Convergent genomic signatures of high-altitude adaptation among domestic mammals

Wu, Dongdong; Yang, Cuiping; Wang, Mingshan; Dong, Kunzhe; Yan, Dawei; Hao, Ziqian; Fan, Songqing; Chu, Shuzhou; Shen, Qingwu; Jiang, Liping; Li, Yan; Zeng, Lin; Liu, He-Qun; Xie, Hailian; Ma, You-Zhi; Kong, Xiaoyan; Yang, Shuli; Dong, Xinxing; Esmailizadeh, Ali; Irwin, David M.; Xiao, Xiao; Li, Ming; Dong, Yang; Wang, Wen; Shi, Peng; Li, Haipeng; Ma, Yue; Gou, Xin; Chen, Yongbin; Zhang, Yaping

doi:10.1093/nsr/nwz213

Cited by 79 publications

(46 citation statements)

References 67 publications

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“…ZFAND2A is predicted to be a target gene of the HIF1A transcription factor using known transcription factor binding site motifs from the TRANSFAC database [48,49]. Moreover, ZFAND2A was recently reported to undergo positive selection and exhibit significantly downregulated expression in the Tibetan pig [50]. Meanwhile, activation of GPER1 by 17β-estradiol (E2) and the specific agonist G-1 will trigger a GPER1-EGFR-MAPK1-FOS signaling pathway, leading to the increased expression level of VEGF through upregulation of HIF1A [51,52].…”

Section: Discussionmentioning

confidence: 99%

Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

Cheng

Liu

et al. 2021

Genome Biol

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Background Structural variation (SV) acts as an essential mutational force shaping the evolution and function of the human genome. However, few studies have examined the role of SVs in high-altitude adaptation and little is known of adaptive introgressed SVs in Tibetans so far. Results Here, we generate a comprehensive catalog of SVs in a Chinese Tibetan (n = 15) and Han (n = 10) population using nanopore sequencing technology. Among a total of 38,216 unique SVs in the catalog, 27% are sequence-resolved for the first time. We systematically assess the distribution of these SVs across repeat sequences and functional genomic regions. Through genotyping in additional 276 genomes, we identify 69 Tibetan-Han stratified SVs and 80 candidate adaptive genes. We also discover a few adaptive introgressed SV candidates and provide evidence for a deletion of 335 base pairs at 1p36.32. Conclusions Overall, our results highlight the important role of SVs in the evolutionary processes of Tibetans’ adaptation to the Qinghai-Tibet Plateau and provide a valuable resource for future high-altitude adaptation studies.

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Section: Discussionmentioning

confidence: 99%

Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

Cheng

Liu

et al. 2021

Genome Biol

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“…However, the approach using Genes 2021, 12, 480 2 of 12 candidate genes/loci did not work well. Notwithstanding the convergent genomic signatures of domestication and high-altitude adaptation that have been explored in sheep and goats [10,11], thus far, there has been a paucity of research on the genetic convergence of prolificacy from a whole-genome perspective. We hypothesize that the genetic convergence of prolificacy occurred in goats and sheep, likely because they were exposed to similar natural and/or artificial selection forces.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analyses Reveal Genetic Convergence of Prolificacy between Goats and Sheep

Lin

Jiang

et al. 2021

Genes

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The litter size of domestic goats and sheep is an economically important trait that shows variation within breeds. Strenuous efforts have been made to understand the genetic mechanisms underlying prolificacy in goats and sheep. However, there has been a paucity of research on the genetic convergence of prolificacy between goats and sheep, which likely arose because of similar natural and artificial selection forces. Here, we performed comparative genomic and transcriptomic analyses to identify the genetic convergence of prolificacy between goats and sheep. By combining genomic and transcriptomic data for the first time, we identified this genetic convergence in (1) positively selected genes (CHST11 and SDCCAG8), (2) differentially expressed genes (SERPINA14, RSAD2, and PPIG at follicular phase, and IGF1, GPRIN3, LIPG, SLC7A11, and CHST15 at luteal phase), and (3) biological pathways (genomic level: osteoclast differentiation, ErbB signaling pathway, and relaxin signaling pathway; transcriptomic level: the regulation of viral genome replication at follicular phase, and protein kinase B signaling and antigen processing and presentation at luteal phase). These results indicated the potential physiological convergence and enhanced our understanding of the overlapping genetic makeup underlying litter size in goats and sheep.

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“…Data analysis was completed using Vcftools (0.1.15) [ 19 ] software. In brief, the Fst value in the chromosome was calculated with 500 kb as the sliding window and 50 kb as the step window [ 20 , 21 ], followed by extraction of the sites in the window where the Fst and θπ ratio were in the top 5% [ 22 ]. These sites were regarded as significant SNP candidate sites for the selective signatures.…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Selective Signatures Reveal Candidate Genes Associated with Hair Follicle Development and Wool Shedding in Sheep

Lei

Sun

Guo

et al. 2021

Genes

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Hair follicle development and wool shedding in sheep are poorly understood. This study investigated the population structures and genetic differences between sheep with different wool types to identify candidate genes related to these traits. We used Illumina ovine SNP 50K chip genotyping data of 795 sheep populations comprising 27 breeds with two wool types, measuring the population differentiation index (Fst), nucleotide diversity (θπ ratio), and extended haplotype homozygosity among populations (XP-EHH) to detect the selective signatures of hair sheep and fine-wool sheep. The top 5% of the Fst and θπ ratio values, and values of XP-EHH < −2 were considered strongly selected SNP sites. Annotation showed that the PRX, SOX18, TGM3, and TCF3 genes related to hair follicle development and wool shedding were strongly selected. Our results indicated that these methods identified important genes related to hair follicle formation, epidermal differentiation, and hair follicle stem cell development, and provide a meaningful reference for further study on the molecular mechanisms of economically important traits in sheep.

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Convergent genomic signatures of high-altitude adaptation among domestic mammals

Cited by 79 publications

References 67 publications

Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

Genome-Wide Analyses Reveal Genetic Convergence of Prolificacy between Goats and Sheep

Genome-Wide Selective Signatures Reveal Candidate Genes Associated with Hair Follicle Development and Wool Shedding in Sheep

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