Special Issue "Domestication Genetics"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 31 October 2020.

Special Issue Editor

Dr. Anna V Kukekova
Website
Guest Editor
Carl R. Woese Institute for Genomic Biology, Univesity of Illinois, Urbana, IL 61801, USA
Interests: animal genetics; domestication; QTL, genomic tools, NGS

Special Issue Information

Dear Colleagues,

The beginning of plant and animal domestication in the early Holocene gave rise to multidimensional changes in human society. A few ancient centers of animal domestication produced most of the agriculturally important species which predetermined human population expansion and on which we continue to rely today. In many species, the timing of domestication as well as the number of domestication events and their geographical origin(s), remain questions of interest, despite long being investigated through the archeological and historical records. Since the development of genomic tools, genomics has emerged as another voice in this debate. Today, the genomes of many common domesticated species have been sequenced and their wild progenitors, existing or extinct, identified. The emergence of next-generation sequencing technologies has presented opportunities to sequence many individuals within species and has begun to reveal the complex history of populations and breeds. The identification of genomic signatures of selection for morphological and production-related traits has been facilitated by the analysis of a growing wealth of such sequencing data. These analyses have revealed that living in close proximity to humans induced changes in the genomes of domesticated species associated with adaption to new environments, climates, and to husbandry itself, in addition to the effects of artificial selection for desirable traits. The primary differences between domesticated animals and their wild progenitors are related to behavior, with domesticated species usually displaying a tame disposition, higher stress resistance, and increased social tolerance. Although understanding the genetic bases of these changes remains a challenge, the molecular processes associated with domesticated behavior have begun to emerge. Animal domestication, which started over 15,000 years ago with the domestication of dogs from wolves, is arguably the most influential and longest-running experiment in the human history, and with genomics it has reached a new epoch. This Special Issue will present recent advances in animal domestication research that are uncovering the genetic changes associated with domestication that have yielded such important consequences for our own species.

Dr. Anna V Kukekova
Guest Editor

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Keywords

  • domestication
  • breed
  • quantitative trait loci
  • selective sweep
  • dog
  • cow
  • pig
  • sheep
  • goat
  • camel

Published Papers (6 papers)

