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Animals
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Conservation and Management of Genetic Resources in Animal Breeding
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Conservation and Management of Genetic Resources in Animal Breeding

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

Deadline for manuscript submissions: closed (20 December 2022) | Viewed by 15434

Special Issue Editors

Dr. Yuehui Ma

E-Mail Website
Guest Editor
Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Beijing 100097, China
Interests: conservation of animal genetic resource; genetic evaluation; population genetics; utilization of genetic resources
Dr. Qianjun Zhao

E-Mail Website
Guest Editor
Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
Interests: population genomics; gene discovery; conservation priority; multi-omics
Prof. Dr. Wei Sun

E-Mail Website
Guest Editor
College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
Interests: conservation of animal genetic resources; genetic evaluation; population genetics; epigenetics; functional genetics; utilization of animal resources

Special Issue Information

Dear Colleagues,

Animal genetic resources provide meat, egg, milk and wool for human, which are important for the sustainable development of husbandry. The genetic diversity of the world’s animal populations is decreasing. Thus, it is vital to evaluate the genetic diversity and identify the genes related to key traits, so as to make rational plans for the conservation and management of animal genetic resources. To this end, scientists involved in this multidisciplinary research field are invited to contribute to the development of knowledge by presenting valuable results representing a precious contribution to genetic resources in animal breeding.

  1. Approaches for animal conservation and the conservation approaches applicable for specific species;
  2. Genetic evaluation and gene discovery of indigenous breeds/populations for animal conservation;
  3. Application of genomics information for conservation breeding plans;
  4. Breeding schemes for animal conservation;
  5. Sustainable utilization and management of animal resources.

Dr. Yuehui Ma
Dr. Qianjun Zhao
Prof. Dr. Wei Sun
Guest Editors

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

  • conservation
  • genetic resources
  • breeding
  • genetic diversity
  • genotyping
  • genomics

Published Papers (7 papers)

