The aim of this study was to detect evidence for signatures of recent selection in the Jinhua pig genome. These results can be useful to better understand the regions under selection in Jinhua pigs and might shed some lights on groups of genes that control production traits. In the present study, we performed extended haplotype homozygosity (EHH) tests to identify significant core regions in 202 Jinhua pigs. A total of 26 161 core regions spanning 636.42 Mb were identified, which occupied approximately 28% of the genome across all autosomes, and 1 158 significant (P<0.01) core haplotypes were selected. Genes in these regions were related to several economically important traits, including meat quality, reproduction, immune responses and exterior traits. A panel of genes including ssc-mir-365-2, KDM8, RABEP2, GSG1L, RHEB, RPH3AL and a signal pathway of PI3K-Akt were detected with the most extreme P-values. The findings in our study could draw a comparatively genome-wide map of selection signature in the pig genome, and also help to detect functional candidate genes under positive selection for further genetic and breeding research in Jinhua and other pigs.

Objective: Porcine respiratory disease is one of the most important health problems causing significant economic losses. To understand the genetic basis for susceptibility to swine enzootic pneumonia (EP) in pigs, we detected 102,809 single nucleotide polymorphisms in a total of 249 individuals based on genome-wide sequencing data. Methods: Genome comparison of susceptibility to swine EP in three pig breeds (Jinhua, Erhualian, and Meishan) with two western lines that are considered more resistant (Duroc and Landrace) using cross-population extended haplotype homozygosity and F-statistic (F-ST) statistical approaches identified 691 positively selected genes. Based on quantitative trait loci, gene ontology terms and literature search, we selected 14 candidate genes that have convincible biological functions associated with swine EP or human asthma. Results: Most of these genes were tested by several methods including transcription analysis and candidate genes association study. Among these genes: cytochrome P450 1A1 and catenin beta 1 (CTNNB1) are involved in fertility; transforming growth factor beta receptor 3 plays a role in meat quality traits; Wnt family member 2, CTNNB1 and transcription factor 7 take part in adipogenesis and fat deposition simultaneously; plasminogen activator, urokinase receptor (completely linked to AXL receptor tyrosine kinase, r(2) = 1) plays an essential role in the successful ovulation of matured oocytes in pigs; colipase like 2 (strongly linked to SAM pointed domain containing ETS transcription factor, r(2) = 0.848) is involved in male fertility. Conclusion: These adverse genes susceptible to swine EP may be selected while selecting for economic traits (especially reproduction traits) due to pleiotropic and hitchhiking effect of linked genes. Our study provided a completely new point of view to understand the genetic basis for susceptibility or resistance to swine EP in pigs thereby, provides insight for designing sustainable breed selection programs. Finally, the candidate genes are crucial due to their potential roles in respiratory diseases in a large number of species, including human.

Chinese indigenous pigs in the Taihu Lake region are well known for their high fecundity and other excellent characteristics. To better understand the characteristics of these breeds in this area as well as to provide the government and breeders the molecular basis for formulating a reasonable conservation policy, we explored the structure of haplotype blocks and genetic diversity of the 7 populations which is relevant for the management and conservation of these important genetic resources using next-generation sequencing data. In this study, a total of 131 300 single-nucleotide polymorphisms with minor allele frequencies ⩾0.05 were obtained for further analysis. In general, there are similar within-breed genetic diversities (He, Ho, Pn, Ar) among these 7 pig populations in the Taihu Lake region. Average values for the inbreeding coefficients estimates in the 7 populations are 0.110 (F1), 0.056 (F2), and 0.078 (F3). All the breeds have seen a continuous decline in Ne estimates over time with FJ and SW populations having a very similar curve. Moreover, the Ne of SMS pig breeds were smaller than other Chinese pig breeds, indicating that SMS pig breeds underwent stronger selection pressure than other Chinese pig breeds. The average genetic distances among the 7 populations in the Taihu Lake region were 0.235 (MMS), 0.240 (SMS), 0.269 (EH), 0.248 (MI), 0.221 (FJ), 0.254 (JX), and 0.212 (SW). A summary of the number of haplotype blocks and haplotype diversity was also presented. This study provide a deep understanding of the current situation of conservation in this region, thereby uncovering the pertinent insight to better formulate more reasonable preservation policies for the government departments and breeding planners to follow-up.

