Genome-wide QTL mapping for three traits related to teat number in a White Duroc × Erhualian pig resource population

<p>Abstract</p> <p>Background</p> <p>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 × Erhualian resource population.</p> <p>Results</p> <p>A sex-average linkage map with a total length of 2350.3 cM and an average marker interval of 12.84 cM was constructed. Eleven genome-wide significant QTL for TTN were detected on 8 autosomes including pig chromosomes (SSC) 1, 3, 4, 5, 6, 7, 8 and 12. Six suggestive QTL for this trait were detected on SSC6, 9, 13, 14 and 16. Eight chromosomal regions each on SSC1, 3, 4, 5, 6, 7, 8 and 12 showed significant associations with LTN. These regions were also evidenced as significant QTL for RTN except for those on SSC6 and SSC8. The most significant QTL for the 3 traits were all located on SSC7. Erhualian alleles at most of the identified QTL had positive additive effects except for three QTL on SSC1 and SSC7, at which White Duroc alleles increased teat numbers. On SSC1, 6, 9, 13 and 16, significant dominance effects were observed on TTN, and predominant imprinting effect on TTN was only detected on SSC12.</p> <p>Conclusion</p> <p>The results not only confirmed the QTL regions from previous experiments, but also identified five new QTL for the total teat number in swine. Minor differences between the QTL regions responsible for LTN and RTN were validated. Further fine mapping should be focused on consistently identified regions with small confidence intervals, such as those on SSC1, SSC7 and SSC12.</p

Identification of loci affecting teat number by genome-wide association studies on three pig populations

Objective Three genome-wide association studies (GWAS) and a meta-analysis of GWAS were conducted to explore the genetic mechanisms underlying variation in pig teat number. Methods We performed three GWAS and a meta-analysis for teat number on three pig populations, including a White Duroc×Erhualian F2 resource population (n = 1,743), a Chinese Erhualian pig population (n = 320) and a Chinese Sutai pig population (n = 383). Results We detected 24 single nucleotide polymorphisms (SNPs) that surpassed the genome-wide significant level on Sus Scrofa chromosomes (SSC) 1, 7, and 12 in the F2 resource population, corresponding to four loci for pig teat number. We highlighted vertnin (VRTN) and lysine demethylase 6B (KDM6B) as two interesting candidate genes at the loci on SSC7 and SSC12. No significant associated SNPs were identified in the meta-analysis of GWAS. Conclusion The results verified the complex genetic architecture of pig teat number. The causative variants for teat number may be different in the three population

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

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

Entschlüsselung von komplexen Merkmalen beim Schwein unter Verwendung von QTL Kartierung und Kandidatengen-Klonierung

Die meisten Merkmale bei Nutztieren werden von vielen Genen bestimmt und werden daher als komplexe Merkmale bezeichnet. In dieser Arbeit beschreiben wir zunächst die molekulare Charakterisierung und die Bestätigung des porcinen SOX9 Gens als positionelles Kandidatengen für Inguinal- und Scrotalhernie. Das SOX9 Gen wurde durch FISH und RH-Panel Analyse in der Region SSC12p13-p14 kartiert. Vier Polymorphismen wurden gefunden und genotypisiert. Assoziationsanalysen zeigten, dass eine 18bp Deletion an Position 223 im 5´-UTR einen signifikanten Effekt auf Inguinal- und Scrotalhernie hatte (p<0.05). Ein Protein bindender Faktor, der spezifisch an die Deletions-Variante bindet, wurde durch "electrophoretic mobility shift assays" (EMSA) entdeckt. In Transfektionsexperimenten wurde gezeigt, dass die Deletions-Variante eine deutlich höhere Transkriptionsaktivierung zeigt als die Insertions-Variante. Wir schlagen vor, dass die Deletion eine Bindestelle für einen Transkriptionsfaktor erzeugt, der die Expression von SOX9 verstärkt. Die erhöhte Expression von SOX9 könnte für die porcine Inguinal- und Scrotalhernie aufgrund seiner Rolle bei der Entwicklung der männlichen Gonaden, beim Kollagenmetabolismus und bei der Apoptosis mit verantwortlich sein.Zusätzlich wurde eine genomweite Analyse zur Identifizierung von"quantitative trait loci" (QTLs) durchgeführt, die mit der Zitzenzahl assoziiert sind. Insgesamt wurden 560 F2 Tiere einer White Duroc×Erhualian Kreuzung genotypisiert. Lineare Regression wurde angewandt, um die QTLs zu kartieren. Vier signifikante QTLs für die Gesamt-Zitzenzahl wurden auf den Chromosomen SSC4, SSC7, SS12 und SSC13 entdeckt. Vier chromosomale Regionen auf den Chromosomen SSC3, SS7, SSC12 und SSC15 wurden identifiziert, die hochsignifikant die Zitzenzahl auf der rechten Seite beeinflussen, während nur 2 signifikante QTLs auf den Chromosomen SSC7 und SSC12 für die Zitzenzahl auf der linken Seite gefunden wurden. Die geschätzten additiven Effekte deuten darauf hin, dass die Erhualian Allele in den signifikantesten QTLs positive additive Effekte im Vergleich zu Duroc Allelen hatten, mit der Ausnahme von einem QTL auf Chromosom SSC7, bei dem Duroc Allele eine erhöhte Zitzenzahl hervorriefen

