In JoVE (1)

Other Publications (34)

Articles by Junwu Ma in JoVE

Other articles by Junwu Ma on PubMed

DNA Prime Followed by Protein Boost Enhances Neutralization and Th1 Type Immunity Against FMDV

Viral Immunology. 2005  |  Pubmed ID: 16212533

Prime-boost strategy has been exhibited its potency to enhance immune responses, which would be important to the success to develop a vaccine against the foot-and-mouth disease virus (FMDV). An eukaryotic expression construct encoding the FMDV capsid VP1 protein with a recombinant VP1 protein or a commercial FMDV vaccine were tested in the prime-boost strategy in mice and cattle trials. The levels of induced specific antibodies, T cell proliferations, and DTH activities were significantly higher in the prime-boost groups than in those vaccinated with DNA, protein or FMDV vaccine alone. More importantly, the levels of neutralizing antibodies in the former groups were significantly higher than others and could last for at least four months in cattle trials. This study suggests that the prime-boost strategy significantly improves the effective immunity and may provide a longer protection against FMDV infection.

Chinese White Rongchang Pig Does Not Have the Dominant White Allele of KIT but Has the Dominant Black Allele of MC1R

The Journal of Heredity. Jan-Feb, 2007  |  Pubmed ID: 17150979

The mast/stem cell growth factor receptor (KIT) and melanocortin receptor 1 (MC1R) mutations are responsible for coat color phenotypes in domestic pigs. Rongchang is a Chinese indigenous pig breed with a white coat color phenotype. To investigate the genetic variability of the KIT and MC1R genes and their possible association with the coat color phenotype in this breed, a gene duplication and splice mutation of KIT were diagnosed in a sample of 93 unrelated Rongchang animals. The results show that Rongchang pigs have a single copy of KIT without the splice mutation at the first nucleotide of intron 17, indicating that the dominant white I allele of KIT is not responsible for their white phenotype. The KIT mRNA and MC1R coding sequences were also determined in this breed. Three putative amino acid substitutions were found in the KIT gene between Rongchang and Western white pigs, their association with the Rongchang white phenotype remains unknown. For the MC1R gene, Rongchang pigs were demonstrated to have the same dominant black allele (E(D1)) as other Chinese breeds, supporting the previous conclusion that Chinese and Western pigs have independent domestication origin. We also clarified that the Rongchang white phenotype was recessive to nonwhite color phenotypes. Our results provide a good starting point for the identification of the mutations underlying the white coat color in Rongchang pigs.

Development and Validation of a 3ABC Indirect ELISA for Differentiation of Foot-and-mouth Disease Virus Infected from Vaccinated Animals

Veterinary Microbiology. Nov, 2007  |  Pubmed ID: 17601688

Non-structural protein (NSP) 3ABC antibody is considered to be the most reliable indicator of present or past infection with foot-and-mouth disease virus (FMDV) in vaccinated animals. An indirect ELISA was established, using purified His-tagged 3ABC fusion protein as antigen, for detection of the antibody response to FMDV NSP 3ABC in different animal species. The method was validated by simultaneous detection of the early antibody responses to NSP and structural protein (SP) in FMDV Asia 1 infected animals. The performance of the method was also validated by detection of antibody in reference sera from the FMD World Reference Laboratory (WRL) in Pirbright, UK, and comparison with two commercial NSP ELISA kits. The results showed that the antibody response to SP developed more quickly than that to NSP 3ABC in FMDV infected animals. In contact-infected cattle, the antibody response to NSP 3ABC was significantly delayed compared with that to SP antibody. The early antibody responses to SP and NSP 3ABC in FMDV inoculated cattle and contact-infected or inoculated sheep and pigs were generally consistent. In pigs, 3ABC antibody was linked to the presence of clinical signs; however, in sheep, subclinical infection was detected by the development of 3ABC antibodies. Therefore, the antibody responses to 3ABC varied between host species. Eight out of 10 positive serum samples from FMD WRL were tested to be positive at cutoff value of 0.2. The rate of agreement with the ceditest FMDV-NS and the UBI NSP ELISA were 98.05% (302/308) and 93.2% (287/308), respectively. The prevalence of 3ABC antibodies reached 71.4% in some diseased cattle herds. The further work is required to evaluation the performance of this method in different animal species and different field situations.

