不同人类免疫缺陷病毒感染途径群体中戊型肝炎病毒的流行情况

本研究旨在了解不同人类免疫缺陷病毒(human immunodeficiency virus,HIV)感染途径群体中戊型肝炎病毒(hepatitis E virus,HEV)抗体情况,探讨HEV疫苗接种的必要性。采集HIV感染者的血清或血浆,利用酶联免疫吸附试验(enzyme-linked immunosorbent assay,ELISA)检测HEV IgG抗体、IgM抗体及抗原,荧光定量聚合酶链反应(polymerase chain reaction,PCR)检测HEV核酸,Roche高纯化HIV-1核酸定量检测试剂盒(PCR荧光法)检测HIV感染者的HIV载量。比较分析不同HIV感染途径群体中HEV流行率的差别。结果显示,HIV感染者中HEV IgG抗体的阳性率为37.4%,静脉吸毒、成分献血和传播途径不明HIV感染群体的HEV IgG抗体阳性率分别为49.3%、39.5%和30.4%。HEV核酸荧光PCR检测结果均为阴性。3种HIV感染群体之间HEV IgG抗体阳性率差异无统计学意义(χ~2=2.978,P0.05)。HEV IgG阳性与阴性感染者之间HIV载量差异无统计学意义(P0.05)。结果提示,为保护HIV感染者免受HEV感染,应考虑接种HEV疫苗。     

北京地区成人呼吸道感染病原体的检测分析

目的探讨北京地区成人呼吸道感染的病原学流行特点,为临床诊疗提供病原学依据。方法采用间接免疫荧光法检测人血清中8种呼吸道病原体的Ig M抗体,根据不同性别、年龄、年份和季节的病原体阳性率进行统计分析。结果 1 219例患者中呼吸道病原体阳性率为49.4%,其中甲型流感病毒阳性率最高,其他依次为嗜肺军团菌、乙型流感病毒、肺炎支原体、副流感病毒、肺炎衣原体、腺病毒和呼吸道合胞病毒;呼吸道感染患者中男性患者病原体阳性率显著高于女性患者(P0.01);不同年龄组病原体阳性率比较差异有统计学意义,以18~39岁年龄组最高,其次为40~59岁年龄组,上述两组病原体阳性率显著高于其他两个年龄组(P0.01);不同年份病原体阳性率比较差异有统计学意义,2014年显著高于2013年(P0.01);不同季节病原体的阳性率比较差异有统计学意义,春季显著高于夏季、秋季和冬季(P0.01)。结论本地区成人呼吸道感染病原体阳性率在性别、年龄、年份和季节性存在差异,病原体以甲型流感病毒和嗜肺军团菌为主。     

三个绵羊品种LHX3基因多态性与生长性状的关联分析

寻找与绵羊生长性状有关的分子标记,以期为绵羊的分子育种提供理论依据。通过琼脂糖凝胶电泳和一代测序技术,在滩羊(TS)、小尾寒羊(STHS)和兰州大尾羊(LFTS)的LHX3基因中检测到了29 bp片段的插入型(AA)、插入/缺失型(AB)以及缺失型(BB)3种基因型,对3个不同品种绵羊的LHX3基因进行遗传多态性分析,并通过一般线性模型分析了3种基因型与3个品种绵羊不同生长性状的相关性。3个品种绵羊LHX3的多态信息含量(PIC)均为0.25 PIC≤0.5,呈中度多态,表明该位点的遗传变异相对较高。LHX3基因型影响3个品种绵羊的一个或多个生长性状,其中LHX3基因型与滩羊的体长(BL)、体重(BW)、胸深(ChD)和管围(CaC)显著相关(P 0.05),且缺失型基因型的生长性状优于插入型基因型和插入/缺失型基因型绵羊;小尾寒羊的缺失型基因型的胸围(ChC)、胸深(ChD)和管围(CaC)显著高于插入型基因型和插入/缺失型基因型绵羊(P 0.01);兰州大尾羊的缺失型基因型的胸围(ChC)、十字部高(HW)、体长(BL)、体重(BW)和管围(CaC)显著高于插入型基因型和插入/缺失型基因型绵羊(P 0.01)。由此可见在绵羊分子育种中,LHX3中29 bp的缺失型可作为绵羊选育的DNA标记位点。     

