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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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2
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Cao Y, Zeng T, Han W, Ma X, Gu T, Chen L, Tian Y, Xu W, Yin J, Li G, Lu L, Gun S. Comparative analysis of liver transcriptome reveals adaptive responses to hypoxia environmental condition in Tibetan chicken. Anim Biosci 2024; 37:28-38. [PMID: 37641844 PMCID: PMC10766467 DOI: 10.5713/ab.23.0126] [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: 04/05/2023] [Revised: 05/25/2023] [Accepted: 07/11/2023] [Indexed: 08/31/2023] Open
Abstract
OBJECTIVE Tibetan chickens, which have unique adaptations to extreme high-altitude environments, exhibit phenotypic and physiological characteristics that are distinct from those of lowland chickens. However, the mechanisms underlying hypoxic adaptation in the liver of chickens remain unknown. METHODS RNA-sequencing (RNA-Seq) technology was used to assess the differentially expressed genes (DEGs) involved in hypoxia adaptation in highland chickens (native Tibetan chicken [HT]) and lowland chickens (Langshan chicken [LS], Beijing You chicken [BJ], Qingyuan Partridge chicken [QY], and Chahua chicken [CH]). RESULTS A total of 352 co-DEGs were specifically screened between HT and four native lowland chicken breeds. Gene ontology and Kyoto encyclopedia of genes and genomes enrichment analyses indicated that these co-DEGs were widely involved in lipid metabolism processes, such as the peroxisome proliferator-activated receptors (PPAR) signaling pathway, fatty acid degradation, fatty acid metabolism and fatty acid biosynthesis. To further determine the relationship from the 352 co-DEGs, protein-protein interaction network was carried out and identified eight genes (ACSL1, CPT1A, ACOX1, PPARC1A, SCD, ACSBG2, ACACA, and FASN) as the potential regulating genes that are responsible for the altitude difference between the HT and other four lowland chicken breeds. CONCLUSION This study provides novel insights into the molecular mechanisms regulating hypoxia adaptation via lipid metabolism in Tibetan chickens and other highland animals.
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Affiliation(s)
- Yongqing Cao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070,
China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Tao Zeng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Wei Han
- Jiangsu Institute of Poultry Science, Yangzhou 225125,
China
- Technology Innovation Co., Ltd., Jiangsu Institute of Poultry Science, Yangzhou 211412,
China
| | - Xueying Ma
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy Agricultural and Animal Husbandry Sciences, Lhasa 850004,
China
| | - Tiantian Gu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Li Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
- China-Ukraine Joint Research Center for Protection, Exploitation and Utilization of Poultry Germplasm Resources, Hangzhou 310021,
China
| | - Yong Tian
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Wenwu Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
| | - Jianmei Yin
- Jiangsu Institute of Poultry Science, Yangzhou 225125,
China
- Technology Innovation Co., Ltd., Jiangsu Institute of Poultry Science, Yangzhou 211412,
China
| | - Guohui Li
- Jiangsu Institute of Poultry Science, Yangzhou 225125,
China
- Technology Innovation Co., Ltd., Jiangsu Institute of Poultry Science, Yangzhou 211412,
China
| | - Lizhi Lu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070,
China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, Hangzhou 310021,
China
- China-Ukraine Joint Research Center for Protection, Exploitation and Utilization of Poultry Germplasm Resources, Hangzhou 310021,
China
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070,
China
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3
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Li S, Zhang X, Dong X, Guo R, Nan J, Yuan J, Schlebusch CM, Sheng Z. Genetic structure and characteristics of Tibetan chickens. Poult Sci 2023; 102:102767. [PMID: 37321029 PMCID: PMC10404676 DOI: 10.1016/j.psj.2023.102767] [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: 12/06/2022] [Revised: 04/21/2023] [Accepted: 04/28/2023] [Indexed: 06/17/2023] Open
Abstract
Tibetan chicken is one of the most common and widely distributed highland breeds, and is often used as a model organism for understanding genetic adaptation to extreme environments in Tibet. Despite its apparent geographical diversity and large variations in plumage patterns, the genetic differences within breed were not accounted for in most studies and have not been systematically investigated. In order to reveal and genetically differentiate the current existing TBC sub-populations that might have major implications for genomic research in TBCs, we systematically evaluated the population structure and demography of current TBC populations. Based on 344 whole-genome sequenced birds including 115 Tibetan chickens that were mostly sampled from family-farms across Tibet, we revealed a clear separation of Tibetan chickens into 4 sub-populations that broadly aligns with their geographical distribution. Moreover, population structure, population size dynamics, and the extent of admixture jointly suggest complex demographic histories of these sub-populations, including possible multiple origins, inbreeding, and introgressions. While most of the candidate selected regions found between the TBC sub-populations and Red Jungle fowls were nonoverlapping, 2 genes RYR2 and CAMK2D were revealed as strong selection candidates in all 4 sub-populations. These 2 previously identified high altitude associated genes indicated that the sub-populations responded to similar selection pressures in an independent but functionally similar fashion. Our results demonstrate robust population structure in Tibetan chickens that will help inform future genetic analyses on chickens and other domestic animals alike in Tibet, recommending thoughtful experimental design.
