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Arias KD, Fernández I, Gutiérrez JP, Álvarez I, Goyache F. Population dynamics of potentially harmful haplotypes: a pedigree analysis. BMC Genomics 2024; 25:487. [PMID: 38755557 PMCID: PMC11097446 DOI: 10.1186/s12864-024-10407-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND The identification of low-frequency haplotypes, never observed in homozygous state in a population, is considered informative on the presence of potentially harmful alleles (candidate alleles), putatively involved in inbreeding depression. Although identification of candidate alleles is challenging, studies analyzing the dynamics of potentially harmful alleles are lacking. A pedigree of the highly endangered Gochu Asturcelta pig breed, including 471 individuals belonging to 51 different families with at least 5 offspring each, was genotyped using the Axiom PigHDv1 Array (658,692 SNPs). Analyses were carried out on four different cohorts defined according to pedigree depth and at the whole population (WP) level. RESULTS The 4,470 Linkage Blocks (LB) identified in the Base Population (10 individuals), gathered a total of 16,981 alleles in the WP. Up to 5,466 (32%) haplotypes were statistically considered candidate alleles, 3,995 of them (73%) having one copy only. The number of alleles and candidate alleles varied across cohorts according to sample size. Up to 4,610 of the alleles identified in the WP (27% of the total) were present in one cohort only. Parentage analysis identified a total of 67,742 parent-offspring incompatibilities. The number of mismatches varied according to family size. Parent-offspring inconsistencies were identified in 98.2% of the candidate alleles and 100% of the LB in which they were located. Segregation analyses informed that most potential candidate alleles appeared de novo in the pedigree. Only 17 candidate alleles were identified in the boar, sow, and paternal and maternal grandparents and were considered segregants. CONCLUSIONS Our results suggest that neither mutation nor recombination are the major forces causing the apparition of candidate alleles. Their occurrence is more likely caused by Allele-Drop-In events due to SNP calling errors. New alleles appear when wrongly called SNPs are used to construct haplotypes. The presence of candidate alleles in either parents or grandparents of the carrier individuals does not ensure that they are true alleles. Minimum Allele Frequency thresholds may remove informative alleles. Only fully segregant candidate alleles should be considered potentially harmful alleles. A set of 16 candidate genes, potentially involved in inbreeding depression, is described.
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Affiliation(s)
- Katherine D Arias
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, Gijón, 33394, Spain
| | - Iván Fernández
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, Gijón, 33394, Spain
| | - Juan Pablo Gutiérrez
- Departamento de Producción Animal, Universidad Complutense de Madrid, Avda. Puerta de Hierro s/n, Madrid, 28040, Spain
| | - Isabel Álvarez
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, Gijón, 33394, Spain
| | - Félix Goyache
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, Gijón, 33394, Spain.
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Zhao X, Hui Q, Azevedo P, Nyachoti CM, O K, Yang C. Calcium-sensing receptor is not expressed in the absorptive enterocytes of weaned piglets. J Anim Sci 2022; 100:6549683. [PMID: 35294536 PMCID: PMC9030235 DOI: 10.1093/jas/skac085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/12/2022] [Indexed: 11/14/2022] Open
Abstract
The calcium-sensing receptor (CaSR) is a kokumi receptor that plays an essential role in nutrient sensing and animal physiology, growth, and development. Pig CaSR (pCaSR) was identified and characterized in the intestine. However, further research is still needed to confirm the expression of CaSR in the epithelial cells isolated from weaned piglets. In this study, primary enterocytes were isolated and characterized from the ileum of weaned piglets by the Weiser distended intestinal sac technique and fluorescence-activated cell sorting (FACS) based on sucrase-isomaltase (SI) as an enterocyte-specific marker. The expression of CaSR was investigated in both primary enterocytes and the intestinal porcine enterocyte cell line-j2 (IPEC-J2) by droplet digital polymerase chain reaction (ddPCR), immunofluorescence staining, and Western blotting. Results demonstrated that porcine enterocytes could be obtained using FACS with the SI as the enterocyte-specific marker and that pCaSR is not expressed in both porcine ileal enterocytes and IPEC-J2 cells, which specifically identified the expression of pCaSR in ileal enterocytes with sensitive and specific approaches.