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Research

Open AccessArticle
Haplotype Purging after Relaxation of Selection in Lines of Chickens That Had Undergone Long-Term Selection for High and Low Body Weight
Genes 2020, 11(6), 630; https://doi.org/10.3390/genes11060630 - 08 Jun 2020
Abstract
Bi-directional selection for increased and decreased 56-day body weights (BW56) has been applied to two lines of White Plymouth Rock chickens—the Virginia high (HWS) and low (LWS) body weight lines. Correlated responses have been observed, including negative effects on traits related to fitness. [...] Read more.
Bi-directional selection for increased and decreased 56-day body weights (BW56) has been applied to two lines of White Plymouth Rock chickens—the Virginia high (HWS) and low (LWS) body weight lines. Correlated responses have been observed, including negative effects on traits related to fitness. Here, we use high and low body weight as proxies for fitness. On a genome-wide level, relaxed lines (HWR, LWR) bred from HWS and LWS purged some genetic variants in the selected lines. Whole-genome re-sequencing was here used to identify individual loci where alleles that accumulated during directional selection were purged when selection was relaxed. In total, 11 loci with significant purging signals were identified, five in the low (LW) and six in the high (HW) body weight lineages. Associations between purged haplotypes in these loci and BW56 were tested in an advanced intercross line (AIL). Two loci with purging signals and haplotype associations to BW56 are particularly interesting for further functional characterization, one locus on chromosome 6 in the LW covering the sour-taste receptor gene PKD2L1, a functional candidate gene for the decreased appetite observed in the LWS and a locus on chromosome 20 in the HW containing a skeletal muscle hypertrophy gene, DNTTIP1. Full article
(This article belongs to the Special Issue Domestication Genetics)
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Open AccessArticle
Genome-Wide Analysis Reveals Human-Mediated Introgression from Western Pigs to Indigenous Chinese Breeds
Genes 2020, 11(3), 275; https://doi.org/10.3390/genes11030275 - 04 Mar 2020
Cited by 1
Abstract
Genetic variations introduced via introgression from Western to Chinese pigs have contributed to the performance of Chinese breeds in traits such as growth rate and feed conversion efficiency. However, little is known about the underlying genomic changes that occurred during introgression and the [...] Read more.
Genetic variations introduced via introgression from Western to Chinese pigs have contributed to the performance of Chinese breeds in traits such as growth rate and feed conversion efficiency. However, little is known about the underlying genomic changes that occurred during introgression and the types of traits affected by introgression. To address these questions, 525 animals were characterized using an SNP array to detect genomic regions that had been introgressed from European to indigenous Chinese breeds. The functions of genes located in introgressed regions were also investigated. Our data show that five out of six indigenous Chinese breeds show evidence of introgression from Western pigs, and eight introgressed genome regions are shared by five of the Chinese breeds. A region located on chr13: 12.8–13.1 M was affected by both introgression and artificial selection, and this region contains the glucose absorption related gene, OXSM, and the sensory related gene, NGLY. The results provide a foundation for understanding introgression from Western to indigenous Chinese pigs. Full article
(This article belongs to the Special Issue Domestication Genetics)
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Open AccessArticle
Complete Range of the Universal mtDNA Gene Pool and High Genetic Diversity in the Thai Dog Population
Genes 2020, 11(3), 253; https://doi.org/10.3390/genes11030253 - 27 Feb 2020
Abstract
The dog population of Southern East Asia is unique in harboring virtually the full range of the universal mtDNA gene pool, and consequently, it has the highest genetic diversity worldwide. Despite this, limited research has been performed on dog genetics within this region. [...] Read more.
The dog population of Southern East Asia is unique in harboring virtually the full range of the universal mtDNA gene pool, and consequently, it has the highest genetic diversity worldwide. Despite this, limited research has been performed on dog genetics within this region. Here we present the first comprehensive study of a sub-region within Southern East Asia, analyzing 528 bp of mtDNA for 265 dogs from Thailand, in the context of dogs from across the Old World. We found that Thailand was the only region in the world that has the full range of the universal mtDNA gene pool, that is, all 10 sub-haplogroups. Consequently, the statistics for diversity are among the highest, especially in North Thailand, which had high values for haplotype diversity and the number of haplotypes, and the lowest proportion of individuals with a universal type-derived haplotype (UTd) among all regions. As previously observed, genetic diversity is distinctly lower outside Southern East Asia and it decreases following a cline to the lowest values in western Eurasia. Thus, the limited geographical region of Thailand harbors a distinctly higher genetic diversity than much larger regions in western Eurasia, for example, Southwest Asia and Europe which have only five and four of the 10 sub-haplogroups, respectively. Within Thailand, diversity statistics for all four sub-regions follow the general pattern of Southern East Asia, but North Thailand stands out with its high diversity compared to the other regions. These results show that a small part of Southern East Asia harbors the full range of the mtDNA gene pool, and they emphasize the exceptional genetic status of Southern East Asia. This indicates that today’s dogs can trace a major part of their ancestry to Southern East Asia or closely situated regions, highlighting Thailand as a region of special interest. Considering the large genetic diversity found in Thailand and that many neighboring regions, e.g., Myanmar and Laos, have not been studied for dog genetics, it is possible that large parts of the dog gene pool remain undiscovered. It will be an important task for future studies to fill in these blanks on the phylogeographic map. Full article
(This article belongs to the Special Issue Domestication Genetics)
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Open AccessArticle
Transcriptome Analysis of the Cecal Tonsil of Jingxing Yellow Chickens Revealed the Mechanism of Differential Resistance to Salmonella
