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Beaudreau N, Page TM, Drolet D, McKindsey CW, Howland KL, Calosi P. Using a metabolomics approach to investigate the sensitivity of a potential Arctic-invader and its Arctic sister-species to marine heatwaves and traditional harvesting disturbances. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170167. [PMID: 38242480 DOI: 10.1016/j.scitotenv.2024.170167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/21/2023] [Accepted: 01/12/2024] [Indexed: 01/21/2024]
Abstract
Coastal species are threatened by fishing practices and changing environmental conditions, such as marine heatwaves (MHW). The mechanisms that confer tolerance to such stressors in marine invertebrates are poorly understood. However, differences in tolerance among different species may be attributed to their geographical distribution. To test the tolerance of species occupying different thermal ranges, we used two closely related bivalves the softshell clam Mya arenaria (Linnaeus, 1758), a cold-temperate invader with demonstrated potential for establishment in the Arctic, and the blunt gaper Mya truncata (Linnaeus, 1758), a native polar species. Clams were subjected to a thermal stress, mimicking a MHW, and harvesting stress in a controlled environment. Seven acute temperature changes (2, 7, 12, 17, 22, 27, and 32 °C) were tested at two harvesting disturbance intensities (with, without). Survival was measured after 12 days and three tissues (gills, mantle, and posterior adductor muscle) collected from surviving individuals for targeted metabolomic profiling. MHW tolerance differed significantly between species: 26.9 °C for M. arenaria and 17.8 °C for M. truncata, with a negligeable effect of harvesting. At the upper thermal limit, M. arenaria displayed a more profound metabolomic remodelling when compared to M. truncata, and this varied greatly between tissue types. Network analysis revealed differences in pathway utilization at the upper MHW limit, with M. arenaria displaying a greater reliance on multiple DNA repair and expression and cell signalling pathways, while M. truncata was limited to fewer pathways. This suggests that M. truncata is ill equipped to cope with warming environments. MHW patterning in the Northwest Atlantic may be a strong predictor of population survival and future range shifts in these two clam species. As polar environments undergo faster rates of warming compared to the global average, M. truncata may be outcompeted by M. arenaria expanding into its native range.
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Affiliation(s)
- Nicholas Beaudreau
- Laboratoire de Physiologie Écologique et Évolutive Marine, Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Québec, Canada
| | - Tessa M Page
- Laboratoire de Physiologie Écologique et Évolutive Marine, Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Québec, Canada
| | - David Drolet
- Fisheries and Oceans Canada, Demersal and Benthic Science Branch, Institut Maurice-Lamontagne, Mont-Joli, Québec, Canada
| | - Christopher W McKindsey
- Fisheries and Oceans Canada, Demersal and Benthic Science Branch, Institut Maurice-Lamontagne, Mont-Joli, Québec, Canada
| | - Kimberly L Howland
- Fisheries and Oceans Canada, Arctic and Aquatic Research Division, Freshwater Institute, Winnipeg, Manitoba, Canada
| | - Piero Calosi
- Laboratoire de Physiologie Écologique et Évolutive Marine, Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, Québec, Canada.
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Wen H, Johnson JS, Freitas PHF, Maskal JM, Gloria LS, Araujo AC, Pedrosa VB, Tiezzi F, Maltecca C, Huang Y, Schinckel AP, Brito LF. Longitudinal genomic analyses of automatically-recorded vaginal temperature in lactating sows under heat stress conditions based on random regression models. Genet Sel Evol 2023; 55:95. [PMID: 38129768 PMCID: PMC10734178 DOI: 10.1186/s12711-023-00868-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Automatic and continuous recording of vaginal temperature (TV) using wearable sensors causes minimal disruptions to animal behavior and can generate data that enable the evaluation of temporal body temperature variation under heat stress (HS) conditions. However, the genetic basis of TV in lactating sows from a longitudinal perspective is still unknown. The objectives of this study were to define statistical models and estimate genetic parameters for TV in lactating sows using random regression models, and identify genomic regions and candidate genes associated with HS indicators derived from automatically-recorded TV. RESULTS Heritability estimates for TV ranged from 0.14 to 0.20 over time (throughout the day and measurement period) and from 0.09 to 0.18 along environmental gradients (EG, - 3.5 to 2.2, which correspond to dew point values from 14.87 to 28.19 ˚C). Repeatability estimates of TV over time and along EG ranged from 0.57 to 0.66 and from 0.54 to 0.77, respectively. TV measured from 12h00 to 16h00 had moderately high estimates of heritability (0.20) and repeatability (0.64), indicating that this period might be the most suitable for recording TV for genetic selection purposes. Significant genotype-by-environment interactions (GxE) were observed and the moderately high estimates of genetic correlations between pairs of extreme EG indicate potential re-ranking of selection candidates across EG. Two important genomic regions on chromosomes 10 (59.370-59.998 Mb) and16 (21.548-21.966 Mb) were identified. These regions harbor the genes CDC123, CAMK1d, SEC61A2, and NUDT5 that are associated with immunity, protein transport, and energy metabolism. Across the four time-periods, respectively 12, 13, 16, and 10 associated genomic regions across 14 chromosomes were identified for TV. For the three EG classes, respectively 18, 15, and 14 associated genomic windows were identified for TV, respectively. Each time-period and EG class had uniquely enriched genes with identified specific biological functions, including regulation of the nervous system, metabolism and hormone production. CONCLUSIONS TV is a heritable trait with substantial additive genetic variation and represents a promising indicator trait to select pigs for improved heat tolerance. Moderate GxE for TV exist, indicating potential re-ranking of selection candidates across EG. TV is a highly polygenic trait regulated by a complex interplay of physiological, cellular and behavioral mechanisms.