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Affiliation(s)
- Xiaoya Zhao
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Qianru Hui
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Paula Azevedo
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | | | - Karmin O
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,CCARM, St. Boniface Hospital Research Centre, Winnipeg, MB R2H 2A6, Canada
| | - Chengbo Yang
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Zhao X, Dong B, Friesen M, Liu S, Zhu C, Yang C. Capsaicin Attenuates Lipopolysaccharide-Induced Inflammation and Barrier Dysfunction in Intestinal Porcine Epithelial Cell Line-J2. Front Physiol 2021; 12:715469. [PMID: 34630139 PMCID: PMC8497985 DOI: 10.3389/fphys.2021.715469] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
Capsaicin is a spicy, highly pungent, colorless, vanilloid compound found in chili peppers with anti-inflammatory, antioxidant, anti-cancer, and analgesic properties. However, the protective effects of capsaicin on the pig intestine during inflammation are yet to be explored. This study investigated the effects of capsaicin on the gut inflammatory response, intestinal epithelial integrity, and gene expression level of nutrient transporters in a model of lipopolysaccharide (LPS)-induced inflammation in non-differentiated intestinal porcine epithelial cell line-J2 (IPEC-J2). The results showed that the pre-treatment of cells with capsaicin (100 μM) significantly decreased the gene expression and secretion of proinflammatory cytokines induced by LPS through Toll-like receptor 4 (TLR4)/NF-κB signaling pathway. In addition, pre-treatment of cells with capsaicin also increased both gene and protein abundance of tight junction proteins. Furthermore, pre-treatment cells with capsaicin significantly increased trans-epithelial electrical resistance (TEER) and decreased permeability of fluorescein isothiocyanate-dextran (FD4) from the apical side to the basolateral side compared with the control (P < 0.05). Additionally, pre-treatment of cells with capsaicin upregulated the mRNA abundance of nutrients transporters such as Na+/glucose cotransporter 1 (SGLT1). These results suggested that capsaicin could attenuate LPS-induced inflammation response through TLR4/NF-κB pathway and improve barrier integrity and glucose absorption.
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Affiliation(s)
- Xiaoya Zhao
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - Bingqi Dong
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - Marissa Friesen
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - Shangxi Liu
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - Changqing Zhu
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Chengbo Yang
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
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Mwaniki AW, Buis QR, Trott D, Huber LA, Yang C, Kiarie EG. Comparative efficacy of commercially available deoxynivalenol detoxifying feed additives on growth performance, total tract digestibility of components, and physiological responses in nursery pigs fed diets formulated with naturally contaminated corn. Transl Anim Sci 2021; 5:txab050. [PMID: 34085027 PMCID: PMC8162626 DOI: 10.1093/tas/txab050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/09/2021] [Indexed: 11/14/2022] Open
Abstract
Comparative efficacy of deoxynivalenol (DON) detoxifying feed additives (FA) was evaluated in growth performance (exp. 1) and apparent total tract digestibility (ATTD; exp. 2) nursery pig studies. Six corn-soybean meal-based diets were used: 1) positive control (PC, formulated with <1.5 ppm DON corn), negative control (NC, formulated with 5.5 ppm DON corn), NC + FA1 (clay plus yeast cell wall extract), NC + FA2 (aluminosilicate), NC + FA3 (aluminosilicate plus fungal extract), and NC + FA4 (sodium metabisulfite, SMB). In exp. 1, 144 pigs (body weight [BW], 10.2 ± 0.1kg) were housed (4 pigs/pen), allocated to diets (n = 6) based on BW, and fed for 4-wk. The BW and feed intake were monitored weekly. On d 7, one pig/pen was bled for plasma and euthanized for organ weight and tissue samples. Assayed DON concentration in PC, NC, NC + FA4 was 0.29, 2.86, and 1.21 ppm, respectively. In wk-1, the average daily gain (ADG) of pigs fed NC + FA4 was not different (P > 0.05) to that of pigs fed PC diet but greater (P = 0.01) than for pigs fed NC without or with other FA. Pigs fed NC and NC + FA2 had lower (P = 0.026) average daily feed intake (ADFI) than pigs fed PC and NC + FA3. Pigs fed NC + FA4 had greater (P = 0.003) G:F than pigs fed the other diets. Diets had no effect (P > 0.05) on ADG, ADFI, and G: F after first week, plasma concentration of urea and creatinine or liver and spleen weight. Pigs fed NC diets had greater (P = 0.01) jejunal mRNA expression of superoxide dismutase 1 relative to pigs fed PC or NC plus FA. Jejunal histomorphology and mRNA expression of nutrient transporters, inflammatory cytokines, and tight junction proteins and ceca digesta concentration of short-chain fatty acids were not affected (P > 0.05) by the diet. In exp. 2, 24 barrows (BW 10.2 ± 0.3 kg) were individually placed in metabolism crates and allocated to four diets: PC, NC, NC + FA3, and NC + FA4 (n = 6) containing TiO2 as digestibility marker. Pigs were adjusted to diets for 5 d, followed by a 2-d grab fecal sample collection. Pigs fed PC and NC + FA4 diets had higher ATTD of dry matter, gross energy, and crude protein than NC fed pigs. The FA3 was intermediate in digestibility response. In conclusion, FA containing sequestering component plus fungal extract or SMB in DON-contaminated feed resulted in commensurate nursery pig performance to PC. The tested FA mitigated intestinal oxidative stress through decreased expression of genes for superoxide dismutase.
