摘要：
Deoxynivalenol (DON), also known as vomitoxin, has a high detection and exceeding rate in feed and is prone to causing symptoms such as loss of appetite, weight loss, vomiting, and diarrhoea in animals, which brings great harm to the aquaculture industry. The common mycotoxin adsorbents have low adsorption rates for DON, and the use of biological methods to remove DON in feeds has gradually become a research trend. One hundred and twenty crossbred barrows were randomly divided into four groups, which included the normal diet group (CON), normal diet + detoxifier group (Det), DON-polluted diet group (DON), and DON-polluted diet + DON detoxifier group (DON + Det); the experiment lasted for 28 d. The results showed that, compared with piglets fed a normal diet, those piglets fed DON-polluted diets significantly decreased their average daily gain (ADG) and average daily feed intake (ADFI) during the 1-14 d and 1-28 d periods; the content of immunoglobulin G (IgG), catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GSH-PX), interleukin-4 (IL-4), and interleukin-10 (IL-10) in serum was decreased; and the content of aminotransferase (AST), alanine aminotransferase (ALT), malondialdehyde (MDA), diamine oxidase (DAO), and endotoxin (LPS) was increased in pigs fed DON-polluted diets; meanwhile, feeding piglets DON-polluted diets significantly reduced the levels of acetic acid, propionic acid, and total short-chain fatty acids (SCFAs) as well as gut microbiota health index (GMHI) in piglet faeces, but increased the relative abundance of Treponema, Prevotellaceae_UGG-001, Lachnospiraceae_XPB1014_group, Frisingicoccus and Sphaerochaeta. In contrast, the addition of a composite detoxifier effectively ameliorated the reduction in ADG and ADFI in piglets caused by DON-polluted diets. It suppressed the reduction in CAT, SOD, GSH-PX, IL-4, and IL-10 and the elevation of TNF-α, IL-2, IL-6, IL-12, MDA, LPS, and DAO in serum; the composite detoxifier also restrained the decrease in SCFA in piglet faeces and increased the relative abundance of Ruminococcus, Lachnospiraceae_NK4A136_group, Lachnospiraceae_AC2044_group, UCG-009, and Eubacterium_siraeum_group bacteria. The composite detoxifier effectively mitigated the adverse effects of a DON-polluted diet on piglet growth performance, blood biochemical indices, and gut microbiota composition.
通讯作者：
Fang, LZ;Zhang, Z;Zhou, HJ;Liu, GE;Li, JJ;Palmer, AA;Frantz, L
作者机构：
[Lund, Mogens Sando; Gong, Mian; Fang, LZ; Sorensen, Peter; Fang, Lingzhao; Lin, Qing; Sahana, Goutam; Bai, Zhonghao; Liu, Xinfeng; Li, Jing] Aarhus Univ, Ctr Quantitat Genet & Genom, Aarhus, Denmark.;[Li, Jiaqi; Zhang, Zhe; Lin, Qing; Gao, Yahui; Pan, Xiangchun; Gong, Wentao; Teng, Jinyan; Yuan, Xiaolong] South China Agr Univ, State Key Lab Swine & Poultry Breeding Ind, Guangdong Prov Key Lab Agroanim Genom & Mol Breed, Natl Engn Res Ctr Breeding Swine Ind,Coll Anim Sc, Guangzhou, Peoples R China.;[Liu, Shuli; Yang, Jian] Westlake Lab Life Sci & Biomed, Hangzhou, Peoples R China.;[Liu, Shuli; Yang, Jian] Westlake Univ, Sch Life Sci, Hangzhou, Peoples R China.;[Guan, Dailu; Zhou, Huaijun; Cheng, Hao] Univ Calif Davis, Dept Anim Sci, Davis, CA 95616 USA.
通讯机构：
[Zhou, HJ ; Palmer, AA ; Li, JJ ] U;[Zhang, Z ] S;[Liu, GE ; Fang, LZ ] A;[Frantz, L ] L;Aarhus Univ, Ctr Quantitat Genet & Genom, Aarhus, Denmark.