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Research

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14 pages, 3501 KiB  
Article
Analysis of Conservation Priorities and Runs of Homozygosity Patterns for Chinese Indigenous Chicken Breeds
by Chaoqun Gao, Wenping Du, Kaiyuan Tian, Kejun Wang, Chunxiu Wang, Guirong Sun, Xiangtao Kang and Wenting Li
Animals 2023, 13(4), 599; https://doi.org/10.3390/ani13040599 - 8 Feb 2023
Cited by 4 | Viewed by 1775
Abstract
To achieve sustainable development of the poultry industry, the effective conservation of genetic resources has become increasingly important. In the present study, we systematically elucidated the population structure, conservation priority, and runs of homozygosity (ROH) patterns of Chinese native chicken breeds. We used [...] Read more.
To achieve sustainable development of the poultry industry, the effective conservation of genetic resources has become increasingly important. In the present study, we systematically elucidated the population structure, conservation priority, and runs of homozygosity (ROH) patterns of Chinese native chicken breeds. We used a high-density genotyping dataset of 157 native chickens from eight breeds. The population structure showed different degrees of population stratification among the breeds. Chahua chicken was the most differentiated breed from the other breeds (Nei = 0.0813), and the Wannan three-yellow chicken (WanTy) showed the lowest degree of differentiation (Nei = 0.0438). On the basis of contribution priority, Xiaoshan chicken had the highest contribution to the total gene diversity (1.41%) and the maximum gene diversity of the synthetic population (31.1%). WanTy chicken showed the highest contribution to the total allelic diversity (1.31%) and the maximum allelic diversity of the syntenic population (17.0%). A total of 5242 ROH fragments and 5 ROH island regions were detected. The longest ROH fragment was 41.51 Mb. A comparison of the overlapping genomic regions between the ROH islands and QTLs in the quantitative trait loci (QTL) database showed that the annotated candidate genes were involved in crucial economic traits such as immunity, carcass weight, drumstick and leg muscle development, egg quality and egg production, abdominal fat precipitation, body weight, and feed intake. In conclusion, our findings revealed that Chahua, Xiaoshan, and WanTy should be the priority conservation breeds, which will help optimize the conservation and breeding programs for Chinese indigenous chicken breeds. Full article
(This article belongs to the Special Issue Conservation and Management of Genetic Resources in Animal Breeding)
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16 pages, 1331 KiB  
Article
Genetic Parameters of Growth Traits and Quantitative Genetic Metrics for Selection and Conservation of Mecheri Sheep of Tamil Nadu
by Balakrishnan Balasundaram, Aranganoor Kannan Thiruvenkadan, Nagarajan Murali, Jaganadhan Muralidharan, Doraiswamy Cauveri and Sunday Olusola Peters
Animals 2023, 13(3), 454; https://doi.org/10.3390/ani13030454 - 28 Jan 2023
Cited by 5 | Viewed by 1712
Abstract
Determining the genetic and non-genetic sources of variation in a breed is vital for the formulation of strategies for its conservation and improvement. The present study was aimed at estimating the (co)variance components and genetic parameters of Mecheri sheep by fitting six different [...] Read more.
Determining the genetic and non-genetic sources of variation in a breed is vital for the formulation of strategies for its conservation and improvement. The present study was aimed at estimating the (co)variance components and genetic parameters of Mecheri sheep by fitting six different animal models in the restricted maximum likelihood method, with a preliminary investigation on the performance of animals for non-genetic sources of variation. A total of 2616 lambs were studied, and varying levels of significance were found for the effects of period, season, parity of dam, and birth type on different body-weight traits. Direct heritability estimates derived from the best animal model for body weight at birth, three months, six months, nine months, and twelve months were 0.21, 0.24, 0.10, 0.15, and 0.09, respectively, and the maternal heritability of the corresponding traits was 0.12, 0.05, 0.04, 0.04, and 0.04, respectively. The genetic correlations between the body-weight traits were all positive and moderate-to-strong, except for the correlation between birth weight and the other body-weight traits. The significance of non-genetic factors studied in this work demanded a correction to improve the accuracy of the direct selection of lambs for body-weight traits. The estimated genetic parameters identified the weaning weight as a selection criterion for the improvement in body weight of Mecheri lambs at different ages. Inbred individuals accounted for approximately 13% of the total population in the Mecheri sheep population studied. There were 877 founders in the population, and the actual effective population size was 128.48. The population’s mean generation interval was 3.26. The mean inbreeding values ranged from 0.005 to 0.010 across generations. The population’s average relatedness ranged from 0.001 to 0.014 across generations. Individual inbreeding was found to be 0.45 per cent for the entire population and 3.4 per cent for the inbred population. Full article
(This article belongs to the Special Issue Conservation and Management of Genetic Resources in Animal Breeding)
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14 pages, 3661 KiB  
Article
Transcriptome Sequencing Reveals Pathways Related to Proliferation and Differentiation of Shitou Goose Myoblasts
by Jiahui Chen, Shuai Zhang, Genghua Chen, Xianqi Deng, Danlu Zhang, Huaqiang Wen, Yunqian Yin, Zetong Lin, Xiquan Zhang and Wen Luo
Animals 2022, 12(21), 2956; https://doi.org/10.3390/ani12212956 - 27 Oct 2022
Cited by 5 | Viewed by 1604
Abstract
Chinese Shitou goose is a type of large goose with high meat yield. Understanding the genetic regulation of muscle development in Shitou goose would be beneficial to improve the meat production traits of geese. Muscle development is regulated by genes related to myoblast [...] Read more.
Chinese Shitou goose is a type of large goose with high meat yield. Understanding the genetic regulation of muscle development in Shitou goose would be beneficial to improve the meat production traits of geese. Muscle development is regulated by genes related to myoblast proliferation and differentiation. In this study, the RNA-seq method was used to construct the mRNA and lncRNA expression profiles of Shitou goose myoblasts and myotubes. A total of 1664 differentially expressed (DE) mRNAs and 244 DE-lncRNAs were identified. The alternative mRNA splicing in proliferation and differentiation stages was also analyzed. Notably, pathways enriched in DE-mRNAs, DE-splicing transcripts, and DE-lncRNAs all point to the Wnt signaling pathway, indicating that the Wnt signaling is a key regulatory pathway of muscle development in Shitou goose. We also constructed the interactive network of DE-lncRNAs and DE-mRNAs and revealed some key genes of lncRNAs regulating the proliferation and differentiation of myoblasts. These results provide new insights for the study of the muscle development of the Shitou goose. Full article