本研究旨在探讨杜洛克(D)、大白(Y)和长白(L)3个知名西方品种与金华猪(J)的杂交利用情况.应用"基于基因组简化与测序的基因型判型(GGRS)"技术平台,检测单核苷酸多态性(SNPs)并判定基因型.利用全基因组性状特异的SNP分子标记估算不同群体间的遗传距离,从胴体与肉品质、繁殖、健康和生长4个性状对金华猪不同杂交模式下的杂种优势进行预测.结果表明:共找到繁殖、生长、胴体与肉品质和健康性状潜在相关基因的SNP分别为1835、2174、196057、17200个;在二元杂交组合中,♂杜 × ♀金(D×J)为较优组合;在三元杂交组合中,♂金 × ♀长大(J×LY)为较优组合;在四元杂交组合中,♂杜金 × ♀长大(DJ×LY)为较优组合.本研究应用生物信息学技术对金华猪不同杂交模式的杂交优势进行预测,可大大减少后续的配合力实验,结果可为金华猪的保种和杂交利用提供一定参考.

Jinhua pig, a well-known Chinese indigenous breed, has evolved as a pig breed with excellent meat quality, greater disease resistance, and higher prolificacy. The reduction in the number of Jinhua pigs over the past years has raised concerns about inbreeding. Runs of homozygosity (ROH) along the genome have been applied to quantify individual autozygosity to improve the understanding of inbreeding depression and identify genes associated with traits of interest. Here, we investigated the occurrence and distribution of ROH using next-generation sequencing data to characterize autozygosity in 202 Jinhua pigs, as well as to identify the genomic regions with high ROH frequencies within individuals. The average inbreeding coefficient, based on ROH longer than 1 Mb, was 0.168 +/- 0.052. In total, 18,690 ROH were identified in all individuals, among which shorter segments (1-5 Mb) predominated. Individual ROH autosome coverage ranged from 5.32 to 29.14% in the Jinhua population. On average, approximately 16.8% of the whole genome was covered by ROH segments, with the lowest coverage on SSC11 and the highest coverage on SSC17. A total of 824 SNPs (about 0.5%) and 11 ROH island regions were identified (occurring in over 45% of the samples). Genes associated with reproduction (HOXA3, HOXA7, HOXA10, and HOXA11), meat quality (MYOD1, LPIN3, and CTNNBL1), appetite (NUCB2) and disease resistance traits (MUC4, MUC13, MUC20, LMLN, ITGB5, HEG1, SLC12A8, and MYLK) were identified in ROH islands. Moreover, several quantitative trait loci for ham weight and ham fat thickness were detected. Genes in ROH islands suggested, at least partially, a selection for economic traits and environmental adaptation, and should be subject of future investigation. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the pig genome.

采用单性状混合模型和多性状混合模型估计了568头体重为70～115 kg的杜洛克猪的饲料转化效率的遗传力及其与生长性状的遗传相关.结果 表明,料重比(feed conversation ratio,FCR)和剩余采食量(residual feed intake,RFI)的遗传力分别为0.38和0.20.饲料转化效率性状之间的遗传相关较高(0.90).FCR与各生长性状间表型相关及遗传相关都高于RFI与生长性状间的相关,尤其是FCR与日增重之间的相关为-0.47.RFI与所有生长性状的表型相关都接近于0,与背膘厚(back fat,BF)呈一定的正遗传相关(0.15),与眼肌面积(loin eye area,LEA)和瘦肉量(lean meat content,LMC)呈较高的负相关(-0.37和-0.48),与日增重之间的相关则接近于0.综上,杜洛克猪70～115 kg体重饲料转化效率指标具有中高等遗传力,与生长性状有一定的遗传相关,尤其是FCR,因此使用该阶段测定数据计算FCR或RFI是合理可行的.