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Affiliation(s)
- Hui Wen
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Jay S Johnson
- USDA-ARS Livestock Behavior Research Unit, West Lafayette, IN, USA
| | - Pedro H F Freitas
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Jacob M Maskal
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Leonardo S Gloria
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Andre C Araujo
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Victor B Pedrosa
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
- Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, Italy
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | | | - Allan P Schinckel
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.
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Wang J, Suo J, Yang R, Zhang CL, Li X, Han Z, Zhou W, Liu S, Gao Q. Genetic diversity, population structure, and selective signature of sheep in the northeastern Tarim Basin. Front Genet 2023; 14:1281601. [PMID: 38028584 PMCID: PMC10666172 DOI: 10.3389/fgene.2023.1281601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Local sheep in the northeastern Tarim Basin can adapt to dry and low-rainfall regional environments. In this study, three local sheep breeds in the northeastern Tarim Basin, LOP (LOP) sheep, Bayinbuluke (BYK) sheep, and Kunlun (KUN, also known as the Qiemo sheep) sheep, and three introduced sheep breeds, Suffolk (SUF) sheep, Dorset (APD) sheep, and Texel (TEX) sheep, were analyzed for genetic diversity, population structure, and selective signature using the Illumina OvineSNP50K BeadChip. We found that LOP, BYK, and KUN had lower observed heterozygosity and expected heterozygosity than TEX, SUF, and ADP, which were differentiated based on geographic distribution. We performed fixation index (FST) analysis on three local sheep breeds in the northeastern Tarim Basin (LOP, BYK, and KUN) and introduced sheep breeds (TEX, SUF, and ADP) to measure genetic differentiation. Nucleotide diversity (PI) analysis was performed on single-nucleotide polymorphism (SNP) data of LOP, BYK, and KUN. A total of 493 candidate genes were obtained by taking the intersection at a threshold of 5%. Among them, SMAD2, ESR2, and HAS2 were related to reproductive traits. PCDH15, TLE4, and TFAP2B were related to growth traits. SOD1, TSHR, and DNAJB5 were related to desert environmental adaptation. Analyzing the genetic patterns of local sheep in the northeastern Tarim Basin can protect the germplasm resources of local sheep and promote the development and utilization of sheep genetic resources.
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Affiliation(s)
- Jieru Wang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Co-Funded by Xinjiang Production and Construction Corps and The Ministry of Science and Technology, College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Jiajia Suo
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Co-Funded by Xinjiang Production and Construction Corps and The Ministry of Science and Technology, College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
| | - Ruizhi Yang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Co-Funded by Xinjiang Production and Construction Corps and The Ministry of Science and Technology, College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
| | - Cheng-Long Zhang
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Xiaopeng Li
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Zhipeng Han
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Wen Zhou
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Shudong Liu
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
| | - Qinghua Gao
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin Co-Funded by Xinjiang Production and Construction Corps and The Ministry of Science and Technology, College of Life Science and Technology, Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology of Xinjiang Production and Construction Corps, College of Animal Science and Technology, Tarim University, Alar, China
- Livestock and Forage Resources in Circum-Tarim Region, Ministry of Agriculture and Rural Affairs, Tarim University, Alar, China
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Tian S, Tang W, Zhong Z, Wang Z, Xie X, Liu H, Chen F, Liu J, Han Y, Qin Y, Tan Z, Xiao Q. Identification of Runs of Homozygosity Islands and Functional Variants in Wenchang Chicken. Animals (Basel) 2023; 13:ani13101645. [PMID: 37238076 DOI: 10.3390/ani13101645] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/11/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
Wenchang chickens, a native breed in the Hainan province of China, are famous for their meat quality and adaptability to tropical conditions. For effective management and conservation, in the present study, we systematically investigated the characteristics of genetic variations and runs of homozygosity (ROH) along the genome using re-sequenced whole-genome sequencing data from 235 Wenchang chickens. A total of 16,511,769 single nucleotide polymorphisms (SNPs) and 53,506 ROH segments were identified in all individuals, and the ROH of Wenchang chicken were mainly composed of short segments (0-1 megabases (Mb)). On average, 5.664% of the genome was located in ROH segments across the Wenchang chicken samples. According to several parameters, the genetic diversity of the Wenchang chicken was relatively high. The average inbreeding coefficient of Wenchang chickens based on FHOM, FGRM, and FROH was 0.060 ± 0.014, 0.561 ± 0.020, and 0.0566 ± 0.01, respectively. A total of 19 ROH islands containing 393 genes were detected on 9 different autosomes. Some of these genes were putatively associated with growth performance (AMY1a), stress resistance (THEMIS2, PIK3C2B), meat traits (MBTPS1, DLK1, and EPS8L2), and fat deposition (LANCL2, PPARγ). These findings provide a better understanding of the degree of inbreeding in Wenchang chickens and the hereditary basis of the characteristics shaped under selection. These results are valuable for the future breeding, conservation, and utilization of Wenchang and other chicken breeds.
