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Deng C, Li M, Wang T, Duan W, Guo A, Ma G, Yang F, Dai F, Li Q. Integrating genomics and transcriptomics to identify candidate genes for high-altitude adaptation and egg production in Nixi chicken. Br Poult Sci 2024:1-13. [PMID: 38922310 DOI: 10.1080/00071668.2024.2367228] [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: 01/30/2024] [Accepted: 05/17/2024] [Indexed: 06/27/2024]
Abstract
1. This study combined genome-wide selection signal analysis with RNA-sequencing to identify candidate genes associated with high altitude adaptation and egg production performance in Nixi chickens (NXC).2. Based on the whole-genome data from 20 NXC (♂:10; ♀:10), the population selection signal was analysed by sliding window analysis. The selected genes were screened by combination with the population differentiation statistic (FST). The sequence diversity statistic (θπ). RNA-seq was performed on the ovarian tissues of NXC (n = 6) and Lohmann laying hens (n = 6) to analyse the differentially expressed genes (DEGs) between the two groups. The functional enrichment analysis of the selected genes and differentially expressed genes was performed.3. There were 742 genes under strong positive selection and 509 differentially expressed genes screened in NXC. Integrated analysis of the genome and transcriptome revealing 26 overlapping genes. The candidate genes for adaptation to a high-altitude environment, as well as for egg production, disease resistance, vision and pigmentation in NXC were preliminarily screened.4. The results provided theoretical guidance for further research on the genetic resource protection and utilisation of NXC.
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Affiliation(s)
- C Deng
- College of Biology and Food Engineering, Southwest Forestry University, Kunming, China
| | - M Li
- School of Mathematics and Computer Science, Yunnan Nationalities University, Kunming, China
| | - T Wang
- School of Pharmacy, Chengdu University, Chengdu, China
| | - W Duan
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - A Guo
- College of Biology and Food Engineering, Southwest Forestry University, Kunming, China
| | - G Ma
- Agricultural and Rural Bureau of Gejiu County, Honghe, China
| | - F Yang
- Agricultural and Rural Bureau of Gejiu County, Honghe, China
| | - F Dai
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Q Li
- College of Biology and Food Engineering, Southwest Forestry University, Kunming, China
- Kunming Xianghao Technology Co. Ltd., Kunming, China
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Liu J, Xiao Y, Ren P, Zhang S, Liu Y, Zhu M. Integrating genomics and transcriptomics to identify candidate genes for high egg production in Wulong geese (Anser cygnoides orientalis). BMC Genomics 2023; 24:481. [PMID: 37620752 PMCID: PMC10464066 DOI: 10.1186/s12864-023-09603-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Wulong geese (Anser cygnoides orientalis) are known for their excellent egg-laying performance. However, they show considerable population differences in egg-laying behavior. This study combined genome-wide selection signal analysis with transcriptome analysis (RNA-seq) to identify the genes related to high egg production in Wulong geese. RESULTS A total of 132 selected genomic regions were screened using genome-wide selection signal analysis, and 130 genes related to high egg production were annotated in these regions. These selected genes were enriched in pathways related to egg production, including oocyte meiosis, the estrogen signaling pathway, the oxytocin signaling pathway, and progesterone-mediated oocyte maturation. Furthermore, a total of 890 differentially expressed genes (DEGs), including 340 up-regulated and 550 down-regulated genes, were identified by RNA-seq. Two genes - GCG and FAP - were common to the list of selected genes and DEGs. A non-synonymous single nucleotide polymorphism was identified in an exon of FAP. CONCLUSIONS Based on genome-wide selection signal analysis and transcriptome data, GCG and FAP were identified as candidate genes associated with high egg production in Wulong geese. These findings could promote the breeding of Wulong geese with high egg production abilities and provide a theoretical basis for exploring the mechanisms of reproductive regulation in poultry.
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Affiliation(s)
- Jingjing Liu
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Yu Xiao
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Pengwei Ren
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Shuer Zhang
- Shandong Animal Husbandry General Station, Jinan, 250010, China
| | - Yang Liu
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Mingxia Zhu
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng, 252000, China.