The Porcine Nuclear Receptor Co-repressor 1 (NCOR1) Gene: Chromosome Location, Expression Profile, and Polymorphism

Biochemical Genetics. Dec, 2007  |  Pubmed ID: 17939029

NCOR1 (nuclear receptor co-repressor1) encodes a protein that represses the expression of the targeted genes by promoting chromatin condensation and disabling access to the transcription machinery. So far, only a few NCOR1 EST sequences are available, and the chromosomal location of NCOR1 is unknown in the porcine genome. In this study, we have localized NCOR1 to the end of pig chromosome (SSC) 12 by a porcine radiation hybrid panel. The expression profile of NCOR1 was clarified using RNA from 18 tissues, and it is expressed ubiquitously in pigs. We did not identify any missense mutation in the exonic region encoding the first SANT domain of the NCOR1 protein, although we found six SNPs and two deletions in intron 12, and three SNPs and one deletion in intron 13, using DNA of 10 founder animals in a White Duroc x Erhualian intercross. These polymorphic markers can be integrated into a genome scan for identifying the QTL affecting economically important traits in pigs.

Experimental Studies with Foot-and-mouth Disease Virus Type Asia-1, Responsible for the 2005 Epidemic in China

Research in Veterinary Science. Oct, 2008  |  Pubmed ID: 18155114

This study was carried out to investigate the biological characteristics of the foot-and-mouth disease (FMD) virus strain Asia-1 China/2005, which is responsible for the 2005 epidemic in China. The result showed that this strain is not host restricted, and could not only cause FMD in cattle and sheep but also in pigs by either inoculation or direct contact.

Genome-wide Identification of QTL for Age at Puberty in Gilts Using a Large Intercross F2 Population Between White Duroc X Erhualian

Genetics, Selection, Evolution : GSE. Sep-Oct, 2008  |  Pubmed ID: 18694548

Puberty is a fundamental development process experienced by all reproductively competent adults, yet the specific factors regulating age at puberty remain elusive in pigs. In this study, we performed a genome scan to identify quantitative trait loci (QTL) affecting age at puberty in gilts using a White Duroc x Erhualian intercross. A total of 183 microsatellites covering 19 porcine chromosomes were genotyped in 454 F2 gilts and their parents and grandparents in the White Duroc x Erhualian intercross. A linear regression method was used to map QTL for age at puberty via QTLexpress. One 1% genome-wise significant QTL and one 0.1% genome-wise significant QTL were detected at 114 cM (centimorgan) on SSC1 and at 54 cM on SSC7, respectively. Moreover, two suggestive QTL were found on SSC8 and SSC17, respectively. This study confirmed the QTL for age at puberty previously identified on SSC1, 7 and 8, and reports for the first time a QTL for age at puberty in gilts on SSC17. Interestingly, the Chinese Erhualian alleles were not systematically favourable for younger age at puberty.

[Cloning of Foot-and-mouth Disease Virus Integrin Receptor Beta1 Subunit and Antibody Production to Its Ligand-binding Domain]

Sheng Wu Gong Cheng Xue Bao = Chinese Journal of Biotechnology. May, 2008  |  Pubmed ID: 18724711

We produced beta1 gene which is about 2400 bp by reverse transcription polymerase chain reaction (RT-PCR) from bovine trachea, reclaimed and purified, then cloned the amplified fragment to pGEM-T easy vector, confirmed by sequencing. The immune-dominant epitope of beta1 gene was chosen by computer analysis and then syncretized ligand-binding domain from 346 bp to 843 bp of ecytoplasm with six histidine, expressed LBD protein massly in E. coli BL21 (DE3), and identified by SDS-PAGE. The fusion protein was purified with Ni-NTA affinity chromatography and immunized New Zealand rabbits preparing of its polyclonal antibody, the specific antibody titer was above 1:12,800 detected by indirect ELISA, the result of Western blot showed that this antibody could be recognized by LBD fusion protein.

A Genome-wide Scan for Quantitative Trait Loci Affecting Limb Bone Lengths and Areal Bone Mineral Density of the Distal Femur in a White Duroc X Erhualian F2 Population

BMC Genetics. Oct, 2008  |  Pubmed ID: 18840302

Limb bone lengths and bone mineral density (BMD) have been used to assess the bone growth and the risk of bone fractures in pigs, respectively. It has been suggested that limb bone lengths and BMD are under genetic control. However, the knowledge about the genetic basis of the limb bone lengths and mineralisatinon is limited in pigs. The aim of this study was to identify quantitative trait loci (QTL) affecting limb bone lengths and BMD of the distal femur in a White Duroc x Erhualian resource population.

Chromosomal Assignment of the Porcine NALP5 Gene, a Candidate Gene for Female Reproductive Traits

Animal Reproduction Science. Jun, 2009  |  Pubmed ID: 18573623

NALP5, also known as MATER (maternal antigen that embryos require), is an oocyte-specific maternal effect gene required for early embryonic development. Because of the specificity of NALP5 expression, and its role in female fertility, NALP5 is an interesting candidate gene for economically important female reproductive traits. Here we describe the chromosomal assignment of the porcine NALP5 gene to the long arm of pig chromosome 6 (SSC6q21-22), a region known to harbour several reproduction quantitative trait loci.