To improve development and utilization of Jinhua pig (JH) resources,we designed the crossings of Duroc × J H (D×J),Duroc × Landrace × JH (D×LJ),JH × Landrace × Yorkshire (J×LY),Duroc × JH × Landrace × Yorkshire (DJ×LY) to see how they affected the growth performance,reproductive performance,slaughter performance and meat quality,respectively,of Jinhua pigs.The results indicated that DJ×LY crossbreeding produced higher total litter size,alive litter size and newborn litter weight than the other three crossbreeding designs;D×LJ and DJ×LY had better dressing percentage and lean percentage;J×LY resulted in the highest carcass length,followed by DJ×LY cross;and DJ×LY led to the highest correct color grading and marbling scores.Taken together,all the JH crossbreeding trials in this study could serve as candidate crosses,with the DJ×LY crossbreedding being a more recommended one,for Jinhua pig production.

小梅山猪(Sus scrofa)是太湖流域独特的地方猪品种,具有肉质鲜美等特点,市场上存在小梅山猪及其肉制品的假冒问题,而传统鉴别技术在实际应用中具有一定的局限性.本研究利用第3代分子标记一单核苷酸多态性(single nucleotide polymorphism,SNP)开发小梅山猪及其制品的分子标记鉴定方法,将小梅山猪与太湖流域其他6个品种及常见西方品种猪进行鉴别区分.对于太湖流域7个品种(品系)(中梅山猪、小梅山猪、二花脸猪、米猪、嘉兴黑猪、枫泾猪和沙乌头猪)和西方5个引进猪品种(杜洛克、长白猪、大白猪、皮特兰、巴克夏)进行简化基因组测序(genotyping by genome reducing and sequencing,GGRS),筛选出小梅山猪与其他猪种具有差异的5个SNP位点,采用Sanger测序进行验证.结果表明,上述5个SNPs在小梅山猪中存在较高等位基因突变率,利用5个候选位点的组合可达到鉴定概率99.35％、准确率100％,无假阳性错判.本研究为小梅山猪遗传资源保护、假冒伪劣品种辨别提供了参考依据.

The objective of this study was to estimate the genetic parameters and analyzed factors (i.e.batch management system and frozen semen) that may influence reproductive performance for Yorkshire pigs,which may establish theoretical basis for genetic evaluation and production management of target population.DMU and ASREML software were used to analyze 4 512 litters for 2 026 Yorkshire pigs,including four traits (i.e.total number born,number born alive,litter weight at 21 d,number weaned).Estimates of heritabilities were all around 0.10 for four traits and estimates of genetic correlations were all strong,positive (P＞0.54).Effects of semen types have not significant difference on litter weight at 21 d and number weaned(P＞0.05),however significant difference were found on total number born and number born alive,the litter size of frozen semen was 1 less than that of fresh semen.The study of batch management system indicate that production performance degradation was found when 1-week batch management system turn into 4-week batch management system,number born alive,litter weight at 21 d and number weaned declined 0.51,0.61,10.13kg,respectively.

剩余采食量(RFI)是如今评价猪饲料转化效率的重要指标之一.与传统的耗料增重比参数不同,RFI是畜禽实际采食量与用于生长和维持的预测采食量之间的差值,通过建立采食量与生产性能和代谢体重的多元线性回归模型获得.猪RFI统计模型的种类很多且各有千秋,不同的统计模型计算的RFI其遗传力、遗传相关、候选基因等具有明显差异.本文着重介绍近年来关于RFI的各种统计模型及不同的统计模型下RFI的遗传参数和候选基因.

