Biology subjects

Otecko, N. O.

Publications and source records attributed to Otecko, N. O..

3 recordsLinked to original sources

bioRxiv2020

Integrating Genomic and Transcriptomic Data to Reveal Genetic Mechanisms Underlying Piao Chicken Rumpless Trait

Piao chicken, a rare Chinese native poultry breed, lacks primary tail structures, such as pygostyle, caudal vertebra, uropygial gland and tail feathers. So far, the molecular mechanisms underlying tail absence in this breed have remained unclear. We employed comprehensive comparative transcriptomic and genomic analyses to unravel potential genetic underpinnings of rumplessness in the Piao chicken. Our results reveal many biological factors involved in tail development and several genomic regions under strong positive selection in this breed. These regions contain candidate genes associated with rumplessness, including IRX4, IL-18, HSPB2, and CRYAB. Retrieval of quantitative trait loci (QTL) and gene functions implied that rumplessness might be consciously or unconsciously selected along with the high-yield traits in Piao chicken. We hypothesize that strong selection pressures on regulatory elements might lead to gene activity changes in mesenchymal stem cells of the tail bud and eventually result in tail truncation by impeding differentiation and proliferation of the stem cells. Our study provides fundamental insights into early initiation and genetic bases of the rumpless phenotype in Piao chicken.

genetics↗

bioRxiv2018

Genomic analysis of dingoes identifies genomic regions under reversible selection during domestication and feralization

Dingoes (Canis dingo) are wild canids living in Australia. They have lived isolated from both the wild and the domestic ancestor and are a unique model for studying feralization, the process in which a domestic species escapes human control, adapts to the wild, and diverges from the domestic ancestor into a genetically distinct population. Here, we sequenced the genomes of 10 dingoes and 2 New Guinea Singing Dogs, to study the origins and feralization process of the dingo. Phylogenetic and demographic analyses show that dingoes originate from domestic dogs in southern East Asia, which migrated via Island Southeast Asia to reach Australia 4300-5000 years ago, and subsequently diverged into a genetically distinct population. Selection analysis identified 99 positively selected genes enriched in starch and fat metabolism pathways, indicating a diet change during feralization of dingoes. Interestingly, we found that 14 genes have shifted allele frequencies compared to dogs but not compared to wolves. This suggests that the selection affecting these genes during domestication of the wolf was reversed in the feralization process. One of these genes, ARHGEF7, may promote the formation of neural spine and synapses in hippocampal neurons. Functional assays showed that an A to G mutation in ARHGEF7, located in a transcription factor-binding site, decreases the endogenous expression. This suggests that ARHGEF7 may have been under selection for behavioral adaptations related to the transitions in environment both from wild to domestic and from domestic back to wild. Our results indicate that adaptation to domestication and feralization primarily affected different genomic regions, but that some genes, related to neurodevelopment, metabolism and reproduction, may have been reversibly affected in the two processes.

genomics↗

bioRxiv2016

Evolutionary history of the brown rat: out of southern East Asia and selection

The brown rat (Rattus norvegicus) is found wherever humans live and transmits many diseases, and its breeding produced the laboratory rat used widely in medical research. Here, we sequenced whole genomes from 118 rats to explore the origin and dispersal routes of the brown rat and the domestication of the laboratory rat. We showed that brown rats migrated about 3600 years ago from southern East Asia, rather than Northern Asia as formerly suggested, to the Middle East and then to Europe and Africa. Many genes involved in the immune system experienced positive selection in the wild brown rat, while genes involved in the nervous system and energy metabolism showed evidence of artificial selection during the domestication of laboratory strains. Our findings demystify the puzzling origin and migration of brown rats and reveal the impact of evolution and domestication on this animal.

evolutionary biology↗