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Animals
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Genomics of Animal Domestication and Trait Evolution
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Genomics of Animal Domestication and Trait Evolution

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 31 August 2024 | Viewed by 2029

Special Issue Editor

Dr. Takeshi Kawakami

E-Mail Website
Guest Editor
Embark Veterinary, Inc., Boston, MA, USA
Interests: genomics; population genetics; trait evolution; selection; domestication; genetic disorders; dogs and other canids

Special Issue Information

Dear Colleagues,

Studying the genetics of domesticated animals can provide valuable insights into the process of trait evolution and is genetic architecture. Domestication by selection has led to the evolution of similar sets of traits across a wide variety of livestock and companion animals. This convergent evolution offers an excellent opportunity for understanding the process of adaptation to novel environments and the underlying genetic basis for phenotypic diversity. Population genetic analysis sheds light on the origin of domesticated animals, extent of bottlenecks, and past and recurrent gene flow between wild and domestic stocks. The detailed understanding of animal domestication processes, along with characterization of molecular and functional basis of key traits in both wild and domesticated animals, holds significant promise in enhancing animal breeding programs. Finally, domesticated animals and humans share common diseases due to shared biological pathways and processes in disease development and progression. Therefore, studying domesticated animals can lead to the identification of genetic factors associated with certain diseases to gain insights into the corresponding disease mechanisms in humans and develop novel treatment strategies by identifying therapeutic targets for human diseases.

In this Special Issue, we would like to invite submissions of high-quality original research or review articles on topics related to the genomics of domesticated animals. We encourage all scientists, using (but not limited to) livestock animals (e.g., cattle, pig, and sheep) and companion animals (e.g., dogs and cats).

Dr. Takeshi Kawakami
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • animal domestication
  • convergent evolution
  • selection
  • genome evolution
  • domestication history
  • population genetics
  • adaptation
  • genetic disorder
  • livestock animals
  • companion animals
  • dog
  • cat

Published Papers (2 papers)

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Research

16 pages, 2192 KiB  
Article
Genome-Wide Association Study Reveals Novel Loci Associated with Body Conformation Traits in Qinchuan Cattle
by Hengwei Yu, Shengchen Yu, Juntao Guo, Gong Cheng, Chugang Mei and Linsen Zan
Animals 2023, 13(23), 3628; https://doi.org/10.3390/ani13233628 - 23 Nov 2023
Viewed by 848
Abstract
A genome-wide association study (GWAS) is an effective tool for identifying the dominant genes of complex economic traits in livestock by statistical analysis of genotype data and measured phenotype data. In this study, we rigorously measured 14 body conformation traits in 254 Qinchuan [...] Read more.
A genome-wide association study (GWAS) is an effective tool for identifying the dominant genes of complex economic traits in livestock by statistical analysis of genotype data and measured phenotype data. In this study, we rigorously measured 14 body conformation traits in 254 Qinchuan cattle, comprising body weight (BW), body height (BOH), back height (BAH), buttock height (BUH), chest depth (CD), chest width (CW), hip cross height (HCH), body length (BL), hip width (HW), rump length (RL), pin bone width (PBW), chest girth (CG), abdomen circumference (AG), and calf circumference (CC). After quality control, 281,889 SNPs were generated for GWAS with different traits. A total of 250 suggestive SNPs (p < 3.54 × 10−6) were screened and 37 candidate genes were annotated. Furthermore, we performed a linkage disequilibrium analysis of SNP loci and considered published studies, identifying the eight genes (ADAMTS17, ALDH1A3, CHSY1, MAGEL2, MEF2A, SYNM, CNTNAP5, and CTNNA3) most likely to be involved in growth traits. This study provides new insights into the regulatory mechanisms of bovine body size development, which can be very useful in the development of management and breeding strategies. Full article
(This article belongs to the Special Issue Genomics of Animal Domestication and Trait Evolution)
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8 pages, 3184 KiB  
Communication
Novel Heredity Basis of the Four-Horn Phenotype in Sheep Using Genome-Wide Sequence Data
by Haoyuan Zhang, Pu Yang, Chengli Liu, Yuehui Ma, Yanguo Han, Yan Zeng, Yongfu Huang, Yongju Zhao, Zhongquan Zhao, Xiaohong He and Guangxin E
Animals 2023, 13(20), 3166; https://doi.org/10.3390/ani13203166 - 10 Oct 2023
Cited by 1 | Viewed by 901
Abstract
Horns are an important breeding trait for sheep. However, no widely recognized viewpoint on the regulatory genes and mechanisms of horns is available, and the genetic basis of the four-horn phenotype (FHP) is unclear. This work conducted a genome-wide association study with 100 [...] Read more.
Horns are an important breeding trait for sheep. However, no widely recognized viewpoint on the regulatory genes and mechanisms of horns is available, and the genetic basis of the four-horn phenotype (FHP) is unclear. This work conducted a genome-wide association study with 100 sheep genomes from multiple breeds to investigate the genetic basis of the FHP. The results revealed three significant associations (corrected as p < 1.64 × 10−8) of the InDels (CHR2: g.133,742,709delA, g.133,743,215insC, and g.133,743,940delT) for FHP in the intergenic sequence (IGS) between the MTX2 and the LOC105609047 of CHR2. Moreover, 14 significant associations (corrected as p < 1.42 × 10−9) of SNPs with the FHP phenotype were identified in CHR2 and CHR16, including five (e.g., CHR16: g.40,351,378G > A and g.40,352,577G > A) located in the intron of the ADAMTS12 gene, eight (e.g., CHR2: g.133,727,513C > T and g.133,732,145T > G) in the IGS between MTX2 and LOC105609047, and only one (CHR2: g.133,930,761A > G) in the IGS between HOXD1 and MTX2. Obvious divergence was also observed in genotype patterns between the FHP and others (two horns and hornless) in the HOXD1 and ADAMTS12 gene regions. An extremely significant linkage also occurred between Loci I and Loci II within 100 individuals (LD = −156.02186, p < 0.00001). In summary, our study indicated that the genomic sequences from CHR2 and CHR16 contributed to the FHP in sheep, specifically the key candidate genes HOXD1 and ADAMTS12. These results improved our understanding of the Mendelian genetic basis of the FHP in sheep. Full article
(This article belongs to the Special Issue Genomics of Animal Domestication and Trait Evolution)
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