全基因组关联分析在德国牧羊犬髋关节发育不良研究中的应用现状

犬髋关节发育不良(canine hip dysplasia,CHD)是犬常见的骨科疾病,传统放射学诊断对降低CHD发病率的作用有限,而基因诊断技术则可以有效促进CHD的育种改良。全基因组关联分析(genome wide association study,GWAS)是一种全基因组范围内的遗传标记的检测技术,对复杂性状功能基因的鉴定十分有效,已成为挖掘畜禽复杂疾病和性状遗传的重要方法。随着犬全基因组测序的完成以及犬不同密度SNP芯片的商业化,GWAS已经成为CHD致病基因筛选的一个重要手段。本文综述了GWAS的定义与影响因素,CHD在国外的育种现状及GWAS在德国牧羊犬中的研究进展。     

A genome‐wide association study for fat‐related traits computed by image analysis in Japanese Black cattle

The objective of this study was to identify genomic regions associated with fat‐related traits using a Japanese Black cattle population in Hyogo. From 1836 animals, those with high or low values were selected on the basis of corrected phenotype and then pooled into high and low groups (n = 100 each), respectively. DNA pool‐based genome‐wide association study (GWAS) was performed using Illumina BovineSNP50 BeadChip v2 with three replicate assays for each pooled sample. GWAS detected that two single nucleotide polymorphisms (SNPs) on BTA7 (ARS‐BFGL‐NGS‐35463 and Hapmap23838‐BTA‐163815) and one SNP on BTA12 (ARS‐BFGL‐NGS‐2915) significantly affected fat percentage (FAR). The significance of ARS‐BFGL‐NGS‐35463 on BTA7 was confirmed by individual genotyping in all pooled samples. Moreover, association analysis between SNP and FAR in 803 Japanese Black cattle revealed a significant effect of SNP on FAR. Thus, further investigation of these regions is required to identify FAR‐associated genes and mutations, which can lead to the development of DNA markers for marker‐assisted selection for the genetic improvement of beef quality.     

Power of a genome scan to detect and locate quantitative trait loci in cattle using dense single nucleotide polymorphisms

There is increasing use of dense single nucleotide polymorphisms (SNPs) for whole‐genome association studies (WGAS) in livestock to map and identify quantitative trait loci (QTL). These studies rely on linkage disequilibrium (LD) to detect an association between SNP genotypes and phenotypes. The power and precision of these WGAS are unknown, and will depend on the extent of LD in the experimental population. One complication for WGAS in livestock populations is that they typically consist of many paternal half‐sib families, and in some cases full‐sib families; unless this subtle population stratification is accounted for, many spurious associations may be reported. Our aim was to investigate the power, precision and false discovery rates of WGAS for QTL discovery, with a commercial SNP array, given existing patterns of LD in cattle. We also tested the efficiency of selective genotyping animals. A total of 365 cattle were genotyped for 9232 SNPs. We simulated a QTL effect as well as polygenic and environmental effects for all animals. One QTL was simulated on a randomly chosen SNP and accounted for 5%, 10% or 18% of the total variance. The power to detect a moderate‐sized additive QTL (5% of the phenotypic variance) with 365 animals genotyped was 37% (p < 0.001). Most importantly, if pedigree structure was not accounted for, the number of false positives significantly increased above those expected by chance alone. Selective genotyping also resulted in a significant increase in false positives, even when pedigree structure was accounted for.     