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Xin Q, Uyanga VA, Jiao H, Zhao J, Wang X, Li H, Zhou Y, Lin H. Insulin-like growth factor-1 is involved in the deteriorated performance of aged laying hens. J Anim Sci 2022; 100:skac286. [PMID: 36049215 PMCID: PMC9667965 DOI: 10.1093/jas/skac286] [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: 06/30/2022] [Accepted: 08/30/2022] [Indexed: 11/12/2022] Open
Abstract
The underlying mechanism behind the deteriorated laying performance of aged laying hens remains unclear. In the present study, the laying performance and gene expression along the hypothalamus-pituitary-gonad axis were determined. A total of 300 healthy 90-wk-old ISA hens with similar body weights were classified into three groups according to their laying rate between 90 and 94 wk of age. The experimental groups were the low laying rate (<60%, LLR), high laying rate (>85%, HLR), and intermediate laying rate (60% < laying rate < 85%, MLR) hens. At the end of 94 wk of age, eight hens were randomly selected from each group for tissue collection. The gene expression of hormones and their receptors were determined in the hypothalamus, pituitary, and follicles. The results showed that the serum 17-β-estradiol had no significant difference among the three groups. However, the level of insulin-like growth factor 1 (IGF1) in LLR hens was significantly decreased in the serum, small white follicles (SWF), and dominant follicles (DF, P < 0.05). Within the hypothalamus and small yellow follicles (SYF), the mRNA expression level of estrogen receptor was higher in the MLR group (P < 0.05). Compared with HLR hens, the steroid hormone-synthesis key gene, CYP19A1 was significantly decreased in the SWF of MLR-hens and DF of MLR- and LLR-hens (P < 0.05). The mRNA expression level of IGF1 receptor was higher in the hypothalamus, pituitary, SWF, large white follicles (LWF), SYF, and DF of LLR hens, compared to the HLR hens (P < 0.05). These results suggest that decreased IGF1 in serum and follicles was associated with the decreased egg production of aged laying hens. The present study provides novel insights into the endocrine changes in aged hens having different egg production.
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Affiliation(s)
- Qian Xin
- Department of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong 271018, P. R. China
| | - Victoria Anthony Uyanga
- Department of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong 271018, P. R. China
| | - Hongchao Jiao
- Department of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong 271018, P. R. China
| | - Jingpeng Zhao
- Department of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong 271018, P. R. China
| | - Xiaojuan Wang
- Department of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong 271018, P. R. China
| | - Haifang Li
- College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, P. R. China
| | - Yunlei Zhou
- College of Chemistry and Material Science, Shandong Agricultural University, Taian, Shandong 271018, P. R. China
| | - Hai Lin
- Department of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, Shandong 271018, P. R. China
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Bhavana K, Foote DJ, Srikanth K, Balakrishnan CN, Prabhu VR, Sankaralingam S, Singha HS, Gopalakrishnan A, Nagarajan M. Comparative transcriptome analysis of Indian domestic duck reveals candidate genes associated with egg production. Sci Rep 2022; 12:10943. [PMID: 35768515 PMCID: PMC9243076 DOI: 10.1038/s41598-022-15099-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/17/2022] [Indexed: 12/12/2022] Open
Abstract
Egg production is an important economic trait and a key indicator of reproductive performance in ducks. Egg production is regulated by several factors including genes. However the genes involved in egg production in duck remain unclear. In this study, we compared the ovarian transcriptome of high egg laying (HEL) and low egg laying (LEL) ducks using RNA-Seq to identify the genes involved in egg production. The HEL ducks laid on average 433 eggs while the LEL ducks laid 221 eggs over 93 weeks. A total of 489 genes were found to be significantly differentially expressed out of which 310 and 179 genes were up and downregulated, respectively, in the HEL group. Thirty-eight differentially expressed genes (DEGs), including LHX9, GRIA1, DBH, SYCP2L, HSD17B2, PAR6, CAPRIN2, STC2, and RAB27B were found to be potentially related to egg production and folliculogenesis. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that DEGs were enriched for functions related to glutamate receptor activity, serine-type endopeptidase activity, immune function, progesterone mediated oocyte maturation and MAPK signaling. Protein-protein interaction network analysis (PPI) showed strong interaction between 32 DEGs in two distinct clusters. Together, these findings suggest a mix of genetic and immunological factors affect egg production, and highlights candidate genes and pathways, that provides an understanding of the molecular mechanisms regulating egg production in ducks and in birds more broadly.
