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.     

一种适用于单胎动物多品种选择的基因组关系矩阵

旨在提出一种新型基因组关系矩阵并验证其在多品种联合群体中的模拟应用效果。本研究利用QMsim软件模拟牛的表型数据和基因型数据;利用Gmatrix软件构建常规G阵;利用R语言构建新型G阵,新型G阵在常规G阵的基础上,将多品种联合群体的非哈代-温伯格平衡位点考虑在内;利用DMU软件使用“一步”法模型计算基因组估计育种值（estimated genomic breeding value,GEBV）;比较不同情况下使用两种G阵的GEBV预测准确性。结果表明,在不同遗传力及QTL数下,不对新型G阵使用A₂₂阵加权就能达到常规G阵使用A₂₂阵加权时的GEBV预测准确性。在系谱部分缺失时,新型G阵不加权较常规G阵加权时GEBV预测准确性高。证明,在系谱有部分缺失时,新型G阵对多品种GEBV的预测有一定优势。     

1株降解黄曲霉毒素B1的解淀粉芽胞杆菌的分离鉴定及其体外脱毒效果

旨在筛选出能够高效降解黄曲霉毒素B₁（AFB₁）的菌株,并对其脱毒活性组分的脱毒效果进行研究,本研究以香豆素为唯一碳源对目标细菌进行初筛,以对AFB₁的降解率为指标进行复筛,并从形态学、生理生化试验和16S rDNA序列分析对筛选菌株进行鉴定;通过测定该菌株不同发酵组分对AFB₁的降解率,来定位其脱毒活性组分,同时采用CCK-8法测定活性组分降解AFB₁后对LMH细胞毒性,并研究了热处理、紫外线照射、强酸、强碱及蛋白酶K处理对活性组分脱毒作用的影响。结果显示,从样品中初筛分离到24株能够在初筛培养基生长良好的菌株,经复筛从中筛选到一株能高效降解AFB₁的菌株Y1-B1,其AFB₁降解率达到73.2%;经形态学、生理生化试验和16S rDNA序列分析确定该菌为解淀粉芽胞杆菌（Bacillus amyloliquefaciens）。对菌株Y1-B1培养物的不同组分进行的脱毒活性研究表明,不同组分对AFB₁的降解率不同,上清液的脱毒能力最强,细菌细胞裂解物的脱毒能力下降明显,菌体悬液和菌体裂解物上清的脱毒能力最差,由此确定解淀粉芽胞杆菌Y1-B1的脱毒能力主要来源于上清液中的某种活性物质;细胞毒性结果显示,与AFB₁对LMH细胞的毒性作用相比,AFB₁被上清液降解后其产物的毒性显著降低。该脱毒活性组分对不同理化因素处理呈现出不同的表现,对高温、紫外照射抵抗力较强,对强酸、强碱抵抗力较差,蛋白酶K仅造成脱毒能力部分减弱。本研究将为解决黄曲霉毒素污染问题提供新的微生物种质资源,同时为后续微生物脱毒制剂的开发奠定基础。     

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.     

抗菌肽粗提物对肉鸡生长性能、粪便微生物菌群结构及经济效益的影响

为分析抗菌肽粗提物对肉鸡生长性能、粪便微生物菌群结构及经济效益的影响,试验选择体重相近的21日龄白羽肉鸡600只,随机分成4组,每组15个重复,每个重复10只,1组为空白对照组饲喂基础日粮,试验2、3、4组在基础日粮中分别添加1.0%、1.5%、2.0%的抗菌肽粗提物,试验期为21 d。结果表明：（1）试验2、3、4组的平均采食均高于1组（P > 0.05）|试验3、4组的平均日增重较1组比分别提高11.0%、9.4%（P ＜ 0.05）,料重比较1组比分别降低18.5%、15.2% （P ＜ 0.05）|（2）试验3、4组粪便中大肠杆菌的含量较1组分别降低14.3%、18.0%（P ＜ 0.05）,试验3、4组粪便中乳酸杆菌、双歧杆菌的含量较1组比分别提高4.6%、6.7%、14.5%、12.3%（P ＜ 0.05）|（3）试验3、4组每只肉鸡经济效益较1组比分别提高19.3%、17.7%。综上,1.5%抗菌肽粗提物添加可以提高白羽肉鸡生长性能,改善粪便微生物菌群结构,提高其经济效益。 [关键词] 抗菌肽粗提物|白羽肉鸡|生长性能|粪便微生物菌群结构|经济效益     