儋州鸡体尺性状全基因组关联分析

【目的】 挖掘影响地方鸡体尺性状的有效SNP位点及功能基因, 给儋州鸡育种工作提供有效的数据基础和理论支撑。【方法】 共采集200只儋州鸡血样并提取基因组DNA, 利用10×全基因组重测序技术获得全基因组SNP标记并对试验个体基因型进行分型。使用EMMAX软件基于混合线性模型对70日龄的儋州鸡体尺性状(胫长、胫围、体斜长、胸宽、髋骨宽、胸深、龙骨长)进行全基因组关联分析。【结果】 共发现与胫长性状和胫围性状基因组水平显著相关的SNPs位点有12和8个, 与胫长性状相关SNPs分别定位于1、2、4和8号染色体上; 与胫围性状相关的SNPs定位于2、4、8和13号染色体上。预测与胫长相关的候选基因为KCNA1、TPK1、EZH2、FSTL5和AMY2A基因, 与胫围相关的候选基因为TPK1、FSTL5、AMY2A、TGFBI、LECT2和IL-9。通过KEGG通路分析和GO注释发现, 8个基因参与钾离子跨膜转运、硫胺素新陈代谢、细胞增殖、钙离子结合、骨骼肌卫星细胞维持与骨骼肌再生、细胞受体相互作用、生长因子活性等生物学进程。【结论】 本研究发现了20个与儋州鸡体尺性状关联的SNPs位点, 并筛选到8个目标性状候选基因, 为儋州鸡育种提供候选的分子标记, 为地方鸡标记辅助选择提供新的思路。     

Precision of estimated QTL positions in granddaughter designs using combined haplotype sharing TDT and linkage analysis

The aim of this study was to develop the linear haplotype sharing transmission disequilibrium test (LHS-TDT) method and combine this method with the simple regression method to estimate the precision of QTL positions in granddaughter designs. This precision was determined by Monte Carlo simulation in granddaughter designs. A single bi-allelic QTL at the midpoint of a linkage group and 26 markers with 1 cM intervals and with two alleles each were simulated. Three linear models, (i.e. the simple regression model, the linear haplotype sharing TDT method and the combination of these two models) were compared. The mean of absolute differences (A) between the estimated and true QTL position of each method was considered for six different scenarios consisting of combinations of a number of markers and the most frequent haplotypes. The mean of A, using the simple regression method, was 4.38 centimorgan (cM). The means of A using the LHS-TDT method were less than the simple regression method in all scenarios and ranged from 1.86 to 3.82 cM depending on the scenario. The mean of A using the combined method was more than the LHS-TDT method and less than the simple regression method. The means of A using the combined method ranged from 2.32 to 4.36 cM. Therefore, for populations similar to those population simulated in this study, the LHS-TDT was better than the simple regression method and the combined method for precision of estimated QTL position in granddaughter designs.     

A genome‐wide association study for canine cryptorchidism in Siberian Huskies

Cryptorchidism is a condition whereby one or both testes fail to descend into the scrotal sac. Here, we performed a genome‐wide association study (GWAS) with both a case–control analysis using the GEMMA software accounting for population structure and a BayesB approach in the GenSel software applied to every 1 Mb window of SNPs or haplotypes. The haplotypes were constructed from a genealogical tree using the population of 204 Siberian Huskies. The BayesB analyses identified six putative genomic candidate regions on CFA6, 9, 24, 27 and X. These regions explained a high percentage of genetic variance when compared with other genomic regions. The positional candidate genes Q9TSI5_CANFA (matrix metalloproteinase 9 precursor) on CFA24, ADAMTS20 (ADAM metallopeptidase with thrombospondin type 1 motif, 20) on CFA27 and MID1IP1 (MID1 interacting protein 1) on CFAX are known to be functionally related to extracellular matrix remodelling, which might be important for gubernaculum elongation and thus interrupting normal testicular descent. Further mutation screening in these candidate regions on CFA6, 9, 24, 27 and X is needed. Next generation sequencing will help to uncover rare variants associated with cryptorchidism in this dog population.     

利用24个微卫星进行猪数量性状座位定位及其遗传效应分析

以 3头英系大白公猪与 7头梅山母猪杂交产生的三代资源家系用来检测猪重要经济性状的数量性状座位(QTL) ,2 0 0 0年下半年随机选留 140头F2代个体 ,进行屠宰测定 ,记录了包括生长、胴体组成等 43个性状 ;从已定位于家猪 3、4和 7号染色体上的遗传标记中选用 2 4个微卫星标记对所有个体进行基因型检测。采用最小二乘回归区间定位法进行QTL检测 ,通过置换实验来确定显著性阈值。在所研究的 32个生长和胴体性状中 ,3条染色体总共 16个QTL达到染色体显著水平 (P <0 0 5 ) ,其中 4个达到染色体极显著性水平 (P <0 0 1) ;同时在 4号和 7号染色体上还检测到了影响器官重性状的 3个QTL ,达到了染色体显著水平 (P <0 0 5 )。在某些QTL座位 ,其有利等位基因来源于具有较低性状平均值的品种。 2QTL模型分析下 ,在 4号染色体上检测到影响板油重的 2个QTL ,并且它们的效应方向相反。     

