猪胃组织中生长激素受体基因表达的发育性变化及品种特点

用相对定量RT PCR的方法研究二花脸猪 (Erhualian)和大白猪 (1argeWhite)胃组织中生长激素受体 (GHr)mR NA发育性变化并进行品种间比较。分别于出生当天、3、2 0、30、4 5、90、12 0和 180日龄随机选取纯种大白猪公猪和二花脸公猪各 4头宰杀并采样 ,同时记录胃重和体重。研究结果表明 :出生时胃组织中GHrmRNA水平较高 ,3日龄时显著下调 (P <0 0 5 ) ;二花脸猪胃组织中GHrmRNA水平在断奶时 (45日龄 )达到高峰 ,随后显著下降 (P <0 0 5 ) ,至 90日龄后维持相对稳定。大白猪公猪在 90日龄时胃组织中GHrmRNA水平达到高峰 ,并维持在较高水平 ;从出生到断奶 ,二花脸猪胃组织GHrmRNA水平高于大白猪 ,2 0日龄时差异显著 (P <0 0 5 ) ;90日龄至 180日龄期间二花脸猪胃组织GHrmRNA水平低于大白猪 ,90日龄时差异显著 (P <0 0 5 )。胃重相对于体重的变化模式和胃组织GHrmRNA水平的发育变化呈中等强度正直线相关 ,相关系数为r=0 5 4 (P <0 0 5 )。以上结果提示 :(1)猪胃组织中GHr基因表达有特定的发育模式 ,并且呈现显著的品种间差异 ;(2 )GH直接作用于胃组织并调节胃的生长 ,GH是否直接参与胃的功能性发育调节 ,尚有待于进一步的实验研究     

Whole-genome sequencing to detect mutations associated with resistance to insecticides and Bt proteins in Spodoptera frugiperda

The fall armyworm (FAW), Spodoptera frugiperda, is a major pest native to the Americas that has recently invaded the Old World. Point mutations in the target-site proteins acetylcholinesterase-1 (ace-1), voltage-gated sodium channel (VGSC) and ryanodine receptor (RyR) have been identified in S. frugiperda as major resistance mechanisms to organophosphate, pyrethroid and diamide insecticides respectively. Mutations in the adenosine triphosphate-binding cassette transporter C2 gene (ABCC2) have also been identified to confer resistance to Cry1F protein. In this study, we applied a whole-genome sequencing (WGS) approach to identify point mutations in the target-site genes in 150 FAW individuals collected from China, Malawi, Uganda and Brazil. This approach revealed three amino acid substitutions (A201S, G227A and F290V) of S. frugiperda ace-1, which are known to be associated with organophosphate resistance. The Brazilian population had all three ace-1 point mutations and the 227A allele (mean frequency = 0.54) was the most common. Populations from China, Malawi and Uganda harbored two of the three ace-1 point mutations (A201S and F290V) with the 290V allele (0.47–0.58) as the dominant allele. Point mutations in VGSC (T929I, L932F and L1014F) and RyR (I4790M and G4946E) were not detected in any of the 150 individuals. A novel 12-bp insertion mutation in exon 15 of the ABCC2 gene was identified in some of the Brazilian individuals but absent in the invasive populations. Our results not only demonstrate robustness of the WGS-based genomic approach for detection of resistance mutations, but also provide insights for improvement of resistance management tactics in S. frugiperda.     

全基因组测序及其在遗传性疾病研究及诊断中的应用

最近,随着测序成本的不断降低,数据分析策略的不断提升,全基因组测序（whole-genome sequencing,WGS）已经在癌症、孟德尔遗传病、复杂疾病的致病基因检测中得到了一定运用,并逐步走向了临床诊断。全基因组测序不但可以检测编码区和非编码区的点突变（SNVs）和插入缺失（InDels）,还可以在全基因组范围内检测拷贝数变异（copy number variation,CNV）以及结构变异（structure variation,SV）。本文详细地介绍了全基因组测序的标准生物信息分析流程与方法,及其在疾病研究、临床诊断中的应用,并对全基因组测序在医学遗传学中的应用与研究进展,以及数据分析方面面临的挑战进行了概述。     