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Affiliation(s)
- Alice W Mwaniki
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Quincy R Buis
- Wallenstein Feed & Supply Ltd., Wallenstein, ON, Canada
| | - David Trott
- Wallenstein Feed & Supply Ltd., Wallenstein, ON, Canada
| | - Lee-Anne Huber
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Chengbo Yang
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - Elijah G Kiarie
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
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Hui Q, Zhao X, Lu P, Liu S, Nyachoti M, O K, Yang C. Molecular distribution and localization of extracellular calcium-sensing receptor (CaSR) and vitamin D receptor (VDR) at three different laying stages in laying hens (Gallus gallus domesticus). Poult Sci 2021; 100:101060. [PMID: 33752067 PMCID: PMC8010884 DOI: 10.1016/j.psj.2021.101060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 11/02/2020] [Accepted: 02/11/2021] [Indexed: 01/06/2023] Open
Abstract
The extracellular calcium-sensing receptor (CaSR) and vitamin D receptor (VDR) play important roles in regulating calcium mobilization, calcium absorption, and calcium homeostasis, and they could be potential therapeutic targets to osteoporosis in laying hens. The present study investigated the molecular distribution of CaSR and VDR and the localization of CaSR in the kidney, proventriculus (true stomach), duodenum, jejunum, ileum, colon, cecum, shell gland, and tibia of laying hens at 3 different laying stages (19, 40, and 55 wk). The results showed that the relative mRNA abundance of CaSR in the kidney, ileum, proventriculus, duodenum, and colon was higher (P < 0.05) than the other tissues at 40 and 55 wk. The relative mRNA abundance of CaSR in the tibia was higher (P < 0.05) at 55 wk than at 40 wk. However, there were no significant differences in the relative protein abundance of CaSR among all tested tissues at peak production or in each tissue at the 3 different laying stages (P > 0.05). The relative mRNA abundance of VDR was higher (P < 0.05) in the small intestine (duodenum, jejunum, and ileum) when compared with other tissues at the 3 different laying stages. The relative protein abundance of VDR in the duodenum was higher (P < 0.05) than that in the proventriculus, colon, and cecum. There were no significant differences in the VDR expression among the tested tissues at the 3 different laying stages (P > 0.05). The immunohistochemical results showed that the positive staining was found widely in each tissue. Moreover, different laying stages did not affect the localization of CaSR except for the tibia tissue. In conclusion, similar to VDR, CaSR was widely expressed not only in the gut but also in the tibia and shell gland in laying hens. The expression level of CaSR and VDR in all tested tissues was unchanged at the different laying stages.
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Affiliation(s)
- Qianru Hui
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Xiaoya Zhao
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Peng Lu
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Shangxi Liu
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Martin Nyachoti
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Karmin O
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada; CCARM, St. Boniface Hospital Research Centre, Winnipeg, Manitoba R2H 2A6, Canada
| | - Chengbo Yang
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada.
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Structural Mechanism of Cooperative Regulation of Calcium-Sensing Receptor-Mediated Cellular Signaling. CURRENT OPINION IN PHYSIOLOGY 2020; 17:269-277. [PMID: 33709045 DOI: 10.1016/j.cophys.2020.08.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Calcaium sensing receptors (CaSRs) play a central role in regulating extracellular calcium (Ca2+) homeostasis and many (patho)physiological processes. This regulation is primarily orchestrated in response to extracellular stimuli via the extracellular domain (ECD). This paper first reviews the modeled structure of the CaSR ECD and the prediction and investigation of the Ca2+ and amino acid binding sites. Several recently solved X-ray structures are then compared to support a proposed CaSR activation model involving functional cooperativity. The review also discusses recent implications for drug development. These studies provide new insights into the molecular basis of diseases and the design of therapeutic agents that target CaSR and other family C G protein-coupled receptors (cGPCRs).