Enantiomeric behaviour of albendazole and fenbendazole sulfoxides in domestic animals: Pharmacological implications

Albendazole and fenbendazole are methylcarbamate benzimidazole anthelmintics extensively used to control gastrointestinal parasites in domestic animals. These parent compounds are metabolised to albendazole sulfoxide and fenbendazole sulfoxide (oxfendazole), respectively. Both sulfoxide derivatives are anthelmintically active and are manufactured for use in animals. They metabolites have an asymmetric centre on their chemical structures and two enantiomeric forms of each sulfoxide have been identified in plasma, tissues of parasite location and within target helminths. Both the flavin-monooxygenase and cytochrome P450 systems are involved in the enantioselective biotransformation of these anthelmintic compounds in ruminant species. A relevant progress on the understanding of the relationship among enantioselective metabolism and systemic availability of each enantiomeric form has been achieved. This article reviews the current knowledge on the pharmacological implications of the enantiomeric behaviour of albendazole sulfoxide and oxfendazole in domestic animals.     

Identification of potential genomic regions for egg weight by a haplotype-based genome-wide association study using Bayesian methods

ABSTRACT

1. Theoretically, haplotype blocks might be a more suitable alternative to SNP genotypes as they are usually better at capturing multi-allelic QTL effects, compared to individual SNP genotypes in genome-wide association studies. The objectives of this study were to identify genomic regions related to egg weight traits by Bayesian methods (BayesA, BayesB, and BayesN) that fit fixed-length haplotypes using GenSel software.

2. Genotypes at 294,705 SNPs, that were common on a 600K Affymetrix chip, were phased for an egg-laying hen population of 1,063 birds. Recorded traits included first egg weight (FEW) and average egg weight at 28, 36, 56, 66, 72 and 80 weeks of age.

2. Fitting 1Mb haplotypes from BayesB resulted in the highest proportion of genetic variance explained for the egg weight traits. Based on the trait, the genetic variance explained by each marker ranged from 27% to 76%.

3. Different haplotype windows associated with egg weight traits only explained a small percentage of the genetic variance.

4. The top one 1-Mb window on GGA1 explained approximately 4.05% of total genetic variance for the FEW. Candidate genes, including PRKAR2B, HMGA2, LEMD3, GRIP1, EHBP1, MAP3K7, and MYH were identified for egg weight traits.

5. Several genomic regions, potentially associated with egg weight traits, were identified, some of which overlapped with known genes and previously reported QTL regions for egg production traits.     

家畜全基因组关联分析研究进展

全基因组关联分析（genome-wide association study,GWAS）是一种研究经济性状候选基因的分析方法。近年来,随着家畜全基因组测序的完成,大量的单核苷酸多态性（single nucleotide polymorphisms,SNPs）被标识,GWAS也越来越多地应用于家畜重要性状的研究领域中,在动物遗传育种中,通过对家畜基因组进行GWAS分析研究,找到控制家畜主要经济性状的重要SNPs,从而挖掘重要经济性状的候选基因。作者详细综述了GWAS的分析方法及其在重要家畜育种中的研究进展。GWAS分析方法包括基因组控制法（genommic control）、分层分析法（stratification analysis）、主成分分析法（principal components analysis,PAC）和混合线性模型分析法（mixed-linear-model association,MLMA）,通路分析方法包括非核算法（基因功能富集分析（gene set enrichment analysis,GSEA）和分层贝叶斯优取（hierarchical Bayes prioritization,HBP））和核算法。依据不同的目标性状选择合理的分析方法,提高GWAS分析结果的准确性,为进一步利用GWAS分析各种性状的遗传基础提供合理的借鉴。     

Practical capability of a DNA pool‐based genome‐wide association study using BovineSNP50 array in a cattle population

