- We found an evidence of admixture between Tibetan chickens and other domestic population. - By comparing the genomes of the Tibetan and lowland fowls, we identified genes associated with high-altitude adaptation in Tibetan chickens were mainly involved in energy metabolism, body size maintenance and available food sources.. - Since the domestication of the red jungle fowl (Gallus gallus) (approximately 8000 to 5400 BC) in Asia [1], domestic chickens (Gallus Gallus domesticus) have been subject to the combined effects of natural and artificial selection. - For example, game fowl are a group of breeds selected specifically for cockfighting, and fighting cocks possess congenital aggres- sion towards all males of the same species [3]. - 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - Full list of author information is available at the end of the article Li et al. - components that are shaped by high-altitude adaptations in the Tibetan chicken.. - To further investigate genomic variations underlying the domestication of chicken breeds and the high-altitude adaptation of Tibetan chickens, the whole genomes of 86 domestic chickens, including 50 lowland chickens from 9 phenotypically diverse breeds in China and 36 Tibetan chickens from 6 Qinghai-Tibetan Plateau lo- calities (Additional file 1: Table S1), together with 5 red jungle fowls (RJFs), were used for a comparative population genomics analysis. - In addition, we per- formed pairwise comparisons of the genome-wide va- riation between the 15 domestic chicken populations.. - Once again, we found that higher population genetic dif- ferentiation was detected in the Z chromosome than in any of the autosomes (Additional file 1: Figure S3). - The overall distribution of the lengths of isochores showed that more than 40% of the isochores had 37–. - The number of SNPs and the GC level are posi- tively correlated in the isochores of the chicken genome (r = 0.73, p = 0) (Fig. - Surprisingly, the number of indels and the GC level in the isochores are negatively correlated in the whole chicken population (r. - The opposite trends of SNP and indel density in the con- text of GC level are probably due to crossing over event, the influence of natural selection and environmental pres- sure. - The isochore families consist of and 2.55% of the chicken genome for L1, L2, H1, H2, and H3 isochore, respectively. - Herein, we show that H1 isochore is the dominant source of genetic variation in the chicken genome. - indels) also represents remarkable variation, while present in small amounts in the genome. - An analysis of SNPs in 91 fowls shows that the single nucleotide mutation rate is highly dependent on the GC content of the genome, which is also the case in humans [10].. - Linkage disequilibrium (LD) analysis showed that Tibetan chicken populations had a faster LD decay rate than other domestic chicken breeds, as did RJFs (Additional file 1: Figure S7A), reflecting a relatively high level of inbreeding under artificial breeding pro- grams and, consequently, lower genomic diversity in the more heavily domesticated chickens. - Interestingly, when K = 4 and K = 5 population clusters were tested, the observed admixture patterns of the Miyi chicken and the Pengxian yellow chicken which is two dis- tinct population living in lowland areas have a different genetic background to other indigenous chickens, respect- ively. - Intensive crossbreeding has occurred in the past, and. - Our population structure analyses indicate a recent history of mutual introgression between Tibetan chickens and other breeds, as well as be- tween wild RJFs and domestic populations. - Introgression signatures were widespread in the domestic chicken popu- lations. - Archaeological discoveries in the Indus Valley and in Hebei Province, China, suggest that chickens were probably domesticated from the red jungle fowl as early as 5400 BC [14]. - More introgression from RJFs to Tibetan chickens (the average number of IBDs is 3144) were found com- pared to others (the average number of IBDs is 2150).. - We found evidence of admixture between Tibetan chickens and other domesticated individuals possibly due to the influence of increased human activity with K changing progressively from 2 to 7. - Genome-wide selective sweep signals in domestic fowls To accurately detect the genomic footprints left by the intense artificial selection pressure, we performed pair- wise comparisons of the genome-wide variation between the wild fowls and 10 geographically close but phenoty- pically diverse domestic breeds. - We identified genomic regions (with a total size of Mb, corresponding to 2.61 to 3.63% of the genome and containing 337–645 genes per. - 10 − 16 , Mann-Whitney U test) in the log 2 (θ π ratio) and F ST. - Stri- kingly, five genes (CH25H, PANK1, LIPA, SLC16A12 and IFIT5) in an 80-kb region Mb) of chromo- some 6 were under positive