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Affiliation(s)
- Shijun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaojian Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinyu Dong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruiyang Guo
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiuhong Nan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingwei Yuan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Carina M Schlebusch
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Zheya Sheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
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4
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Zhang T, Li C, Deng J, Jia Y, Qu L, Ning Z. Chicken Hypothalamic and Ovarian DNA Methylome Alteration in Response to Forced Molting. Animals (Basel) 2023; 13:ani13061012. [PMID: 36978553 PMCID: PMC10044502 DOI: 10.3390/ani13061012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/12/2023] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
Epigenetic modifications play an important role in regulating animal adaptation to external stress. To explore how DNA methylation regulates the expression levels of related genes during forced molting (FM) of laying hens, the hypothalamus and ovary tissues were analyzed at five periods using Whole-Genome Bisulfite Sequencing. The results show that methylation levels fluctuated differently in the exon, intron, 5′UTR, 3′UTR, promoter, and intergenic regions of the genome during FM. In addition, 16 differentially methylated genes (DMGs) regulating cell aging, immunity, and development were identified in the two reversible processes of starvation and redevelopment during FM. Comparing DMGs with differentially expressed genes (DEGs) obtained in the same periods, five hypermethylated DMGs (DSTYK, NKTR, SMOC1, SCAMP3, and ATOH8) that inhibited the expression of DEGs were found. Therefore, DMGs epigenetically modify the DEGs during the FM process of chickens, leading to the rapid closure and restart of their reproductive function and a re-increase in the egg-laying rate. Therefore, this study further confirmed that epigenetic modifications could regulate gene expression during FM and provides theoretical support for the subsequent optimization of FM technology.
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Affiliation(s)
- Tongyu Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Chengfeng Li
- Hubei Shendan Healthy Food Co., Ltd., Xiaogan 432600, China
| | - Jianwen Deng
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yaxiong Jia
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100091, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Zhonghua Ning
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Animal Nutrition, Beijing 100193, China
- Correspondence:
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5
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Analysis of genome and methylation changes in Chinese indigenous chickens over time provides insight into species conservation. Commun Biol 2022; 5:952. [PMID: 36097156 PMCID: PMC9467985 DOI: 10.1038/s42003-022-03907-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/26/2022] [Indexed: 11/08/2022] Open
Abstract
Conservation of natural resources is a vital and challenging task. Numerous animal genetic resources have been effectively conserved worldwide. However, the effectiveness of conservation programmes and the variation information of species have rarely been evaluated. Here, we performed whole-genome and whole-genome bisulfite sequencing of 90 Chinese indigenous chickens, which belonged to the Tibetan, Wenchang and Bian chicken breeds, and have been conserved under different conservation programmes. We observed that low genetic diversity and high DNA methylation variation occurs during ex situ in vivo conservation, while higher genetic diversity and differentiation occurs during in situ conservation. Further analyses revealed that most DNA methylation signatures are unique within ex situ in vivo conservation. Moreover, a high proportion of differentially methylated regions is found in genomic selection regions, suggesting a link between the effects of genomic variation and DNA methylation. Altogether our findings provide valuable information about genetic and DNA methylation variations during different conservation programmes, and hold practical relevance for species conservation. Comparisons of genomic and methylomic changes during the conservation of indigenous chicken breeds in China provide insight into conservation programmes for these breeds and their adaptations to unique environments.