Physiological responses of growing Large White boars in three management environments

Growth and physiological responses in Large White boars were studied under three different management environments at the Teaching and Research Farm of the Federal University of Technology, Akure. The management environments were shed with concrete floor (SCF), open space with concrete floor (OSCF) and open space with earth floor (OSEF). Two studies were carried out, one between December 1990 and March 1991 and the other from December 1991 to April 1992. Meteorological parameters in all management environments were monitored simultaneously with physiological variables. Growth of the animals was assessed by monitoring body weights of the animals. Data analysis showed that mean ambient temperatures, mean relative humidity and net radiation differed significantly (P<0.05) among the management environments. Ambient temperature and net radiation of the pigs were highest (P<0.05) in the OSEF environment, which also had the lowest (P<0.05) relative humidity. Although growth rates did not differ significantly among environments, body weight was lowest (P<0.05) in the OSEF environment. Mean respiratory rates and rectal temperatures were lowest (P<0.05) in the SCF environment. The study shows correlations between some meteorological parameters and body weights. Pigs under shade and in concrete-floored pens were more comfortable and had higher body weight and lower respiratory rates and rectal temperatures.     

大白猪和通城猪全基因组选择性清扫分析

长期的人工选择使猪的生产性能得到显著提高,与选择相关的基因组区域也随之发生特定遗传变异表征(选择信号)。不同类型品种所受到选择强度不一,选择信号亦不相同,选择性清扫分析已逐渐成为选择信号的主要检测手段。文章基于商用型大白猪(n=45)和地方猪品种通城猪(n=45)的猪60K SNP芯片分型数据,借助遗传分化系数Fst法进行选择信号检测分析。利用gPLINK软件设定质控标准,共计34 304个SNPs被筛选出用于统计分析。使用Genepop软件包计算两个猪品种之间的遗传分化参数Fst,所得Fst平均值为0.3209。选取Fst>0.7036(即占总Fst值数目的 1%),共计344个SNPs被选择出来。SNP位置注释显示这些位点涉及到79个候选基因(Sus scrofa Build 9)。利用在线软件Ingenuity Pathway Analysis对候选基因的生物学通路进行网络分析,发现它们多与生长繁殖及免疫应答有关,如NCOA6、ERBB4、RUNX2和APOB等基因。研究结果为进行猪产肉、抗病等性状候选基因和致因突变深入挖掘提供了有益参考。     

雄烯二酮高产菌新金分枝杆菌MN4的全基因组测序及序列分析北大核心CSCD

【目的】新金分枝杆菌(Mycobacterium neoaurum)MN4是1株经诱变育种获得的高产雄烯二酮,并且能够耐受高浓度底物植物甾醇的突变菌株。为深入研究MN4菌株耐底物的机制及雄烯二酮的生物合成途径,有必要解析MN4菌株的全基因组序列信息。【方法】本研究采用高通量测序技术对MN4进行全基因组测序,然后使用相关软件对测序数据进行基因组装、基因预测与功能注释、COG聚类分析以及次级代谢产物合成基因簇预测等。【结果】新金分枝杆菌MN4基因组装获得33个Contigs,整个基因组大小为5.39 Mb,GC含量为66.9%,编码4920个蛋白基因,序列提交至Gen Bank数据库,登录号为JXYZ00000000。【结论】本研究首次报道了1株高产雄烯二酮菌株MN4的全基因组序列,分析了基因组的基本特征,初步解析了该菌株降解植物甾醇生产雄烯二酮的关键基因,将为MN4的功能基因组学研究及相关次级代谢产物的生物合成途径与异源表达研究提供基础。     

Genome‐wide analysis reveals artificial selection on coat colour and reproductive traits in Chinese domestic pigs