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Affiliation(s)
- Shuaishuai Tian
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Wendan Tang
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Ziqi Zhong
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Ziyi Wang
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Xinfeng Xie
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Hong Liu
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Fuwen Chen
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Jiaxin Liu
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Yuxin Han
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Yao Qin
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Zhen Tan
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Qian Xiao
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
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Cheruiyot EK, Haile-Mariam M, Cocks BG, Pryce JE. Improving Genomic Selection for Heat Tolerance in Dairy Cattle: Current Opportunities and Future Directions. Front Genet 2022; 13:894067. [PMID: 35769985 PMCID: PMC9234448 DOI: 10.3389/fgene.2022.894067] [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: 03/11/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Heat tolerance is the ability of an animal to maintain production and reproduction levels under hot and humid conditions and is now a trait of economic relevance in dairy systems worldwide because of an escalating warming climate. The Australian dairy population is one of the excellent study models for enhancing our understanding of the biology of heat tolerance because they are predominantly kept outdoors on pastures where they experience direct effects of weather elements (e.g., solar radiation). In this article, we focus on evidence from recent studies in Australia that leveraged large a dataset [∼40,000 animals with phenotypes and 15 million whole-genome sequence variants] to elucidate the genetic basis of thermal stress as a critical part of the strategy to breed cattle adapted to warmer environments. Genotype-by-environment interaction (i.e., G × E) due to temperature and humidity variation is increasing, meaning animals are becoming less adapted (i.e., more sensitive) to changing environments. There are opportunities to reverse this trend and accelerate adaptation to warming climate by 1) selecting robust or heat-resilient animals and 2) including resilience indicators in breeding goals. Candidate causal variants related to the nervous system and metabolic functions are relevant for heat tolerance and, therefore, key for improving this trait. This could include adding these variants in the custom SNP panels used for routine genomic evaluations or as the basis to design specific agonist or antagonist compounds for lowering core body temperature under heat stress conditions. Indeed, it was encouraging to see that adding prioritized functionally relevant variants into the 50k SNP panel (i.e., the industry panel used for genomic evaluation in Australia) increased the prediction accuracy of heat tolerance by up to 10% units. This gain in accuracy is critical because genetic improvement has a linear relationship with prediction accuracy. Overall, while this article used data mainly from Australia, this could benefit other countries that aim to develop breeding values for heat tolerance, considering that the warming climate is becoming a topical issue worldwide.
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Affiliation(s)
- Evans K. Cheruiyot
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
- Centre for AgriBiosciences, Agriculture Victoria Research, AgriBio, Bundoora, VIC, Australia
| | - Mekonnen Haile-Mariam
- Centre for AgriBiosciences, Agriculture Victoria Research, AgriBio, Bundoora, VIC, Australia
- *Correspondence: Mekonnen Haile-Mariam,
| | - Benjamin G. Cocks
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
- Centre for AgriBiosciences, Agriculture Victoria Research, AgriBio, Bundoora, VIC, Australia
| | - Jennie E. Pryce
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
- Centre for AgriBiosciences, Agriculture Victoria Research, AgriBio, Bundoora, VIC, Australia
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Mohamadipoor Saadatabadi L, Mohammadabadi M, Amiri Ghanatsaman Z, Babenko O, Stavetska R, Kalashnik O, Kucher D, Kochuk-Yashchenko O, Asadollahpour Nanaei H. Signature selection analysis reveals candidate genes associated with production traits in Iranian sheep breeds. BMC Vet Res 2021; 17:369. [PMID: 34861880 PMCID: PMC8641187 DOI: 10.1186/s12917-021-03077-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 11/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sheep were among the first animals to be domesticated. They are raised all over the world and produce a major scale of animal-based protein for human consumption and play an important role in agricultural economy. Iran is one of the important locations for sheep genetic resources in the world. Here, we compared the Illumina Ovine SNP50 BeadChip data of three Iranian local breeds (Moghani, Afshari and Gezel), as a population that does not undergone artificial breeding programs as yet, and five other sheep breeds namely East Friesian white, East Friesian brown, Lacaune, DorsetHorn and Texel to detect genetic mechanisms underlying economical traits and daptation to harsh environments in sheep. RESULTS To identify genomic regions that have been targeted by positive selection, we used fixation index (Fst) and nucleotide diversity (Pi) statistics. Further analysis indicated candidate genes involved in different important traits such as; wool production included crimp of wool (PTPN3, NBEA and KRTAP20-2 genes), fiber diameter (PIK3R4 gene), hair follicle development (LHX2 gene), the growth and development of fiber (COL17A1 gene)), adaptation to hot arid environments (CORIN gene), adaptive in deficit water status (CPQ gene), heat stress (PLCB4, FAM107B, NBEA, PIK3C2B and USP43 genes) in sheep. CONCLUSIONS We detected several candidate genes related to wool production traits and adaptation to hot arid environments in sheep that can be applicable for inbreeding goals. Our findings not only include the results of previous researches, but also identify a number of novel candidate genes related to studied traits. However, more works will be essential to acknowledge phenotype- genotype relationships of the identified genes in our study.