摘要：
Genetic mutation and drift, coupled with natural and human-mediated selection and migration, have produced a wide variety of genotypes and phenotypes in farmed animals. We here introduce the Farm Animal Genotype–Tissue Expression (FarmGTEx) Project, which aims to elucidate the genetic determinants of gene expression across 16 terrestrial and aquatic domestic species under diverse biological and environmental contexts. For each species, we aim to collect multiomics data, particularly genomics and transcriptomics, from 50 tissues of 1,000 healthy adults and 200 additional animals representing a specific context. This Perspective provides an overview of the priorities of FarmGTEx and advocates for coordinated strategies of data analysis and resource-sharing initiatives. FarmGTEx aims to serve as a platform for investigating context-specific regulatory effects, which will deepen our understanding of molecular mechanisms underlying complex phenotypes. The knowledge and insights provided by FarmGTEx will contribute to improving sustainable agriculture-based food systems, comparative biology and eventual human biomedicine. The FarmGTEx Project aims to understand genetic control of gene activity under diverse biological and environmental contexts in domestic animals, providing a foundation for improving animal precision breeding, adaptation and human health.
摘要：
This study aimed to explore the effects of glutamate (Glu) supplementation on the growth performance, carcass traits, meat quality, composition of amino acids and fatty acids in the longissimus dorsi muscle, and the colonic microbial community of Shaziling pigs. A total of 48 healthy male Shaziling pigs (150 d, 31.56 ± 0.95 kg) were randomly assigned to two groups, and fed a basal diet with no supplement (control group) or supplemented with 1% Glu (Glu group) for 51 d, and 6 pigs per group were finally slaughtered. Glu significantly increased the average daily gain ( P = 0.039), lean percentage ( P = 0.023), and intramuscular fat (IMF) content ( P = 0.015), and decreased the fat percentage ( P = 0.021) of Shaziling pigs. In the muscle, Glu increased the concentrations of inosine-5′-monophosphate ( P = 0.094), Fe ( P = 0.002), Cu ( P = 0.052), and monounsaturated fatty acids (MUFAs) ( P = 0.024), and decreased the content of C18:2n6 ( P = 0.011), n-6 polyunsaturated fatty acids (n-6 PUFAs) ( P = 0.014), and PUFAs ( P = 0.014). Moreover, Glu significantly upregulated the mRNA expression of adipogenesis-related genes ( FAS , SREBP-1C ) ( P = 0.032, P = 0.026) and muscle growth-related genes ( MyHCⅡb , MyHCⅡx ) ( P = 0.038, P = 0.019) in the muscle, and increased the relative abundance of Spirochaetota ( P < 0.001) and the acetic acid content in the colon ( P = 0.039). Correlation analysis indicated that the acetic acid content was positively correlated with the relative Spirochaetota abundance and the IMF content, and a negative trend with the fat percentage of Shaziling pigs. In conclusion, these results indicated that Glu could simultaneously increase the lean percentage and IMF content and decrease the fat percentage of Shaziling pigs, and these beneficial effects may be related to increased colonic Spirochaetota abundance and acetic acid concentrations.
This study aimed to explore the effects of glutamate (Glu) supplementation on the growth performance, carcass traits, meat quality, composition of amino acids and fatty acids in the longissimus dorsi muscle, and the colonic microbial community of Shaziling pigs. A total of 48 healthy male Shaziling pigs (150 d, 31.56 ± 0.95 kg) were randomly assigned to two groups, and fed a basal diet with no supplement (control group) or supplemented with 1% Glu (Glu group) for 51 d, and 6 pigs per group were finally slaughtered. Glu significantly increased the average daily gain ( P = 0.039), lean percentage ( P = 0.023), and intramuscular fat (IMF) content ( P = 0.015), and decreased the fat percentage ( P = 0.021) of Shaziling pigs. In the muscle, Glu increased the concentrations of inosine-5′-monophosphate ( P = 0.094), Fe ( P = 0.002), Cu ( P = 0.052), and monounsaturated fatty acids (MUFAs) ( P = 0.024), and decreased the content of C18:2n6 ( P = 0.011), n-6 polyunsaturated fatty acids (n-6 PUFAs) ( P = 0.014), and PUFAs ( P = 0.014). Moreover, Glu significantly upregulated the mRNA expression of adipogenesis-related genes ( FAS , SREBP-1C ) ( P = 0.032, P = 0.026) and muscle growth-related genes ( MyHCⅡb , MyHCⅡx ) ( P = 0.038, P = 0.019) in the muscle, and increased the relative abundance of Spirochaetota ( P < 0.001) and the acetic acid content in the colon ( P = 0.039). Correlation analysis indicated that the acetic acid content was positively correlated with the relative Spirochaetota abundance and the IMF content, and a negative trend with the fat percentage of Shaziling pigs. In conclusion, these results indicated that Glu could simultaneously increase the lean percentage and IMF content and decrease the fat percentage of Shaziling pigs, and these beneficial effects may be related to increased colonic Spirochaetota abundance and acetic acid concentrations.