Pigs from Asia and Europe were independently domesticated from c. 9000 years ago. During this period, strong artificial selection has led to dramatic phenotypic changes in domestic pigs. However, the genetic basis underlying these morphological and behavioural adaptations is relatively unknown, particularly for indigenous Chinese pigs. Here, we performed a genome‐wide analysis to screen 196 regions with selective sweep signals in Tongcheng pigs, which are a typical indigenous Chinese breed. Genes located in these regions have been found to be involved in lipid metabolism, melanocyte differentiation, neural development and other biological processes, which coincide with the evolutionary phenotypic changes in this breed. A synonymous substitution, c.669T>C, in ESR1, which colocalizes with a major quantitative trait locus for litter size, shows extreme differences in allele frequency between Tongcheng pigs and wild boars. Notably, the variant C allele in this locus exhibits high allele frequency in most Chinese populations, suggesting a consequence of positive selection. Five genes (PRM1, PRM2, TNP2, GPR149 and JMJD1C) related to reproductive traits were found to have high haplotype similarity in Chinese breeds. Two selected genes, MITF and EDNRB, are implied to shape the two‐end black colour trait in Tongcheng pig. Subsequent SNP microarray studies of five Chinese white‐spotted breeds displayed a concordant signature at both loci, suggesting that these two genes are responsible for colour variations in Chinese breeds. Utilizing massively parallel sequencing, we characterized the candidate sites that adapt to artificial and environmental selections during the Chinese pig domestication. This study provides fundamental proof for further research on the evolutionary adaptation of Chinese pigs.     

Genome‐wide scans to detect positive selection in Large White and Tongcheng pigs

Due to the direction, intensity, duration and consistency of genetic selection, especially recent artificial selection, the production performance of domestic pigs has been greatly changed. Therefore, we reasoned that there must be footprints or selection signatures that had been left during domestication. In this study, with porcine 60K BeadChip genotyping data from both commercial Large White and local Chinese Tongcheng pigs, we calculated the extended haplotype homozygosity values of the two breeds using the long‐range haplotype method to detect selection signatures. We found 34 candidate regions, including 61 known genes, from Large White pigs and 25 regions comprising 57 known genes from Tongcheng pigs. Many selection signatures were found on SSC1, SSC4, SSC7 and SSC14 regions in both populations. According to quantitative trait loci and network pathway analyses, most of the regions and genes were linked to growth, reproduction and immune responses. In addition, the average genetic differentiation coefficient F_ST was 0.254, which means that there had already been a significant differentiation between the breeds. The findings from this study can contribute to further research on molecular mechanisms of pig evolution and domestication and also provide valuable references for improvement of their breeding and cultivation.     

枫泾猪、香猪和长白猪的DNA指纹图分析

本文用M13和3个人源小卫星探针(33.6、 33.15、α-珠蛋白-3’HVR)获得了枫泾猪、香猪及长白猪的DNA指纹图,分析了各品种内和品种间的遗传变异性。结果表明,各品种的平均DNA指纹图相似系数在0.440-0.532的范围内,极显著地高于品种间的相似系数(0.223-0.307)。各品种的DNA指纹图还存在着一些品种特异性图带,这些图带在以后的基因定位中值得重视。 Abstract:This paper demonstrated DNA fingerprints of Fengjing,Xiang and Large White breeds of swine generated by M13 and three human minisatellite probes(33.6,33.15 andα-globin-3’HVR),and determined the intrabreed and interbreed variabilities of swine DNA fingerprints.It was shown that the mean band sharing probability within breeds was 0.440-0.532,significantly higher than that between breeds(0.223-0.307).Some breed-specific bands were noted in each breed,which should draw our attention in the course of gene mapping.     

Detection of quantitative trait loci for androstenone, skatole and boar taint in a cross between Large White and Meishan pigs