Genes 2019, 10(12), 979; https://doi.org/10.3390/genes10120979 - 28 Nov 2019
Abstract
Salmonella is one of the most common food-borne pathogens. It can be transmitted between chickens, as well as to people by contaminated poultry products. In our study, we distinguished chickens with different resistances mainly based on bacterial loads. We compared the cecal tonsil [...] Read more.
Salmonella is one of the most common food-borne pathogens. It can be transmitted between chickens, as well as to people by contaminated poultry products. In our study, we distinguished chickens with different resistances mainly based on bacterial loads. We compared the cecal tonsil transcriptomes between the susceptible and resistant chickens after Salmonella infection, aiming to identify the crucial genes participating in the antibacterial activity in the cecal tonsil. A total of 3214 differentially expressed genes (DEGs), including 2092 upregulated and 1122 downregulated genes, were identified between the two groups (fold change ≥ 2.0, padj < 0.05). Many DEGs were mainly involved in the regulation of two biological processes: crosstalk between the cecal tonsil epithelium and pathogenic bacteria, such as focal adhesion, extracellular-matrix–receptor interaction, and regulation of the actin cytoskeleton and host immune response including the cytokine–receptor interaction. In particular, the challenged resistant birds exhibited strong activation of the intestinal immune network for IgA production, which perhaps contributed to the resistance to Salmonella infection. These findings give insight into the mRNA profile of the cecal tonsil between the two groups after initial Salmonella stimulation, which may extend the known complexity of molecular mechanisms in chicken immune response to Salmonella. Full article
(This article belongs to the Special Issue Domestication Genetics)
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Open AccessArticle
Evidence for Early European Neolithic Dog Dispersal: New Data on Southeastern European Subfossil Dogs from the Prehistoric and Antiquity Ages
Genes 2019, 10(10), 757; https://doi.org/10.3390/genes10100757 - 26 Sep 2019
Cited by 1
Abstract
The history of dog domestication is still under debate, but it is doubtless the process of an ancient partnership between dogs (Canis familiaris) and humans. Although data on ancient DNA for dog diversity are still incomplete, it is clear that several [...] Read more.
The history of dog domestication is still under debate, but it is doubtless the process of an ancient partnership between dogs (Canis familiaris) and humans. Although data on ancient DNA for dog diversity are still incomplete, it is clear that several regional dog populations had formed in Eurasia up to the Holocene. During the Neolithic Revolution and the transition from hunter-gatherer to farmer societies, followed by civilization changes in the Antiquity period, the dog population structure also changed. This process was due to replacement with newly formed dog populations. In this study, we present for the first time mitochondrial data of ancient dog remains from the Early Neolithic (8000 years before present (BP)) to Late Antiquity (up to 3th century AD) from southeastern Europe (the Balkans). A total of 16 samples were analyzed, using the mitochondrial D-loop region (HVR1). The results show the presence of A (70%) and B (25%) clades throughout the Early and Late Neolithic Period. In order to clarify the position of our results within the ancient dog population in Eneolithic Eurasia, we performed phylogenetic analysis with the available genetic data sets. This data showed a similarity of the ancient Bulgarian dogs to Italian (A, B, and C clades) and Iberian (clades A and C) dogs’ populations. A clear border can be seen between southern European genetic dog structure, on the one hand, and on the other hand, central-western (clade C), eastern (clade D) and northern Europe (clades A and C). This corresponds to genetic data for European humans during the same period, without admixture between dog populations. Also, our data have shown the presence of clade B in ancient Eurasia. This is not unexpected, as the B haplogroup is widely distributed in extant Balkan dogs and wolves. The presence of this clade both in dogs and in wolves on the Balkans may be explained with hybridization events before the Neolithic period. The spreading of this clade across Europe, together with the A clade, is related to the possible dissemination of newly formed dog breeds from Ancient Greece, Thrace, and the Roman Empire. Full article
(This article belongs to the Special Issue Domestication Genetics)
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Open AccessArticle
Transcriptomic Analysis of Porcine Granulosa Cells Overexpressing Retinol Binding Protein 4
Genes 2019, 10(8), 615; https://doi.org/10.3390/genes10080615 - 13 Aug 2019
Cited by 1
Abstract
Retinol binding protein 4 (RBP4), mainly secreted by the liver and adipocytes, is a transporter of vitamin A. RBP4 has been shown to be involved in several pathophysiological processes, such as obesity, insulin resistance, and cardiovascular risk. Reports have indicated the high expression [...] Read more.
Retinol binding protein 4 (RBP4), mainly secreted by the liver and adipocytes, is a transporter of vitamin A. RBP4 has been shown to be involved in several pathophysiological processes, such as obesity, insulin resistance, and cardiovascular risk. Reports have indicated the high expression levels of RBP4 in cystic follicles. However, the role of RBP4 in mammalian follicular granulosa cells (GCs) remains largely unknown. To illustrate the molecular pathways associated with the effects of RBP4 on GCs, we used high-throughput sequencing to detect differential gene expression in GCs overexpressing RBP4. A total of 113 differentially expressed genes (DEGs) were identified in RBP4-overexpressing GCs, and they included 71 upregulated and 42 downregulated genes. The differential expressions of the top 10 DEGs were further confirmed by real-time quantitative polymerase chain reaction. Pathway analysis indicated that the DEGs are mostly involved in oxidative phosphorylation, Parkinson’s disease, non-alcoholic fatty liver disease, Huntington’s disease, cardiac muscle contraction, Alzheimer’s disease, fatty acid biosynthesis, AMP-activated protein kinase signaling pathway, and insulin signaling pathway. Genes in these pathways should be useful for future studies on GCs. Altogether, the results of our study establish a framework for understanding the potential functions of RBP4 in porcine GCs. Full article
(This article belongs to the Special Issue Domestication Genetics)
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