摘要：
The current study aims to investigate the potential interaction between glycosylation profiles of the Ningxiang breed (NX) and Western Duroc × Landrace × Yorkshire breed (DLY) weaned piglets, and their characteristic microbes, employing integrated analyses of transcriptomics and metagenomics. Twenty-four (12 NX and 12 DLY) at 28 days of age were transported into an experimental house and fed the same weaned piglet diet. The trail period was 7 days. Results revealed that the NX piglets had a higher growth-to-feed ratio, body weight gain scale, and lower pathological score of intestinal injury compared with the DLY piglets ( P < 0.01). DLY piglets displayed elevated mRNA expression levels of MUC2 and MUC5AC in colonic mucosal tissue than NX piglets ( P < 0.05). Within the O-linked glycosylated differentially expressed genes (DEGs), FNTA , GALNT18 , POMGNT1 , POMGNT2 , and POMT1 were significantly upregulated in DLY piglets relative to NX piglets ( P < 0.05). Conversely, C1GALT2 , GALNT1 , KMT2C , and OGT were significantly downregulated in DLY piglets compared to NX piglets ( P < 0.05). The KMT2C gene was hardly expressed in the transcriptome of DLY piglets. At the phylum taxonomic level, NX piglets had a higher abundance of Firmicutes, while DLY piglets had a higher abundance of Proteobacteria. At the genus taxonomic level, NX piglets had a higher abundance of Lactobacillus , whereas DLY piglets had a higher abundance of Collinsella , Enterococcus and Escherichia . The results of the correlation between intestinal differential bacteria and O-chain glycosylated DEG showed that C1GALT2 , GALNT1 and KMT2 were associated with Lactobacillus_pontis showed a positive correlation ( R = 0.67). Through comparative analysis of differentially glycosylated genes and their associated functions, this study highlights the potential role of reduced expression of GALNT1 and KMT2C genes, involved in O-linked protein and glycan reactions, in impairing the intestinal barrier function of DLY piglets. Furthermore, members of the Lactobacillus and Prevotella genera may actively contribute to the regulation of piglet colon glycosylation profiles.
The current study aims to investigate the potential interaction between glycosylation profiles of the Ningxiang breed (NX) and Western Duroc × Landrace × Yorkshire breed (DLY) weaned piglets, and their characteristic microbes, employing integrated analyses of transcriptomics and metagenomics. Twenty-four (12 NX and 12 DLY) at 28 days of age were transported into an experimental house and fed the same weaned piglet diet. The trail period was 7 days. Results revealed that the NX piglets had a higher growth-to-feed ratio, body weight gain scale, and lower pathological score of intestinal injury compared with the DLY piglets ( P < 0.01). DLY piglets displayed elevated mRNA expression levels of MUC2 and MUC5AC in colonic mucosal tissue than NX piglets ( P < 0.05). Within the O-linked glycosylated differentially expressed genes (DEGs), FNTA , GALNT18 , POMGNT1 , POMGNT2 , and POMT1 were significantly upregulated in DLY piglets relative to NX piglets ( P < 0.05). Conversely, C1GALT2 , GALNT1 , KMT2C , and OGT were significantly downregulated in DLY piglets compared to NX piglets ( P < 0.05). The KMT2C gene was hardly expressed in the transcriptome of DLY piglets. At the phylum taxonomic level, NX piglets had a higher abundance of Firmicutes, while DLY piglets had a higher abundance of Proteobacteria. At the genus taxonomic level, NX piglets had a higher abundance of Lactobacillus , whereas DLY piglets had a higher abundance of Collinsella , Enterococcus and Escherichia . The results of the correlation between intestinal differential bacteria and O-chain glycosylated DEG showed that C1GALT2 , GALNT1 and KMT2 were associated with Lactobacillus_pontis showed a positive correlation ( R = 0.67). Through comparative analysis of differentially glycosylated genes and their associated functions, this study highlights the potential role of reduced expression of GALNT1 and KMT2C genes, involved in O-linked protein and glycan reactions, in impairing the intestinal barrier function of DLY piglets. Furthermore, members of the Lactobacillus and Prevotella genera may actively contribute to the regulation of piglet colon glycosylation profiles.