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     

子午岭黑山羊与辽宁绒山羊产肉性能、肉品质、肌肉营养成分和脂肪酸含量比较

1990年,甘肃省庆阳市开始引入辽宁绒山羊对子午岭黑山羊进行杂交改良,但目前尚不清楚2个品种在脂肪酸含量、肌肉营养成分等方面的差异,影响了杂交改良效果。试验旨在分析两个绒山羊品种的产肉性能、肉品质、肌肉营养成分和脂肪酸含量差异,为绒山羊的杂交改良提供理论依据。本研究选取相同饲养管理条件下、9月龄的子午岭黑山羊和辽宁绒山羊公羊各5只,测定其屠宰性能以及背最长肌、前腿肌和后腿肌处的肉品质、脂肪酸含量和肌肉营养成分。结果表明：子午岭黑山羊的胴体重、屠宰率、净肉重、净肉率、眼肌面积、GR值、剪切力和滴水损失低于辽宁绒山羊（P<0.05）,但其肌肉的平均亮度值、色度值、pH₁和pH₂₄高于辽宁绒山羊（P<0.01）。营养成分测定结果表明,子午岭黑山羊肌肉的水分和粗灰分含量高于辽宁绒山羊（P<0.05）,但肌内脂肪和粗蛋白含量低于辽宁绒山羊。在2个山羊品种的肌肉中均检测到11 种饱和脂肪酸（SFA,以棕榈酸和硬脂酸为主）、10种多不饱和脂肪酸（PUFA,以亚油酸和顺-11,14-二十碳二烯酸为主）和6种单不饱和脂肪酸（MUFA,以油酸为主）,子午岭黑山羊肉中的SFA、PUFA、n-3 PUFA、n-6 PUFA含量和PUFA/SFA值均高于辽宁绒山羊（P<0.01）,但MUFA含量低于辽宁绒山羊（P<0.01）。结果表明,辽宁绒山羊有更高的产肉力,但子午岭黑山羊肌肉品质和营养成分更佳,脂肪酸组成和含量更符合人类健康膳食标准。     

妊娠后期营养限制对蒙古绵羊胎儿生物原胺类神经递质的影响

本试验旨在研究妊娠后期营养限制对蒙古绵羊胎儿生物原胺类神经递质的影响。选择健康、体况相近的蒙古绵羊18只,对其进行同期发情、配种后,从妊娠第90天开始,随机分为3个组:营养限制1组[NG1组,n=6,代谢能(ME)=0.175 MJ/(kg BW 0.75·d)]、营养限制2组[NG2组,n=6,ME=0.330 MJ/(kg BW 0.75·d)]和对照组[CG组,n=6,ME=0.670 MJ/(kg BW 0.75·d)],在妊娠第140天时屠宰,取各组胎儿及其脑组织和血液。结果显示:NG1组胎儿的脑重较CG组显著增高(P<0.05),并且NG1组胎儿脑中5-羟色胺(5-HT)(P<0.01)、肾上腺素(EPI)(P<0.05)含量显著或极显著高于CG组,去甲肾上腺素(NA)的含量极显著低于CG组(P<0.01)。NG2组胎儿脑中5-HT含量极显著高于CG组(P<0.01),而NA(P<0.01)、多巴胺(DA)(P<0.05)含量显著或极显著低于CG组。另外,NG1组胎儿血浆中5-HT(P<0.01)、EPI(P<0.01)、NA(P<0.05)、DA(P<0.01)含量显著或极显著低于CG组;NG2组胎儿血浆中5-HT(P<0.01)、NA(P<0.01)、DA(P<0.05)含量显著或极显著低于CG组。由此得出,妊娠后期营养限制使得蒙古绵羊胎儿脑中5-HT、EPI含量升高和NA含量降低,血浆中5-HT、EPI、NA、DA含量降低。     

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。