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Affiliation(s)
- Karippadakam Bhavana
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Dustin J Foote
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
| | - Krishnamoorthy Srikanth
- Department of Animal Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | | | - Vandana R Prabhu
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India.,ICAR-Central Marine Fisheries Research Institute, Ernakulam North PO, Kochi, Kerala, 682 018, India
| | - Shanmugam Sankaralingam
- Department of Poultry Science, College of Veterinary and Animal Sciences, Mannuthy, Thrissur, Kerala, 680 651, India
| | - Hijam Surachandra Singha
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | | | - Muniyandi Nagarajan
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India.
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Ovarian Transcriptomic Analysis of Ninghai Indigenous Chickens at Different Egg-Laying Periods. Genes (Basel) 2022; 13:genes13040595. [PMID: 35456401 PMCID: PMC9027236 DOI: 10.3390/genes13040595] [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: 03/01/2022] [Revised: 03/17/2022] [Accepted: 03/23/2022] [Indexed: 11/25/2022] Open
Abstract
Egg production is an essential indicator of poultry fertility. The ovary is a crucial organ involved in egg production; however, little is known about the key genes and signaling pathways involved in the whole egg-laying cycle of hens. In order to explore the mechanism of egg production at different stages of the egg-laying process, ovarian tissues from four chickens were randomly selected for transcriptome analysis at each of the three ages (145 d, 204 d, and 300 d in the early, peak, and late stages of egg laying). A total of 12 gene libraries were constructed, and a total of 8433 differential genes were identified from NH145d vs. NH204d, NH145d vs. NH300d and NH300d vs. NH204d (Ninghai 145-day-old, Ninghai 204-day-old, and Ninghai 300-day-old), with 1176, 1653 and 1868 up-regulated genes, and 621, 1955 and 1160 down-regulated genes, respectively. In each of the two comparison groups, 73, 1004, and 1030 differentially expressed genes were found to be co-expressed. We analyzed the differentially expressed genes and predicted nine genes involved in egg production regulation, including LRP8, BMP6, ZP4, COL4A1, VCAN, INHBA, LOX, PTX3, and IHH, as well as several essential egg production pathways, such as regulation adhesion molecules (CAMs), calcium signaling pathways, neuroactive ligand–receptor interaction, and cytokine–cytokine receptor interaction. Transcriptional analysis of the chicken ovary during different phases of egg-lay will provide a useful molecular basis for study of the development of the egg-laying ovary.
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Abstract
The lack of preclinical models of spontaneous ovarian cancer (OVCA), a fatal gynecological malignancy, is a significant barrier to generating information on early changes indicative of OVCA. In contrast to rodents, laying hens develop OVCA spontaneously, with remarkable similarities to OVCA in women regarding tumor histology, OVCA dissemination, immune responses, and risk factors. These important features of OVCA will be useful to develop an early detection test for OVCA, which would significantly reduce mortality rates; preventive strategies; immunotherapeutics; prevention of resistance to chemotherapeutics; and exploration of gene therapies. A transvaginal ultrasound (TVUS) imaging method for imaging of hen ovarian tumors has been developed. Hens can be monitored prospectively by using serum markers, together with TVUS imaging, to detect early-stage OVCA, provided that a panel of serum markers can be established and imaging agents developed. Recent sequencing of the chicken genome will further facilitate the hen model to explore gene therapies against OVCA.
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Affiliation(s)
- Animesh Barua
- Laboratory of Translational Research on Ovarian Cancer, Department of Cell and Molecular Medicine, Rush University Medical Center, Chicago, Illinois, USA;
| | - Janice M Bahr
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA;
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