通讯机构：
[Zhou, HJ ] U;[Hu, XX ; Yang, N ] C;[Fang, LZ ] A;Univ Calif Davis, Dept Anim Sci, Davis, CA 95616 USA.;Aarhus Univ, Ctr Quantitat Genet & Genom QGG, Aarhus, Denmark.
摘要：
The chicken is a valuable model for understanding fundamental biology and vertebrate evolution and is a major global source of nutrient-dense and lean protein. Despite being the first non-mammalian amniote to have its genome sequenced, a systematic characterization of functional variation on the chicken genome remains lacking. Here, we integrated bulk RNA sequencing (RNA-seq) data from 7,015 samples, single-cell RNA-seq data from 127,598 cells and 2,869 whole-genome sequences to present a pilot atlas of regulatory variants across 28 chicken tissues. This atlas reveals millions of regulatory effects on primary expression (protein-coding genes, long non-coding RNA and exons) and post-transcriptional modifications (alternative splicing and 3′-untranslated region alternative polyadenylation). We highlighted distinct molecular mechanisms underlying these regulatory variants, their context-dependent behavior and their utility in interpreting genome-wide associations for 39 chicken complex traits. Finally, our comparative analyses of gene regulation between chickens and mammals demonstrate how this resource can facilitate cross-species gene mapping of complex traits. This study introduces a ChickenGTEx atlas of regulatory variants across 28 tissues and illustrates its utility in deciphering association signals for 39 complex traits in chickens.
作者：
Gui, Jue;Azad, Md. Abul Kalam;Lin, Wenchao;Meng, Chengwen;Hu, Xin;...
期刊：
Frontiers in Microbiology,2025年16:1628339 ISSN：1664-302X
作者机构：
[Gui, Jue; Azad, Md. Abul Kalam; Meng, Chengwen; Kong, Xiangfeng] Institute of Subtropical Agriculture, Chinese Academy of Sciences (CAS), Changsha, China;[Lin, Wenchao; He, Jianhua] College of Animal Science and Technology, Hunan Agricultural University, Changsha, China;[Hu, Xin; Cui, Yadong; Lan, Wei] School of Biology and Food Engineering, Fuyang Normal University, Fuyang, China
关键词：
Chinese herb;intestinal barrier function;microbiota;Ultrafine powder;Xinyang black-feather hens
摘要：
Corrigendum on: Gui J, Azad MAK, Lin W, Meng C, Hu X, Cui Y, Lan W, He J and Kong X (2023) Dietary supplementation with Chinese herb ultrafine powder improves intestinal morphology and physical barrier function by altering jejunal microbiota in laying hens. Front. Microbiol. 14:1185806. doi: 10.3389/fmicb.2023.1185806.In the published article, there was an error in the legend for Table 1 as published. In our study, due to our error, "The premix provided the following per kg of diets" should be revised to "The ingredients provided per kilogram of premix", and " vitamin Κ, 3.18 g " should be revised to " vitamin Κ3, 0.18 g ". The corrected legend appears below.a The ingredients provided per kilogram of premix: vitamin A, 140,000 IU; vitamin D3, 50,000 IU; vitamin E, 480 mg; vitamin Κ3, 0.18 g; vitamin B1, 63 mg; vitamin B2, 200 mg; vitamin B6, 140 mg; vitamin B12, 0.7 mg; nicotinic acid, 1000 mg; D-pantothenic acid, 500 mg; folic acid, 50 mg; D-biotin, 5.0 mg; choline chloride, 900 mg; Fe, 2.0 g; Cu, 0.3 g; Mn, 1.8 g; Zn, 2.0 g; I, 70 mg; Se, 9 mg; and phytase, 3000 IU.b Crude protein and ether extract were measured values, while the others were calculated values.The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.End of template, if you would like to request a correction for a reason not seen here, please contact the journal's Editorial Office
摘要：