(This article belongs to the Special Issue Conservation and Management of Genetic Resources in Animal Breeding)
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14 pages, 3071 KiB  
Article
Genomic Tools for the Characterization of Local Animal Genetic Resources: Application in Mascaruna Goat
by Marco Tolone, Maria Teresa Sardina, Gabriele Senczuk, Giorgio Chessari, Andrea Criscione, Angelo Moscarelli, Silvia Riggio, Ilaria Rizzuto, Rosalia Di Gerlando, Baldassare Portolano and Salvatore Mastrangelo
Animals 2022, 12(20), 2840; https://doi.org/10.3390/ani12202840 - 19 Oct 2022
Cited by 5 | Viewed by 2803
Abstract
Italy contains a large number of local goat populations, some of which do not have a recognized genetic structure. The “Mascaruna” is a goat population reared for milk production in Sicily. In this study, a total of 72 individuals were genotyped with the [...] Read more.
Italy contains a large number of local goat populations, some of which do not have a recognized genetic structure. The “Mascaruna” is a goat population reared for milk production in Sicily. In this study, a total of 72 individuals were genotyped with the Illumina Goat_IGGC_65K_v2 BeadChip with the aim to characterize the genetic diversity, population structure and relatedness with another 31 Italian goat populations. The results displayed a moderate level of genetic variability for Mascaruna, in concordance with the estimated values for Italian goats. Runs of homozygosity islands are linked to genes involved in milk production, immune response and local adaptation. Population structure analyses separated Mascaruna from the other goat populations, indicating a clear genetic differentiation. Although they are not conclusive, our current results represent a starting point for the creation of monitoring and conservation plans. Additional analyses and a wider sampling would contribute to refine and validate these results. Finally, our study describing the diversity and structure of Mascaruna confirms the usefulness of applied genomic analyses as valid tools for the study of the local uncharacterized genetic resources. Full article
(This article belongs to the Special Issue Conservation and Management of Genetic Resources in Animal Breeding)
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15 pages, 2242 KiB  
Article
Genetic Diversity and Selection Signatures in Jianchang Black Goats Revealed by Whole-Genome Sequencing Data
by Xueliang Sun, Jiazhong Guo, Li Li, Tao Zhong, Linjie Wang, Siyuan Zhan, Juan Lu, Decheng Wang, Dinghui Dai, George E. Liu and Hongping Zhang
Animals 2022, 12(18), 2365; https://doi.org/10.3390/ani12182365 - 10 Sep 2022
Cited by 7 | Viewed by 2333
Abstract
Understanding the genetic composition of indigenous goats is essential to promote the scientific conservation and sustainable utilization of these breeds. The Jianchang Black (JC) goat, a Chinese native breed, is solid black and exhibits crude feed tolerance, but is characterized by a low [...] Read more.
Understanding the genetic composition of indigenous goats is essential to promote the scientific conservation and sustainable utilization of these breeds. The Jianchang Black (JC) goat, a Chinese native breed, is solid black and exhibits crude feed tolerance, but is characterized by a low growth rate and small body size. Based on the whole-genome sequencing data for 30 JC, 41 Jintang Black (JT), and 40 Yunshang Black (YS) goats, and 21 Bezoar ibexes, here, we investigated the genetic composition of JC goats by conducting analyses of the population structure, runs of homozygosity (ROH), genomic inbreeding, and selection signature. Our results revealed that JT and YS showed a close genetic relationship with a non-negligible amount of gene flows but were genetically distant from JC, apart from Bezoars. An average of 2039 ROHs were present in the autosomal genome per individual. The ROH-based inbreeding estimates in JC goats generally showed moderate values ranging from 0.134 to 0.264, mainly due to rapid declines in the effective population size during recent generations. The annotated genes (e.g., IL2, IL7, and KIT) overlapping with ROH islands were significantly enriched in immune-related biological processes. Further, we found 61 genes (e.g., STIM1, MYO9A, and KHDRBS2) under positive selection in JC goats via three complementary approaches, which may underly genetic adaptations to local environmental conditions. Our findings provided references for the conservation and sustainable utilization of JC goats. Full article
(This article belongs to the Special Issue Conservation and Management of Genetic Resources in Animal Breeding)
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14 pages, 2126 KiB  
Article
Genome-Wide Population Structure Analysis and Genetic Diversity Detection of Four Chinese Indigenous Duck Breeds from Fujian Province
by Ruiyi Lin, Jiaquan Li, Yue Yang, Yinhua Yang, Jimin Chen, Fanglu Zhao and Tianfang Xiao
Animals 2022, 12(17), 2302; https://doi.org/10.3390/ani12172302 - 5 Sep 2022
Cited by 4 | Viewed by 1869
Abstract
The assessment of population genetic structure is the basis for understanding the genetic information of indigenous breeds and is important for the protection and management of indigenous breeds. However, the population genetic differentiation of many local breeds still remains unclear. Here, we performed [...] Read more.
The assessment of population genetic structure is the basis for understanding the genetic information of indigenous breeds and is important for the protection and management of indigenous breeds. However, the population genetic differentiation of many local breeds still remains unclear. Here, we performed a genome-wide comparative analysis of Jinding, Liancheng white, Putian black, and Shanma ducks based on the genomic sequences using RAD sequencing to understand their population structure and genetic diversity. The population parameters showed that there were obvious genetic differences among the four indigenous breeds, which were separated groups. Among them, Liancheng white and Shanma ducks may come from the same ancestor because the phylogenetic tree forms three tree trunks. In addition, during the runs of homozygosity (ROH), we found that the average inbreeding coefficient of Liancheng white and Putian black ducks was the lowest and the highest, respectively. Five genomic regions were considered to be the hotspots of autozygosity among these indigenous duck breeds, and the candidate genes involved a variety of potential variations, such as muscle growth, pigmentation, and neuroregulation. These findings provide insights into the further improvement and conservation of Fujian duck breeds. Full article
(This article belongs to the Special Issue Conservation and Management of Genetic Resources in Animal Breeding)
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Review