2003-2008年我国实验猴BV抗体检测结果及抗体水平变化规律的分析

目的对近年来我国实验猴BV（猴疱疹病毒Ⅰ型）抗体检测结果进行比较分析,以了解我国实验猴BV感染情况及其抗体水平变化规律,为我国实验猴质量控制及标准化提供依据。方法根据国标中ELISA方法 ,对2003～2008年我国11个单位送检的2个品种猴血清进行BV抗体检测,并对检测结果进行统计分析。结果检测的4612份猴血清中,有1843份BV抗体呈阳性,阳性率为39.96%;6年中检测猴群BV抗体阳性率基本在30%～50%。幼年（≤2岁）、青年（2.1～4.0岁）、成年（4.1～6.5岁）、老年（≥6.5岁）4个不同年龄段猴BV感染率分别为26.28%、31.53%、53.74%、87.27%。不同年龄感染率差异显著（P〈0.01）。雌猴BV感染率（35.91%）高于雄猴（34.93%）,但两者差异不显著（P〉0.05）。结论不同年龄猴BV感染率不同,随着年龄的增长BV感染率升高。     

2018年河南省健康人群脊髓灰质炎抗体水平监测结果分析

目的了解2018年河南省健康人群脊髓灰质炎(poliomyelitis,简称脊灰)抗体水平,为评价脊灰疫苗免疫效果、保持河南省无脊灰状态提供科学依据。方法选取漯河市舞阳县、许昌市建安区和濮阳市清丰县作为监测点,通过中和抗体测定法对健康人群进行脊灰抗体检测。结果共检测636份健康人血标本,其中脊灰I型和III型抗体阳性率分别为96.54%和93.55%,抗体几何平均滴度(geometric mean titer,GMT)分别为1∶137.70和1∶47.27,I型、III型抗体阳性率和GMT之间差异均有统计学意义(P0.05),I型抗体阳性率和GMT均高于III型。不同年龄组之间脊灰I型、III型抗体阳性率和GMT差异均有统计学意义(P0.05),GMT随着年龄的增加而降低。不同免疫史之间脊灰I型、III型抗体阳性率和GMT差异有统计学意义(P0.05),接种过脊灰疫苗人群的抗体阳性率和GMT均高于未接种或者免疫史不详人群。不同性别和不同地区之间脊灰I型、III型抗体阳性率和GMT差异均无统计学意义(P0.05)。结论 2018年河南省健康人群脊灰抗体处于较高水平,已形成了有效的免疫屏障,但保持河南省无脊灰的发生工作依然严峻。脊灰防治需加强人群的疫苗免疫规划和常规免疫,定期对健康人群脊灰抗体的检测是防止脊灰病毒传播较为有效的方法之一。     

大学新生戊型肝炎病毒现/近期隐性感染的筛查

为了解大学新生戊型肝炎病毒(HEV)现/近期隐性感染的状况,探讨引起隐性感染与急性戊型肝炎(HE)的HEV毒株间有无差异,本实验利用ELISA一步法检测了正常大学新生血清标本中抗-HEV IgM,对抗-HEV IgM阳性者检测抗-HEV IgG,并进行HEV逆转录-巢式PCR(RT-nPCR). 结果2223份血清中抗-HEV IgM阳性18份,阳性率0.8%,P/N值在2.0~3.0之间.17份标本抗-HEV IgM、IgG同时阳性,1份抗-HEV IgM单独阳性,但用RT-nPCR检测抗-HEV IgM阳性标本, HEV RNA均阴性.提示正常大学新生中存在HEV现/近期隐性感染,应注意感染者作为传染源的可能性;HEV隐性感染时,产生的抗体滴度或亲和力较低,病毒血症时间短,病毒滴度低,或毒株的基因序列与引起急性HE的毒株的序列有一定差异.     

