Evolution of Genetic Diversity 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: closed (31 December 2021) | Viewed by 9589

Special Issue Editor


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Guest Editor
Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
Interests: population genetics; animals; diversity; ecology; genomics

Special Issue Information

Dear Colleagues,

Domestic animals have an important place in human society synonymous to richness, particularly in developing countries, providing food security or even heritage in regions where they are tightly linked to landscape. The domestication of animals started during the Paleolithic with dogs deriving from wolves to protect humans from wild animals. From then many other species have been domesticated and selected for multiple purposes ranging from production (e.g., milk, meat, wool, eggs, leather) to traction (e.g., workhorses) or as pets. Selection was specific to each purpose and each environment, leading to a huge level of diversity between breeds within the same species. Conservation of domestic animals and of their numerous breeds is thus a main concern in many places over the world.

Genetic diversity within breeds, plays a key role in the sustainability of animal breeding through the conservation of breeds. It acts at three time scales: i) short-term, through the expression of inbreeding depression with potential strong deleterious effects on both performance and fitness traits, ii) middle-term, through the maintenance of additive genetic variance and subsequent genetic gain toward selection goals, and iii) long-term, allowing adaptation to new, potentially harsh, environments (climate change, pathogens, free-range agriculture...). For these reasons, characterizing, monitoring, and managing genetic diversity are essential for the development of sustainable breeding and conservation of domestic animals with a particular emphasis on small breeds which are likely to first suffer from genetic depletion.

We invite original research papers that address the question of genetic diversity in domestic animal populations. This could involve the fine characterization of genetic diversity and its evolution in response to breeding conditions or the environment. We are also interested in papers helping to refine our knowledge on the management and use of genetic diversity through real data or simulation studies. Additional topics include opinion papers about the use of genetic resources not only from a genetic perspective but also from a policy perspective, with particular emphasis on stakeholders.

Dr. Gwendal Restoux
Guest Editor

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Keywords

  • breeds
  • genetic diversity
  • genetic resources
  • conservation
  • population genetics
  • genomics
  • pedigrees
  • management

Published Papers (3 papers)

