In JoVE (1)

Other Publications (9)

Articles by Yanyu Duan in JoVE

Other articles by Yanyu Duan on PubMed

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.

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 Missense Mutation in PPARD Causes a Major QTL Effect on Ear Size in Pigs

PLoS Genetics. May, 2011  |  Pubmed ID: 21573137

Chinese Erhualian is the most prolific pig breed in the world. The breed exhibits exceptionally large and floppy ears. To identify genes underlying this typical feature, we previously performed a genome scan in a large scale White Duroc × Erhualian cross and mapped a major QTL for ear size to a 2-cM region on chromosome 7. We herein performed an identical-by-descent analysis that defined the QTL within a 750-kb region. Historically, the large-ear feature has been selected for the ancient sacrificial culture in Erhualian pigs. By using a selective sweep analysis, we then refined the critical region to a 630-kb interval containing 9 annotated genes. Four of the 9 genes are expressed in ear tissues of piglets. Of the 4 genes, PPARD stood out as the strongest candidate gene for its established role in skin homeostasis, cartilage development, and fat metabolism. No differential expression of PPARD was found in ear tissues at different growth stages between large-eared Erhualian and small-eared Duroc pigs. We further screened coding sequence variants in the PPARD gene and identified only one missense mutation (G32E) in a conserved functionally important domain. The protein-altering mutation showed perfect concordance (100%) with the QTL genotypes of all 19 founder animals segregating in the White Duroc × Erhualian cross and occurred at high frequencies exclusively in Chinese large-eared breeds. Moreover, the mutation is of functional significance; it mediates down-regulation of β-catenin and its target gene expression that is crucial for fat deposition in skin. Furthermore, the mutation was significantly associated with ear size across the experimental cross and diverse outbred populations. A worldwide survey of haplotype diversity revealed that the mutation event is of Chinese origin, likely after domestication. Taken together, we provide evidence that PPARD G32E is the variation underlying this major QTL.

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 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.

The G32E Functional Variant Reduces Activity of PPARD by Nuclear Export and Post-translational Modification in Pigs

PloS One. 2013  |  Pubmed ID: 24058710

Peroxisome proliferator-activated receptor beta/delta (PPARD) is a crucial and multifaceted determinant of diverse biological functions including lipid metabolism, embryonic development, inflammatory response, wound healing and cancer. Recently, we proposed a novel function of porcine PPARD (sPPARD) in external ear development. A missense mutation (G32E) in an evolutionary conservative domain of sPPARD remarkably increases external ear size in pigs. Here, we investigated the underlying molecular mechanism of the causal mutation at the cellular level. Using a luciferase reporter system, we showed that the G32E substitution reduced transcription activity of sPPARD in a ligand-dependent manner. By comparison of the subcellular localization of wild-type and mutated sPPARD in both PK-15 cells and pinna cartilage-derived primary chondrocytes, we found that the G32E substitution promoted CRM-1 mediated nuclear exportation of sPPARD. With the surface plasmon resonance technology, we further revealed that the G32E substitution had negligible effect on its ligand binding affinity. Finally, we used co-immunoprecipitation and luciferase reporter assays to show that the G32E substitution greatly reduced ubiquitination level by blocking ubiquitination of the crucial A/B domain and consequently decreased transcription activity of sPPARD. Taken together, our findings strongly support that G32E is a functional variant that plays a key role in biological activity of sPPARD, which advances our understanding of the underlying mechanism of sPPARD G32E for ear size in pigs.

Porcine SOX9 Gene Expression Is Influenced by an 18 Bp Indel in the 5'-Untranslated Region

PloS One. 2015  |  Pubmed ID: 26430891

Sex determining region Y-box 9 (SOX9) is an important regulator of sex and skeletal development and is expressed in a variety of embryonal and adult tissues. Loss or gain of function resulting from mutations within the coding region or chromosomal aberrations of the SOX9 locus lead to a plethora of detrimental phenotypes in humans and animals. One of these phenotypes is the so-called male-to-female or female-to-male sex-reversal which has been observed in several mammals including pig, dog, cat, goat, horse, and deer. In 38,XX sex-reversal French Large White pigs, a genome-wide association study suggested SOX9 as the causal gene, although no functional mutations were identified in affected animals. However, besides others an 18 bp indel had been detected in the 5'-untranslated region of the SOX9 gene by comparing affected animals and controls. We have identified the same indel (Δ18) between position +247 bp and +266 bp downstream the transcription start site of the porcine SOX9 gene in four other pig breeds; i.e., German Large White, Laiwu Black, Bamei, and Erhualian. These animals have been genotyped in an attempt to identify candidate genes for porcine inguinal and/or scrotal hernia. Because the 18 bp segment in the wild type 5'-UTR harbours a highly conserved cAMP-response element (CRE) half-site, we analysed its role in SOX9 expression in vitro. Competition and immunodepletion electromobility shift assays demonstrate that the CRE half-site is specifically recognized by CREB. Both binding of CREB to the wild type as well as the absence of the CRE half-site in Δ18 reduced expression efficiency in HEK293T, PK-15, and ATDC5 cells significantly. Transfection experiments of wild type and Δ18 SOX9 promoter luciferase constructs show a significant reduction of RNA and protein levels depending on the presence or absence of the 18 bp segment. Hence, the data presented here demonstrate that the 18 bp indel in the porcine SOX9 5'-UTR is of functional importance and may therefore indeed be a causative variation in SOX9 associated traits.

Genome-wide Identification of Quantitative Trait Transcripts for Blood Traits in the Liver Samples of a White Duroc × Erhualian F2 Pig Resource Population

Physiological Genomics. Aug, 2016  |  Pubmed ID: 27260842

Blood cell counts are important clinical indicators for health status. The liver plays a crucial role in food digestion and metabolism and is also a blood-forming organ. Here, we conducted a whole-genome quantitative trait transcript (QTT) analysis on 497 liver samples for 16 hematological traits in a White Duroc × Erhualian F2 pig resource population. A total of 20,108 transcripts were explored to detect their association with hematological traits. By using Spearman correlation coefficients, we identified 1,267 QTTs for these 16 hematological traits at the significance threshold of P < 0.001. We found 31 candidate genes for erythrocyte and leukocyte-related traits by a look-up of human and pig genome-wide association study results. Furthermore, we constructed coexpression networks for leukocyte-related QTTs using weighted gene coexpression analysis. These QTTs were clustered into two to eight modules. The highest connection strength in intramodules was identified in a module for white blood cell count. In the module, USP18, RSAD2, and OAS1 appeared to be important genes involved in interferon-stimulated innate immune system. The findings improve our understanding of intrinsic relationships between the liver and blood cells and provide novel insights into the potential therapeutic targets of hematologic diseases.

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