我国蒙古羊系统不同生态型绵羊品种遗传多样性及距离隔离机制的研究

以我国主要地方绵羊品种湖羊、同羊、小尾寒羊、滩羊和洼地绵羊为研究对象,检测位于不同染色体的微卫星位点的基因频率分布,进行比较分析.结果表明 1) 就本研究涉及的微卫星标记而言,湖羊处于Hardy-Weinberg极不平衡状态 (P ＜ 0.01),而其余群体包括同羊、小尾寒羊、滩羊和洼地绵羊却处于Hardy-Weinberg平衡 (P ＜ 0.05).2) 就本研究涉及的微卫星标记而言,平均杂合度、多型信息含量和有效等位基因数三个遗传变异指标的方差分析表明不同群体间杂合度、多型信息含量均不存在显著差异 (P ＞ 0.05),有效等位基因数遗传变异指标在、滩羊、湖羊、同羊和洼地羊相互之间以及洼地羊与小尾寒羊之间亦差异不显著(P ＞ 0.05),但是有效等位基因数在前3个群体与后2个群体之间存在显著差异 (0.01 ＜ P ＜ 0.05).5个绵羊群体的变异水平以小尾寒羊最高,其次为洼地绵羊、同羊和滩羊,最低的是湖羊.3) 本研究涉及的我国蒙古羊系统内5个绵羊群体间的系统发生关系不满足距离隔离模式,绵羊群体间的遗传分化关系的远近与其地理分布并未表现出紧密的线性相关.这与5个绵羊起源于不同时期的蒙古羊始祖群体,同时在品种间存在一定程度的基因交流,并在各自特有的生态环境中经历不同程度的自然选择和人为选择品种培育史实相符.     

18～60岁健康人群肺炎链球菌IgG抗体水平调查

目的了解18~60岁健康人群肺炎链球菌IgG抗体水平,为肺炎链球菌性疾病的预防与控制提供参考依据。方法选取甘肃、宁夏健康献浆员为调查对象,分为18~30、31~40、41~50、51~60岁4个年龄组,共调查347人。采用WHO推荐的标准化酶联免疫吸附试验检测12种肺炎链球菌血清型IgG抗体水平,并计算IgG抗体阳性率和几何平均浓度(Geometric mean concentration,GMC)。结果质控血清QC907的IgG抗体浓度均值与参考值之间的误差百分数均未超过±40%,测定值符合其参考值范围,各血清型抗体浓度检测结果的CV均30%。347份血清样品肺炎链球菌IgG抗体总阳性率为64.8%~96.0%,GMC为0.37~2.24μg/m L。不同血清型间IgG抗体GMC差异具有统计学意义(P0.05)。不同年龄组同种血清型IgG抗体阳性率及GMC均无统计学意义(P0.05)。除19F型外,不同地区同种血清型IgG抗体阳性率均有统计学意义(P0.05);除4、7F、14和18C型外,不同地区同种血清型IgG抗体GMC间差异均有统计学意义(P0.05)。结论 18~60岁健康人群肺炎链球菌IgG抗体水平普遍较高,对肺炎链球菌主要流行血清型均具有一定的保护力。     

石家庄市儿童呼吸道感染病原体IgM抗体结果分析

目的分析石家庄市儿童呼吸道感染病原体的流行特点,为临床预防和治疗呼吸道感染提供病原学依据。方法纳入就诊于儿科的呼吸道感染患儿936例,运用间接免疫荧光法检测儿童血清的八种呼吸道病原体的IgM型抗体。根据不同季节、不同年龄和不同性别分组,分析其病原体阳性率和感染类型。结果 936例患儿血清标本中,检出病原体IgM抗体共424例,阳性率为45.30%。其中肺炎支原体阳性率(28.63%)最高,其次依次为流感病毒B型、呼吸道合胞病毒、流感病毒A型、肺炎衣原体、腺病毒、副流感病毒,未检出嗜肺军团菌。不同季节病原体的阳性率有差异,冬季的病原体阳性率(50.33%)显著高于夏、秋季的阳性率(33.71%和41.46%),差异均有统计学意义;不同年龄组中,婴儿组病原体阳性率(16.05%)显著低于其他3个年龄组,差异均有统计学意义;检出病原体的424例阳性患儿中,单一病原体感染类型者为290例(30.98%),混合感染者134例(14.32%);全部936例患儿中,男童病原体阳性率(42.33%)显著低于女童阳性率(52.29%);病原体混合感染类型中以肺炎支原体和流感病毒B型混合感染最常见,其中婴儿组混合感染病原体检出率均显著低于幼儿组、学龄前组和学龄组。结论肺炎支原体全年在儿童呼吸道感染中占主要地位。年龄和性别是石家庄市儿童呼吸道病原体感染的特异性因素,冬季为呼吸道病原体感染高峰期。     