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Affiliation(s)
| | | | - Zeinab Amiri Ghanatsaman
- Department of Animal Science, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Shiraz, Iran
| | - Olena Babenko
- Department of Animal Science, Bila Tserkva National Agrarian University, Soborna, Bila Tserkva, Kyivska Oblast, Ukraine
| | - Ruslana Stavetska
- Department of Animal Science, Bila Tserkva National Agrarian University, Soborna, Bila Tserkva, Kyivska Oblast, Ukraine
| | - Oleksandr Kalashnik
- Department of Animal Science, Sumy National Agrarian University, Sumy, Ukraine
| | - Dmytro Kucher
- Department of Breeding, Animal Genetics and Biotechnology, Polissia National University, Zhytomyr, Ukraine
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Yasoob TB, Khalid AR, Zhang Z, Zhu X, Hang S. Liver transcriptome of rabbits supplemented with oral Moringa oleifera leaf powder under heat stress is associated with modulation of lipid metabolism and up-regulation of genes for thermo-tolerance, antioxidation and immunity. Nutr Res 2021; 99:25-39. [DOI: 10.1016/j.nutres.2021.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 12/19/2022]
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Beer MA, Kane RA, Micheletti SJ, Kozakiewicz CP, Storfer A. Landscape genomics of the streamside salamander: Implications for species management in the face of environmental change. Evol Appl 2021; 15:220-236. [PMID: 35233244 PMCID: PMC8867708 DOI: 10.1111/eva.13321] [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: 01/29/2021] [Revised: 09/27/2021] [Accepted: 10/18/2021] [Indexed: 11/28/2022] Open
Abstract
Understanding spatial patterns of genetic differentiation and local adaptation is critical in a period of rapid environmental change. Climate change and anthropogenic development have led to population declines and shifting geographic distributions in numerous species. The streamside salamander, Ambystoma barbouri, is an endemic amphibian with a small geographic range that predominantly inhabits small, ephemeral streams. As A. barbouri is listed as near‐threatened by the IUCN, we describe range‐wide patterns of genetic differentiation and adaptation to assess the species’ potential to respond to environmental change. We use outlier scans and genetic‐environment association analyses to identify genomic variation putatively underlying local adaptation across the species’ geographic range. We find evidence for adaptation with a polygenic architecture and a set of candidate SNPs that identify genes putatively contributing to local adaptation. Our results build on earlier work that suggests that some A. barbouri populations are locally adapted despite evidence for asymmetric gene flow between the range core and periphery. Taken together, the body of work describing the evolutionary genetics of range limits in A. barbouri suggests that the species may be unlikely to respond naturally to environmental challenges through a range shift or in situ adaptation. We suggest that management efforts such as assisted migration may be necessary in future.
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Affiliation(s)
- Marc A. Beer
- School of Biological Sciences Washington State University Pullman WA 99164 USA
| | - Rachael A. Kane
- School of Biological Sciences Washington State University Pullman WA 99164 USA
| | | | - Christopher P. Kozakiewicz
- Department of Microbiology, Immunology, and Pathology Colorado State University Fort Collins CO 80523 USA
| | - Andrew Storfer
- School of Biological Sciences Washington State University Pullman WA 99164 USA
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Cheruiyot EK, Haile-Mariam M, Cocks BG, MacLeod IM, Xiang R, Pryce JE. New loci and neuronal pathways for resilience to heat stress in cattle. Sci Rep 2021; 11:16619. [PMID: 34404823 PMCID: PMC8371109 DOI: 10.1038/s41598-021-95816-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
While understanding the genetic basis of heat tolerance is crucial in the context of global warming's effect on humans, livestock, and wildlife, the specific genetic variants and biological features that confer thermotolerance in animals are still not well characterized. We used dairy cows as a model to study heat tolerance because they are lactating, and therefore often prone to thermal stress. The data comprised almost 0.5 million milk records (milk, fat, and proteins) of 29,107 Australian Holsteins, each having around 15 million imputed sequence variants. Dairy animals often reduce their milk production when temperature and humidity rise; thus, the phenotypes used to measure an individual's heat tolerance were defined as the rate of milk production decline (slope traits) with a rising temperature-humidity index. With these slope traits, we performed a genome-wide association study (GWAS) using different approaches, including conditional analyses, to correct for the relationship between heat tolerance and level of milk production. The results revealed multiple novel loci for heat tolerance, including 61 potential functional variants at sites highly conserved across 100 vertebrate species. Moreover, it was interesting that specific candidate variants and genes are related to the neuronal system (ITPR1, ITPR2, and GRIA4) and neuroactive ligand-receptor interaction functions for heat tolerance (NPFFR2, CALCR, and GHR), providing a novel insight that can help to develop genetic and management approaches to combat heat stress.