A Genome Wide Detection of Quantitative Trait Loci on Pig Maternal Infanticide Behavior in a Large Scale White Duroc X Erhualian Resource Population

Behavior Genetics. Mar, 2009  |  Pubmed ID: 19130209

Maternal behavior around parturition is important to piglet survival. An extreme form of failure of maternal behavior, also called maternal infanticide, often occurs in some sows. This is defined as an active attack to piglets using the jaws, resulting in serious or fatal bite wounds within 24 h of birth. It leads to considerable economic losses to the pig industry and severe problems in pig welfare. In this study, maternal behaviors from 5 h before to 24 h after parturition were recorded in detail on 288 White Duroc x Erhualian intercross F(2) sows over their three continuous farrowings. In the F(2) population 12.8% gilts showed maternal infanticide in their first litter, while the incidences of maternal infanticide at their second and third farrowing reduced to 7.5% and 4.5%, respectively. All F(2) sows were genotyped for 194 microsatellite markers spanning the whole pig genome. A whole genome linkage analysis was performed using the non-parametric linkage test by SimWalk2 software. The results identified that seven chromosome regions on SSC2, SSC6, SSC14, SSC15 and SSCX were significantly linked with maternal infanticide (P < 0.05). The quantitative trait loci (QTL) on SSC2 and SSCX achieved P < 0.01 significance level. The most promising QTLs, however, were detected on X chromosome where three peaks of negative logarithm of P-value located at marker SW980, SW2456 and SW1608. QTLs on SSC2 and SSCX from this experiment were consistent with published results from the Western commercial lines.

Genome-wide QTL Mapping for Three Traits Related to Teat Number in a White Duroc X Erhualian Pig Resource Population

BMC Genetics. Feb, 2009  |  Pubmed ID: 19226448

Teat number is an important fertility trait for pig production, reflecting the mothering ability of sows. It is also a discrete and often canalized trait presenting bilateral symmetry with minor differences between the two sides, providing a potential power to evaluate fluctuating asymmetry and developmental instability. The knowledge of its genetic control is still limited. In this study, a genome-wide scan was performed with 183 microsatellites covering the pig genome to identify quantitative trait loci (QTL) for three traits related to teat number including the total teat number (TTN), the teat number at the left (LTN) and right (RTN) sides in a large scale White Duroc x Erhualian resource population.

Recombinational Landscape of Porcine X Chromosome and Individual Variation in Female Meiotic Recombination Associated with Haplotypes of Chinese Pigs

BMC Genomics. Mar, 2010  |  Pubmed ID: 20211033

Variations in recombination fraction (theta) among chromosomal regions, individuals and families have been observed and have an important impact on quantitative trait loci (QTL) mapping studies. Such variations on porcine chromosome X (SSC-X) and on other mammalian chromosome X are rarely explored. The emerging assembly of pig sequence provides exact physical location of many markers, facilitating the study of a fine-scale recombination landscape of the pig genome by comparing a clone-based physical map to a genetic map. Using large offspring of F1 females from two large-scale resource populations (Large White male symbol x Chinese Meishan female symbol, and White Duroc male symbol x Chinese Erhualian female symbol), we were able to evaluate the heterogeneity in theta for a specific interval among individual F1 females.

A Global View of Porcine Transcriptome in Three Tissues from a Full-sib Pair with Extreme Phenotypes in Growth and Fat Deposition by Paired-end RNA Sequencing

BMC Genomics. 2011  |  Pubmed ID: 21906321

Elucidation of the pig transcriptome is essential for interpreting functional elements of the genome and understanding the genetic architecture of complex traits such as fat deposition, metabolism and growth.

A Comprehensive Survey of Copy Number Variation in 18 Diverse Pig Populations and Identification of Candidate Copy Number Variable Genes Associated with Complex Traits

BMC Genomics. Dec, 2012  |  Pubmed ID: 23270433

Copy number variation (CNV) is a major source of structural variants and has been commonly identified in mammalian genome. It is associated with gene expression and may present a major genetic component of phenotypic diversity. Unlike many other mammalian genomes where CNVs have been well annotated, studies of porcine CNV in diverse breeds are still limited.

Effect of Temperature and PH on Postmortem Color Development of Porcine M. Longissimus Dorsi and M. Semimembranosus

Journal of the Science of Food and Agriculture. Mar, 2013  |  Pubmed ID: 23165775

Purchasing pork that is boned within 1 h postmortem and not aged is customary in China, and final pork color would not be fully realized. The relationship between early postmortem, pre-rigor meat color and 24 h postmortem, post-rigor pork color was investigated and related to the rate of pH and temperature decline within the longissimus dorsi (LD) and the semimembranosus (SM) muscles of pork carcasses. Muscle color, pH and temperature were measured at 45 min and at 3, 9, 15 and 24 h postmortem in carcasses of F₂ White Duroc and Chinese Erhualian pigs.