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Ragsdale A, Ortega-Recalde O, Dutoit L, Besson AA, Chia JHZ, King T, Nakagawa S, Hickey A, Gemmell NJ, Hore T, Johnson SL. Paternal hypoxia exposure primes offspring for increased hypoxia resistance. BMC Biol 2022; 20:185. [PMID: 36038899 PMCID: PMC9426223 DOI: 10.1186/s12915-022-01389-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 08/10/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND In a time of rapid environmental change, understanding how the challenges experienced by one generation can influence the fitness of future generations is critically needed. Using tolerance assays and transcriptomic and methylome approaches, we use zebrafish as a model to investigate cross-generational acclimation to hypoxia. RESULTS We show that short-term paternal exposure to hypoxia endows offspring with greater tolerance to acute hypoxia. We detected two hemoglobin genes that are significantly upregulated by more than 6-fold in the offspring of hypoxia exposed males. Moreover, the offspring which maintained equilibrium the longest showed greatest upregulation in hemoglobin expression. We did not detect differential methylation at any of the differentially expressed genes, suggesting that other epigenetic mechanisms are responsible for alterations in gene expression. CONCLUSIONS Overall, our findings suggest that an epigenetic memory of past hypoxia exposure is maintained and that this environmentally induced information is transferred to subsequent generations, pre-acclimating progeny to cope with hypoxic conditions.
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Affiliation(s)
| | | | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Anne A Besson
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Jolyn H Z Chia
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Tania King
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Shinichi Nakagawa
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Anthony Hickey
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Timothy Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Sheri L Johnson
- Department of Zoology, University of Otago, Dunedin, New Zealand.
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7
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Zhao Q, Ge Z, Fu S, Wan S, Shi J, Wu Y, Zhang Y. DNA methylation plays an important role in iron-overloaded Tibetans. Gene 2022; 97:55-66. [PMID: 35644542 DOI: 10.1266/ggs.21-00006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The prevalence of iron overload in Tibetans in Tibet is higher than that in Han. DNA methylation (DNAm) is closely related to iron metabolism and iron level. Nevertheless, the epigenetic status of Tibetans with iron overload is unknown, and we therefore aimed to explore whether the phenomenon observed in the Tibetan population is regulated by epigenetics. The results showed that 2.26% of cytosine was methylated in the whole genome, and that the rate of CG cytosine methylation was higher in individuals in the iron overload (TH) group than in those in the iron normal (TL) group. We analyzed differentially methylated genes (DMGs) in whole-genome bisulfite sequencing data from the TH and TL groups of high-altitude Tibetans. Protein-protein interaction and pathway analyses of candidate DMGs related to iron uptake and transport showed that epigenetic changes in 10 candidate genes (ACO1, CYBRD1, FLVCR1, HFE, HMOX2, IREB2, NEDD8, SLC11A2, SLC40A1 and TFRC) are likely to relate to iron overload. This work reveals, for the first time, changes of DNAm in Tibetan people with iron overload, which suggest that DNAm is a mechanism underlying differences in iron content between individuals in the high-altitude Tibetan population. Our findings should contribute to the study of iron metabolism and the overall health status of Tibetans.
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Affiliation(s)
- Qin Zhao
- Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital C.T.)
| | - Zhijing Ge
- School of Basic Medical Sciences, Tibet University
| | - Suhong Fu
- Laboratory of Natural Medicine, West China Hospital, West China Medical School, Sichuan University
| | - Sha Wan
- Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital C.T.)
| | - Jing Shi
- Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital C.T.)
| | - Yunhong Wu
- Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital C.T.)
| | - Yongqun Zhang
- Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital C.T.)