Genome‐wide association mapping for complex traits in cattle populations is a powerful, but expensive, selection tool. The DNA pooling technique can potentially reduce the cost of genome‐wide association studies. However, in DNA pooling design, the additional variance generated by pooling‐specific errors must be taken into account. Therefore, this study aimed to investigate factors such as: (i) the accuracy of allele frequency estimation; (ii) the magnitude of errors in pooling construction and in the array; and (iii) the effect of the number of replicate arrays on P‐values estimated by a genome‐wide association study. Results showed that the Illumina correction method is the most effective method to correct the allele frequency estimation; pooling errors, especially array variance, should be taken into account in DNA pooling design; and the risk of a type I error can be reduced by using at least two replicate arrays. These results indicate the practical capability and cost‐effectiveness of pool‐based genome‐wide association studies using the BovineSNP50 array in a cattle population.     

Genome‐wide association study of cell‐mediated immune response in chicken

Cell‐mediated immunity (CMI) causes the intracellular destruction of the antigen or elimination of the host cell to make animals resistant against exogenous antigens and cancers. In this study, a genome‐wide association study (GWAS) was carried out to identify genomic regions associated with CMI in chicken using chicken 60k high‐density single nucleotide polymorphism (SNP) array. Genomic relationships were taken into account to adjust for population structure. In order to account for multiple testing, chromosome‐wise false discovery rate was controlled at 5% and 10% levels. Moreover, a comparison of the power of fixed and mixed linear models based on genomic inflation factor was carried out. Mixed linear model (MLM) had better inflation rate, and therefore the results from MLM were used for subsequent analysis. Three significantly associated SNPs (FDR < 0.05) on chromosome 24 and linkage group E22C19W28_E50C23, and three suggestively associated SNPs (FDR < 0.1) on chromosome 1, 5 and 16 were identified. Pathway analysis showed that two biological pathways, which are related to immune response, were strongly associated with the candidate genes surrounding identified SNPs, and their influences were mostly on antigen processing and presentation, and cellular structure.     

家蚕茧丝性状的遗传基础研究

蚕业是中国农业的重要组成部分,对经济建设和人民生活具有重要意义.丝绸及相关产业使用的原料为茧丝,茧丝性状可谓被直接利用的家蚕最重要的经济性状,主要由蚕品种遗传基础决定.因此,茧丝性状的遗传学研究一直是蚕业科技的重要领域,备受家蚕育种学家关注.然而,茧丝性状为数量性状,其遗传基础的解析是蚕学研究的难点之一.鉴于对茧丝性状遗传控制机制的认识对于家蚕育种的重要意义,从经典遗传到分子层面均具有众多研究,但至今尚无任一控制家蚕茧丝性状的QTL位点获得功能上的实验验证.本文综述了该领域的主要研究进展.     

The first survey and molecular identification of Entamoeba spp. in farm animals on Qinghai-Tibetan Plateau of China

Protozoans of Entamoeba spp. are globally distributed zoonotic parasites that infect diverse animal hosts and humans. Prevalence and species/genotypes distribution of Entamoeba spp. in domestic animals are not fully investigated on Qinghai-Tibetan Plateau (QTP), an animal husbandry and agriculture region of China. In a survey, 528 fecal samples were collected from 7 species of domestic animals on multiple locations across QTP region and analyzed by PCR and sequencing analysis. The overall prevalence of Entamoeba spp. infection in all examined animals was 97.9 %. Four Entamoeba species, E. bovis, E. moshkovskii, E. ecuadoriensis and E. histolytica were found, and majority (94.2 %) of Entamoeba-infected animals harbored E. bovis. Six Entamoeba genotypes, Entamoeba ribosomal lineages (RL) 1, 2, 3, 4, 8 and 9 were identified by sequencing analysis. Two zoonotic species, E. moshkovskii and E. histolytica, were present in horses, while E. ecuadoriensis and E. bovis were found in horses and all species of seven farm animals, respectively. It was also observed that six Entamoeba genotypes were distributed in animals in specific pattern. The results revealed high prevalence of Entamoeba spp. infection in livestock, broad range of hosts as well as diversity and species/genotype distribution of Entamoeba spp. in farm animals inhabiting on the high altitude QTP region.     

