Applications in the search for genomic selection signatures in fish
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Selection signatures are genomic regions harboring DNA sequences functionally involved in the genetic variation of traits subject to selection. Selection signatures have been intensively studied in recent years because of their relevance to evolutionary biology and their potential association with genes that control phenotypes of interest in wild and domestic populations. Selection signature research in fish has been confined to a smaller scale, due in part to the relatively recent domestication of fish species and limited genomic resources such as molecular markers, genetic mapping, DNA sequences, and reference genomes. However, recent genomic technology advances are paving the way for more studies that may contribute to the knowledge of genomic regions underlying phenotypes of biological and productive interest in fish.In this paper, different definitions of animal domestication are examined. Methods for identifying the domestication processes are outlined, including zooarchaeological and biomolecular techniques, along with archaeological evidence of associated economic and social changes. The extent to which animal domestications can be seen as hunter-gatherer innovations rather than a later addition by plant agriculturalists is discussed. The undisputed hunter-gatherer innovation of dog domestication is taken as a case study, and horse domestication in central Asia is also considered in depth. Other possible examples of domestication of animals by hunter-gatherers either before, or synchronously with, plant domestication are highlighted, including cattle in North Africa, camelids in South America, and reindeer in northern Eurasia. The reasons why animal domestication usually post-dates plant domestication are explored.
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This chapter contains sections titled: Introduction The Domestication Process Centers of Agricultural Origins Time Frame of Domestication The Domestication Syndrome Inheritance and Molecular Basis of the Domestication Syndrome Genetic Bottlenecks Is There a Potential for Domestication among Plant and Animal Species? Summary Literature Cited
Inheritance
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Crop domestication and further breeding improvement have long been important areas of genetics and genomics studies. With the rapid advancing of next-generation sequencing (NGS) technologies, the amount of population genomics data has surged rapidly. Analyses of the mega genomics data have started to uncover a previously unknown pattern of genome-wide changes with crop domestication and breeding. Selection during domestication and breeding drastically reshaped crop genomes, which have ended up with regions of greatly reduced genetic diversity and apparent enrichment of potentially beneficial alleles located in both genic and non-genic regions. Increasing evidences suggest that epigenetic modifications also played an important role during domestication and breeding.
Molecular breeding
Population genomics
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Phenotypic trait
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Summary Crop grasses were among the first plants to be domesticated c . 12 000 yr ago, and they still represent the main staple crops for humans. During domestication, as did many other crops, grasses went through dramatic genetic and phenotypic changes. The recent massive increase in genomic data has provided new tools to investigate the genetic basis and consequences of domestication. Beyond the genetics of domestication, many aspects of grass biology, including their phylogeny and developmental biology, are also increasingly well studied, offering a unique opportunity to analyse the domestication process in a comparative way. Taking such a comparative point of view, we review the history of domesticated grasses and how domestication affected their phenotypic and genomic diversity. Considering recent theoretical developments and the accumulation of genetic data, we revisit more specifically the role of mating systems in the domestication process. We close by suggesting future directions for the study of domestication in grasses. Contents Summary 273 I. Introduction 274 II. A brief history of domestication in grasses 275 III. Domestication genes 278 IV. Models of the domestication process 280 V. Evolutionary consequences of domestication for grass genomes 281 VI. Mating systems and the evolutionary dynamics of domestication in grasses 284 VII. Conclusion 286 Acknowledgements 287 References 287
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Summary Domesticated food crops are derived from a phylogenetically diverse assemblage of wild ancestors through artificial selection for different traits. Our understanding of domestication, however, is based upon a subset of well‐studied ‘model’ crops, many of them from the Poaceae family. Here, we investigate domestication traits and theories using a broader range of crops. We reviewed domestication information (e.g. center of domestication, plant traits, wild ancestors, domestication dates, domestication traits, early and current uses) for 203 major and minor food crops. Compiled data were used to test classic and contemporary theories in crop domestication. Many typical features of domestication associated with model crops, including changes in ploidy level, loss of shattering, multiple origins, and domestication outside the native range, are less common within this broader dataset. In addition, there are strong spatial and temporal trends in our dataset. The overall time required to domesticate a species has decreased since the earliest domestication events. The frequencies of some domestication syndrome traits (e.g. nonshattering) have decreased over time, while others (e.g. changes to secondary metabolites) have increased. We discuss the influences of the ecological, evolutionary, cultural and technological factors that make domestication a dynamic and ongoing process. Contents Summary 29 I. Introduction 30 II. Key concepts and definitions 30 III. Methods of review and analysis 35 IV. Trends identified from the review of 203 crops 37 V. Life cycle 38 VI. Ploidy level 40 VII. Reproductive strategies 42 VIII. The domestication syndrome 42 IX. Spatial and temporal trends 42 X. Utilization of plant parts 44 XI. Conclusions 44 Acknowledgements 45 References 45
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This chapter discusses how societal demands can affect the domestication process and how this affects domestic animals compared with their wild counterparts. The different conceptions of domestication, domestication from a modern ethological point of view will, the animals' perception of humans and changes in the way that animal domestication processes are considered are also included.
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The far Southwest Ethiopians transplant wild plant species to their gardens. One of such plant is the Dioscorea that we studied to assess the knowledge of wild yam and process of domestication. The study links two types of evidence to obtain insight about the process of yam domestication. We analyze two data sets derived from (1) ethnobotanical survey using 231 semi-structured interviews; and (2) morphological study in 47 yam accessions. Our study revealed that domestication is still active in some villages. Knowledge of yam domestication was shared by 44% of the farmers' even by those that have never practiced its domestication. Farmers who can describe the trend of domestication and the morphotypes of domesticate represented 21 and 28%, respectively. Farmers who have recent transplants in their garden varied from 4% in Bench to 10% in Sheko. The domestication process described by the two ethnic groups is similar. The duration of domestication can take up to six years, but with most of the individuals, it only takes three to five years. By linking the two types of evidence, two evolutionary processes are distinguished: (1) populations of recent domesticate expressing a domestication syndrome possibly belongs to the wild D. abyssinica or D. praehensilis, and (2) plants of incipient domesticate that might be derived from volunteers or diverse types of hybrids. Each of these processes can lead to integration of wild genotypes into the cultivated gene pool, and hence, enhance genetic diversity of cultivated yams. The domestication practices of traditional farmers should thus be taken into account if yam conservation and improvement plans need to be established.
Ethnobotany
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The pig appears to have been among the earliest domesticated animals in China, with evidence for pig domestication at Cishan from 8000 BP. The authors propose a model for the development of animal domestication.
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