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Abdelmanova AS, Dotsev AV, Romanov MN, Stanishevskaya OI, Gladyr EA, Rodionov AN, Vetokh AN, Volkova NA, Fedorova ES, Gusev IV, Griffin DK, Brem G, Zinovieva NA. Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens. BIOLOGY 2021; 10:biology10090876. [PMID: 34571753 PMCID: PMC8469556 DOI: 10.3390/biology10090876] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 01/14/2023]
Abstract
Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by FST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding.
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Affiliation(s)
- Alexandra S. Abdelmanova
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Arsen V. Dotsev
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
- K.I. Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, 23 Akademika Skryabina St., 109472 Moscow, Russia
- Correspondence: (M.N.R.); (N.A.Z.); Tel.: +798-57154351 (M.N.R.); +749-67651163 (N.A.Z.)
| | - Olga I. Stanishevskaya
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (O.I.S.); (E.S.F.)
| | - Elena A. Gladyr
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Andrey N. Rodionov
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Anastasia N. Vetokh
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Natalia A. Volkova
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Elena S. Fedorova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (O.I.S.); (E.S.F.)
| | - Igor V. Gusev
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK;
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, 142132 Podolsk, Russia; (A.S.A.); (A.V.D.); (E.A.G.); (A.N.R.); (A.N.V.); (N.A.V.); (I.V.G.)
- Correspondence: (M.N.R.); (N.A.Z.); Tel.: +798-57154351 (M.N.R.); +749-67651163 (N.A.Z.)
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Zhang Y, Su W, Zhang B, Ling Y, Kim WK, Zhang H. Comprehensive analysis of coding and non-coding RNA transcriptomes related to hypoxic adaptation in Tibetan chickens. J Anim Sci Biotechnol 2021; 12:60. [PMID: 33934713 PMCID: PMC8091548 DOI: 10.1186/s40104-021-00582-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 03/08/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Tibetan chickens, a unique native breed in the Qinghai-Tibet Plateau of China, possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment. Increasing evidence suggests that long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) play roles in the hypoxic adaptation of high-altitude animals, although their exact involvement remains unclear. RESULTS This study aimed to elucidate the global landscape of mRNAs, lncRNAs, and miRNAs using transcriptome sequencing to construct a regulatory network of competing endogenous RNAs (ceRNAs) and thus provide insights into the hypoxic adaptation of Tibetan chicken embryos. In total, 354 differentially expressed genes (DE genes), 389 differentially expressed lncRNAs (DE lncRNAs), and 73 differentially expressed miRNAs (DE miRNAs) were identified between Tibetan chickens (TC) and control Chahua chickens (CH). GO and KEGG enrichment analysis revealed that several important DE miRNAs and their target DE lncRNAs and DE genes are involved in angiogenesis (including blood vessel development and blood circulation) and energy metabolism (including glucose, carbohydrate, and lipid metabolism). The ceRNA network was then constructed with the predicted DE gene-DE miRNA-DE lncRNA interactions, which further revealed the regulatory roles of these differentially expressed RNAs during hypoxic adaptation of Tibetan chickens. CONCLUSIONS Analysis of transcriptomic data revealed several key candidate ceRNAs that may play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and energy metabolism. These results provide insights into the molecular mechanisms of hypoxic adaptation regulatory networks from the perspective of coding and non-coding RNAs.
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Affiliation(s)
- Ying Zhang
- National Engineering Laboratory for Animal Breeding, Plateau Animal Genetic Resources Center, China Agricultural University, No. 2 Yuanmingyuan West Rd, Haidian District, Beijing, 100193, China
| | - Woyu Su
- National Engineering Laboratory for Animal Breeding, Plateau Animal Genetic Resources Center, China Agricultural University, No. 2 Yuanmingyuan West Rd, Haidian District, Beijing, 100193, China
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding, Plateau Animal Genetic Resources Center, China Agricultural University, No. 2 Yuanmingyuan West Rd, Haidian District, Beijing, 100193, China
| | - Yao Ling
- National Engineering Laboratory for Animal Breeding, Plateau Animal Genetic Resources Center, China Agricultural University, No. 2 Yuanmingyuan West Rd, Haidian District, Beijing, 100193, China
| | - Woo Kyun Kim
- Department of Poultry Science, University of Georgia, 303 Poultry Science Building, Athens, GA, 30602, USA.
