Whole genome-wide analysis of DEP family members in sheep (Ovis aries) reveals their potential roles in regulating lactation

Gai, Zhongchao; Hu, Songhao; Ma, Jun; Wang, Yujiao; Gong, Guoli; Zhao, Jieqiong

doi:10.1186/s40538-022-00336-w

Cited by 2 publications

(1 citation statement)

References 57 publications

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“…DEPDC5 or DEP domain containing 5 is a gene located on OAR17 and involved in stimulus response and associated with growth traits [ 115 ]. Whole-genome analyses [ 116 ] have also shown that this gene family plays a role in the regulation of lactation in sheep. On OAR22, CFAP46 or cilia and flagella associated protein 46, has been associated to lactose content [ 117 ] whereas RBM34 or RNA-binding protein 34 gene on OAR25 has role in nucleic acid binding and nucleotide binding, and it was found by GWAS study on cattle to be associated with milk yield [ 118 ].…”

Section: Discussionmentioning

confidence: 99%

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

Lukic,

Curik,

Drzaic

et al. 2023

J Animal Sci Biotechnol

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Background The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations. Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production (carcass, wool and milk yield). Therefore, eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation (EAS), are generally considered as multipurpose breeds (milk, meat and wool), not specialised for a particular type of production, but known for their robustness and resistance to certain environmental conditions. Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures, decipher their biological and productive functionality, and provide a "genomic" characterization of EAS adaptation and determine its production type. Results We identified positive selection signatures in EAS using several methods based on reduced local variation, linkage disequilibrium and site frequency spectrum (eROHi, iHS, nSL and CLR). Our analyses identified numerous genomic regions and genes (e.g., desmosomal cadherin and desmoglein gene families) associated with environmental adaptation and economically important traits. Most candidate genes were related to meat/production and health/immune response traits, while some of the candidate genes discovered were important for domestication and evolutionary processes (e.g., HOXa gene family and FSIP2). These results were also confirmed by GO and QTL enrichment analysis. Conclusions Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type, ultimately providing a new opportunity for future breeding programmes. At the same time, the numerous genes identified will improve our understanding of ruminant (sheep) robustness and resistance in the harsh and specific Mediterranean environment.

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Section: Discussionmentioning

confidence: 99%

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

Lukic,

Curik,

Drzaic

et al. 2023

J Animal Sci Biotechnol

View full text Add to dashboard Cite

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Whole genome level analysis of the DEATH protein superfamily in sheep (Ovis aries) and their coordination relationship in regulating lactation

Gai

et al. 2023

Chem. Biol. Technol. Agric.

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Background Sheep milk is a nutritional and health-promoting food source for humans. The DEATH superfamily is a conserved protein family, and some of its members are closely related to lactation. Systematic studies of the members of the DEATH superfamily are important for further understanding its functions in the mammary gland during lactation; however, there studies are currently lacking. Results Herein, 74 members of the DEATH superfamily were identified in sheep, and phylogenetic analyses indicated that four subfamilies were strongly correlated in evolution. The Ka/Ks calculations demonstrated that negative selection was the primary pressure acting on DEATH members; however, the immune-related gene IFI203 was undergoing strong positive selection in sheep. Furthermore, in the late pregnancy and lactation period, these DEATH genes exhibited similar expression patterns under different nutritional conditions in the mammary gland, and four subfamilies were positively correlated in expression patterns. Additionally, half or more DEATH genes were upregulated in the lactation period, which implied their crucial roles in the lactation of sheep. Conclusions The current research contributes to a better understanding of the evolutionary characteristics of the DEATH superfamily and their roles in sheep lactation, and it also provides potential target genes for the molecular breeding of dairy sheep. Graphical Abstract

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Whole genome-wide analysis of DEP family members in sheep (Ovis aries) reveals their potential roles in regulating lactation

Cited by 2 publications

References 57 publications

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

Whole genome level analysis of the DEATH protein superfamily in sheep (Ovis aries) and their coordination relationship in regulating lactation

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