selection in at least five of the domestic populations, which had the highest values of F ST , at and of zF ST , at p <. - IFIT5 confers antiviral defense by disrupting protein-protein in- teractions in the host translation initiation machinery [16], and its expression is induced in ducks upon infection with influenza virus [17]. - SLC16A12 is a member of the carboxylic acid transporter family, essential for the establishment and/or maintenance of homeostasis in the lenses and kidneys. - Mutations in SLC16A12 lead to deficiency in the transportation of metabolites, contributing to the development of cataracts and renal glycosuria in humans [20]. - correlation between variations and GC content of the genome and population structures. - a Boxplot showing the difference in the number of heterozygous SNP per base pair between the Z chromosome and all autosomes.. - Correlation between the number of SNPs (b) or the number of indels (c) in 91 chickens and the GC level in the isochores of the chicken genome. - causative mutation is located 103 base pairs upstream of the coding sequence of PDSS2. - In addition, in this study, we found a SNP (chr located in the coding region of PDSS2 that is specific for this breed, and the function of this mutation has not been reported yet.. - The length of the genomic region with strong selective sweep signals is shown for each breed. - The numbers of shared genes and breed- specific genes in the region are also listed. - Violin plots show the zF ST values and the θ π ratio for the regions of the breeds that have undergone selection (grey) versus the whole genome (red) (bottom panels). - b Genomic region with strong selective sweep signals on chromosome 6 in the domestic chicken breeds. - c A heatmap shows the selected SNP sites and the region containing SLC16A12 , LIPA, PDSS2, MC1R, TUBB3 and IFIT5 from RJFs, Tibetan chickens and other domestic chicken breeds. - the sweep was located in the upstream non-coding region of the SMPD3 gene. - The highest differentiation peak in the Shimian Caoke fowl occurred in a region containing the GLI3 gene (F ST = 0.66, zF ST = 7.04, p <. - 0.001), which plays a role in the patterning of the brain and limbs [25]. - In chicken, BMP7 was found to be upregulated in hyperpigmentation of the visceral peritoneum (HVP) affected chickens [31]. - They found that a complex genomic rearrangement involving the endothelin 3 locus causes dermal hyperpigmentation in the Chicken [32]. - It seems that positive selection of game fowls leads to convergence of neural activity, and defects in relevant genes have been implicated in the pathogenesis of Alzheimer’s and Parkin- son’ s diseases. - For example, APP , SNCA and PPT1 are in- volved in neural activity, and defects in those genes have been implicated in the pathogenesis of Alzheimer’s disease, Parkinson’ s disease, and infantile neuronal ceroid lipofusci- nosis, respectively [33–35]. - In addition, many genes related to muscle development and cardiovascular activity, such as FGF14 [36], VCL [37], MYH11 and SYNE1 [38] were also found to be altered in the game breeds. - A network of the proteins encoded by specific genes (Fig. - High-altitude adaptation in Tibetan chickens. - We discovered five genes under selection in all Tibetan chickens (TRIT1, HPCAL4, NT5C1A, LOC419677, and HEYL) in a small region (40 kb) of chromosome 23 that showed high zF ST. - This gene has been identified among a set of tran- scripts that are differentially expressed during high-altitude acclimatization in the Indian Air Force and Army Aviation Corps populations and is postulated to allow for more efficient oxygen utilization [42]. - HEYL is a member of the Hairy-related transcription factor (HRT) family. - Therefore, NT5C1A and HEYL may be involved in the high-altitude adaption of oxygen delivery in Tibetan chickens. - Several candidate genes in the calcium-signaling pathway may be involved in the hypoxia adaptation experienced by Tibetan chick- ens [45]. - Additionally, few of the positively selected genes were involved in the hypoxia-inducible factor 1 signaling pathway, which is primarily utilized in response to hypoxia in mammals such as humans [46, 47], Tibetan Mastiffs [48, 49] and horses [50]. - However, none of the candidates occurred at a high frequency in these Tibetan chicken lineages. - PKD2L1 encodes a member of the polycystin protein family that is an integral membrane protein involved in cell-cell/matrix interactions. - WHDG feed is potentially part of why PKD2L1 has been under selection in Tibetan chickens. - EVI5 is involved in the regulation of GTPase activity. - Muta- tions in the coding region of EVI5 aligned with the ortholo- gous protein sequences from 4 other vertebrates were shown in Additional file 1: Figure S12B. - Further studies are needed to confirm whether ZDHHC9 is involved in high-altitude adaption.. - In summary, we