Two experiments were conducted to determine digestible energy (DE), metabolizable energy (ME), and standardized ileal digestibility (SID) of crude protein (CP) and amino acids (AA) in Chinese paddy rice for growing pigs, and to establish prediction equations for DE, ME and SID of CP and AA based on its chemical composition including amylase-treated neutral detergent fiber (aNDF), acid detergent fiber (ADF), and calcium (Ca). In Exp. 1, twenty-four castrated barrows (20 ± 1.3 kg) were selected and allotted to a replicated 12 × 3 incomplete Latin square design, including 12 diets and 3 consecutive periods. A basal diet and 11 Chinese paddy rice diets were prepared and maintained a consistent ratio of corn to soybean meal. Each period had 7 d of adaptation and 5 d of fecal and urine collection. In Exp. 2, twenty-four ileal-cannulated pigs (15.4 ± 1.8 kg) were used in a duplicated 12 × 3 incomplete Latin square design with 12 diets and three consecutive periods, and each period had 5 d of adaptation and 2 d of ileal digesta collection. Chinese paddy rice was the sole nitrogen (N) source in 11 test diets, and an N-free diet was used for calculating the basal endogenous N losses. The results revealed that DE and ME values (as-fed basis) in Chinese paddy rice averaged 12.17 MJ/kg and 11.57 MJ/kg, respectively. The optimal prediction equations for DE and ME were DE (MJ/kg) = 20.12 − (0.56 × aNDF, %) + (130.01 × Ca, %) − (3.94 × phytic acid, %); R2 = 0.94, RSD = 0.44, P < 0.001, and ME (MJ/kg) = −0.263 + (0.972 × DE, MJ/kg); R2 = 0.96, RSD = 0.32, P < 0.001, respectively. The values for SID of CP (SIDCP), Lys (SIDLys), Met (SIDMet), Thr (SIDThr), and Trp (SIDTrp) in Chinese paddy rice were 0.735, 0.766, 0.687, 0.736, and 0.862, respectively. The best-fit equations for SIDCP, SIDLys, and SIDThr were SIDCP = 0.67 − (0.03 × ADF, %) + (0.06 × CP, %); R2 = 0.79, RSD = 0.04, P = 0.002, SIDLys = 1.18 + (4.34 × non-phytate phosphorus, %) − (6.71 × Trp, %) − (6.59 × Ca, %); R2 = 0.93, RSD = 0.03, P < 0.001, and SIDThr = 0.82 + (2.88 × Met, %) − (1.61 × Lys, %); R2 = 0.83, RSD = 0.03, P = 0.001, respectively. In conclusion, our study revealed the relationships between the chemical composition of Chinese paddy rice and DE, ME, and the SID of the first four limiting AA for growing pigs, establishing the predicted models for the nutritive value of Chinese paddy rice fed to growing pigs. The aNDF, ADF, phytic acid, phytate phosphorus, non-phytate phosphorus, total phosphorus, CP, and Ca were the common key predictors for DE and ME. Dry matter, aNDF, and ADF were the common key predictors of SIDCP and SIDLys. Crude fiber, ADF, and Met can be the single predictors of SIDThr.
Two experiments were conducted to determine digestible energy (DE), metabolizable energy (ME), and standardized ileal digestibility (SID) of crude protein (CP) and amino acids (AA) in Chinese paddy rice for growing pigs, and to establish prediction equations for DE, ME and SID of CP and AA based on its chemical composition including amylase-treated neutral detergent fiber (aNDF), acid detergent fiber (ADF), and calcium (Ca). In Exp. 1, twenty-four castrated barrows (20 ± 1.3 kg) were selected and allotted to a replicated 12 × 3 incomplete Latin square design, including 12 diets and 3 consecutive periods. A basal diet and 11 Chinese paddy rice diets were prepared and maintained a consistent ratio of corn to soybean meal. Each period had 7 d of adaptation and 5 d of fecal and urine collection. In Exp. 2, twenty-four ileal-cannulated pigs (15.4 ± 1.8 kg) were used in a duplicated 12 × 3 incomplete Latin square design with 12 diets and three consecutive periods, and each period had 5 d of adaptation and 2 d of ileal digesta collection. Chinese paddy rice was the sole nitrogen (N) source in 11 test diets, and an N-free diet was used for calculating the basal endogenous N losses. The results revealed that DE and ME values (as-fed basis) in Chinese paddy rice averaged 12.17 MJ/kg and 11.57 MJ/kg, respectively. The