体系用于检测17种耐药基因。在特异性试验中,两套体系中的检测信号无干扰,具有较高的特异性数值;敏感性试验中,体系一的单一质粒最低检测量为102~104 copies/μL,混合质粒为103~105 copies/μL;体系二的单一质粒最低检测量为102~105 copies/μL,混合质粒为104~106 copies/μL;有效性试验中,液态芯片法与PCR检测结果的Kappa值多在0.60以上,具有高度一致性。结果表明,本研究建立的2套液态芯片检测体系具有高通量、高灵敏和高特异性的优点,可同时对17种耐药基因进行检测,能够达到快速检测的目的。     

Ultrasound-guided modified subcostal transversus abdominis plane block and influence of recumbency position on dye spread in equine cadavers

ObjectiveTo describe and evaluate an ultrasound-guided modified subcostal approach for the transversus abdominis plane (TAP) block in horse cadavers in lateral or dorsal recumbency.Study designProspective, experimental cadaveric study.AnimalsStudy of one preserved foal and eight fresh adult horse cadavers.MethodsThe lateral and ventral abdominal wall of a preserved cadaver was dissected to identify the muscles and nerves. A unilateral standard TAP block technique was performed (60 mL of methylene blue dye–bupivacaine) on a fresh cadaver in right lateral recumbency. A modified subcostal technique was performed on the opposite side using a linear ultrasound transducer and in-plane approach. Injection points (two 30 mL dye) were at the level of the TAP (between the rectus abdominis and transversus abdominis muscles and ventral to the cutaneous trunci muscle) perpendicular to: 1) the mid-point between the xiphoid cartilage and umbilical scar; and 2) at a point between the caudal and middle thirds of the abdomen measured from the first injection point to the umbilical scar. The modified subcostal approach was performed in seven additional cadavers in both hemiabdomens, with three cadavers in lateral and four cadavers in dorsal recumbency. Ultrasound guidance was used with all injections.ResultsThe standard approach stained the sixteenth to eighteenth thoracic nerves (T16–T18). The modified subcostal approach performed in lateral recumbency provided greater spread (T9–T17) than dorsal recumbency (T12–T18) (p = 0.016).Conclusions and clinical relevanceThe modified subcostal TAP approach resulted in extensive staining exceeding the standard approach. The nerves stained are consistent with production of ventral abdominal wall anesthesia in horses. Clinical studies are needed to verify these findings.     

Effects of perioperative saphenous and sciatic nerve blocks,lumbosacral epidural or morphine–lidocaine–ketamine infusion on postoperative pain and sedation in dogs undergoing tibial plateau leveling osteotomy

ObjectiveTo compare the quality of postoperative analgesia and sedation after preoperative saphenous and sciatic nerve blockade, preoperative lumbosacral epidural injection and perioperative intravenous (IV) morphine, lidocaine and ketamine infusions in dogs undergoing stifle arthroscopy and tibial plateau leveling osteotomy (TPLO) under general anesthesia.Study designProspective, blinded, randomized, clinical comparison study.AnimalsA total of 45 dogs weighing 33.9 (15.9–56.7) kg and aged 5.2 (1.0–12.0) years, mean (range), undergoing elective unilateral TPLO for spontaneous cranial cruciate ligament rupture.MethodsClient-owned dogs were enrolled. Dogs were randomly assigned to one of three groups: group MLK, perioperative IV morphine, lidocaine and ketamine infusion; group EPID, lumbosacral epidural with ropivacaine and morphine; or group SSNB, saphenous and sciatic nerve blockade with ropivacaine. Routine stifle arthroscopy followed by TPLO surgery was performed. Sedation and pain scores were assessed at 0, 2, 4, 8 and 24 hours following extubation. Rescue analgesia was administered as prescribed by Glasgow composite pain score–short form score >5.ResultsSedation scores for MLK were higher than EPID and SSNB. Pain scores for SSNB were lower than those for EPID and MLK. No significant differences were found in anesthesia duration or surgery duration among groups. No dogs required rescue analgesia.Conclusions and clinical relevanceAlthough analgesia was adequate in all groups, the best combination of analgesia without increased sedation was recorded for SSNB.     

两种无抗制剂对育肥猪生长性能及肠道健康的影响

本试验通过在生长育肥猪饲粮中添加两种不同的无抗制剂,探究其对育肥猪生长及肠道健康的影响。选取体重为（85.95±3.48） kg的LDY三元杂交猪60头,分为对照组、试验1、2组,每组5个重复,每个重复4头猪（阉公猪和母猪各半）。对照组饲喂基础饲粮,试验1组在基础饲粮中添加0.5%的红曲合生元酵母硒锗复合制剂,试验2组在基础饲粮中添加0.5%的复方中药提取物。结果表明：①3组间生长性能各项指标均差异不显著（P>0.05）。②与对照组相比,试验1组空肠的绒毛高度（VH）、绒毛高度/隐窝深度（V/C）以及回肠的绒毛高度均显著增加（P<0.05）,试验2组空肠和回肠的绒毛高度均显著增加（P<0.05）;试验1组空肠和回肠的绒毛高度显著高于试验2组（P<0.05）。③与对照组相比,试验1和2组盲肠菌群香浓指数均显著升高（P<0.05）、辛普森指数均显著降低（P<0.05）;试验1组的香浓指数显著高于试验2组（P<0.05）。④在门水平上,与对照组相比,试验1组盲肠菌群变形菌门和放线菌门丰度均显著升高（P<0.05）,厚壁菌门丰度显著降低（P<0.05）;试验2组厚壁菌门和变形菌门丰度显著升高（P<0.05）,拟杆菌门丰度显著降低（P<0.05）;试验1组放线菌门丰度显著高于试验2组（P<0.05）,厚壁菌门丰度显著低于试验2组（P<0.05）。在属水平上,与对照组相比,试验1组链球菌属丰度显著升高（P<0.05）,苏黎世杆菌属、uncultured_bacterium_f_Muribaculaceae和乳杆菌属丰度显著降低（P<0.05）;试验2组瘤胃菌属和链球菌属丰度显著升高（P<0.05）,苏黎世杆菌属、梭菌属_13、乳杆菌属丰度显著降低（P<0.05）;试验1组梭菌属_13和链球菌属丰度显著高于试验2组（P<0.05）,试验1组uncultured_bacterium_f_Muribaculaceae、瘤胃菌属显著低于试验2组（P<0.05）。⑤试验1组Occludin、Zo-1、Claudin-1表达量显著高于对照组（P<0.05）,Occludin、Claudin-1表达量显著高于试验2组（P<0.05）。以上结果表明,红曲合生元酵母硒锗复合制剂和复方中药提取物对育肥猪肠道健康均有改善作用,但红曲合生元酵母硒锗复合制剂组饲喂效果优于复方中药提取物组。