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Li H, Li S, Zhang H, Gu J, Dai Y, Wu R, Wang Y, Han R, Sun G, Zhang Y, Li H, Zhao Y, Li G. Integrated GWAS and transcriptome analysis reveals key genes associated with muscle fibre and fat traits in Gushi chicken. Br Poult Sci 2024:1-11. [PMID: 39364777 DOI: 10.1080/00071668.2024.2400685] [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: 02/07/2024] [Accepted: 05/13/2024] [Indexed: 10/05/2024]
Abstract
1. In the following experiment meat quality traits of a Gushi-Anka F2 resource population were measured, and their heritability estimated. Intramuscular fat (IMF) had medium heritability (0.35) but leg muscle fibre density (LMD), leg muscle fibre diameter (LMF), breast muscle fibre density (BMD), fresh fat content (FFA), and absolute dry fat content (AFC) had low heritability (0-0.2). The IMF presented the most important genetic additive effect among the poultry meat quality-related traits studied.2. The phenotypic data of meat quality traits in the Gushi-Anka F2 resource population were combined with genotyping by sequencing (GBS) data to obtain genotype data. Six meat quality traits in 734 birds were analysed by GWAS. Based on these variants, 83 significant (-log10(p) > 4.42) single nucleotide polymorphisms and four quantitative trait loci (QTL) regions corresponding to 175 genes were identified. Further linkage disequilibrium (LD) analysis was conducted on chromosome 13 (Chr13) and chromosome 27 (Chr27) QTL regions.3. Based on the transcriptome data and GWAS results, 12 shared genes - ITGB3, DNAJC27, ETV4, C7orf50, FKBP1B, G3BP1, IGF2BP1, KCNH6, LOC416263, SCARA5, SMIM5 and TBL1XR1 were identified as candidate genes influencing muscle fibre and fat traits.
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Affiliation(s)
- H Li
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou, Henan, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - S Li
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou, Henan, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - H Zhang
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou, Henan, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - J Gu
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou, Henan, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Y Dai
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou, Henan, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - R Wu
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou, Henan, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Y Wang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - R Han
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou, Henan, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - G Sun
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou, Henan, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Y Zhang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - H Li
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Y Zhao
- College of Biological Engineering, Henan University of Technology, Zheng Zhou, Henan, China
| | - G Li
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou, Henan, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
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Kang X, Li XD, Zhou HY, Wang F, Lin LB. Genome-Wide and 16S rRNA Sequencing-Based Analysis on the Health Effects of Lacticaseibacillus paracasei XLK401 on Chicks. Microorganisms 2023; 11:2140. [PMID: 37763985 PMCID: PMC10538037 DOI: 10.3390/microorganisms11092140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/17/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
Lacticaseibacillus paracasei, serves as a growth promoter used in the poultry industry, contributeing to broiler development. However, practical studies are needed to determine the probiotic potential and growth-promoting effects of specific L. paracasei strains. This study aims to determine whether L. paracasei XLK401 influences broiler chicken growth and the mechanisms involved. Notably, we identified several bile salt and acid tolerance-related genes (Asp23, atpD, atpA, atpH, and atpF) in L. paracasei XLK401. This bacterium demonstrates robust probiotic properties under acidic conditions (pH 2.0) and 0.3% bile salt conditions. It also contains a variety of antioxidant-related genes (trxA, trxB, and tpx), carbohydrate-related genes, gene-encoding glycosidases (e.g., GH and GT), and three clusters of genes associated with antimicrobial compounds. Supplementation with L. paracasei XLK401 significantly increased the body weight of the chicks. In addition, it significantly increased hepatic antioxidant enzyme activities (GSH-Px, SOD, and T-AOC) while significantly decreasing the levels of oxidative damage factors and inflammatory factors (MDA and IL-6), resulting in improved chick health. Improvements in body weight and health status were associated with significant increases in α-amylase activity and the remodeling of the host gut microbiota by L. paracasei XLK401. Among them, actinobacteria abundance in chicken intestines after feeding them L. paracasei XLK401 was significantly decreased, Bifidobacterium sp. abundance was also significantly decreased, and Subdoligranulum sp. abundance was significantly increased. This suggests that L. paracasei XLK401 can regulate the abundance of certain bacteria without changing the overall microbial structure. In addition, in the correlation analysis, Subdoligranulums sp. were positively correlated with SOD and negatively correlated with IL-1β and MDA. Overall, our study demonstrates that L. paracasei XLK401 effectively promotes healthy chick growth. This is made possible by the modulation of gut microbe abundance and the underlying probiotic effect of L. paracasei XLK401. Based on these findings, we postulate L. paracasei XLK401 as a potential efficient growth promoter in broiler farming.
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Affiliation(s)
- Xin Kang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China; (X.K.); (X.-D.L.); (H.-Y.Z.)