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Research

13 pages, 2416 KiB  
Article
Assessing Genomic Diversity and Selective Pressures in Bohai Black Cattle Using Whole-Genome Sequencing Data
by Xiaohui Ma, Haijian Cheng, Yangkai Liu, Luyang Sun, Ningbo Chen, Fugui Jiang, Wei You, Zhangang Yang, Baoheng Zhang, Enliang Song and Chuzhao Lei
Animals 2022, 12(5), 665; https://doi.org/10.3390/ani12050665 - 7 Mar 2022
Cited by 4 | Viewed by 3017
Abstract
Bohai Black cattle are one of the well-known cattle breeds with black coat color in China, which are cultivated for beef. However, no study has conducted a comprehensive analysis of genomic diversity and selective pressures in Bohai Black cattle. Here, we performed a [...] Read more.
Bohai Black cattle are one of the well-known cattle breeds with black coat color in China, which are cultivated for beef. However, no study has conducted a comprehensive analysis of genomic diversity and selective pressures in Bohai Black cattle. Here, we performed a comprehensive analysis of genomic variation in 10 Bohai Black cattle (five newly sequenced and five published) and the published whole-genome sequencing (WGS) data of 50 cattle representing five “core” cattle populations. The population structure analysis revealed that Bohai Black cattle harbored the ancestry with European taurine, Northeast Asian taurine, and Chinese indicine. The Bohai Black cattle demonstrated relatively high genomic diversity from the other cattle breeds, as indicated by the nucleotide diversity (pi), the expected heterozygosity (HE) and the observed heterozygosity (HO), the linkage disequilibrium (LD) decay, and runs of homozygosity (ROH). We identified 65 genes containing more than five non-synonymous SNPs (nsSNPs), and an enrichment analysis revealed the “ECM-receptor interaction” pathways associated with meat quality in Bohai Black cattle. Five methods (CLR, θπ, FST, θπ ratio, and XP-EHH) were used to find several pathways and genes carried selection signatures in Bohai Black cattle, including black coat color (MC1R), muscle development (ITGA9, ENAH, CAPG, ABI2, and ISLR), fat deposition (TBC1D1, CYB5R4, TUSC3, and EPS8), reproduction traits (SPIRE2, KHDRBS2, and FANCA), and immune system response (CD84, SLAMF1, SLAMF6, and CDK10). Taken together, our results provide a valuable resource for characterizing the uniqueness of Bohai Black cattle. Full article
(This article belongs to the Special Issue Evolution of Genetic Diversity in Domestic Animals)
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23 pages, 5090 KiB  
Article
Process of Introduction of Australian Braford Cattle to South America: Configuration of Population Structure and Genetic Diversity Evolution
by Araceli Rocío Marisel González, Francisco Javier Navas González, Gustavo Ángel Crudeli, Juan Vicente Delgado Bermejo, María Esperanza Camacho Vallejo and Celia Raquel Quirino
Animals 2022, 12(3), 275; https://doi.org/10.3390/ani12030275 - 23 Jan 2022
Cited by 3 | Viewed by 2485
Abstract
This study analyzes the evolution of the population structure and genetic diversity of Braford cattle in South America from 1949 to 2019 to suggest effective strategies for breeding in the future. The percentage of bulls historically increased. The average generational interval decreased to [...] Read more.
This study analyzes the evolution of the population structure and genetic diversity of Braford cattle in South America from 1949 to 2019 to suggest effective strategies for breeding in the future. The percentage of bulls historically increased. The average generational interval decreased to 11.78 years for the current population. Average inbreeding (F) and coancestry (C) are low and show a historically increasing trend (0.001% to 0.002%, respectively). The degree of nonrandom mating (α) increased from −0.0001 to 0.0001 denoting a change in the trend to mate similar individuals. The average relatedness coefficient (ΔR) increased in the current period from 0.002% to 0.004%. A single ancestor explained 4.55% to 7.22% of the population’s gene pool. While the effective population size based on the individual inbreeding rate (NeFi) was 462.963, when based on the individual coancestry rate (NeCi), it was 420.168. Genetic diversity loss is small and mainly ascribed to bottlenecks (0.12%) and to unequal contributions of the founders (0.02%). Even if adequate levels of diversity can be found, practices that consider the overuse of individual bulls (conditioned by nature or not), could lead to a long-term reduction in diversity. The present results permit tailoring genetic management strategies that are perfectly adapted to the needs that the population demands internationally. Full article
(This article belongs to the Special Issue Evolution of Genetic Diversity in Domestic Animals)
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10 pages, 260 KiB  
Article
Analysis of MC1R, MITF, TYR, TYRP1, and MLPH Genes Polymorphism in Four Rabbit Breeds with Different Coat Colors
by Xianbo Jia, Peng Ding, Shiyi Chen, Shaokang Zhao, Jie Wang and Songjia Lai
Animals 2021, 11(1), 81; https://doi.org/10.3390/ani11010081 - 5 Jan 2021
Cited by 15 | Viewed by 2551
Abstract
Pigmentation genes such as MC1R, MITF, TYR, TYRP1, and MLPH play a major role in rabbit coat color. To understand the genotypic profile underlying coat color in indigenous Chinese rabbit breeds, portions of the above-mentioned genes were amplified and variations in them [...] Read more.
Pigmentation genes such as MC1R, MITF, TYR, TYRP1, and MLPH play a major role in rabbit coat color. To understand the genotypic profile underlying coat color in indigenous Chinese rabbit breeds, portions of the above-mentioned genes were amplified and variations in them were analyzed by DNA sequencing. Based on the analysis of 24 Tianfu black rabbits, 24 Sichuan white rabbits, 24 Sichuan gray rabbits, and 24 Fujian yellow rabbits, two indels in MC1R, three SNPs in MITF, five SNPs (single nucleotide polymorphisms) in TYR, one SNP in TYRP1, and three SNPs in MLPH were discovered. These variations have low-to-moderate polymorphism, and there are significant differences in their distribution among the different breeds (p < 0.05). These results provide more information regarding the genetic background of these native rabbit breeds and reveal their high-quality genetic resources. Full article
(This article belongs to the Special Issue Evolution of Genetic Diversity in Domestic Animals)
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