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Affiliation(s)
- Evans K. Cheruiyot
- grid.1018.80000 0001 2342 0938School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083 Australia ,grid.452283.a0000 0004 0407 2669Agriculture Victoria Research, Centre for AgriBiosciences, AgriBio, Bundoora, VIC 3083 Australia
| | - Mekonnen Haile-Mariam
- grid.452283.a0000 0004 0407 2669Agriculture Victoria Research, Centre for AgriBiosciences, AgriBio, Bundoora, VIC 3083 Australia
| | - Benjamin G. Cocks
- grid.1018.80000 0001 2342 0938School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083 Australia ,grid.452283.a0000 0004 0407 2669Agriculture Victoria Research, Centre for AgriBiosciences, AgriBio, Bundoora, VIC 3083 Australia
| | - Iona M. MacLeod
- grid.452283.a0000 0004 0407 2669Agriculture Victoria Research, Centre for AgriBiosciences, AgriBio, Bundoora, VIC 3083 Australia
| | - Ruidong Xiang
- grid.452283.a0000 0004 0407 2669Agriculture Victoria Research, Centre for AgriBiosciences, AgriBio, Bundoora, VIC 3083 Australia ,grid.1008.90000 0001 2179 088XFaculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC 3052 Australia
| | - Jennie E. Pryce
- grid.1018.80000 0001 2342 0938School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083 Australia ,grid.452283.a0000 0004 0407 2669Agriculture Victoria Research, Centre for AgriBiosciences, AgriBio, Bundoora, VIC 3083 Australia
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Wang K, Wu P, Wang S, Ji X, Chen D, Xiao W, Gu Y, Zeng Y, Xu X, Tang G. Differential DNA methylation analysis reveals key genes in Chinese Qingyu and Landrace pigs. Genome 2021; 65:1-8. [PMID: 34242523 DOI: 10.1139/gen-2021-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Chinese Qingyu pig is a typical domestic fatty pig breed and an invaluable indigenous genetic resource in China. Compared with the Landrace pig, the Qingyu pig has unique meat characteristics, including muscle development, intramuscular fat, and other meat quality traits. At present, few studies have explored epigenetic differences due to DNA methylation between the Qingyu pig and the Landrace pig. In this study, 30 Qingyu pigs and 31 Landrace pigs were subjected to reduced representation bisulfite sequencing (RRBS). Genome-wide differential DNA methylation analysis was conducted. Six genomic regions, including regions on Sus scrofa chromosome (SSC) 1: 266.09-274.23 Mb, SSC5: 0.88-10.68 Mb, SSC8: 41.23-48.51 Mb, SSC12: 45.43-54.38 Mb, SSC13: 202.15-207.95 Mb, and SSC14: 126.43-139.85 Mb, were regarded as key regions that may be associated with phenotypic differences between the Qingyu pig and the Landrace pig. Furthermore, according to further analysis, five differentially methylated genes (ADCY1, FUBP3, GRIN2B, KIT, and PIK3R6) were identified as key candidate genes that might be associated with meat characteristics. Our findings provide new insights into the differences in DNA methylation between the Qingyu pig and the Landrace pig. These results enrich the epigenetic research of the Chinese Qingyu pig.
