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Animals
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Genetic Analysis of Important Traits in Domestic Animals
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Genetic Analysis of Important Traits in Domestic Animals

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

Deadline for manuscript submissions: 31 December 2024 | Viewed by 4456

Special Issue Editor

Dr. Sunday Peters

E-Mail Website
Guest Editor
Department of Animal Science, Berry College, Mount Berry, GA, USA
Interests: quantitative genetics; molecular genetics; statistical genetics; genomics; metabolomics; proteomics; metatranscriptomics; transcriptomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Domestic animals, including livestock, companion animals, and agricultural species, have been selectively bred for centuries to enhance their desirable traits, such as productivity, disease resistance, and temperament. The genetic analysis of these important traits plays a crucial role in understanding the underlying genetic mechanisms and developing targeted breeding strategies to improve animal health, welfare, and performance.

Advancements in genomic technologies, such as high-throughput sequencing and genotyping platforms, have revolutionized the field of genetic analysis in domestic animals. These technologies enable researchers to efficiently analyze large-scale genomic data and identify the genetic variants associated with specific traits. Additionally, the integration of multi-omics data, including transcriptomics, proteomics, and metabolomics, provides a comprehensive understanding of the molecular mechanisms underlying these traits.

The genetic analysis of important traits in domestic animals has wide-ranging implications for various sectors. In livestock production, genetic analysis can help improve traits related to meat and milk production, feed efficiency, and disease resistance, leading to more sustainable and efficient animal agriculture. In companion animals, genetic analyses can contribute to the identification of genetic markers associated with breed-specific diseases, behavior traits, and overall health.

Call to publish in a Special Issue:

We invite researchers and scientists working in the field of genetic analysis of any important traits in domestic animals to contribute their original research articles, reviews, and perspectives to a Special Issue on "Genetic Analysis of Important Traits in Domestic Animals." This Special Issue aims to showcase the latest advancements in genetic analysis methods, novel findings on the genetic basis of important traits, and their implications for animal breeding, health, and welfare.

Topics of interest for this Special Issue include, but are not limited to, the following:

  1. Identification and characterization of genetic variants associated with important traits in domestic animals, including livestock, companion animals, and agricultural species.
  2. Genomic selection and marker-assisted breeding strategies for improving important traits in domestic animal populations.
  3. Functional genomics approaches to elucidate the molecular mechanisms underlying important traits.
  4. Integration of multi-omics data to gain a comprehensive understanding of the genetic architecture of important traits.
  5. Genomic technologies and bioinformatics tools for efficient analysis of large-scale genomic data in domestic animals.
  6. Ethical considerations and societal implications of genetic analyses in domestic animals.

We encourage researchers from diverse disciplines, including genetics, genomics, animal science, veterinary medicine, and agriculture, to contribute their expertise and insights to this Special Issue. By bringing together cutting-edge research on the genetic analysis of important traits in domestic animals, we aim to foster collaborations, exchange knowledge, and accelerate the development of innovative breeding strategies for sustainable animal production and welfare.

Submission guidelines:

- Manuscripts should be prepared according to the Animals journal's guidelines for authors.

- All submissions will undergo a rigorous peer review process to ensure the scientific rigor and quality of the published articles.

- The deadline for manuscript submission is December 31, 2024.

- Authors should indicate their interest in the Special Issue “Genetic Analysis of Important Traits in Domestic Animals” during the submission process.

We look forward to receiving your contributions and sharing the latest advancements in the genetic analysis of important traits in domestic animals with the scientific community. Together, we will pave the way for a more productive, sustainable, and welfare-conscious future in animal breeding and production.

Dr. Sunday Peters
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

  • genetic variants
  • important traits
  • genetic analysis
  • genomic selection
  • breeding strategies
  • multi-omics
  • bioinformatics

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Published Papers (4 papers)