产前应激子代大鼠海马核转录因子-кB表达的性别差异

;本研究采用免疫组织化学和Western blot检测NF-кB p65/p50在产前应激子代海马的表达,并探讨其表达是否存在性别差异.研究结果显示,在雌性子代,中、晚期应激组海马齿状回p65表达显著低于对照组(P＜0.01),而海马各区p50表达均显著高于对照组(P＜0.01),中、晚期应激组间p65和p50表达均有显著差异(P＜0.01).在雄性子代,中、晚期应激组海马齿状回p65表达显著高于对照组(P＜0.01),晚期应激组海马各区p50表达均显著低于对照组(P＜0.05,P＜0.01),中、晚期应激组间p65和p50表达均有显著差异(P＜0.01).雌、雄子代比较,对照组雌、雄p65表达差异极显著(P＜0.01),p50仅在海马CA1区表达差异极显著(P＜0.01);中期应激组雌、雄子代大鼠海马p65/p50表达无显著差异;晚期应激组雌、雄海马p65/p50表达均有极显著差异(P＜0.01).Western blot与免疫组织化学结果基本一致.结果表明,产前不同时期的应激显著影响子代海马NF-кB p65和p50表达,且有性别差异,这可能是产前应激对子代雌、雄大鼠学习记忆能力影响差异的机制之一.     

Influence of somatic cell donor breed on reproductive performance and comparison of prenatal growth in cloned canines

Using in vivo–flushed oocytes from a homogenous dog population and subsequent embryo transfer after nuclear transfer, we studied the effects of donor cells collected from 10 different breeds on cloning efficiency and perinatal development of resulted cloned puppies. The breeds were categorized into four groups according to their body weight: small (≤9 kg), medium (>9–20 kg), large (>20–40 kg), and ultra large (>40 kg). A total of 1611 cloned embryos were transferred into 454 surrogate bitches for production of cloned puppies. No statistically significant differences were observed for initial pregnancy rates at Day 30 of embryo transfer for the donor cells originated from different breeds. However, full-term pregnancy rates were 16.5%, 11.0%, 10.0%, and 7.1% for the donor cells originated from ultra-large breed, large, medium, and small breeds, respectively, where pregnancy rate in the ultra-large group was significantly higher compared with the small breeds (P < 0.01). Perinatal mortality until weaning was significantly higher in small breeds (33.3%) compared with medium, large, or ultra-large breeds where no mortality was observed. The mean birth weight of cloned pups significantly increased proportional to breed size. The highest litter size was examined in ultra-large breeds. There was no correlation between the number of embryo transferred and litter size. Taken together, the efficiency of somatic cell cloning and fetal survival after embryo transfer may be affected significantly by selecting the appropriate genotype.     

Immunogenetic and population genetic analyses of Iberian cattle

Blood samples were collected from more than 100 animals in each of 2 Spanish cattle breeds (Retinto and De Lidia), 2 Portuguese breeds (Alentejana and Mertolenga), and American Longhorn cattle. All samples for the 4 Iberian breeds were tested for 20 polymorphic systems; American Longhorn were tested for 19 of the 20. For each breed an average inbreeding coefficient was estimated by a comparison of the observed and expected heterozygosity at 7 or 8 codominant systems tested. All breeds had positive values but only 3 breeds had estimates of inbreeding that were statistically significantly different from 0: De Lidia with = 0.17, Retinto with = 0.08 and Mertolenga with f = 0.05. The De Lidia breed especially may be suffering from inbreeding depression since this high value is greater than expected if all of the animals were progeny of half-sib matings. Genetic distances were calculated from the gene frequency data on these 5 breeds plus 9 other European breeds. Analyses of these distances show a closely related group of the 4 Iberian breeds and American Longhorn, confirming the close relationships among the Iberian breeds and the Iberian, probably Portuguese, origin of American Longhorn cattle.     