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, Plateau Animal Genetic Resources Center, China Agricultural University, No. 2 Yuanmingyuan West Rd, Haidian District, Beijing, 100193, China.
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10
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Wang T, Guo Y, Liu S, Zhang C, Cui T, Ding K, Wang P, Wang X, Wang Z. KLF4, a Key Regulator of a Transitive Triplet, Acts on the TGF-β Signaling Pathway and Contributes to High-Altitude Adaptation of Tibetan Pigs. Front Genet 2021; 12:628192. [PMID: 33936161 PMCID: PMC8082500 DOI: 10.3389/fgene.2021.628192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/10/2021] [Indexed: 11/13/2022] Open
Abstract
Tibetan pigs are native mammalian species on the Tibetan Plateau that have evolved distinct physiological traits that allow them to tolerate high-altitude hypoxic environments. However, the genetic mechanism underlying this adaptation remains elusive. Here, based on multitissue transcriptional data from high-altitude Tibetan pigs and low-altitude Rongchang pigs, we performed a weighted correlation network analysis (WGCNA) and identified key modules related to these tissues. Complex network analysis and bioinformatics analysis were integrated to identify key genes and three-node network motifs. We found that among the six tissues (muscle, liver, heart, spleen, kidneys, and lungs), lung tissue may be the key organs for Tibetan pigs to adapt to hypoxic environment. In the lung tissue of Tibetan pigs, we identified KLF4, BCL6B, EGR1, EPAS1, SMAD6, SMAD7, KDR, ATOH8, and CCN1 genes as potential regulators of hypoxia adaption. We found that KLF4 and EGR1 genes might simultaneously regulate the BCL6B gene, forming a KLF4-EGR1-BCL6B complex. This complex, dominated by KLF4, may enhance the hypoxia tolerance of Tibetan pigs by mediating the TGF-β signaling pathway. The complex may also affect the PI3K-Akt signaling pathway, which plays an important role in angiogenesis caused by hypoxia. Therefore, we postulate that the KLF4-EGR1-BCL6B complex may be beneficial for Tibetan pigs to survive better in the hypoxia environments. Although further molecular experiments and independent large-scale studies are needed to verify our findings, these findings may provide new details of the regulatory architecture of hypoxia-adaptive genes and are valuable for understanding the genetic mechanism of hypoxic adaptation in mammals.
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Affiliation(s)
- Tao Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Yuanyuan Guo
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Shengwei Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Chaoxin Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Tongyan Cui
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
| | - Kun Ding
- College of Computer Science and Technology, Inner Mongolia Normal University, Hohhot, China
| | - Peng Wang
- HeiLongJiang Provincial Husbandry Department, Harbin, China
| | - Xibiao Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Zhipeng Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,Bioinformatics Center, Northeast Agricultural University, Harbin, China
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11
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Gong P, Jing Y, Liu Y, Wang L, Wu C, Du Z, Li H. Whole-genome bisulfite sequencing of abdominal adipose reveals DNA methylation pattern variations in broiler lines divergently selected for fatness. J Anim Sci 2021; 99:skaa408. [PMID: 33373456 PMCID: PMC8611762 DOI: 10.1093/jas/skaa408] [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: 09/08/2020] [Accepted: 12/23/2020] [Indexed: 11/14/2022] Open
Abstract
The methylation status of pivotal genes involved in fat deposition in chickens has been extensively studied. However, the whole-genome DNA methylation profiles of broiler abdominal adipose tissue remain poorly understood. Using whole-genome bisulfite sequencing, we generated DNA methylation profiles of chicken abdominal adipose tissue from Northeast Agricultural University broiler lines divergently selected for abdominal fat content. We aimed to explore whether DNA methylation was associated with abdominal fat deposition in broilers. The whole-genome DNA methylation profiles of fat- and lean-line broilers abdominal adipose tissue were constructed. The DNA methylation levels of functional genomic regions in the fat broiler were higher than those in the lean broiler, especially in the 3' untranslated regions (UTRs) and exons in the non-CG contexts. Additionally, we identified 29,631 differentially methylated regions and, subsequently, annotated 6,484 and 2,016 differentially methylated genes (DMGs) in the gene body and promoter regions between the two lines, respectively. Functional annotation showed that the DMGs in promoter regions were significantly enriched mainly in the triglyceride catabolic process, lipid metabolism-related pathways, and extracellular matrix signal pathways. When the DMG in promoter regions and differentially expressed genes were integrated, we identified 30 genes with DNA methylation levels that negatively correlated with their messenger RNA (mRNA) expression, of which CMSS1 reached significant levels (false discovery rate < 0.05). These 30 genes were mainly involved in fatty acid metabolism, peroxisome-proliferator-activated receptor signaling, Wnt signaling pathways, transmembrane transport, RNA degradation, and glycosaminoglycan degradation. Comparing the DNA methylation profiles between fat- and lean-line broilers demonstrated that DNA methylation is involved in regulating broiler abdominal fat deposition. Our study offers a basis for further exploring the underlying mechanisms of abdominal adipose deposition in broilers.
