Genetics and genomics of crop domestication TABLE OF CONTENTS Plants and Domestication . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Scope . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Domesticated crops . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Weeds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 Invasive species . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 Model species and crop sciences . . . . . . . . . . . . . . . . . 5 Understanding Domestication Processes . . . . . . . . . . . . . . . 5 Evidence of relatives and processes of early domestication . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Genes of domestication . . . . . . . . . . . . . . . . . . . . . . . . . 6 Genetic variation and domestication . . . . . . . . . . . . . . . 6 Genetic control related to diversity and speciation . . . . 6 Domestication of maize . . . . . . . . . . . . . . . . . . . . . . . . . 7 Domestication of legumes . . . . . . . . . . . . . . . . . . . . . . . 7 Yield traits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 Hybrid Species and New Polyploids in Domestication . . . . 8 Post-Domestication Selection . . . . . . . . . . . . . . . . . . . . . . . . 8 Modi.cations in crop characteristics . . . . . . . . . . . . . . . 8 New Domestication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9 Domesticated species . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Lost crops . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Trees and biofuels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Genetics and breeding for new uses: Ecosystem services . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 Features of Domesticated Genomes . . . . . . . . . . . . . . . . . . 11 Superdomestication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 Plants and Domestication Scope In this review of genetics and genomics related to plant bio-technology and agriculture, we consider the nature of species that are grownas crops and used by mankind, or otherwise associated with people. We will thenreview aspects of the genetics and genome changes that have beenassociated with cropplants and their domestication from their wild rela-tives before speculating about some of the new opportunities forplant biotechnology to meet the challenges faced in the twenty-.rst century. Domesticated crops Domesticated crops are a subset of all plants. Domesticated species, whetherplants oranimals, are considered as those grown by people for economic or otherreasons, and that dif-fer from their closest wild relatives. Domesticated species are reliant on human intervention for theirreproduction, nutri-tion, health, planting, and dispersal. They are harvested with the possibility that a different species will be planted in theirplace. Additional characteristics selected for domesticationinclude size of harvested parts, yield or yield stability, and quality for the use of the product. There are extensive genetic differences inall of these characteristics between individu-als withina species, as well as between species, and multiple characteristics are selected at the time of domestication that make the crop worth growing by farmers for millenniaand now by today’s plant breeders. . 2012 Elsevier Inc. All rights reserved. DOI: 10.1016/B978-0-12-381466-1.00001-8 Genomic techniques allow the underlying selectionproc-esses to be understood, exploited, and re.ned for cropimprovement. Genomic scientists cannow understand and improve the ef. ciency of exploitation of genes, genetic diversity, and controls present in crop species and their wild relatives. Domestication of plants, including selection of appropriate species and genetic changes, is one of the features of agriculture, but agriculture also requires knowledge beyond suitable genotypes ( Janick, 2005 ), such as the planting, grow-ing, protection, and harvest of the plants and the accurate timing of the various farming operations. Domesticated plants are grown by the humanpopulation to meet arange of needs that can be summarized by the six “Fs”: food, feed, fuel, . bers (and chemicals), . owers, and pharma-ceuticals. Plants within each of these classes have substan-tial economic impact. Nevertheless, out of 400,000 species of . owering plants, less than 200 have been domesticated as food and feed plants, and just 12 species provide 75% of the food eaten (FAOStat, 2010 ). Very few of the 1000 gymno-sperms, and arguably none of the 15,000 ferns and allies, have been domesticated. New knowledge of genetics and improved techniques of selection, hybridization, or gene transfer have the potential to enable more species to be domesticated. As well as domesticated crop species, there are many spices, pharmaceutical (and medicinal), horticultural, and garden (“. owers”) plants collected over the last millenniafrom the wild and cultivated ona small-scale. These plants may be genetically similarand as diverse as their wild rela-tives, although one ora small number of genes may have beenselected. Many of the selections require human interventionto survive, often because they are grown outside theirnatu-ral climate range or have abnormalities that are regarded as attractive or useful but reduce plant . tness. However, with the exception of some hybrids, the limited changes mean they are not normally considered as domesticated. Weeds Weeds and invasive species are associated with human farm-ing and habitation, although they are not normally considered as domesticated species. There has been limited genomic and genetic work on most of these species with notable excep-tions, inparticularArabidopsis thaliana. Harlanand deWet (1965) de.ned a weed as “a generally unwanted organism that thrives in habitats disturbed by man”; like crops, weed species are extremely diverse, and have different strategies for sur-vival. The effect of weeds onagriculture can be devastating, such as taking nutrition from the crop, making harvest dif. -cult, orreducing the value and quality of the harvest. Most cropplants will not establish themselves inan envi-ronment where weeds thrive and active intervention is needed to remove competition. Inan extensive study of feral oil seed rape (canola orBrassica napus), Crawley and Brown (1995) showed the very high level of turnover of site occupancy onhighway verges, with local extinction occurring within three years in the absence of new seeding and soil disturbance. Incontrast, weeds can be notably persistent, with; for exam-ple, nettles (Urtica dioica) remaining as markers of sites of habitationafter hundreds of years innorthern Europe in the absence of further habitation or evidence of crops. There are strong selectionpressures on weeds to bene. t from the human-created habitat at the farm (rather thanplant breeder) level, working with potentially much largerand more widely distributed populations than breeders use. Weeds may mimic the growth forms or seeds of crops and are distributed orgrow along with them. The selection is not applied to yield and quality characteristics, but on survival and popula-tion distribution or expansion, with key genes such as those for seed dormancy or dehiscence (see the sectionGenes of Domestication) potentially selected in the opposite directionfrom the seeds of a crop. Crops can become weeds. In the Brassicas, for example, the same genotype may be a weed with low yield and poorcharacteristics in one environment, but arobust crop with desirable properties inanother. Volunteers ― plants from aprevious crop on the same land ― are a major challenge ingrowing many . eld crops. They thrive in the crop conditions; the economic damage from these weeds includes acting as reservoirs of crop-speci. c diseases over several seasons inarotation. Weeds have no harvest value ina crop, reducing yields, and making crop management dif.cult, so farmers have beenimproving their weed control methods since the start of agri-culture. Inadvanced commercial farms weed control is anexpensive part of the agronomy, while for smallholders and subsistence farmers, the continuous laborrequired can be one of the most tedious and demeaning operations for the people, usually womenand children, that are involved. The removal and control of weeds is environmentally costly and involves burning, herbicides, deepplowing and multiple soil cultivations, processes leading to erosion, poor soil moisture conservation, use of large amounts of energy, loss of soil struc-ture, uncontrolled .res, and smoke orpollution. Approaches to weed control have changed continuously over millennia, including use of .re, planting methods, and plowing. As well a
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