Genome-wide Association Study Reveals Constant and Specific Loci for Hematological Traits at Three Time Stages in a White Duroc × Erhualian F2 Resource Population

PloS One. 2013  |  Pubmed ID: 23691082

Hematological traits are important indicators of immune function and have been commonly examined as biomarkers of disease and disease severity in humans. Pig is an ideal biomedical model for human diseases due to its high degree of similarity with human physiological characteristics. Here, we conducted genome-wide association studies (GWAS) for 18 hematological traits at three growth stages (days 18, 46 and 240) in a White Duroc × Erhualian F2 intercross. In total, we identified 38 genome-wide significant regions containing 185 genome-wide significant SNPs by single-marker GWAS or LONG-GWAS. The significant regions are distributed on pig chromosomes (SSC) 1, 4, 5, 7, 8, 10, 11, 12, 13, 17 and 18, and most of significant SNPs reside on SSC7 and SSC8. Of the 38 significant regions, 7 show constant effects on hematological traits across the whole life stages, and 6 regions have time-specific effects on the measured traits at early or late stages. The most prominent locus is the genomic region between 32.36 and 84.49 Mb on SSC8 that is associated with multiple erythroid traits. The KIT gene in this region appears to be a promising candidate gene. The findings improve our understanding of the genetic architecture of hematological traits in pigs. Further investigations are warranted to characterize the responsible gene(s) and causal variant(s) especially for the major loci on SSC7 and SSC8.

Genome-wide Association Study of Meat Quality Traits in a White Duroc×Erhualian F2 Intercross and Chinese Sutai Pigs

PloS One. 2013  |  Pubmed ID: 23724019

Thousands of QTLs for meat quality traits have been identified by linkage mapping studies, but most of them lack precise position or replication between populations, which hinder their application in pig breeding programs. To localize QTLs for meat quality traits to precise genomic regions, we performed a genome-wide association (GWA) study using the Illumina PorcineSNP60K Beadchip in two swine populations: 434 Sutai pigs and 933 F2 pigs from a White Duroc×Erhualian intercross. Meat quality traits, including pH, color, drip loss, moisture content, protein content and intramuscular fat content (IMF), marbling and firmness scores in the M. longissimus (LM) and M. semimembranosus (SM) muscles, were recorded on the two populations. In total, 127 chromosome-wide significant SNPs for these traits were identified. Among them, 11 SNPs reached genome-wise significance level, including 1 on SSC3 for pH, 1 on SSC3 and 3 on SSC15 for drip loss, 3 (unmapped) for color a*, and 2 for IMF each on SSC9 and SSCX. Except for 11 unmapped SNPs, 116 significant SNPs fell into 28 genomic regions of approximately 10 Mb or less. Most of these regions corresponded to previously reported QTL regions and spanned smaller intervals than before. The loci on SSC3 and SSC7 appeared to have pleiotropic effects on several related traits. Besides them, a few QTL signals were replicated between the two populations. Further, we identified thirteen new candidate genes for IMF, marbling and firmness, on the basis of their positions, functional annotations and reported expression patterns. The findings will contribute to further identification of the causal mutation underlying these QTLs and future marker-assisted selection in pigs.

Fine Mapping of Fatness QTL on Porcine Chromosome X and Analyses of Three Positional Candidate Genes

BMC Genetics. Jun, 2013  |  Pubmed ID: 23725562

Porcine chromosome X harbors four QTL strongly affecting backfat thickness (BFT), ham weight (HW), intramuscular fat content (IMF) and loin eye area (LEA). The confidence intervals (CI) of these QTL overlap and span more than 30 cM, or approximately 80 Mb. This study therefore attempts to fine map these QTL by joint analysis of two large-scale F₂ populations (Large White × Meishan and White Duroc × Erhualian constructed by INRA and JXAU respectively) and furthermore, to determine whether these QTL are caused by mutations in three positional candidate genes (ACSL4, SERPINA7 and IRS4) involved in lipid biosynthesis.