optimal prediction equations for DE and ME were DE (MJ/kg) = 20.12 − (0.56 × aNDF, %) + (130.01 × Ca, %) − (3.94 × phytic acid, %); R2 = 0.94, RSD = 0.44, P < 0.001, and ME (MJ/kg) = −0.263 + (0.972 × DE, MJ/kg); R2 = 0.96, RSD = 0.32, P < 0.001, respectively. The values for SID of CP (SIDCP), Lys (SIDLys), Met (SIDMet), Thr (SIDThr), and Trp (SIDTrp) in Chinese paddy rice were 0.735, 0.766, 0.687, 0.736, and 0.862, respectively. The best-fit equations for SIDCP, SIDLys, and SIDThr were SIDCP = 0.67 − (0.03 × ADF, %) + (0.06 × CP, %); R2 = 0.79, RSD = 0.04, P = 0.002, SIDLys = 1.18 + (4.34 × non-phytate phosphorus, %) − (6.71 × Trp, %) − (6.59 × Ca, %); R2 = 0.93, RSD = 0.03, P < 0.001, and SIDThr = 0.82 + (2.88 × Met, %) − (1.61 × Lys, %); R2 = 0.83, RSD = 0.03, P = 0.001, respectively. In conclusion, our study revealed the relationships between the chemical composition of Chinese paddy rice and DE, ME, and the SID of the first four limiting AA for growing pigs, establishing the predicted models for the nutritive value of Chinese paddy rice fed to growing pigs. The aNDF, ADF, phytic acid, phytate phosphorus, non-phytate phosphorus, total phosphorus, CP, and Ca were the common key predictors for DE and ME. Dry matter, aNDF, and ADF were the common key predictors of SIDCP and SIDLys. Crude fiber, ADF, and Met can be the single predictors of SIDThr.
摘要：
Simple Summary The aim of this study was to explore the genetic resources of the Huitang duck (HT) in Hunan Province, China, and investigate its population structure and genetic potential through comparative analysis with various duck populations. The results showed that HT belonged to the versatile duck breed, exhibiting significant phenotypic and genetic differences compared to other duck breeds in Hunan Province. The inspection of genomic selective signals in their genome showed that selected candidate genes were involved in the growth and development of skeletal muscle and ovary. These findings provide valuable information for future breeding programs and genetic preservation of HT.Abstract The Huitang duck (HT), a long-domesticated elite local breed from Hunan Province, China, with excellent meat quality, has not had its population genetic structure and genomic selective sweeps extensively studied to date. This study measured the phenotypic characteristics of HT and conducted comparative analysis between HT and 16 different duck breeds, including wild, indigenous, and meat breeds, to characterize its population structure and genetic potential. The results revealed that HT is a dual-purpose indigenous breed with a genetic background closely related to the Youxian sheldrake and Linwu ducks. In the selective sweep analysis between HT and Linwu ducks, genes such as PLCG2, FN1, and IGF2BP2, which are associated with muscle growth and development, were identified near the 27 selection signals. The comparison between HT and Jinding ducks revealed 68 selective signals that contained important genes associated with ovarian development (GRIK4, MAP3K8, and TGIF1) and egg-laying behaviors (ERBB4). Selective sweep analysis between HT and Youxian sheldrake ducks found 93 selective regions covering genes related to both meat (IGF1R and IGFBP5) and egg-production (FOXO3 and ITPR1) traits. Our study may provide novel knowledge for exploring the population structure and genetic potential of HT, offering a theoretical basis for its breeding strategies in the future.
通讯机构：
[Yi, GQ; Tang, ZL ] C;[Groenen, MAM ] W;Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Guangdong Lab Lingnan Modern Agr, Shenzhen Branch,Key Lab Livestock & Poultry Multio, Shenzhen 518124, Peoples R China.;Wageningen Univ & Res, Anim Breeding & Genom Grp, POB 338, NL-6700 AH Wageningen, Netherlands.