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Affiliation(s)
- Kai Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Pingxian Wu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Shujie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiang Ji
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Dong Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Weihang Xiao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yiren Gu
- Sichuan Animal Science Academy, Chengdu, 610066, Sichuan, China
| | - Yangshuang Zeng
- Sichuan Animal Husbandry Station, Chengdu, 610041, Sichuan, China
| | - Xu Xu
- Sichuan Animal Husbandry Station, Chengdu, 610041, Sichuan, China
| | - Guoqing Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
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11
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Lee J, Lee S, Son J, Lim H, Kim E, Kim D, Ha S, Hur T, Lee S, Choi I. Analysis of circulating-microRNA expression in lactating Holstein cows under summer heat stress. PLoS One 2020; 15:e0231125. [PMID: 32866172 PMCID: PMC7458322 DOI: 10.1371/journal.pone.0231125] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 08/18/2020] [Indexed: 12/24/2022] Open
Abstract
Korean peninsula weather is rapidly becoming subtropical due to global warming. In summer 2018, South Korea experienced the highest temperatures since the meteorological observations recorded in 1907. Heat stress has a negative effect on Holstein cows, the most popular breed of dairy cattle in South Korea, which is susceptible to heat. To examine physiological changes in dairy cows under heat stress conditions, we analyzed the profiles circulating microRNAs isolated from whole blood samples collected under heat stress and non-heat stress conditions using small RNA sequencing. We compared the expression profiles in lactating cows under heat stress and non-heat stress conditions to understand the regulation of biological processes in heat-stressed cows. Moreover, we measured several heat stress indicators, such as rectal temperature, milk yield, and average daily gain. All these assessments showed that pregnant cows were more susceptible to heat stress than non-pregnant cows. In addition, we found the differential expression of 11 miRNAs (bta-miR-19a, bta-miR-19b, bta-miR-30a-5p, and several from the bta-miR-2284 family) in both pregnant and non-pregnant cows under heat stress conditions. In target gene prediction and gene set enrichment analysis, these miRNAs were found to be associated with the cytoskeleton, cell junction, vasculogenesis, cell proliferation, ATP synthesis, oxidative stress, and immune responses involved in heat response. These miRNAs can be used as potential biomarkers for heat stress.
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Affiliation(s)
- Jihwan Lee
- Dairy Science Division, National Institute of Animal Science, RDA, Cheon-an, Republic of Korea
| | - Soohyun Lee
- Department of Animal and Dairy Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Junkyu Son
- Dairy Science Division, National Institute of Animal Science, RDA, Cheon-an, Republic of Korea
| | - Hyeonju Lim
- Dairy Science Division, National Institute of Animal Science, RDA, Cheon-an, Republic of Korea
| | - Euntae Kim
- Dairy Science Division, National Institute of Animal Science, RDA, Cheon-an, Republic of Korea
| | - Donghyun Kim
- Dairy Science Division, National Institute of Animal Science, RDA, Cheon-an, Republic of Korea
| | - Seungmin Ha
- Dairy Science Division, National Institute of Animal Science, RDA, Cheon-an, Republic of Korea
| | - Taiyoung Hur
- Dairy Science Division, National Institute of Animal Science, RDA, Cheon-an, Republic of Korea
| | - Seunghwan Lee
- Department of Animal and Dairy Sciences, Chungnam National University, Daejeon, Republic of Korea
- * E-mail: (IC); (SL)
| | - Inchul Choi
- Department of Animal and Dairy Sciences, Chungnam National University, Daejeon, Republic of Korea
- * E-mail: (IC); (SL)
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12
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Liver Transcriptome Changes of Hyla Rabbit in Response to Chronic Heat Stress. Animals (Basel) 2019; 9:ani9121141. [PMID: 31847222 PMCID: PMC6940982 DOI: 10.3390/ani9121141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 12/11/2019] [Indexed: 01/04/2023] Open
Abstract
Simple Summary It has been widely acknowledged in farm animals that environmental heat stress would have comprehensive influences on many kinds of physiological aspects, including the metabolic characteristics, production performances, welfare concerns, etc. The rabbit is a small herbivore and needs to regulate the body temperature in a fine mechanism. Little is known, however, about the genes and pathways that are involved in the regulatory responses under chronic heat stress conditions. In the present study, we investigated the liver transcriptome changes in response to chronic heat stress for Hyla rabbit, that is a commercial meat breed recently introduced into China. We successfully revealed the differentially expressed genes that were significantly enriched in heat stress related biological processes. The results would help us for better understanding the molecular mechanisms underlying physiological responses against heat stress in rabbits. Abstract Rabbit is an economically important farm animal in China and also is a widely used animal model in biological researches. Rabbits are very sensitive to the environmental conditions, therefore we investigated the liver transcriptome changes in response to chronic heat stress in the present study. Six Hyla rabbits were randomly divided into two groups: chronic heat stress (HS) and controls without heat stress (CN). Six RNA-Seq libraries totally yielded 380 million clean reads after the quality filtering. Approximately 85.07% of reads were mapped to the reference genome. After assembling transcripts and quantifying gene expression levels, we detected 51 differentially expressed genes (DEGs) between HS and CN groups with thresholds of the adjusted p-value < 0.05 and |log2(FoldChange)| > 1. Among them, 33 and 18 genes were upregulated and downregulated, respectively. Gene ontology analyses further revealed that these DEGs were mainly associated with metabolism of lipids, thyroid hormone metabolic process, and cellular modified amino acid catabolic process. The upregulated ACACB, ACLY, LSS, and CYP7A1 genes were found to be inter-related through biological processes of thioester biosynthetic process, acyl-CoA biosynthetic process, acetyl-CoA metabolic process, and others. Six DEGs were further validated by quantitative real-time PCR analysis. The results revealed the candidate genes and biological processes that will potentially be considered as important regulatory factors involved in the heat stress response in rabbits.