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Affiliation(s)
- Pengfei Gong
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and
Rural Affairs, Harbin, P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education
Department of Heilongjiang Province, Harbin, P.R.
China
- College of Animal Science and Technology, Northeast Agricultural
University, Harbin, P.R. China
| | - Yang Jing
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and
Rural Affairs, Harbin, P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education
Department of Heilongjiang Province, Harbin, P.R.
China
- College of Animal Science and Technology, Northeast Agricultural
University, Harbin, P.R. China
| | - Yumeng Liu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and
Rural Affairs, Harbin, P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education
Department of Heilongjiang Province, Harbin, P.R.
China
- College of Animal Science and Technology, Northeast Agricultural
University, Harbin, P.R. China
| | - Lijian Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and
Rural Affairs, Harbin, P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education
Department of Heilongjiang Province, Harbin, P.R.
China
- College of Animal Science and Technology, Northeast Agricultural
University, Harbin, P.R. China
| | - Chunyan Wu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and
Rural Affairs, Harbin, P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education
Department of Heilongjiang Province, Harbin, P.R.
China
- College of Animal Science and Technology, Northeast Agricultural
University, Harbin, P.R. China
| | - Zhiqiang Du
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and
Rural Affairs, Harbin, P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education
Department of Heilongjiang Province, Harbin, P.R.
China
- College of Animal Science and Technology, Northeast Agricultural
University, Harbin, P.R. China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and
Rural Affairs, Harbin, P.R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education
Department of Heilongjiang Province, Harbin, P.R.
China
- College of Animal Science and Technology, Northeast Agricultural
University, Harbin, P.R. China
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12
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Tang R, Wang J, Zhou M, Lan Y, Jiang L, Price M, Yue B, Li D, Fan Z. Comprehensive analysis of lncRNA and mRNA expression changes in Tibetan chicken lung tissue between three developmental stages. Anim Genet 2020; 51:731-740. [DOI: 10.1111/age.12990] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 06/04/2020] [Accepted: 07/06/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Ruixiang Tang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
| | - Jiao Wang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
| | - Min Zhou
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
| | - Yue Lan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife College of Life Sciences Sichuan University Chengdu 610064 China
| | - Lan Jiang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife College of Life Sciences Sichuan University Chengdu 610064 China
| | - Megan Price
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
| | - Diyan Li
- Sichuan Agricultural University Chengdu 611130 China
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
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13
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Zhang Y, Gou W, Zhang Y, Zhang H, Wu C. Insights into hypoxic adaptation in Tibetan chicken embryos from comparative proteomics. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 31:100602. [PMID: 31212116 DOI: 10.1016/j.cbd.2019.100602] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/08/2019] [Accepted: 06/09/2019] [Indexed: 01/23/2023]
Abstract
Tibetan chicken, an indigenous breed, is highly adapted to the extreme environment of the Qinghai-Tibet Plateau. It serves as a model organism to identify genetic differences between hypoxia-adapted and lowland breeds. However, the mechanisms underlying hypoxia adaptation are yet unclear. This study aimed to identify differently abundant proteins (DAPs) and elucidate the mechanisms involved in hypoxic adaptation in the Tibetan chicken. In this study, we obtained proteome data for the embryonic heart tissues of Tibetan and Chahua chickens incubated under hypoxia (TCH and CHH) and normoxia (TCN and CHN) using isobaric tags for relative and absolute quantitation (iTRAQ) technology. We identified 4210 proteins from 53,352 unique peptides in the heart tissue of chicken embryos. Pairwise TCH vs. CHH, TCH vs. TCN, CHH vs. CHN, and TCN vs. CHN comparisons revealed 118, 176, 103, and 162 differently abundant proteins, respectively. Several key proteins (EGLN1, MAP2K2, MYLK, QARS, NOTCH2, and MYH7) and pathways (glutathione metabolism, PPAR signaling pathway, and vascular smooth muscle contraction) were identified and considered important candidates for high-altitude adaptation in Tibetan chicken. This study provides novel insights into the chicken embryonic heart tissue and furthers the current understanding of the mechanisms of survival among animals in high-altitude environments.