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14 pages, 904 KiB  
Review
Assessment of Genetic Diversity and Conservation in South African Indigenous Goat Ecotypes: A Review
by Aletta Matshidiso Magoro, Bohani Mtileni, Khanyisile Hadebe and Avhashoni Zwane
Animals 2022, 12(23), 3353; https://doi.org/10.3390/ani12233353 - 29 Nov 2022
Cited by 3 | Viewed by 2529
Abstract
Goats were amongst the first livestock to be domesticated more than 10,000 years ago for their meat, milk, skin, and fiber. They were introduced to Southern Africa by migrating nations from Central Africa to the south. Due to local adaptation to the different [...] Read more.
Goats were amongst the first livestock to be domesticated more than 10,000 years ago for their meat, milk, skin, and fiber. They were introduced to Southern Africa by migrating nations from Central Africa to the south. Due to local adaptation to the different agro-ecological zones and selection, indigenous goats are identified as ecotypes within the indigenous veld goat breed. Their ability to thrive in a resource-limited production system and in challenging environmental conditions makes them valuable animal resources for small-scale and emerging farmers. They play important roles in household agriculture and cultural activities as well as in poverty alleviation. Studies have described the phenotypic and genetic variations in indigenous goats, targeting the major goat-producing regions and the breeds of South Africa. In turn, information is restricted to certain breeds and regions, and the experimental design is often not adequate to inform the conservation status and priorities in changing environments. Advances in genomics technologies have availed more opportunities for the assessment of the biodiversity, demographic histories, and detection regions associated with local adaptation. These technologies are essential for breeding and conservation strategies for sustainable production for food security. This review focuses on the status of indigenous goats in South Africa and the application of genomics technologies for characterization, with emphasis on prioritization for conservation and sustainable utilization. Full article
(This article belongs to the Special Issue Conservation and Management of Genetic Resources in Animal Breeding)
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