Dataset Information

Whole-genome sequences of 89 Chinese sheep suggest role of RXFP2 in the development of unique horn phenotype as response to semi-feralization.

ABSTRACT: Background:Animal domestication has been extensively studied, but the process of feralization remains poorly understood. Results:Here, we performed whole-genome sequencing of 99 sheep and identified a primary genetic divergence between 2 heterogeneous populations in the Tibetan Plateau, including 1 semi-feral lineage. Selective sweep and candidate gene analysis revealed local adaptations of these sheep associated with sensory perception, muscle strength, eating habit, mating process, and aggressive behavior. In particular, a horn-related gene, RXFP2, showed signs of rapid evolution specifically in the semi-feral breeds. A unique haplotype and repressed horn-related tissue expression of RXFP2 were correlated with higher horn length, as well as spiral and horizontally extended horn shape. Conclusions:Semi-feralization has an extensive impact on diverse phenotypic traits of sheep. By acquiring features like those of their wild ancestors, semi-feral sheep were able to regain fitness while in frequent contact with wild surroundings and rare human interventions. This study provides a new insight into the evolution of domestic animals when human interventions are no longer dominant.

SUBMITTER: Pan Z

PROVIDER: S-EPMC5905515 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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Whole-genome sequences of 89 Chinese sheep suggest role of RXFP2 in the development of unique horn phenotype as response to semi-feralization.

Pan Zhangyuan Z Li Shengdi S Liu Qiuyue Q Wang Zhen Z Zhou Zhengkui Z Di Ran R Miao Benpeng B Hu Wenping W Wang Xiangyu X Hu Xiaoxiang X Xu Ze Z Wei Dongkai D He Xiaoyun X Yuan Liyun L Guo Xiaofei X Liang Benmeng B Wang Ruichao R Li Xiaoyu X Cao Xiaohan X Dong Xinlong X Xia Qing Q Shi Hongcai H Hao Geng G Yang Jean J Luosang Cuicheng C Zhao Yiqiang Y Jin Mei M Zhang Yingjie Y Lv Shenjin S Li Fukuan F Ding Guohui G Chu Mingxing M Li Yixue Y

GigaScience 20180401 4

<h4>Background</h4>Animal domestication has been extensively studied, but the process of feralization remains poorly understood.<h4>Results</h4>Here, we performed whole-genome sequencing of 99 sheep and identified a primary genetic divergence between 2 heterogeneous populations in the Tibetan Plateau, including 1 semi-feral lineage. Selective sweep and candidate gene analysis revealed local adaptations of these sheep associated with sensory perception, muscle strength, eating habit, mating proce ...[more]

PMID: 29668959

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Project description:BackgroundThe mode of inheritance of horn status in sheep is far more complex than a superficial analysis might suggest. Observations, which were mostly based on crossbreeding experiments, indicated that the allele that results in horns is dominant in males and recessive in females, and some authors even speculated about the involvement of more than two alleles. However, all recent genome-wide association analyses point towards a very strong effect of a single autosomal locus on ovine chromosome 10, which was narrowed down to a putatively causal insertion polymorphism in the 3'-untranslated region of the relaxin/insulin-like family peptide receptor 2 gene (RXFP2). The main objective of this study was to test this insertion polymorphism as the causal mutation in diverse sheep breeds, including breeds with a variable and/or sex-dependent horn status.ResultsAfter re-sequencing a region of about 246 kb that covered the RFXP2 gene and its flanking regions for 24 sheep from six completely horned and six completely polled breeds, we identified the same insertion polymorphism that was previously published as segregating with horn status in these breeds. Multiplex PCR genotyping of 489 sheep from 34 breeds and some crosses between sheep breeds showed a nearly perfect segregation of the insertion polymorphism with horn status in sheep breeds of Central and Western European origin. In these breeds and their crossings, heterozygous males were horned and heterozygous females were polled. However, this segregation pattern was not, or at least not completely, reproducible in breeds with sex-dependent and/or variable horn status, especially in sheep that originated from even more southern European regions and from Africa. In such breeds, we observed almost all possible combinations of genotype, sex and horn status phenotype.ConclusionsThe 1.78-kb insertion polymorphism in the 3'-untranslated region of RXFP2 and SNPs in the 3'-UTR, exon 14 and intron 11 of this gene that we analyzed in this study cannot be considered as the only cause of polledness in sheep and are not useful as a universal marker to define the genetic horn status in sheep.

Project description:BACKGROUND:Tardigrades are renowned for their ability to enter cryptobiosis (latent life) and endure extreme stress, including desiccation and freezing. Increased focus is on revealing molecular mechanisms underlying this tolerance. Here, we provide the first transcriptomes from the heterotardigrade Echiniscoides cf. sigismundi and the eutardigrade Richtersius cf. coronifer, and compare these with data from other tardigrades and six eukaryote models. Investigating 107 genes/gene families, our study provides a thorough analysis of tardigrade gene content with focus on stress tolerance. RESULTS:E. cf. sigismundi, a strong cryptobiont, apparently lacks expression of a number of stress related genes. Most conspicuous is the lack of transcripts from genes involved in classical Non-Homologous End Joining. Our analyses suggest that post-cryptobiotic survival in tardigrades could rely on high fidelity transcription-coupled DNA repair. Tardigrades seem to lack many peroxins, but they all have a comprehensive number of genes encoding proteins involved in antioxidant defense. The "tardigrade unique proteins" (CAHS, SAHS, MAHS, RvLEAM), seem to be missing in the heterotardigrade lineage, revealing that cryptobiosis in general cannot be attributed solely to these proteins. Our investigation further reveals a unique and highly expressed cold shock domain. We hypothesize that the cold shock protein acts as a RNA-chaperone involved in regulation of translation following freezing. CONCLUSIONS:Our results show common gene family contractions and expansions within stress related gene pathways in tardigrades, but also indicate that evolutionary lineages have a high degree of divergence. Different taxa and lineages may exhibit unique physiological adaptations towards stress conditions involving possible unknown functional homologues and/or novel physiological and biochemical mechanisms. To further substantiate the current results genome assemblies coupled with transcriptome data and experimental investigations are needed from tardigrades belonging to different evolutionary lineages.

Dataset Information

Whole-genome sequences of 89 Chinese sheep suggest role of RXFP2 in the development of unique horn phenotype as response to semi-feralization.

Publications

Whole-genome sequences of 89 Chinese sheep suggest role of RXFP2 in the development of unique horn phenotype as response to semi-feralization.

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