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Affiliation(s)
- Yawen Zhang
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wenyu Gou
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ying Zhang
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China.
| | - Changxin Wu
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
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14
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Bacterial Lipopolysaccharide Induced Alterations of Genome-Wide DNA Methylation and Promoter Methylation of Lactation-Related Genes in Bovine Mammary Epithelial Cells. Toxins (Basel) 2019; 11:toxins11050298. [PMID: 31137708 PMCID: PMC6563294 DOI: 10.3390/toxins11050298] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/16/2019] [Accepted: 05/24/2019] [Indexed: 12/21/2022] Open
Abstract
Bacterial lipopolysaccharide (LPS) could result in poor lactation performance in dairy cows. High methylation of DNA is associated with gene repression. However, it is unclear whether LPS could suppress the expression of lactation-related genes by inducing DNA methylation. Therefore, the objective of this study was to investigate the impact of LPS on genome-wide DNA methylation, using methylated DNA immunoprecipitation with high-throughput sequencing (MeDIP-seq) and on the promoter methylation of lactation-related genes using MassArray analysis in bovine mammary epithelial cells. The bovine mammary epithelial cell line MAC-T cells were treated for 48 h with LPS at different doses of 0, 1, 10, 100, and 1000 endotoxin units (EU)/mL (1 EU = 0.1 ng). The results showed that the genomic methylation levels and the number of methylated genes in the genome as well as the promoter methylation levels of milk genes increased when the LPS dose was raised from 0 to 10 EU/mL, but decreased after further increasing the LPS dose. The milk gene mRNA expression levels of the 10 EU/mL LPS treatment were significantly lower than these of untreated cells. The results also showed that the number of hypermethylated genes was greater than that of hypomethylated genes in lipid and amino acid metabolic pathways following 1 and 10 EU/mL LPS treatments as compared with control. By contrast, in the immune response pathway the number of hypomethylated genes increased with increasing LPS doses. The results indicate LPS at lower doses induced hypermethylation of the genome and promoters of lactation-related genes, affecting milk gene mRNA expression. However, LPS at higher doses induced hypomethylation of genes involved in the immune response pathway probably in favor of immune responses.