关键词：
epigenetics;genomic variation;pan-genome;phenotype differentiation;pig;skeletal muscle development
摘要：
By combining nine high‐quality pig genomes and 1081 resequencing data sets, researchers constructed a comprehensive pan‐genome and genetic variation data set for pigs, laying the groundwork for analyzing complex traits. This data set identified selective sweep signals and genes related to fat deposition, muscle growth, and immune function, providing genetic markers for breeding. Integration of transcriptome and methylome data from 27 muscle development stages revealed epigenetic mechanisms behind muscle growth differences between Eastern and Western pig breeds. Artificial selection influenced DNA methylation and gene regulation, affecting muscle growth and meat quality. Key genes, such as GHSR and BDH1, regulate skeletal muscle development and meat production, while ABCA3 impacts immune response and lung injury, and BRCA1 is linked to adipocyte growth and fat deposition. Abstract The genetic basis of complex traits and phenotypic differentiation remains unclear in pigs. Using nine genomes—seven of which were newly generated, high‐quality de novo assembled genomes—and 1081 resequencing genomes, we built a pan‐genome and identified 134.24 Mb nonredundant nonreference sequences, 1099 novel protein‐coding genes, 187,927 structural variations (SVs) and 30,143,962 single‐nucleotide polymorphisms (SNPs). Analysis of selective domestication revealed BRCA1 associated with enhanced adipocyte growth and fat deposition, and ABCA3 linked to an alleviated immune response and reduced lung injury. Integrating 162 transcriptomes and 162 methylomes of skeletal muscle across 27 developmental stages revealed the regulatory mechanism of phenotypic differentiation between Eastern and Western breeds. Artificial selection reshaped local DNA methylation status and imparted regulatory effects on the progression patterns of heterochronic genes such as GHSR and BDH1, particularly during embryonic development. Altogether, our work provides valuable resources for understanding molecular mechanisms behind phenotypic variations and enhancing the genetic improvement programs in pigs.
摘要：
Weaning stress can trigger diarrhea, cause intestinal damage, and disrupt the intestinal flora of piglets, ultimately resulting in retarded growth or even the death of the animals. Traditional Chinese medicine residues encompass numerous bioactive compounds and essential nutrients; however, their efficient utilization remains a challenge. Consequently, our study sought to explore the impact of traditional Chinese medicine residues, specifically Isatidis Root residue (IRR), on the growth performance, intestinal function, and occurrence of weaning diarrhea in newly weaned piglets. Forty healthy, castrated Duroc × Landrace × Yorkshire males, weaned at 21 days old and exhibiting similar body conditions, were randomly allocated into five groups, with eight piglets in each group. The results indicated that the dietary inclusion of IRR at concentrations ranging from 0.5% to 4.0% notably decreased the incidence of diarrhea in weaned piglets compared to the control group (p < 0.05). Serum LDL-C and globulin (GLB) contents were reduced in response to dietary IRR concentrations (0.5% to 4.0%), while serum albumin (ALB) and albumin/globulin (A/G) contents were enhanced (p < 0.05). Dietary 0.5%, 1.0%, and 2.0% IRR resulted in significant increases in villus height (VH) and villus height/crypt depth (V/C) ratios in the jejunum, V/C ratios in the ileum, and the number of villi goblet cells both in the jejunum and ileum. IRR also led to a significant decrease in the crypt depth (CD) of the jejunum and ileum (p < 0.05). Furthermore, the expression of IL-6 in the jejunum was significantly increased in IRR-fed piglets (0.5% to 4.0%) (p < 0.05). IRR demonstrated inhibitory effects on harmful bacteria in the gastrointestinal microbiome, including Campylobacter, Actinobacillus minor, and Ralstonia pickettii, indicating its broad-spectrum bacteriostatic properties. In conclusion, dietary IRR alleviated diarrhea in weaned piglets and improved gut function and microbial compositions.
关键词：
lipid metabolism;machine learning;melatonin;meta-analysis;obesity mice;obesity rat
摘要：
Melatonin appears to be a promising supplement for obesity treatment. The antiobesity effects of melatonin on obese rodents are influenced by various factors, including the species, sex, the dosage of melatonin, treatment duration, administration via, daily treatment time, and initial body weight (IBW). Therefore, we conducted a meta-analysis and machine learning study to evaluate the antiobesity effect of melatonin on obese mice or rats from 31 publications. The results showed that melatonin significantly reduced body weight, serum glucose (GLU), triglycerides (TGs), low-density lipoprotein (LDL), and cholesterol (TC) levels in obese mice or rats but increased high-density lipoprotein (HDL) levels. Melatonin showed a slight positive effect on clock-related genes, although the number of studies was limited. Meta-regression analysis and machine learning indicated that the dosage of melatonin was the primary factor influencing body weight, with higher melatonin dosages leading to a stronger weight reduction effect. Together, male obese C57BL/6 mice and Sprague-Dawley rats with an IBW of 100-200 g showed better body weight reduction when supplemented with a dose of 10-30 mg/kg melatonin administered at night via injection for 5-8weeks.