Genome‐wide association study for feedlot average daily gain in Nellore cattle (Bos indicus)

The genome‐wide association study (GWAS) results are presented for average daily gain (ADG) in Nellore cattle. Phenotype of 720 male Bos indicus animals with information of ADG in feedlots and 354 147 single‐nucleotide polymorphisms (SNPs) obtained from a database added by information from Illumina Bovine HD (777 962 SNPs) and Illumina BovineSNP50 (54 609) by imputation were used. After quality control and imputation, 290 620 SNPs remained in the association analysis, using R package Genome‐wide Rapid Association using Mixed Model and Regression method GRAMMAR‐Gamma. A genomic region with six significant SNPs, at Bonferroni‐corrected significance, was found on chromosome 3. The most significant SNP (rs42518459, BTA3: 85849977, p = 9.49 × 10^?8) explained 5.62% of the phenotypic variance and had the allele substitution effect of ?0.269 kg/day. Important genes such as PDE4B, LEPR, CYP2J2 and FGGY are located near this region, which is overlapped by 12 quantitative trait locus (QTLs) described for several production traits. Other regions with markers with suggestive effects were identified in BTA6 and BTA10. This study showed regions with major effects on ADG in Bos indicus in feedlots. This information may be useful to increase the efficiency of selecting this trait and to understand the physiological processes involved in its regulation.     

Interval mapping of growth quantitative trait loci in Japanese Black beef cattle using microsatellite DNA markers and half-sib regression analysis

A confirmatory scan for the regions of bovine chromosome 1 segregating the quantitative trait loci (QTL) influencing birthweight, weaning weight, yearling weight, and preweaning and postweaning average daily gains was performed by genotyping half‐sib progeny of four Japanese Black sires using microsatellite DNA markers. Data were analyzed by generating an F‐statistic every 1 cM on a linkage map by the regression of phenotype on the probabilities of inheriting an allele from the sire after adjusting for the fixed effects of sire, sex, parity and season of birth as well as age as a covariate. Permutation tests at chromosome‐wide significance thresholds were carried out over 10 000 iterations. A significant QTL for birthweight at 114 cM was detected in the sire 2 family. This identification of a birthweight QTL in Japanese Black cattle may be useful for the implementation of marker‐assisted selection.     

凉山半细毛羊初生重QTL的研究

选取凉山半细毛羊7个父系半同胞家系,利用绵羊1号染色体上11个微卫星标记,通过聚合酶链式反应（polymerase chain reaction,PCR）对凉山半细毛羊初生重QTL进行了研究。QTL分析的结果表明,在其中一个家系B3K5055中,1号染色体微卫星标记ILSTS004与CSSM004之间检测到影响初生重的QTL,其LOD值为3.338,位于置信区间95%（2.73）和99%（3.49）之间。     

Identification of candidate markers on bovine chromosome 14 (BTA14) under milk production trait quantitative trait loci in Holstein

The objective of this study was to identify single-nucleotide polymorphisms using a bovine chromosome 14 high-density SNP panel after accounting for the effect of DGAT1. Linkage disequilibrium information and sire heterozygosity were used to select markers for linkage analysis on bovine chromosome 14 for milk production traits in 321 Holstein animals. Results show putative milk peaks at 42 and 61 cM, both at p<0.10, a fat yield peak at 42 and 63 cM, both at p<0.05; a protein yield peak at 42 (p<0.01) and 84 cM (p<0.05); fat per cent peaks at 3 (p<0.01) and 29 cM (p<0.05), and a protein per cent peak at 4 cM (p<0.05). Once quantitative trait loci positions were established, allele substitution effects for all markers were evaluated using the same statistical model. Overlaying information between quantitative trait loci (QTL) and allele effect analysis enabled the identification (p<0.01) of 20 SNPs under the milk yield QTL, 2 under both of the fat yield peaks, 8 and 9 under the protein yield peaks, 2 and 6 for the fat per cent peaks and 5 for the protein per cent peak. One SNP in particular, ss61514555:A>C, showed association with 3 of the 5 traits: milk (p=1.59E-04), fat (p=6.88E-05) and protein yields (p=5.76E-05). Overall, combining information from linkage disequilibrium, sire heterozygosity and genetic knowledge of traits enabled the characterization of additional markers with significant associations with milk production traits.