- Engineering Research Center for Replacement Technology, Feed Antibiotics of Yunnan College, Kunming 650500, China
| | - Xin-Dong Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China; (X.K.); (X.-D.L.); (H.-Y.Z.)
- Engineering Research Center for Replacement Technology, Feed Antibiotics of Yunnan College, Kunming 650500, China
| | - Huan-Yu Zhou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China; (X.K.); (X.-D.L.); (H.-Y.Z.)
- Engineering Research Center for Replacement Technology, Feed Antibiotics of Yunnan College, Kunming 650500, China
| | - Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China; (X.K.); (X.-D.L.); (H.-Y.Z.)
- Engineering Research Center for Replacement Technology, Feed Antibiotics of Yunnan College, Kunming 650500, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China; (X.K.); (X.-D.L.); (H.-Y.Z.)
- Engineering Research Center for Replacement Technology, Feed Antibiotics of Yunnan College, Kunming 650500, China
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Alsoufi MA, Liu Y, Cao C, Zhao J, Kang J, Li M, Wang K, He Y, Ge C. Integrated Transcriptomics Profiling in Chahua and Digao Chickens' Breast for Assessment Molecular Mechanism of Meat Quality Traits. Genes (Basel) 2022; 14:95. [PMID: 36672833 PMCID: PMC9859260 DOI: 10.3390/genes14010095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/27/2022] [Accepted: 12/02/2022] [Indexed: 12/31/2022] Open
Abstract
Meat quality traits are an important economic trait and remain a major argument, from the producer to the consumer. However, there are a few candidate genes and pathways of chicken meat quality traits that were reported for chicken molecular breeding. The purpose of the present study is to identify the candidate genes and pathways associated with meat quality underlying variations in meat quality. Hence, transcriptome profiles of breast tissue in commercial Digao (DG, 5 male) and Chahua (CH, 5 male) native chicken breeds were analyzed at the age of 100 days. The results found 3525 differentially expressed genes (DEGs) in CH compared to DG with adjusted p-values of ≤0.05 and log2FC ≥ 0.1 FDR ≤ 0.05. Functional analysis of GO showed that the DEGs are mainly involved in the two types of processes of meat quality, such as positive regulation of the metabolic process, extracellular structure organization, collagen trimer, cellular amino acid metabolic process, cellular amino acid catabolic process, and heme binding. Functional analysis of KEGG showed that the DEGs are mainly involved in the two types of processes of meat quality, such as oxidative phosphorylation, carbon metabolism, valine, leucine, and isoleucine degradation, and fatty acid degradation. Many of the DEGs are well known to be related to meat quality, such as COL28A1, COL1A2, MB, HBAD, HBA1, ACACA, ACADL, ACSL1, ATP8A1, CAV1, FADS2, FASN, DCN, CHCHD10, AGXT2, ALDH3A2, and MORN4. Therefore, the current study detected multiple pathways and genes that could be involved in the control of the meat quality traits of chickens. These findings should be used as an essential resource to improve the accuracy of selection for meat traits in chickens using marker-assisted selection based on differentially expressed genes.
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Affiliation(s)
- Mohammed Abdulwahid Alsoufi
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Department of Animal Production, Faculty of Agriculture, Sana’a University, Alwehdah Street, Sana’a P.O. Box 19509, Yemen
| | - Yong Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Changwei Cao
- Department of Food Science and Engineering, College of Biological Sciences, Southwest Forestry University, Kunming 650224, China
| | - Jinbo Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Jiajia Kang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Mengyuan Li
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Kun Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Yang He
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Changrong Ge
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
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Leija-Montoya AG, González-Ramírez J, Martínez-Coronilla G, Mejía-León ME, Isiordia-Espinoza M, Sánchez-Muñoz F, Chávez-Cortez EG, Pitones-Rubio V, Serafín-Higuera N. Roles of microRNAs and Long Non-Coding RNAs Encoded by Parasitic Helminths in Human Carcinogenesis. Int J Mol Sci 2022; 23:ijms23158173. [PMID: 35897749 PMCID: PMC9331937 DOI: 10.3390/ijms23158173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 12/14/2022] Open
Abstract
Infectious agents such as viruses, bacteria, and parasites can lead to cancer development. Infection with the helminthic parasite Schistosoma haematobium can cause cancer of the urinary bladder in humans, and infection with the parasites Clonorchis sinensis and Opisthorchis viverrini can promote cholangiocarcinoma. These three pathogens have been categorized as “group 1: carcinogenic to humans” by the International Agency for Research on Cancer (IARC). Additionally, the parasite Schistosoma japonicum has been associated with liver and colorectal cancer and classified as “group 2B: possibly carcinogenic to humans”. These parasites express regulatory non-coding RNAs as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), which modulate genic expression in different biological processes. In this review, we discuss the potential roles of miRNAS and lncRNAs encoded by helminthic parasites that are classified by the IARC as carcinogenic and possibly carcinogenic to humans. The miRNAs of these parasites may be involved in carcinogenesis by modulating the biological functions of the pathogen and the host and by altering microenvironments prone to tumor growth. miRNAs were identified in different host fluids. Additionally, some miRNAs showed direct antitumoral effects. Together, these miRNAs show potential for use in future therapeutic and diagnostic applications. LncRNAs have been less studied in these parasites, and their biological effects in the parasite–host interaction are largely unknown.