Chinese Meishan pig is well-known for its high prolificacy and superior meat quality.In order to detect the current situation of the conservation population,the sequencing data of 143 pigs from the four state-owned conservation farms were selected in this study.We found that all of the farms have low effective population sizes.The Middle Meishan populations have a higher proportion of polymorphic markers,and the Small Meishan populations have a higher observed heterozygosity and expected heterozygosity.It has been observed that there is an obvious genetic difference between the Middle and the Small Meishan population as the value of genetic differentiation (Fst) was 0.111 and the genetic distance (D) was 0.287.There is a weak differentiation between the two conservation farms of the Small Meishan pigs (Fst=0.055,D=0.239) but a moderate differentiation between the two conservation farms of the Middle Meishan pigs (Fst=0.127,D=0.273).This work may provide the molecular basis for the better protection and utilization of the Meishan pigs.

China has been importing enormous numbers of pigs abroad.However,whether the information offered by the exporters is reliable and whether participating in foreign breeding evaluation systems (NSR,etc.) are controversial issues.Taking one national level core breeding farm as an example which had imported pig from USA and then been a member of NSR,this study made systematic correlation analysis for four traits including "Days to 115kg","Backfat thickness","LoinMuscle Area" and "Predicted Percent Lean",and the results shown that.The breeding values offered by NSR is real,but it is not useful.For the trait of "Days to 115 kg",there seems to be a significant negative correlation between the breeding values estimated by NSR and by our method for imported ones and their progenies,which means that the results of selection based on our methods are probably opposite to the results according to NSR evaluation system.But for the other three traits,the coefficients of relationship are positively significant.However,as the selection index is composed of the sum of the weights of breeding values of "days to 115kg" and other traits,the whole index will be unreliable.Therefore,this is to say that we cannot blindly participate in the international evaluation system.When it comes to the reason of the results,it may be the interaction between genotype and environment.And further analysis is still needed to validate this hypothesis.

This study was aimed to investigate the genetic diversity and the reason for the degradation of the reproductive performance of Pudong White pig.The genetic diversity of Pudong White pig, six Taihu pig breeds and three Western pig breeds were analyzed based on the genome-wide SNPs.The genetic diversity and population structure of these pig breeds were also explored based on the SNPs related to reproductive traits.The results showed that Pudong White pig displayed a lower level of the genetic diversity than the Taihu area pig breeds.For the reproductive-related loci, except for Fengjing pig, Pudong White pig displayed the lowest propotion of polymorphic markers, expected heterozygosities and allelic richness (excluded Duroc pig).The result of PCA showed that Pudong White pig displayed its uniqueness in the reproductive-related SNPs.With the comparsion of Taihu pigs and Western populations, Pudong White pig displayed a lower level of the genetic diversity and more homozygous reproductive-related loci.Nevertheless, a certain number of favorable alleles were still harbored in Pudong White pig, which might result high heterosis in the offsprings.In conclusion, the results of this study might provide some valuable information for the breeding, conservation and utilization of this breed.

Selection index is composed of weighted breeding values of each breeding-related trait.The weights of the traits involve their economic importance and their variance-covariance in the specific population and the specific market background,so the application of a specific set of weights has certain limit while their estimation is very difficult.In view of this,we recommend using the breeding importance based on the current situation and the breeding goal as a weight.This paper introduces the concepts and formulas,gives software and an example,and discusses some related problems in the application,hoping to benefit the farms and then promote the development of the National Pig Improvement Program (2009-2020).