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Mejicanos GA, González-Ortiz G, Nyachoti CM. Effect of dietary supplementation of xylanase in a wheat-based diet containing canola meal on growth performance, nutrient digestibility, organ weight, and short-chain fatty acid concentration in digesta when fed to weaned pigs. J Anim Sci 2020; 98:skaa064. [PMID: 32103244 PMCID: PMC7097717 DOI: 10.1093/jas/skaa064] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/25/2020] [Indexed: 12/14/2022] Open
Abstract
This study was designed to determine the effect of dietary supplementation of xylanase on growth performance, nutrient digestibility, organ weight, digesta pH, and concentration of short-chain fatty acids (SCFA) of weaned pigs fed wheat-canola meal (CM) diets over a 35-d period. A total of 144 piglets (72 barrows and 72 gilts) weaned at 18 ± 2 d of age, with initial body weight (BW) of 6.2 ± 0.7 kg, received one of eight dietary treatments based on randomized complete block design. BW and feed intake were recorded weekly to calculate average daily gain (ADG), average daily feed intake (ADFI), and feed efficiency (G:F). Treatments consisted of a control wheat-soybean meal-based diet and wheat-regular (RCM), dehulled (DCM), or coarse CM (CCM) without and with 16,000 BXU/kg xylanase (Econase XT). All diets contained 500 FTU/kg of phytase (Quantum Blue 5G) and titanium dioxide (0.3%). Apparent total tract digestibility (ATTD) of neutral detergent fiber (NDF), crude protein (CP), phosphorous (P), calcium (Ca), dry matter, and diet were determined. On day 35, one pig per pen was euthanized to evaluate the main factors of protein, xylanase supplementation, and sex on organ weight, ileal and colon digesta pH, and colon digesta concentrations of SCFA. The main factors did not affect growth performance. Xylanase supplementation improved nutrient digestibilities in all diets and increased ileal and colonic digesta pH without affecting the growth performance of weaned pigs fed wheat and CM-based diets. A protein-xylanase effect (P < 0.05) resulted in increasing the ATTD of NDF from 28% to 32% and from 29% to 37% for RCM and DCM, respectively. The ATTD of CP was greater (P < 0.05) with xylanase supplementation (75% vs. 70%). Xylanase supplementation increased ATTD of P and Ca. A three-way interaction (P < 0.05) for protein-xylanase-gender for colon pH, acetic, and propionic acid in the colon digesta of pigs indicated that, in addition to the protein source, piglet sex could have influenced how xylanase works. Xylanase supplementation increased (P < 0.05) the weight of the liver and spleen and tended (P < 0.10) to increase the size of the kidney. In conclusion, dietary supplementation of xylanase increased nutrient digestibility and digesta pH but did not influence the growth performance of weaned pigs fed wheat and CM-based diets over a 35-d period.
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Amino Acids Influencing Intestinal Development and Health of the Piglets. Animals (Basel) 2019; 9:ani9060302. [PMID: 31159180 PMCID: PMC6617173 DOI: 10.3390/ani9060302] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/25/2019] [Accepted: 05/28/2019] [Indexed: 12/16/2022] Open
Abstract
Simple Summary The health of piglets is an important issue in pig production. Nutritional support for intestinal development is a significant component of piglet care, and amino acids are essential for intestinal growth and development. For suckling piglets, the sows’ milk and the maternal environment shape the structure and support the function of the intestinal tract. The composition of milk affects intestinal morphology and the digestive, absorption and barrier function. After weaning, the optimal nutritional strategies of their diet are necessary to guarantee the piglets’ intestinal development and growth performance. Amino acids are the most important ingredient in piglet diets. The aim of this review is to collect and analyze the relationship between amino acid nutrition and intestinal development of piglets, and elucidate the impacts on piglet health. Abstract The amino acids and other components of diet provide nourishment for piglet intestinal development and maturation. However, early-weaned piglets struggle with tremendous stress, impairing normal intestinal health and leading to intestinal dysfunction and even death. The high prevalence worldwide of post-weaning diarrhoea syndrome (PWDS) in piglets has led to much interest in understanding the important role of nutrients in the establishment and maintenance of a functional intestinal tract. In particular, the impacts of amino acids on these functions must be considered. Amino acid levels greatly influence intestinal development in weaning piglets. The lack of amino acids can cause marked structural and functional changes in the intestine. Therefore, a comprehensive understanding of the functions of amino acids is necessary to optimize amino acid requirements of the developing intestinal tract to maximize piglet health and growth performance. This review summarizes the role of specific amino acids (arginine, glutamate, threonine, sulphur-containing amino acids (SCAAs), and branched-chain amino acids (BCAAs)) that have been proven to be beneficial for the intestinal health of weaned piglets.
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