Artificial insemination with frozen semen in dogs: a retrospective study of 10 years using a non-surgical approach

From 1994 to 2003, a total of 526 bitches of 99 different breeds were artificially inseminated in 685 estrus cycles with domestic (n = 353) or imported (n = 332) frozen-thawed semen from 368 males. The overall whelping rate was 73.1% and mean (+/- S.E.M.) litter size 5.7 +/- 0.1 pups. The whelping rate was higher after intrauterine insemination (75.0%; n = 665) than after intravaginal insemination (10.0%, n = 20; P < 0.05). Insemination at the optimal time resulted in a higher whelping rate (78%, n = 559; P < 0.01) and larger litter size (5.8 +/- 0.2; P < 0.05) than inseminations performed late or too late (55.7% and 4.5 +/- 0.5, n = 61). Two inseminations (n = 384) yielded a higher whelping rate (P < 0.05) and mean litter size (P < 0.01) than one insemination (n = 241), 78.1% and 6.0 +/- 0.2 and 70.5% and 5.1 +/- 0.2, respectively. For inseminations performed at the optimal time, however, the whelping rate was not significantly different for bitches inseminated twice (79.3%, n = 358) versus once (76.8%, n = 168), but the litter size was larger (6.0 +/- 0.2 and 5.3 +/- 0.3). Semen classified as of poor quality (progressive motility < 50% or percentage abnormal sperm > 20%) resulted in a lower whelping rate (P < 0.01) than semen classified as of good quality (progressive motility > or = 50% and percentage abnormal sperm < or = 20%), 61 and 77%, respectively. Small breeds (n = 50) had a smaller litter size (3.9 +/- 0.3; P < 0.01) than larger breeds (medium [5.7 +/- 0.3, n = 94], large [5.9 +/- 0.2, n = 295] or giant breeds [6.1 +/- 0.5, n = 62] [P < 0.01]). Bitches older than 6 years had a lower whelping rate (68.2%) than younger ones (77.0%; P < 0.05). The duration of pregnancy was longer (P < 0.01) for bitches with a litter size of < 3 pups (61.7 +/- 0. 4 days, n = 30) than for bitches with larger litters (60.5 +/- 0.1 days, n = 177). These results show the potential of transcervical intrauterine insemination for routine artificial insemination in dogs. The results with frozen semen inseminations were optimised by inseminating bitches < or = 6 years old 2 and 3 days after ovulation with semen of good quality from males < or = 8 years old.     

不同植茶年限土壤团聚体碳氮磷生态化学计量学特征

试验选取了四川雅安12～15年、20～22年、30～33年和>50年的茶园,研究其土壤团聚体有机碳、全氮、全磷的含量分布及其生态化学计量学特征,以阐明不同植茶年限土壤团聚体碳氮磷生态化学计量学特征的指示意义.结果表明: 0～20 cm和20～40 cm土层土壤有机碳、全氮和全磷含量的变异系数分别为17.5%、16.3%、9.4%和24.0%、21.0%、9.2%;全磷的空间变异性低于有机碳和全氮,但三者呈极显著的正相关关系.有机碳与全氮含量集中分布于小粒径团聚体中,且均在植茶50年后达到最大值,土壤全磷在各粒径团聚体中分布则较为均匀,在种植年限上的变化也不大;0～20 cm和20～40 cm土层土壤C/N、C/P和N/P的变异系数分别为9.4%、14.0%、14.8%和7.4%、24.9%、21.8%;土壤C/N的变异性较低,土壤C/P和N/P均在小粒径中较高,且在植茶50年后达到最大值. 土壤C/N、C/P和N/P对土壤有机碳储量具有良好的指示作用.
     