'Boar taint' is a strong perspiration-like, urine-like unpleasant odour given off upon heating or cooking of meat from some intact (uncastrated) male pigs. Data from the F(2) generation of a Large White (LW) x Meishan (MS) crossbred population were analysed to detect quantitative trait loci (QTL) for traits associated with boar taint. Fat samples from 178 intact male pigs slaughtered at 85 +/- 5 kg were analysed for the major contributors to boar taint (androstenone, indole and skatole). Fat and lean samples from cooked meat were scored for boar, abnormal and pork flavour and odour by a trained sensory panel (SP). A scan with 117 markers covering the whole genome was performed in the F(2) individuals, together with their F(1) parents and purebred grandparents. At the 5% chromosomal significance threshold (approximately equal to the genome-wide suggestive significance threshold), QTL were detected for the laboratory estimate of androstenone on chromosomes 2, 4, 6, 7 and 9. However, only on chromosome 6 were there QTL for boar flavour (BF) traits in the same or adjacent marker intervals as a QTL for the laboratory estimate of androstenone. On chromosome 14, QTL were detected for the laboratory estimates of indole and skatole, the SP score for skatole and the scores for BF in lean and BF in fat. In all five cases, the MS allele generally increased the estimate or score, compared with the LW allele, but it appeared that desirable and undesirable alleles were present in both breeds. This locus on chromosome 14 has considerable potential for use to reduce the incidence of boar taint, especially if further research can identify the causative polymorphism or strongly associated markers.     

Assessment of relationships between pigs based on pedigree and genomic information

Relationships play a very important role in studies on quantitative genetics. In traditional breeding, pedigree records are used to establish relationships between animals; while this kind of relationship actually represents one kind of relatedness, it cannot distinguish individual specificity, capture the variation between individuals or determine the actual genetic superiority of an animal. However, with the popularization of high-throughput genotypes, assessments of relationships among animals based on genomic information could be a better option. In this study, we compared the relationships between animals based on pedigree and genomic information from two pig breeding herds with different genetic backgrounds and a simulated dataset. Two different methods were implemented to calculate genomic relationship coefficients and genomic kinship coefficients, respectively. Our results show that, for the same kind of relative, the average genomic relationship coefficients (G matrix) were very close to the pedigree relationship coefficients (A matrix), and on average, the corresponding values were halved in genomic kinship coefficients (K matrix). However, the genomic relationship yielded a larger variation than the pedigree relationship, and the latter was similar to that expected for one relative with no or little variation. Two genomic relationship coefficients were highly correlated, for farm1, farm2 and simulated data, and the correlations for the parent-offspring, full-sib and half-sib were 0.95, 0.90 and 0.85; 0.93, 0.96 and 0.89; and 0.52, 0.85 and 0.77, respectively. When the inbreeding coefficient was measured, the genomic information also yielded a higher inbreeding coefficient and a larger variation than that yielded by the pedigree information. For the two genetically divergent Large White populations, the pedigree relationship coefficients between the individuals were 0, and 62 310 and 175 271 animal pairs in the G matrix and K matrix were greater than 0. Our results demonstrated that genomic information outperformed the pedigree information; it can more accurately reflect the relationships and capture the variation that is not detected by pedigree. This information is very helpful in the estimation of genomic breeding values or gene mapping. In addition, genomic information is useful for pedigree correction. Further, our findings also indicate that genomic information can establish the genetic connection between different groups with different genetic background. In addition, it can be used to provide a more accurate measurement of the inbreeding of an animal, which is very important for the assessment of a population structure and breeding plan. However, the approaches for measuring genomic relationships need further investigation.     

全基因组测序揭示两株泡菜源植物乳杆菌基因型差异和潜在益生特性北大核心

【目的】为了探究植物乳杆菌(Lactiplantibacillus plantarum)基因型差异和潜在益生特性,采用全基因组测序技术对其进行测序并解析基因组序列及生物特性。【方法】本研究基于HiSeq和PacBio测序平台,对团队前期从四川多代泡菜中分离获得、体外益生特性评价良好的潜在益生菌菌株L.plantarum Eden-Star PC06和L.plantarum Eden-Star PC108的全基因组进行测序。利用相关生物信息学软件对原始数据进行组装及其后续的功能注释、分子进化、菌株安全性、次级代谢产物合成基因簇以及益生特性相关基因进行分析。【结果】通过基因组装得到了2株植物乳杆菌的全基因组信息,L.plantarum Eden-Star PC06和Eden-Star PC108基因组大小分别为3163902 bp和3205054 bp;GC含量分别为44.68%和44.67%;分别包含3161个和3197个DNA编码序列;功能基因数据库比对结果显示2株菌在碳水化合物利用、氨基酸利用和糖基转移酶等基因上得到大量注释;通过比对数据库,在2株植物乳杆菌全基因组上发现了4个与肠液耐受相关的胆盐水解酶基因、完整的植物乳杆菌细菌素合成相关基因簇和抵御多种胁迫的益生相关基因。【结论】本研究通过全基因组测序在基因水平上探究了L.plantarum Eden-Star PC06和Eden-Star PC108基因型差异和益生特性基因,证明L.plantarum Eden-Star PC06和Eden-Star PC108是2株有应用前景的益生菌菌株,以期为筛选优良益生菌菌株和评价其益生特性提供遗传学基础。     