Genome-wide Association Analyses for Fatty Acid Composition in Porcine Muscle and Abdominal Fat Tissues

PloS One. 2013  |  Pubmed ID: 23762394

Fatty acid composition is an important phenotypic trait in pigs as it affects nutritional, technical and sensory quality of pork. Here, we reported a genome-wide association study (GWAS) for fatty acid composition in the longissimus muscle and abdominal fat tissues of 591 White Duroc×Erhualian F2 animals and in muscle samples of 282 Chinese Sutai pigs. A total of 46 loci surpassing the suggestive significance level were identified on 15 pig chromosomes (SSC) for 12 fatty acids, revealing the complex genetic architecture of fatty acid composition in pigs. Of the 46 loci, 15 on SSC5, 7, 14 and 16 reached the genome-wide significance level. The two most significant SNPs were ss131535508 (P = 2.48×10(-25)) at 41.39 Mb on SSC16 for C20∶0 in abdominal fat and ss478935891 (P = 3.29×10(-13)) at 121.31 Mb on SSC14 for muscle C18∶0. A meta-analysis of GWAS identified 4 novel loci and enhanced the association strength at 6 loci compared to those evidenced in a single population, suggesting the presence of common underlying variants. The longissimus muscle and abdominal fat showed consistent association profiles at most of the identified loci and distinct association signals at several loci. All loci have specific effects on fatty acid composition, except for two loci on SSC4 and SSC7 affecting multiple fatness traits. Several promising candidate genes were found in the neighboring regions of the lead SNPs at the genome-wide significant loci, such as SCD for C18∶0 and C16∶1 on SSC14 and ELOVL7 for C20∶0 on SSC16. The findings provide insights into the molecular basis of fatty acid composition in pigs, and would benefit the final identification of the underlying mutations.

A Splice Mutation in the PHKG1 Gene Causes High Glycogen Content and Low Meat Quality in Pig Skeletal Muscle

PLoS Genetics. Oct, 2014  |  Pubmed ID: 25340394

Glycolytic potential (GP) in skeletal muscle is economically important in the pig industry because of its effect on pork processing yield. We have previously mapped a major quantitative trait loci (QTL) for GP on chromosome 3 in a White Duroc × Erhualian F2 intercross. We herein performed a systems genetic analysis to identify the causal variant underlying the phenotype QTL (pQTL). We first conducted genome-wide association analyses in the F2 intercross and an F19 Sutai pig population. The QTL was then refined to an 180-kb interval based on the 2-LOD drop method. We then performed expression QTL (eQTL) mapping using muscle transcriptome data from 497 F2 animals. Within the QTL interval, only one gene (PHKG1) has a cis-eQTL that was colocolizated with pQTL peaked at the same SNP. The PHKG1 gene encodes a catalytic subunit of the phosphorylase kinase (PhK), which functions in the cascade activation of glycogen breakdown. Deep sequencing of PHKG1 revealed a point mutation (C>A) in a splice acceptor site of intron 9, resulting in a 32-bp deletion in the open reading frame and generating a premature stop codon. The aberrant transcript induces nonsense-mediated decay, leading to lower protein level and weaker enzymatic activity in affected animals. The mutation causes an increase of 43% in GP and a decrease of>20% in water-holding capacity of pork. These effects were consistent across the F2 and Sutai populations, as well as Duroc × (Landrace × Yorkshire) hybrid pigs. The unfavorable allele exists predominantly in Duroc-derived pigs. The findings provide new insights into understanding risk factors affecting glucose metabolism, and would greatly contribute to the genetic improvement of meat quality in Duroc related pigs.

Sexually Dimorphic Genetic Architecture of Complex Traits in a Large-scale F2 Cross in Pigs

Genetics, Selection, Evolution : GSE. Nov, 2014  |  Pubmed ID: 25374066

It is common for humans and model organisms to exhibit sexual dimorphism in a variety of complex traits. However, this phenomenon has rarely been explored in pigs.

Genome-wide Association Analysis Reveals Genetic Loci and Candidate Genes for Meat Quality Traits in Chinese Laiwu Pigs

Mammalian Genome : Official Journal of the International Mammalian Genome Society. Apr, 2015  |  Pubmed ID: 25678226

Meat quality traits have economically significant impacts on the pig industry, and can be improved using molecular approaches in pig breeding. Since 1994 when the first genome-wide scan for quantitative trait loci (QTLs) in pig was reported, over the past two decades, numerous QTLs have been identified for meat quality traits by family based linkage analyses. However, little is known about the genetic variants for meat quality traits in Chinese purebred or outbred populations. To unveil it, we performed a genome-wide association study for 10 meat quality traits in Chinese purebred Laiwu pigs. In total, 75 significant SNPs (P < 1.01 × 10(-6)) and 33 suggestive SNPs (P < 2.03 × 10(-5)) were identified. On SSC12, a region between 56.22 and 61.49 Mb harbored a cluster of SNPs that were associated with meat color parameters (L*, lightness; a*, redness; b*, yellowness) and moisture content of longissimus muscle (LM) and semimembranosus muscle at the genome-wide significance level. A region on SSC4 also has pleiotropic effects on moisture content and drip loss of LM. In addition, this study revealed at least five novel QTLs and several candidate genes including 4-linked MYH genes (MYH1, MYH2, MYH3, and MYH13), MAL2, LPAR1, and PRKAG3 at four significant loci. Except for the SSC12 QTL, other QTLs are likely tissue-specific. These results provide new insights into the genetic basis of meat quality traits in Chinese Laiwu pigs and some significant SNPs reported here could be incorporated into the selection programs involving this breed.