Genetic Variation and Association of Insulin-Like Growth Factor Binding Protein-3 with Performance in Swine

Genetic variation of insulin-like growth factor binding protein-3 was analyzed in 17 pig breeds (14 native Chinese and 3 European). Using PCR-single strand conformation polymorphism, we found a polymorphism in intron 2, and this SNP was the combined mutation of G897T-G903A-C911T. The Chinese breeds carried a higher TAT/TAT genotype frequency (over 50%), except for Bamei (22%), Yujiang Black (0.0%), and Erhualian (10.0%); the European breeds had a higher GGC/GGC genotype frequency (Large White 1.67%, Landrace 13.89%, Duroc 0.0%). The allelic frequency of TAT in Chinese breeds was over 50%, except for Yujiang Black (12.5%); the allelic frequency of GGC was over 50% in all European breeds. The effect of genotype on 43 performance traits was investigated in one population (Lantang × Landrace). Pigs with the TAT/TAT genotype had higher B-point and C-point back-fat thickness than pigs with the GGC/GGC genotype. The TAT/TAT pigs also scored higher in meat color than the GGC/GGC pigs. These results implied that IGFBP-3 may affect meat quality and carcass traits.     

Polymorphisms of caprine <Emphasis Type="Italic">POU1F1</Emphasis> gene and their association with litter size in Jining Grey goats

Seven pairs of primers were designed to amplify 5′ promoter region, six exons and partial introns and to detect the polymorphisms of POU1F1 gene in five goat breeds with different prolificacy. The results showed that six mutations were identified in caprine POU1F1 gene including C256T in exon 3, C53T and T123G in intron 3, and G682T (A228S), T723G and C837T in exon 6. The former four mutations were novel SNPs in goat POU1F1 gene. The 53 and 123 loci were in complete linkage disequilibrium in five caprine breeds. Regarding the 256 locus, the Jining Grey goat does with genotype CT had 0.66 kids more than those with genotype CC (P < 0.05), while does with genotype GT had 0.63 (P < 0.05) kids more than those with genotype GG at the 682 locus. The present study preliminarily showed an association between allele T at the 256 and 682 loci of POU1F1 gene and high litter size in Jining Grey goats. Totally 16 haplotypes and 50 genotypes were identified at the above six loci in POU1F1 gene of five goat breeds. Three common haplotypes (hap2, hap3 and hap4) were identified in five goat breeds joined. Four specific haplotypes (hap7, hap9, hap11 and hap13) were detected in Jining Grey goats. The predominant haplotype was hap1 (35.29% and 48.25%) in both Jining Grey and Guizhou White goats, while hap4 (50%) in Boer goats, and hap2 (42.86% and 38.75%) in both Wendeng Dairy and Liaoning Cashmere goats. The most frequent genotypes at six loci in the above five goat breeds were hap1/hap2 (14.38%) and hap1/hap4 (14.38%), hap1/hap2 (38.60%), hap4/hap4 (40.91%), hap2/hap4 (26.53%), hap2/hap5 (20.00%), respectively. The Jining Grey goat does with nine genotypes analyzed of POU1F1 gene showed no obvious difference in litter size.     

High genetic divergence in miniature breeds of Japanese native chickens compared to Red Junglefowl, as revealed by microsatellite analysis

A wide diversity of domesticated chicken breeds exist due to artificial selection on the basis of human interests. Miniature variants (bantams) are eminently illustrative of the large changes from ancestral junglefowls. In this report, the genetic characterization of seven Japanese miniature chicken breeds and varieties, together with institute-kept Red Junglefowl, was conducted by means of typing 40 microsatellites located on 21 autosomes. We drew focus to genetic differentiation between the miniature chicken breeds and Red Junglefowl in particular. A total of 305 alleles were identified: 27 of these alleles (8.9%) were unique to the Red Junglefowl with high frequencies (>20%). Significantly high genetic differences ( F _ST) were obtained between Red Junglefowl and all other breeds with a range of 0.3901–0.5128. Individual clustering (constructed from combinations of the proportion of shared alleles and the neighbour-joining method) indicated high genetic divergence among breeds including Red Junglefowl. There were also individual assignments on the basis of the Bayesian and distance-based approaches. The microsatellite differences in the miniature chicken breeds compared to the presumed wild ancestor reflected the phenotypic diversity among them, indicating that each of these miniature chicken breeds is a unique gene pool.     