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Li YX, Feng XP, Wang HL, Meng CH, Zhang J, Qian Y, Zhong JF, Cao SX. Transcriptome analysis reveals corresponding genes and key pathways involved in heat stress in Hu sheep. Cell Stress Chaperones 2019; 24:1045-1054. [PMID: 31428918 PMCID: PMC6882975 DOI: 10.1007/s12192-019-01019-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/17/2019] [Accepted: 06/20/2019] [Indexed: 12/20/2022] Open
Abstract
Heat stress (HS) seriously affects animal performance. In view of global warming, it is essential to understand the regulatory mechanisms by which animals adapt to heat stress. In this study, our aim was to explore the genes and pathways involved in heat stress in sheep. To this end, we used transcriptome analysis to understand the molecular responses to heat stress and thereby identify means to protect sheep from heat shock. To obtain an overview of the effects of heat stress on sheep, we used the hypothalamus for transcriptome sequencing and identified differentially expressed genes (DEGs; false discovery rate (FDR) < 0.01; fold change > 2) during heat stress. A total of 1423 DEGs (1122 upregulated and 301 downregulated) were identified and classified into Gene Ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Heat stress triggered dramatic and complex alterations in gene expression in the hypothalamus. We hypothesized that heat stress induced apoptosis and dysfunction in cells and vital organs and affected growth, development, reproduction, and circadian entrainment via the calcium signaling pathway, which influences ribosome assembly and function. Real-time PCR was used to evaluate the expression of the genes regulating important biological functions or whose expression profiles were significantly changed after acute heat stress (FDR < 0.01; fold change > 4), and the results showed that the expression patterns of these genes were consistent with the results of transcriptome sequencing, indicating that the credibility of the sequencing results. Our data indicated that heat stress induced calcium dyshomeostasis, blocked biogenesis, caused ROS accumulation, impaired the antioxidant system and innate defense, and induced apoptosis through the P53 signaling pathway activated by PEG3, decreased growth and development, and enhanced organ damage. These data is very important and helpful to elucidate the molecular mechanism of heat stress and finally to find ways to deal with heat stress damage in sheep.
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Affiliation(s)
- Y X Li
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China
- Key Laboratory of Crop and Animal Integrated Farming, Ministry of Agriculture, Nanjing, 210014, China
| | - X P Feng
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China
- Key Laboratory of Crop and Animal Integrated Farming, Ministry of Agriculture, Nanjing, 210014, China
| | - H L Wang
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China
- Key Laboratory of Crop and Animal Integrated Farming, Ministry of Agriculture, Nanjing, 210014, China
| | - C H Meng
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China
- Key Laboratory of Crop and Animal Integrated Farming, Ministry of Agriculture, Nanjing, 210014, China
| | - J Zhang
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China
- Key Laboratory of Crop and Animal Integrated Farming, Ministry of Agriculture, Nanjing, 210014, China
| | - Y Qian
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China
- Key Laboratory of Crop and Animal Integrated Farming, Ministry of Agriculture, Nanjing, 210014, China
| | - J F Zhong
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China
- Key Laboratory of Crop and Animal Integrated Farming, Ministry of Agriculture, Nanjing, 210014, China
| | - S X Cao
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
- The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, 210014, China.
- Key Laboratory of Crop and Animal Integrated Farming, Ministry of Agriculture, Nanjing, 210014, China.
- Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, China.
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14
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A Discovery of Relevant Hepatoprotective Effects and Underlying Mechanisms of Dietary Clostridium butyricum Against Corticosterone-Induced Liver Injury in Pekin Ducks. Microorganisms 2019; 7:microorganisms7090358. [PMID: 31527489 PMCID: PMC6780423 DOI: 10.3390/microorganisms7090358] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/30/2019] [Accepted: 09/12/2019] [Indexed: 02/06/2023] Open
Abstract
Clostridium butyricum (C. butyricum) can attenuate oxidative stress, inflammation, and hepatic fatty deposition in poultry, however, the underlying mechanisms for this in Pekin ducks remain unclear. This study evaluated these hepatoprotective effects and the underlying mechanisms in a corticosterone (CORT)-induced liver injury model in Pekin ducks fed a C. butyricum intervention diet. A total of 500 Pekin ducks were randomly divided into five groups: one group (CON group) was only provided with a basal diet, three groups were provided a basal diet with 200 mg/kg (LCB group), 400 mg/kg (MCB group), or 600 mg/kg (HCB group) C. butyricum, respectively, and one group was provided a basal diet with 150 mg/kg aureomycin (ANT group) for 42 d. At 37 days-old, all ducks received daily intraperitoneal injections of CORT for five days to establish a liver injury model. C. butyricum intervention alleviated liver injury by decreasing the liver organ indices, hepatic steatosis and hepatocyte necrosis, and improving liver function, antioxidant capacity, and inflammatory factors. Hepatic RNA-seq revealed 365 differentially expressed genes (DEGs) between the MCB and CON groups, with 229 up- and 136 down-regulated DEGs in the MCB group. Between the MCB and ANT groups, 407 DEGs were identified, including 299 up- and 108 down-regulated genes in MCB group. Some DEGs in the MCB group related to oxidative stress and inflammatory responses such as Sod3, Tlr2a/b, and Il10, which were up-regulated, while Apoa1, Cyp7a1, Acsl1/5, Fasn, Ppar-γ, and Scd, which are involved in lipid metabolism, were down-regulated, indicating that these genes were responsive to dietary C. butyricum for the alleviation of corticosterone-induced hepatic injury. Toll-like receptor signaling, PI3K-Akt signaling pathway, cytokine-cytokine receptor interaction, peroxisome proliferator-activated receptor (PPAR) signaling pathway, adipocytokine and glycerophospholipid metabolism signaling pathway were significantly enriched in the MCB group. These findings indicate that C. butyricum intervention can protect Pekin ducks from corticosterone-induced liver injury by the modulation of immunoregulatory- and lipid metabolism-related genes and pathways.