Genome-wide Association Analyses Reveal Significant Loci and Strong Candidate Genes for Growth and Fatness Traits in Two Pig Populations

Genetics, Selection, Evolution : GSE. Mar, 2015  |  Pubmed ID: 25885760

Recently, genome-wide association studies (GWAS) have been reported on various pig traits. We performed a GWAS to analyze 22 traits related to growth and fatness on two pig populations: a White Duroc × Erhualian F2 intercross population and a Chinese Sutai half-sib population.

Genome-wide Association Analyses for Meat Quality Traits in Chinese Erhualian Pigs and a Western Duroc × (Landrace × Yorkshire) Commercial Population

Genetics, Selection, Evolution : GSE. May, 2015  |  Pubmed ID: 25962760

Understanding the genetic mechanisms that underlie meat quality traits is essential to improve pork quality. To date, most quantitative trait loci (QTL) analyses have been performed on F2 crosses between outbred pig strains and have led to the identification of numerous QTL. However, because linkage disequilibrium is high in such crosses, QTL mapping precision is unsatisfactory and only a few QTL have been found to segregate within outbred strains, which limits their use to improve animal performance. To detect QTL in outbred pig populations of Chinese and Western origins, we performed genome-wide association studies (GWAS) for meat quality traits in Chinese purebred Erhualian pigs and a Western Duroc × (Landrace × Yorkshire) (DLY) commercial population.

A Meta Analysis of Genome-wide Association Studies for Limb Bone Lengths in Four Pig Populations

BMC Genetics. Jul, 2015  |  Pubmed ID: 26219668

Limb bone length is an economically important trait in pigs, because it is negatively correlated with backfat thickness, and is also a determinant to the yield of hip and loin. Moreover, abnormal growth of the limb bone leads to leg structural weakness. Until now, the genetic architecture of the pig lime bone length remains poorly understood. The object of this study was to map genomic loci for limb bone length by genome-wide association study (GWAS) on 4 pig populations.

Genetic Architecture of Fatty Acid Composition in the Longissimus Dorsi Muscle Revealed by Genome-wide Association Studies on Diverse Pig Populations

Genetics, Selection, Evolution : GSE. Jan, 2016  |  Pubmed ID: 26796620

Fatty acid composition in muscle is an important factor that affects the nutritive value and taste of pork. To investigate the genetic architecture of fatty acid composition of pork, we measured fatty acid contents in longissimus dorsi muscle of 1244 pigs from three divergent populations and conducted genome-wide association studies (GWAS) for fatty acid contents.

Production of Transgenic Pigs with an Introduced Missense Mutation of the Bone Morphogenetic Protein Receptor Type IB Gene Related to Prolificacy

Asian-Australasian Journal of Animal Sciences. Jul, 2016  |  Pubmed ID: 26954151

In the last few decades, transgenic animal technology has witnessed an increasingly wide application in animal breeding. Reproductive traits are economically important to the pig industry. It has been shown that the bone morphogenetic protein receptor type IB (BMPR1B) A746G polymorphism is responsible for the fertility in sheep. However, this causal mutation exits exclusively in sheep and goat. In this study, we attempted to create transgenic pigs by introducing this mutation with the aim to improve reproductive traits in pigs. We successfully constructed a vector containing porcine BMPR1B coding sequence (CDS) with the mutant G allele of A746G mutation. In total, we obtained 24 cloned male piglets using handmade cloning (HMC) technique, and 12 individuals survived till maturation. A set of polymerase chain reactions indicated that 11 of 12 matured boars were transgene-positive individuals, and that the transgenic vector was most likely disrupted during cloning. Of 11 positive pigs, one (No. 11) lost a part of the terminator region but had the intact promoter and the CDS regions. cDNA sequencing showed that the introduced allele (746G) was expressed in multiple tissues of transgene-positive offspring of No.11. Western blot analysis revealed that BMPR1B protein expression in multiple tissues of transgene-positive F1 piglets was 0.5 to 2-fold higher than that in the transgene-negative siblings. The No. 11 boar showed normal litter size performance as normal pigs from the same breed. Transgene-positive F1 boars produced by No. 11 had higher semen volume, sperm concentration and total sperm per ejaculate than the negative siblings, although the differences did not reached statistical significance. Transgene-positive F1 sows had similar litter size performance to the negative siblings, and more data are needed to adequately assess the litter size performance. In conclusion, we obtained 24 cloned transgenic pigs with the modified porcine BMPR1B CDS using HMC. cDNA sequencing and western blot indicated that the exogenous BMPR1B CDS was successfully expressed in host pigs. The transgenic pigs showed normal litter size performance. However, no significant differences in litter size were found between transgene-positive and negative sows. Our study provides new insight into producing cloned transgenic livestock related to reproductive traits.