Danish A.I. field data with sexed semen

The objective of this study was to compare conception rates, non-return rates and sex ratios of sexed and conventional semen from the same sires in commercial dairy herds in Denmark. The semen was produced from three bulls from each of the three major dairy breeds in Denmark: Holstein, Jersey and Danish Red Dairy Breed (nine bulls total), in order to answer questions on breeds differences in field results. AI was performed by trained technicians using a minimum of 150 doses of sorted sperm and 50 control doses from each bull. During the trial, a total of 2087 doses were used in 63 herds.The trial showed that the conception rate using sorted semen was 5% points lower than with conventional doses for Danish Reds, 7% points for Jerseys, and 12% points for Holsteins. Translating this into non-return rate revealed differences of 10-20% points among bulls. These differences are thought to be a good indicator of what to expect from commercial use of sexed semen.The sex ratios varied from 89% to 93% female calves among breeds, which on average is consistent with the theoretical average sex ratio of 93% females considering the low number of inseminations.     

High-density marker imputation accuracy in sixteen French cattle breeds

Background

Genotyping with the medium-density Bovine SNP50 BeadChip^® (50K) is now standard in cattle. The high-density BovineHD BeadChip^®, which contains 777 609 single nucleotide polymorphisms (SNPs), was developed in 2010. Increasing marker density increases the level of linkage disequilibrium between quantitative trait loci (QTL) and SNPs and the accuracy of QTL localization and genomic selection. However, re-genotyping all animals with the high-density chip is not economically feasible. An alternative strategy is to genotype part of the animals with the high-density chip and to impute high-density genotypes for animals already genotyped with the 50K chip. Thus, it is necessary to investigate the error rate when imputing from the 50K to the high-density chip.

Methods

Five thousand one hundred and fifty three animals from 16 breeds (89 to 788 per breed) were genotyped with the high-density chip. Imputation error rates from the 50K to the high-density chip were computed for each breed with a validation set that included the 20% youngest animals. Marker genotypes were masked for animals in the validation population in order to mimic 50K genotypes. Imputation was carried out using the Beagle 3.3.0 software.

Results

Mean allele imputation error rates ranged from 0.31% to 2.41% depending on the breed. In total, 1980 SNPs had high imputation error rates in several breeds, which is probably due to genome assembly errors, and we recommend to discard these in future studies. Differences in imputation accuracy between breeds were related to the high-density-genotyped sample size and to the genetic relationship between reference and validation populations, whereas differences in effective population size and level of linkage disequilibrium showed limited effects. Accordingly, imputation accuracy was higher in breeds with large populations and in dairy breeds than in beef breeds. More than 99% of the alleles were correctly imputed if more than 300 animals were genotyped at high-density. No improvement was observed when multi-breed imputation was performed.

Conclusion

In all breeds, imputation accuracy was higher than 97%, which indicates that imputation to the high-density chip was accurate. Imputation accuracy depends mainly on the size of the reference population and the relationship between reference and target populations.     

Fat body catalase activity as a biochemical index for the recognition of thermotolerant breeds of mulberry silkworm, Bombyx mori L.

The fifth instar larvae of the silkworm Bombyx mori L. were exposed to selected high temperatures (35 and 40 °C) in order to understand the changes in the level of catalase activity in the three tissues of fat body, midgut and haemolymph of the five selected bivoltine breeds and their 9 quantitative traits, namely larval weight, cocoon weight, shell weight, shell ratio, filament length, filament weight, denier, renditta and effective rearing rate (ERR), also the correlation between them under high temperature conditions were examined. Catalase activity resulting in fat body revealed a positive correlation between the control (28±1 °C) and 40±1 °C. The CSR₂ breed showed the most level of thermotolerance and catalase activity, compared with the CSR₄, JROP, NB₄D₂ and KA breeds. It was found that the level of catalase activity in fat body may be a reliable biochemical index to recognize thermotolerant breeds in order to develop resistant hybrids for tropical areas.