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

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

Ultrahigh removal performance of lead from wastewater by tricalcium aluminate via precipitation combining flocculation with amorphous aluminum

Lead (Pb) removal is an urgent issue of industrial wastewater treatment due to its fatal harm on human health. In this study, for the first time, the efficient removal of Pb by cement-based material tricalcium aluminate (C(3)A) have been reported. The ultrahigh removal capacity of 1747.1 mg.g(-1) for Pb by C(3)A was achieved at the dosage of 0.5 g.L-1 within 1 h. The removal behaviors investigated by batch experiments illustrated that the C(3)A dosage and initial Pb concentration significantly influenced the removal behavior. And the removal process was identified to be a pH-independence process accompanying with a chemical reaction. X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, Raman spectroscopy, scanning electron microscopy (SEM), transmission electron microscopy (TEM), and the chemical precipitation thermodynamic model PHREEQC were employed to elucidate the removal mechanism. Amorphous aluminum released by C(3)A hydration played a major role in Pb removal via flocculation at low Pb concentration (600 mg.L-1). C(3)A could remove Pb to an acceptable level (WHO standard) from authentic wastewaters at low Pb concentration (similar to 20 mg.L-1), or remove similar to 70% Pb from authentic wastewaters at high concentration (ca. 700 mg.L-1). This work presents C(3)A as an excellent material for lead removal and broadens the potential application of cement-based materials in environmental remediation. (C) 2019 Elsevier Ltd. All rights reserved

The tetracyclines removal by MgAl layered double oxide in the presence of phosphate or nitrate: Behaviors and mechanism exploration

Pollution of tetracyclines (TCs) in swine wastewater has been a critical concern worldwide. Notably, multiple anions (e.g. PO , NO ) coexist in the actual environments, which could significantly influence the TCs removal. In the current study, MgAl layered double oxide (MgAl-LDO) was adopted for investigating the TC removal performance with/without PO or NO . In all systems, the adsorption performance exhibited two different approaches between low and high TC concentrations. In the single system, pseudo-second-order and the Freundlich model fitted well to the equilibrium adsorption data when TC concentration was below 125 mg·L, while the pseudo-first-order and the linear model could describe the removal process at high TC concentration (>125 mg·L). The maximum adsorption capacity was 83.56 mg·g. In the co-existing system, the adsorption capacity was slightly enhanced when TC concentration below 150 mg·L however was inhibited at high concentration (>150 mg·L). Combined with the characterization analyses, the interaction mechanism at low concentration was primarily surface adsorption on reconstructed LDH from LDO in the TC-alone system. It is worth mention that both PO and NO facilitated the formation of LDH via rehydration of LDO which enhanced surface adsorption in the co-existing system. At high TC concentration, the formation of tetracycline-metal complexes played a dominant role in TC removal in the single system, whereas diminished complexation in the binary system led to the decreased TC removal. This study provides a theoretical and practical guidance for MgAl-LDO on the efficient remediation of actual tetracyclines wastewater

Antiviral Activities of Carbazole Derivatives against Porcine Epidemic Diarrhea Virus In Vitro

Porcine epidemic diarrhea virus (PEDV), an enteric coronavirus, causes neonatal pig acute gastrointestinal infection with a characterization of severe diarrhea, vomiting, high morbidity, and high mortality, resulting in tremendous damages to the swine industry. Neither specific antiviral drugs nor effective vaccines are available, posing a high priority to screen antiviral drugs. The aim of this study is to investigate anti-PEDV effects of carbazole alkaloid derivatives. Eighteen carbazole derivatives (No.1 to No.18) were synthesized, and No.5, No.7, and No.18 were identified to markedly reduce the replication of enhanced green fluorescent protein (EGFP) inserted-PEDV, and the mRNA level of PEDV N. Flow cytometry assay, coupled with CCK8 assay, confirmed No.7 and No.18 carbazole derivatives displayed high inhibition effects with low cell toxicity. Furthermore, time course analysis indicated No.7 and No.18 carbazole derivatives exerted inhibition at the early stage of the viral life cycle. Collectively, the analysis underlines the benefit of carbazole derivatives as potential inhibitors of PEDV, and provides candidates for the development of novel therapeutic agents

Organization and location of the proximal promoter of the porcine <i>SOX9</i> gene.

<p>The 18bp sequence and the <i>CRE</i> half-site are indicated. The sequence alignment in the lower panel shows conserved regions between pig, cattle, buffalo, roe deer, and horse. (B) Sequence alignment of the wild type and 18bp indel (Δ18) region.</p