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Research

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14 pages, 1421 KiB  
Article
Genetic Evaluation of Monthly Test-Day Milk Yields of Jersey Crossbred Cattle Under Farmers’ Production System in Tamil Nadu, India
by Dhanukodialagar Kasiviswanathan, Palaniappan Devendran, Ragothaman Venkataramanan, Subramanian Meenakshisundaram, Ganesamoorthy Senthilkumar and Sunday O. Peters
Animals 2024, 14(21), 3152; https://doi.org/10.3390/ani14213152 - 2 Nov 2024
Viewed by 730
Abstract
Tamil Nadu, a state in southern India, is bereft of any native dairy or dual-purpose cattle breeds, and the state depends chiefly on crossbred cattle for milk production. Jersey crossbred cattle account for 90% of the state’s milk production. This genetic evaluation study [...] Read more.
Tamil Nadu, a state in southern India, is bereft of any native dairy or dual-purpose cattle breeds, and the state depends chiefly on crossbred cattle for milk production. Jersey crossbred cattle account for 90% of the state’s milk production. This genetic evaluation study aimed to assess milk production traits, including test-day milk yields (TDMYs), total lactation milk yield (TMY), and 305-day milk yield (305MY), in these cattle reared under farmers’ conditions. Data on monthly TDMYs (TDMY1 to TDMY10) of Jersey crossbred cows (n = 75,627) reared by the farmers over 11 years (2012–2022) were collected for evaluation. The influence of non-genetic factors viz., location (agroclimatic zones), period and season of calving, and parity on TDMYs, TMY and 305MY were assessed, and the variance and covariance components for genetic parameters (heritability and genetic correlation) of the traits were estimated by the method of restricted maximum likelihood (REML) under a multivariate animal model and by a random regression model (RRM). The overall means of various TDMYs ranged from 4.98 (TDMY10) to 9.95 kg (TDMY2), and for TMY and 305MY, the means were 2480.33 and 2393.71 kg, respectively. The heritabilities estimated by the multivariate animal model for TDMYs were moderate and ranged from 0.26 ± 0.02 to 0.37 ± 0.02 and the estimates were less variable throughout lactation, while the estimates obtained by RRM were medium to high and ranged between 0.29 ± 0.01 and 0.67 ± 0.02 for milk yield on day 5 to 305 (DIM 5–DIM 305). The heritabilities estimated for TMY and 305MY were 0.43 ± 0.02 and 0.43 ± 0.02, respectively. The estimates of heritability for mid-lactation yields were comparatively less than those at the beginning and the end of lactation. The moderate to high estimates of heritabilities for TDMYs, TMY, and 305MY obtained in the present study offer ample scope for improving milk production through selective breeding. Genetic correlations between TDMYs estimated by the multivariate animal model were positive and high, with a range between 0.75 ± 0.03 and 0.99 ± 0.00. Considerably higher estimates (0.98–0.99) were observed between adjacent TDMYs showing strong genetic associations. By RRM, genetic correlations estimated between DIMs were positive (except for DIM 5 with DIM 125 to DIM 185 and DIM 125 with DIM 305), and the magnitude of genetic correlation decreased with an increase in the interval between the DIMs. The high genetic correlation observed between the TDMYs (in the early stage of lactation) and total lactation milk yield suggested that these test-day yields could be used favorably for the early selection of cows for milk production, which facilitates reduction in the generation interval and consequently increases the annual genetic gain for the milk production traits. Full article
(This article belongs to the Special Issue Genetic Analysis of Important Traits in Domestic Animals)
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12 pages, 2732 KiB  
Article
Relationship between Indel Variants within the JAK2 Gene and Growth Traits in Goats
by Xian-Feng Wu, Qian Xu, Ao Wang, Ben-Zhi Wang, Xian-Yong Lan, Wen-Yang Li and Yuan Liu
Animals 2024, 14(13), 1994; https://doi.org/10.3390/ani14131994 - 6 Jul 2024
Viewed by 879
Abstract
Janus kinase 2 (JAK2) plays a critical role in myoblast proliferation and fat deposition in animals. Our previous RNA-Seq analyses identified a close association between the JAK2 gene and muscle development. To date, research delving into the relationship between the JAK2 [...] Read more.
Janus kinase 2 (JAK2) plays a critical role in myoblast proliferation and fat deposition in animals. Our previous RNA-Seq analyses identified a close association between the JAK2 gene and muscle development. To date, research delving into the relationship between the JAK2 gene and growth traits has been sparse. In this study, we sought to investigate the relationship between novel mutations within the JAK2 gene and goat growth traits. Herein, two novel InDel (Insertion/Deletion) polymorphisms within the JAK2 gene were detected in 548 goats, and only two genotypes were designated as ID (Insertion/Deletion) and DD (Deletion/Deletion). The results indicate that the two InDels, the del19008 locus in intron 2 and del72416 InDel in intron 6, showed significant associations with growth traits (p < 0.05). Compared to Nubian and Jianzhou Daer goats, the del72416 locus displayed a more pronounced effect in the Fuqing breed group. In the Nubian breed (NB) group, both InDels showed a marked influence on body height (BH). There were strong linkages observed for these two InDels between the Fuqing (FQ) and Jianzhou (JZ) populations. The DD-ID diplotype was associated with inferior growth traits in chest width (ChW) and cannon circumference (CaC) in the FQ goats compared to the other diplotypes. In the NB population, the DD-DD diplotype exhibited a marked negative impact on BH and HuWI (hucklebone width index), in contrast to the other diplotypes. In summary, our findings suggest that the two InDel polymorphisms within the JAK2 gene could serve as valuable molecular markers for enhancing goat growth traits in breeding programs. Full article
(This article belongs to the Special Issue Genetic Analysis of Important Traits in Domestic Animals)
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14 pages, 2788 KiB  
Article
Identification of Differentially Expressed Genes and microRNAs in the Gray and White Feather Follicles of Shitou Geese
by Pengyun Guo, Junpeng Chen, Lei Luo, Xumeng Zhang, Xiujin Li, Yunmao Huang, Zhongping Wu and Yunbo Tian
Animals 2024, 14(10), 1508; https://doi.org/10.3390/ani14101508 - 20 May 2024
Viewed by 1211
Abstract
The Shitou goose, a highly recognized indigenous breed with gray plumage originating from Chaozhou Raoping in Guangdong Province, China, is renowned for being the largest goose species in the country. Notably, during the pure breeding process of Shitou geese, approximately 2% of the [...] Read more.
The Shitou goose, a highly recognized indigenous breed with gray plumage originating from Chaozhou Raoping in Guangdong Province, China, is renowned for being the largest goose species in the country. Notably, during the pure breeding process of Shitou geese, approximately 2% of the offspring in each generation unexpectedly exhibited white plumage. To better understand the mechanisms underlying white plumage color formation in Shitou geese, we conducted a comparative transcriptome analysis between white and gray feather follicles, aiming to identify key genes and microRNAs that potentially regulate white plumage coloration in this unique goose breed. Our results revealed a number of pigmentation genes, encompassing TYR, TYRP1, EDNRB2, MLANA, SOX10, SLC45A2, GPR143, TRPM1, OCA2, ASIP, KIT, and SLC24A5, which were significantly down-regulated in the white feather follicles of Shitou geese. Among these genes, EDNRB2 and KIT emerged as the most promising candidate genes for white plumage coloration in Shitou geese. Additionally, our analysis also uncovered 46 differentially expressed miRNAs. Of these, miR-144-y may play crucial roles in the regulation of feather pigmentation. Furthermore, the expression of novel-m0086-5p, miR-489-y, miR-223-x, miR-7565-z, and miR-3535-z exhibits a significant negative correlation with the expression of pigmentation genes including TYRP1, EDNRB2, MLANA, SOX10, TRPM1, and KIT, suggesting these miRNAs may indirectly regulate the expression of these genes, thereby influencing feather color. Our findings provide valuable insights into the genetic mechanisms underlying white plumage coloration in Shitou geese and contribute to the broader understanding of avian genetics and coloration research. Full article
(This article belongs to the Special Issue Genetic Analysis of Important Traits in Domestic Animals)
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Review