found that genes associated with high-altitude adaptation in Tibetan chickens were mainly involved in energy metabolism, body size maintenance and digestion, which could be related the chilly climate of the highlands, the high body temperature characteristic of. - Transcriptome data from lowland and Tibetan chickens are needed to further explore the high-altitude hypoxia adaption of birds.. - Comparison of the genome sequences of red jungle fowls, nine lowland domestic chicken breeds and Tibetan chickens provided insights into the distinct evolu- tionary scenarios occurring under artificial selection for agricultural production and under natural selection for success at a high altitude. - Our results indicate that Tibetan chickens evolved in adaptation to a high-altitude alpine environ- ment during their long history of living at high altitudes.. - Genome sequencing, analysis of the population structure and evolutionary history. - Description and quantification of the phenotypic diversity of each breed are provided in Additional file 1: Table S7. - To detect characteristics that have under- gone selection associated with high altitude or domesti- cation, we measured the genome-wide variation between the highland (Qinghai-Tibetan Plateau) and lowland groups (Sichuan Basin) and the genome-wide variation between the domesticated breeds and the RJFs. - The gene annotation is performed in the selected genomic regions according to the reference chicken genome. - Genes were submitted to DAVID (https://david.ncifcrf.gov/) for enrichment analysis of the significant overrepresentation of GO biological process (GO-BP) and molecular function (GO-MF) terms, as well as InterPro domains and KEGG pathways. - In all tests, the whole set of known chicken genes was defined as the background, and p values (i.e., EASE scores), indi- cating the significance of the overlap between various gene sets, were calculated using a modified Fisher’s exact test corrected by the Benjamini-Hochberg procedure.. - The design and initiation of the study were supported by grants from the Sichuan Provincial Department of Science &. - Sample collection and main body of the work were funded by the National Natural Science Foundation of China (31402063 and the China Agricultural Research System (CARS-41), the 13th Five-Year Plan for breeding programs in Sichuan – Selective breeding of new breeds and synthetic strains of broiler (2016NYZ0025 and 2016NYZ0043). - Genome sequencing and publication costs of this article were supported by the National Program for Support of Top-notch Young Professionals and the Young Scholars of the Yangtze River.. - All data generated or analyzed in the present study are included in this article and can be found in the Additional files 1 and 2. - The genomic signature of sexual selection in the genetic diversity of the sex chromosomes and autosomes. - CpG mutation rates in the human genome are highly dependent on local GC content. - Next-generation sequencing reveals genomic features in the Japanese quail. - Multiple maternal origins of chickens: out of the Asian jungles. - Cholesteryl ester storage disease: review of the findings in 135 reported patients with an underdiagnosed disease. - Genome-wide analysis of the ovodefensin gene family: monophyletic origin, independent gene duplication and presence of different selection patterns. - Neutral sphingomyelinase 2 (smpd3) in the control of postnatal growth and development. - Temporally regulated expression of Lin-28 in diverse tissues of the developing mouse. - Impact of high altitude on the hepatic fatty acid oxidation and synthesis in rats. - Genetic parameters and genome-wide association study of hyperpigmentation of the visceral peritoneum in chickens. - A complex genomic rearrangement involving the endothelin 3 locus causes dermal hyperpigmentation in the chicken. - A mutation in the fibroblast growth factor 14 gene is associated with autosomal dominant cerebellar ataxia [corrected]. - Evaluation of the effects of different culture media on the myogenic differentiation potential of adipose tissue- or bone marrow-derived human mesenchymal stem cells. - The cytoplasmic and nuclear populations of the eukaryote tRNA-isopentenyl transferase have distinct functions with implications in human cancer. - Hypoxic signature of high altitude acclimatization: a gene expression study. - Blood characteristics for high altitude adaptation in Tibetan chickens. - Genomic analyses reveal potential independent adaptation to high altitude in Tibetan chickens. - A genetic mechanism for Tibetan high-altitude adaptation. - Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia. - Population variation revealed high-altitude adaptation of Tibetan mastiffs. - A genome wide study of genetic adaptation to high altitude in feral Andean horses of the paramo
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