Gene expression in Large White or Duroc-sired female and castrated male pigs and relationships with pork quality

This study assessed expression of 12 genes in 24 pig longissimus samples earlier subjected to a proteomic study by our group. Genes were selected on the basis of the earlier proteomic results. Pigs differed in rearing environment (indoors or outdoors), sire breed (Duroc or Large White) and gender (female or castrated male). At slaughter they experienced different stress conditions. The proportion of gene expression changes influenced by treatment factors was consistent with the proportion of protein changes in an earlier proteomic analysis of the same pigs. Expression levels of genes were often correlated. Gene expression was generally not correlated with the levels of the corresponding protein. Finally, most meat quality traits were correlated with the expression of at least one of the studied genes. The most meaningful of these was the association of a slower pH decline with lower levels of HSP72 expression and higher levels of HSP72 protein. ANXA2 and cMDH expression were also associated with various meat quality traits. These relationships may be related to pre-slaughter stress levels and fibre type composition.     

第二代测序技术用于水稻和稻瘟菌互作早期转录组的分析

稻瘟菌为了实现对水稻的有效侵染,在侵染水稻时可能通过表达和转运一定数量的效应蛋白进入到水稻细胞,抑制和干扰水稻的先天免疫机制。文章利用Solexa第二代测序技术,通过开展水稻和稻瘟菌互作早期转录组的测定和分析,克隆和鉴定在互作早期表达的稻瘟菌效应蛋白基因。利用序列同源比对,我们从总计约12.5 M条序列标签中,分离和鉴定了338 942条来源于稻瘟菌的序列,并最终定位到779个稻瘟菌预测基因。其中108个基因很可能参与了水稻和稻瘟菌互作过程,42个基因为预测的分泌蛋白基因。通过RT-PCR分析,最终确认了42个预测分泌蛋白基因中有12个基因在侵染水稻早期有显著的表达,而其中有4个基因表现为侵染早期特异表达。文章尝试利用第二代测序技术实现稻瘟菌侵染早期特异表达基因,尤其是分泌蛋白基因的快速克隆和鉴定,为稻瘟菌效应蛋白基因的克隆和功能鉴定提供了较为有意义的探索。     

Next Generation Semiconductor Based-Sequencing of a Nutrigenetics Target Gene (GPR120) and Association with Growth Rate in Italian Large White Pigs

The GPR120 gene (also known as FFAR4 or O3FAR1) encodes for a functional omega-3 fatty acid receptor/sensor that mediates potent insulin sensitizing effects by repressing macrophage-induced tissue inflammation. For its functional role, GPR120 could be considered a potential target gene in animal nutrigenetics. In this work we resequenced the porcine GPR120 gene by high throughput Ion Torrent semiconductor sequencing of amplified fragments obtained from 8 DNA pools derived, on the whole, from 153 pigs of different breeds/populations (two Italian Large White pools, Italian Duroc, Italian Landrace, Casertana, Pietrain, Meishan, and wild boars). Three single nucleotide polymorphisms (SNPs), two synonymous substitutions and one in the putative 3′-untranslated region (g.114765469C > T), were identified and their allele frequencies were estimated by sequencing reads count. The g.114765469C > T SNP was also genotyped by PCR-RFLP confirming estimated frequency in Italian Large White pools. Then, this SNP was analyzed in two Italian Large White cohorts using a selective genotyping approach based on extreme and divergent pigs for back fat thickness (BFT) estimated breeding value (EBV) and average daily gain (ADG) EBV. Significant differences of allele and genotype frequencies distribution was observed between the extreme ADG-EBV groups (P < 0.001) whereas this marker was not associated with BFT-EBV.