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15
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Makarova AV, Mitrofanova OV, Vakhrameev AB, Dementeva NV. Molecular-genetic bases of plumage coloring in chicken. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.499] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The color of plumage in birds is an important feature, often determining descent to a particular species or breed. It serves as a key factor in the interaction of birds with each other due to their well-developed visual perception of the surrounding world. In poultry including chickens, the color of the plumage can be treated as a genetic marker, useful for identifying breeds, populations and breeding groups with their specific traits. The origin of diverse color plumage is the result of two interrelated physical processes, chemical and optical, due to which pigment and structural colors in the color are formed. The pigment melanin, which is presented in two forms, eumelanin and pheomelanin, is widely spread in birds. The basis for the formation of melanin is the aromatic amino acid tyrosine. The process of melano-genesis involves many loci, part of the complex expression of plumage color genes. In birds, the solid black color locus encodes the melanocortin 1 receptor (MC1R), mutations in which lead to a change in receptor activation and form different variants of the E locus. Using the GWAS analysis, possible genes affecting the formation of color in chickens were detected. The biosynthesis and types of melanin are affected by the activity of the enzyme tyrosine, and mutations in the tyrosinase gene (TYR) cause albinism in different species. The formation mechanism of brown, silver, gold, lavender and a number of other shades is determined by the influence on the work of the MC1R genes and TYR specific modifier genes. Thus, locus I currently associated with the PMEL17 gene inhibits the expression of eumelanin, and the MLPH gene affects tyrosinase function. Research on the mechanisms of formation of the secondary coloring of plumage in chickens is being actively conducted nowadays. The formation of a marble feather pattern is associated with the mutation of the endothelin B2 receptor (EDNRB2), in the coding part of the gene of which a polymorphism is found associated with the mo locus. The molecular base that causes the feather banding (locus B and autosomal recessive banding) is identified. Today, only some genes that determine the color of the plumage of chickens are studied and described. Different genes can produce similar plumage patterns, and different phenotypes can be determined by the polymorphism of a single gene. Using molecular methods, you can more accurately identify these differences. This overview shows the nature of melanin coloration in birds using the example of chickens of various breeds and also attempts to systematize knowledge about the molecular-genetic mechanisms of the appearance of various types of coloration.
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Affiliation(s)
- A. V. Makarova
- Russian Research Institute of Farm Animal Genetics and Breeding – Branch of the L.K. Ernst Federal Science Center for Animal Husbandry
| | - O. V. Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding – Branch of the L.K. Ernst Federal Science Center for Animal Husbandry
| | - A. B. Vakhrameev
- Russian Research Institute of Farm Animal Genetics and Breeding – Branch of the L.K. Ernst Federal Science Center for Animal Husbandry
| | - N. V. Dementeva
- Russian Research Institute of Farm Animal Genetics and Breeding – Branch of the L.K. Ernst Federal Science Center for Animal Husbandry
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16
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Zhang B, Ban D, Gou X, Zhang Y, Yang L, Chamba Y, Zhang H. Genome-wide DNA methylation profiles in Tibetan and Yorkshire pigs under high-altitude hypoxia. J Anim Sci Biotechnol 2019; 10:25. [PMID: 30867905 PMCID: PMC6397503 DOI: 10.1186/s40104-019-0316-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 01/04/2019] [Indexed: 12/21/2022] Open
Abstract
Background Tibetan pigs, which inhabit the Tibetan Plateau, exhibit distinct phenotypic and physiological characteristics from those of lowland pigs and have adapted well to the extreme conditions at high altitude. However, the genetic and epigenetic mechanisms of hypoxic adaptation in animals remain unclear. Methods Whole-genome DNA methylation data were generated for heart tissues of Tibetan pigs grown in the highland (TH, n = 4) and lowland (TL, n = 4), as well as Yorkshire pigs grown in the highland (YH, n = 4) and lowland (YL, n = 4), using methylated DNA immunoprecipitation sequencing. Results We obtained 480 million reads and detected 280679, 287224, 259066, and 332078 methylation enrichment peaks in TH, YH, TL, and YL, respectively. Pairwise TH vs. YH, TL vs. YL, TH vs. TL, and YH vs. YL comparisons revealed 6829, 11997, 2828, and 1286 differentially methylated regions (DMRs), respectively. These DMRs contained 384, 619, 192, and 92 differentially methylated genes (DMGs), respectively. DMGs that were enriched in the hypoxia-inducible factor 1 signaling pathway and pathways involved in cancer and hypoxia-related processes were considered to be important candidate genes for high-altitude adaptation in Tibetan pigs. Conclusions This study elucidates the molecular and epigenetic mechanisms involved in hypoxic adaptation in pigs and may help further understand human hypoxia-related diseases.
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Affiliation(s)
- Bo Zhang
- 1National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Dongmei Ban
- 1National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xiao Gou
- 2College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
| | - Yawen Zhang
- 1National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Lin Yang
- 1National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Yangzom Chamba
- 3College of Animal Science, Tibet Agriculture and Animal Husbandry University, Linzhi, 860000 Tibet China
| | - Hao Zhang
- 1National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, 100193 China
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