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34 pages, 2762 KiB  
Review
Genome-Wide Association Study as an Efficacious Approach to Discover Candidate Genes Associated with Body Linear Type Traits in Dairy Cattle
by Mingxue Long, Bo Wang, Zhangping Yang and Xubin Lu
Animals 2024, 14(15), 2181; https://doi.org/10.3390/ani14152181 - 26 Jul 2024
Viewed by 981
Abstract
Body shape traits are very important and play a crucial role in the economic development of dairy farming. By improving the accuracy of selection for body size traits, we can enhance economic returns across the dairy industry and on farms, contributing to the [...] Read more.
Body shape traits are very important and play a crucial role in the economic development of dairy farming. By improving the accuracy of selection for body size traits, we can enhance economic returns across the dairy industry and on farms, contributing to the future profitability of the dairy sector. Registered body conformation traits are reliable and cost-effective tools for use in national cattle breeding selection programs. These traits are significantly related to the production, longevity, mobility, health, fertility, and environmental adaptation of dairy cows. Therefore, they can be considered indirect indicators of economically important traits in dairy cows. Utilizing efficacious genetic methods, such as genome-wide association studies (GWASs), allows for a deeper understanding of the genetic architecture of complex traits through the identification and application of genetic markers. In the current review, we summarize information on candidate genes and genomic regions associated with body conformation traits in dairy cattle worldwide. The manuscript also reviews the importance of body conformation, the relationship between body conformation traits and other traits, heritability, influencing factors, and the genetics of body conformation traits. The information on candidate genes related to body conformation traits provided in this review may be helpful in selecting potential genetic markers for the genetic improvement of body conformation traits in dairy cattle. Full article
(This article belongs to the Special Issue Genetic Analysis of Important Traits in Domestic Animals)
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