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Affiliation(s)
- Ana Gabriela Leija-Montoya
- Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Centro Cívico, Mexicali 21000, BC, Mexico; (A.G.L.-M.); (G.M.-C.); (M.E.M.-L.)
| | - Javier González-Ramírez
- Facultad de Enfermería, Universidad Autónoma de Baja California, Av. Álvaro Obregón y Calle “G” S/N, Col. Nueva, Mexicali 21100, BC, Mexico;
| | - Gustavo Martínez-Coronilla
- Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Centro Cívico, Mexicali 21000, BC, Mexico; (A.G.L.-M.); (G.M.-C.); (M.E.M.-L.)
| | - María Esther Mejía-León
- Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Centro Cívico, Mexicali 21000, BC, Mexico; (A.G.L.-M.); (G.M.-C.); (M.E.M.-L.)
| | - Mario Isiordia-Espinoza
- Instituto de Investigación en Ciencias Médicas, Departamento de Clínicas, División de Ciencias Biomédicas, Centro Universitario de Los Altos, Universidad de Guadalajara, Av. Rafael Casillas Aceves 1200, Tepatitlán de Morelos 47600, JAL, Mexico;
| | - Fausto Sánchez-Muñoz
- Departamento de Inmunología, Instituto Nacional de Cardiología, Juan Badiano No. 1, Col. Sección XVI, Tlapan 140080, DF, Mexico;
| | - Elda Georgina Chávez-Cortez
- Centro de Ciencias de la Salud, Facultad de Odontología, Universidad Autónoma de Baja California, Zotoluca s/n, Fracc. Calafia, Mexicali 21040, BC, Mexico; (E.G.C.-C.); (V.P.-R.)
| | - Viviana Pitones-Rubio
- Centro de Ciencias de la Salud, Facultad de Odontología, Universidad Autónoma de Baja California, Zotoluca s/n, Fracc. Calafia, Mexicali 21040, BC, Mexico; (E.G.C.-C.); (V.P.-R.)
| | - Nicolas Serafín-Higuera
- Centro de Ciencias de la Salud, Facultad de Odontología, Universidad Autónoma de Baja California, Zotoluca s/n, Fracc. Calafia, Mexicali 21040, BC, Mexico; (E.G.C.-C.); (V.P.-R.)
- Correspondence:
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Liu X, Luo M, Li M, Wei J. Transcriptomic Analysis Reveals LncRNAs Associated with Flowering of Angelica sinensis during Vernalization. Curr Issues Mol Biol 2022; 44:1867-1888. [PMID: 35678657 PMCID: PMC9164074 DOI: 10.3390/cimb44050128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/19/2022] [Accepted: 04/23/2022] [Indexed: 11/16/2022] Open
Abstract
Angelica sinensis is a “low-temperature and long-day” perennial plant that produces bioactive compounds such as phthalides, organic acids, and polysaccharides for various types of clinical agents, including those with cardio-cerebrovascular, hepatoprotective, and immunomodulatory effects. To date, the regulatory mechanism of flowering under the photoperiod has been revealed, while the regulatory network of flowering genes during vernalization, especially in the role of lncRNAs, has yet to be identified. Here, lncRNAs associated with flowering were identified based on the full-length transcriptomic analysis of A. sinensis at vernalization and freezing temperatures, and the coexpressed mRNAs of lncRNAs were validated by qRT-PCR. We obtained a total of 2327 lncRNAs after assessing the protein-coding potential of coexpressed mRNAs, with 607 lncRNAs aligned against the TAIR database of model plant Arabidopsis, 345 lncRNAs identified, and 272 lncRNAs characterized on the SwissProt database. Based on the biological functions of coexpressed mRNAs, the 272 lncRNAs were divided into six categories: (1) chromatin, DNA/RNA and protein modification; (2) flowering; (3) stress response; (4) metabolism; (5) bio-signaling; and (6) energy and transport. The differential expression levels of representatively coexpressed mRNAs were almost consistent with the flowering of A. sinensis. It can be concluded that the flowering of A. sinensis is positively or negatively regulated by lncRNAs, which provides new insights into the regulation mechanism of the flowering of A. sinensis.
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Affiliation(s)
- Xiaoxia Liu
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.L.); (M.L.)
| | - Mimi Luo
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.L.); (M.L.)
| | - Mengfei Li
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.L.); (M.L.)
- Correspondence: (M.L.); (J.W.)
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Correspondence: (M.L.); (J.W.)
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