Mycoplasmal pneumonia of swine (MPS,also referred to as'enzootic pneumonia',EP) caused by Mycoplasma hyopneumoniae (Mhp),is a chronic respiratory disease with the clinical sign of persistent dry cough.Epidemic of MPS has a negative impact on growth rate and feed conversion.The causative agent Mhp is easily infected and it will become worse with co-infections,which always gives rise to huge economic damage to the swine (Sus scrofa) industry,both at home and abroad.At present,most research is centered on pathological diagnosis,immunity,prevention and control.However,these medical treatments and public health measures are incapable of alleviating the negative impacts from MPS.For better solving the occurrence of MPS,we intend to adopt bioinformatics analysis methods to explore MPS from the molecular level for better illustrating its mechanism.For the purpose,this study was mainly based on Gene Ontology (GO) enrichment analysis,KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis,text mining and other bioinformatics tools to complete the PigQTLdb (pig QTL Database) retrieval and biological annotations for MPS candidate genes.The results showed that 47 possible QTLs were associated with MPS with the full use of PigQTLdb,2 of which were related to MPS susceptibility,and the others were involved in immunity.38 GO terms linked to MPS were searched by CoPub,a text-mining tool,and then 3 379 genes contained in 47 QTLs were effective after semantic similarities calculation with R programming and GOSim package.Among them,36 genes were statistically significant.For another,there were 53 genes found in GO enrichment analysis,and 16 genes in'Asthma'pathway from KEGG analysis.In addition,six candidate genes were from the results of text-mining,including TNFα (tumor necrosis factor),NRAMP1 (natural resistance-associated macrophage protein 1),TCRs (T-cell receptor genes),CYP1A1 (cytochrome P450 family 1 subfamily A member 1),CYP3A29 (cytochrome P450 3A29v4) and SERPING1 (serpin family G member 1).As a result,there were totally 104 optimized genes for the MPS candidate gene set.Special attention should be paid on gene TNF,for it was involved in both GO enrichment analysis and KEGG pathway analysis results,and appeared in the text mining results as well.To be specific,TNF was one of the crucial factors to induce inflammation,which ranked fourth in significance among all candidate genes during calculations.We inferred that TNF and POU5F1 were the candidate genes of vital importance during MPS infections.These findings will offer a new aspect for the further research in the future,though there would be some improvements in the analysis,and these conclusions remained to be proved.In next step,we will make efforts to explain the relationship between MPS and other important economic traits and explore the molecular differences between Chinese indigenous pigs and western imported pigs for further to indicate its heritance mechanism and provide insights for human asthma study one day.

The Dongxiang Blue-shelled chicken is one of the most valuable Chinese indigenous poultry breeds. However, compared to the Italian native White Leghorn, although this Chinese breed possesses numerous favorable characteristics, it also exhibits lower growth performance and fertility. Here, we utilized genotyping sequencing data obtained via genome reduction on a sequencing platform to detect 100,114 single nucleotide polymorphisms and perform further biological analysis and functional annotation. We employed cross-population extended haplotype homozygosity, eigenvector decomposition combined with genome-wide association studies (EigenGWAS), and efficient mixed-model association expedited methods to detect areas of the genome that are potential selected regions (PSR) in both chicken breeds, and performed gene ontology (GO) enrichment and quantitative trait loci (QTL) analyses annotating using the Kyoto Encyclopedia of Genes and Genomes. The results of this study revealed a total of 2424 outlier loci (p-value <0.01), of which 2144 occur in the White Leghorn breed and 280 occur in the Dongxiang Blue-shelled chicken. These correspond to 327 and 94 PSRs containing 297 and 54 genes, respectively. The most significantly selected genes in Blue-shelled chicken are TMEM141 and CLIC3, while the SLCO1B3 gene, related to eggshell color, was identified via EigenGWAS. We show that the White Leghorn genes JARID2, RBMS3, GPC3, TRIB2, ROBO1, SAMSN1, OSBP2, and IGFALS are involved in immunity, reproduction, and growth, and thus might represent footprints of the selection process. In contrast, we identified six significantly enriched pathways in the Dongxiang Blue-shelled chicken that are related to amino acid and lipid metabolism as well as signal transduction. Our results also reveal the presence of a GO term associated with cell metabolism that occurs mainly in the White Leghorn breed, while the most significant QTL regions mapped to the Chicken QTL Database (GG_4.0) for the Dongxiang Blue-shelled breed are predominantly related to lesions, bone mineral content, and other related traits compared to tibia length and body weight (i.e., at 14, 28, 42, and 70 d) in the White Leghorn. The results of this study highlight differences in growth, immunity, and egg quality traits between the two breeds, and provide a foundation for the exploration of their genetic mechanisms.