Immunoprotective Mechanisms in Swine Within the "grey Zone" in Antibody Response After Immunization with Foot-and-mouth Disease Vaccine

Virus Research. Jul, 2016  |  Pubmed ID: 27067203

Foot-and-mouth disease (FMD) is a highly contagious disease of cloven-hoofed animals caused by the FMD virus (FMDV). Vaccination represents one approach for limiting the effects of FMD. The level of protection in vaccinated animals after challenge with foot and mouth disease virus (FMDV) is closely related to the antibody titer, which can be classified into three zones: a "white zone", a "grey zone", and a "black zone". The aim of the present study was to clarify the immunoprotective mechanisms operating in the grey zone, in which vaccinated animals have intermediate antibody titers, making it difficult to predict the level of protection. Thirty-three pigs were used to analyze the distribution of lymphocyte subpopulations in whole blood and the expression levels of 40 cytokines before vaccination and challenge. The antibody titer in pigs in the grey zone ranged from 1:6-1:45. Cytotoxic T lymphocyte subpopulations, expression levels of Th1 cytokines such as tumor necrosis factor-α (TNF-α), interferon-γ (IFN-γ), interleukin (IL)-12, IL-15, IL-18, and monocyte interferon gamma inducing factor (MIG), and of granulocyte-macrophage colony-stimulating factor (GM-CSF), IL-1α, transforming growth factor-α (TGF-α), and TWEAK R varied between protected and unprotected animals. The results of this study suggest that the cellular immune response is the key factor responsible for immunoprotection in vaccinated animals with antibody titers within the grey zone.

Genome-wide Association Studies for Fatty Acid Metabolic Traits in Five Divergent Pig Populations

Scientific Reports. Apr, 2016  |  Pubmed ID: 27097669

Fatty acid composition profiles are important indicators of meat quality and tasting flavor. Metabolic indices of fatty acids are more authentic to reflect meat nutrition and public acceptance. To investigate the genetic mechanism of fatty acid metabolic indices in pork, we conducted genome-wide association studies (GWAS) for 33 fatty acid metabolic traits in five pig populations. We identified a total of 865 single nucleotide polymorphisms (SNPs), corresponding to 11 genome-wide significant loci on nine chromosomes and 12 suggestive loci on nine chromosomes. Our findings not only confirmed seven previously reported QTL with stronger association strength, but also revealed four novel population-specific loci, showing that investigations on intermediate phenotypes like the metabolic traits of fatty acids can increase the statistical power of GWAS for end-point phenotypes. We proposed a list of candidate genes at the identified loci, including three novel genes (FADS2, SREBF1 and PLA2G7). Further, we constructed the functional networks involving these candidate genes and deduced the potential fatty acid metabolic pathway. These findings advance our understanding of the genetic basis of fatty acid composition in pigs. The results from European hybrid commercial pigs can be immediately transited into breeding practice for beneficial fatty acid composition.

Research Progress in the Genetics of Hyperuricaemia and Gout

Yi Chuan = Hereditas. Apr, 2016  |  Pubmed ID: 27103454

Gout is one of the most common inflammatory arthritis caused by hyperuricaemia, which is affected by both genetic factors and environmental factors. Early researches show that a few of rare monogenic mutations, such as PRPS1 and HPRT1 mutations, lead to abnormal purine anabolism and then cause hyperuricaemia and gout. In recent years, genome-wide association studies (GWAS) have identified dozens of susceptibility loci and/or candidate genes associated with hyperuricemia and gout. Loss-of-function mutations in SLC2A9, SLC22A11, and SLC22A12 cause hereditary hypouricaemia, while their overexpression may increase the reabsorption of uric acid. In contrast, loss-of-function mutations in ABCG2, SLC17A1, and SLC17A3 cause urate underexcretion of renal and intestinal. These variations leading to blood uric acid excretion disorder (excess reabsorption and underexcretion) are the main genetic factors affecting hyperuicemia and gout. Moreover, to some degree, inhibins-activins growth factor system, transcription factors, cytoskeleton and gene-environment interaction can also affect the level of blood uric acid. In addition, two risk genes, RFX3 and KCNQ1, which might impair immune response and lead to functional deficiency of beta cell were recently discovered to influence hyperuiceamia and gout in Han Chinese. This paper systematically reviews genetic studies on hyperuricaemia and gout to improve our understanding of pathogenesis of hyperuricaemia and gout.