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15
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Te Pas MFW, Park W, Srikanth K, Kemp S, Kim JM, Lim D, Park JE. Transcriptomic profiles of muscle, heart, and spleen in reaction to circadian heat stress in Ethiopian highland and lowland male chicken. Cell Stress Chaperones 2019; 24:175-194. [PMID: 30565091 PMCID: PMC6363629 DOI: 10.1007/s12192-018-0954-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 11/14/2018] [Accepted: 11/24/2018] [Indexed: 01/25/2023] Open
Abstract
Temperature stress impacts both welfare and productivity of livestock. Global warming is expected to increase the impact, especially in tropical areas. We investigated the biological mechanisms regulated by temperature stress due to the circadian temperature cycle in temperature adapted and non-adapted chicken under tropical conditions. We studied transcriptome profiles of heart, breast muscle, and spleen tissues of Ethiopian lowland chicken adapted to high circadian temperatures and non-adapted Ethiopian highland chicken under lowland conditions at three points during the day: morning, noon, and evening. Functional annotations and network analyses of genes differentially expressed among the time points of the day indicate major differences in the reactions of the tissues to increasing and decreasing temperatures, and also the two chickens lines differ. However, epigenetic changes of chromatin methylation and histone (de)acetylation seemed to be central regulatory mechanisms in all tissues in both chicken lines. Finally, all tissues showed differentially expressed genes between morning and evening times indicating biological mechanisms that need to change during the night to reach morning levels again the next day.
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Affiliation(s)
- Marinus F W Te Pas
- Wageningen UR Livestock Research, Animal Breeding and Genomics, Wageningen, The Netherlands.
| | - Woncheoul Park
- Department of Animal Biotechnology and Environment, Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Krishnamoorthy Srikanth
- Department of Animal Biotechnology and Environment, Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Steve Kemp
- Animal Biosciences, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Dajeong Lim
- Department of Animal Biotechnology and Environment, Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Jong-Eun Park
- Department of Animal Biotechnology and Environment, Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea.
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16
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Park W, Srikanth K, Lim D, Park M, Hur T, Kemp S, Dessie T, Kim MS, Lee SR, te Pas MFW, Kim JM, Park JE. Comparative transcriptome analysis of Ethiopian indigenous chickens from low and high altitudes under heat stress condition reveals differential immune response. Anim Genet 2018; 50:42-53. [DOI: 10.1111/age.12740] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2018] [Indexed: 01/22/2023]
Affiliation(s)
- W. Park
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science, RDA; Wanju 55365 Korea
| | - K. Srikanth
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science, RDA; Wanju 55365 Korea
| | - D. Lim
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science, RDA; Wanju 55365 Korea
| | - M. Park
- Animal Breeding and Genomics Division; National Institute of Animal Science, RDA; Wanju 55365 Korea
| | - T. Hur
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science, RDA; Wanju 55365 Korea
| | - S. Kemp
- Animal Biosciences; International Livestock Research Institute (ILRI); P.O. Box 30709 Nairobi 00100 Kenya
| | - T. Dessie
- Animal Biosciences; International Livestock Research Institute (ILRI); P.O. Box 5689 Addis Ababa Ethiopia
| | - M. S. Kim
- Department of Animal Science; College of Agriculture and Life Sciences; Chonnam National University; Republic of Korea Gwangju 61186 Korea
| | - S.-R. Lee
- Department of Agro-biotechnology Convergence; Jeonju University; Republic of Korea 55069 Jeonju Korea
| | - M. F. W. te Pas
- Animal Breeding and Genomics; Wageningen UR Livestock Research; 6700AH Wageningen The Netherlands
| | - J.-M. Kim
- Department of Animal Science and Technology; Chung-Ang University; Anseong Gyeonggi-do 17546 Korea
| | - J.-E. Park
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science, RDA; Wanju 55365 Korea
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