奶牛乳房炎是奶牛的常见病和多发病之一,给奶牛业带来巨大的经济损失,严重制约着奶牛业的发展.为了进一步了解乳房炎的调控机理,对已发表的5套大肠杆菌感染奶牛乳腺上皮细胞的表达谱芯片数据统一进行预处理,并整合大肠杆菌感染1、6、24 h的基因富集分析,以期得到更可靠的影响奶牛乳房炎的关键基因和通路.结果发现,感染1、6和24 h数据集的分析结果中共同下调通路分别为9、30和17个,分析结果确定了一些奶牛乳房炎相关的通路及基因,为进一步揭示其调控机理提供参考.

Single nucleotide polymorphisms (SNPs) are essential for identifying the genetic mechanisms of complex traits. In the present study, we applied genotyping by genome reducing and sequencing (GGRS) method to construct a 252-plex sequencing library for SNP discovery and genotyping in chicken. The library was successfully sequenced on an Illumina HiSeq 2500 sequencer with a paired-end pattern; approximately 400 million raw reads were generated, and an average of approximately 1.4 million good reads per sample were generated. A total of 91,767 SNPs were identified after strict filtering, and all of the 252 samples and all of the chromosomes were well represented. Compared with the Illumina 60K chicken SNP chip data, approximately 34,131 more SNPs were identified using GGRS, and a higher SNP density was found using GGRS, which could be beneficial for downstream analysis. Using the GGRS method, more than 3528 samples can be sequenced simultaneously, and the cost is reduced to $18 per sample. To the best of our knowledge, this study describes the first report of such highly multiplexed sequencing in chicken, indicating potential applications for genome-wide association and genomic selection in chicken.

在梅山猪保种群和法系大白猪群体中采用直接测序法和PCR-RFLP法对基因VEGFA、HIF1A和EPAS1进行了基因多态位点的寻找及多态性检测并对不同基因型的总产仔数、产活仔数等繁殖性状进行了相关分析.在所获得的基因VEGFA的扩增片段中共检测到17个多态位点,其中有4个位点可进行PCR-RFLP检测,分别为BstH2I-RFLP,PspEI-RFLP,Eco32 I-RFLP和BcnI-RFLP,而在HIF1A和EPAS1扩增片段中未获得可进行PCR-RFLP检测的多态位点.在2个实验猪群中对VEGFA基因的4个多态位点进行基因型及等位基因频率分析,结果表明:VEGFA基因的BstH2I、Eco32I、PspEI 3个多态位点在梅山猪群体中A等位基因占优势,BcnI多态位点在梅山猪群体中B等位基因占优势,而在法系大白猪群体中VEGFA基因的BstH2I、Eco32I、PspEI和BcnI 4个多态位点的相关基因型和等位基因分布极不均衡.BstH2I和PspEI多态位点相关的A等位基因频率在法系大白猪群体中为0,而Eco32I和BcnI多态位点相关的A、B等位基因频率在法系大白猪群体中不到1％.单倍体型推断结果表明VEGFA基因4个多态位点在梅山猪群体中共存在10种单倍体型,而在法系大白猪群体中只存在2种单倍体型BBBA和BBAB,且只有一个个体的单倍体型是BBAB.通过性状关联分析,发现梅山猪群体中VEGFA基因单倍体型BBBA对初产总仔数影响显著(P＜0.05);单倍体型BABA对经产总仔数和经产活仔数影响显著(P＜0.05);单倍体型BBAA对初生窝重影响显著(P＜0.05).使用辐射杂种克隆板将基因VEGFA定位于SSC7q11-12;基因HIF1A定位于SSC1;基因EPAS1定位于SSC3q11-14.而所获得的基因HIF1A和EPAS1的扩增片段无PCR-RFLP可识别的SNP位点.研究结果表明猪VEGFA基因具有成为影响猪繁殖性状分子遗传标记的潜力.