Multi-breed Genome-wide Association Study Reveals Heterogeneous Loci Associated with Loin Eye Area in Pigs

Journal of Applied Genetics. Nov, 2016  |  Pubmed ID: 27183999

Numerous quantitative trait loci (QTL) for loin eye area had been identified by linkage mapping studies, but the lack of their precise position hinders their application in the pig breeding industry. To map QTL for loin eye area to a precise genomic region, we conducted a genome-wide association study (GWAS) using Illumina 60 K PorcineSNP60 Beadchip in four swine populations: 819 F2 pigs, 273 Laiwu pigs, 434 Sutai pigs, and 326 Erhualian pigs. In total, 26 single nucleotide polymorphisms (SNPs) deposited on seven chromosomes associated with loin eye area were identified, 11 of which surpassed the genome-wide significant threshold; of the 11 SNPs, seven located on SSC2 in F2 pigs and four located on SSC12 and SSC18 in Laiwu pigs. Of note, all of the identified QTL were breed specific and no common QTL was identified across the four populations in our study. These findings not only confirmed a previous QTL on SSC2 harboring the candidate gene insulin-like growth factor 2 (IGF2), but also identified some novel candidate genes, far upstream element binding protein 3 (FUBP3), myosin heavy chain (MYH) family, leucine-rich repeats and guanylate kinase domain containing (LRGUK). Our study will contribute to the further identification of the causal mutation underlying these QTL and improve our knowledge of the complex genetic architecture for loin eye area in pigs.

A GWA Study Reveals Genetic Loci for Body Conformation Traits in Chinese Laiwu Pigs and Its Implications for Human BMI

Mammalian Genome : Official Journal of the International Mammalian Genome Society. Dec, 2016  |  Pubmed ID: 27473603

Pigs share numerous physiological and phenotypic similarities with human and thus have been considered as a good model in nonrodent mammals for the study of genetic basis of human obesity. Researches on candidate genes for obesity traits have successfully identified some common genes between humans and pigs. However, few studies have assessed how many similarities exist between the genetic architecture of obesity in pigs and humans by large-scale comparative genomics. Here, we performed a genome-wide association study (GWAS) using the porcine 60 K SNP Beadchip for BMI and other four conformation traits at three different ages in a Chinese Laiwu pig population, which shows a large variability in fat deposition. In total, 35 SNPs were found to be significant at Bonferroni-corrected 5 % chromosome-wise level (P = 2.13 × 10(-5)) and 88 SNPs had suggestive (P < 10(-4)) association with the conformation traits. Some SNPs showed age-dependent association. Intriguingly, out of 32 regions associated with BMI in pigs, 18 were homologous with the loci for BMI in humans. Furthermore, five closest genes to GWAS peaks including HIF1AN, SMYD3, COX10, SLMAP, and GBE1 have been already associated with BMI in humans, which makes them very promising candidates for these QTLs. The result of GO analysis provided strong support to the fact that mitochondria and synapse play important roles in obesity susceptibility, which is consistent with previous findings on human obesity, and it also implicated new gene sets related to chromatin modification and Ig-like C2-type 5 domain. Therefore, these results not only provide new insights into the genetic architecture of BMI in pigs but also highlight that humans and pigs share the significant overlap of obesity-related genes.

Genome-wide Association Study Identifies 22 New Loci for Body Dimension and Body Weight Traits in a White Duroc × Erhualian F2 Intercross Population

Asian-Australasian Journal of Animal Sciences. Jan, 2017  |  Pubmed ID: 28111436

Growth-related traits are important economic traits in the swine industry. However, the genetic mechanism of growth-related traits is little known. The aim of this study is to screen the candidate genes and molecular markers associated with body dimension and body weight traits in pigs.

Genome-wide Detection of Genetic Markers Associated with Growth and Fatness in Four Pig Populations Using Four Approaches

Genetics, Selection, Evolution : GSE. Feb, 2017  |  Pubmed ID: 28196480

Genome-wide association studies (GWAS) have been extensively used to identify genomic regions associated with a variety of phenotypic traits in pigs. Until now, most GWAS have explored single-trait association models. Here, we conducted both single- and multi-trait GWAS and a meta-analysis for nine fatness and growth traits on 2004 pigs from four diverse populations, including a White Duroc × Erhualian F2 intercross population and Chinese Sutai, Laiwu and Erhualian populations.

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