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Genetics and Genomics of Crop Domestication J.S Genetics and genomics of crop domestication J.S. (Pat) Heslop-Harrison and Trude Schwarzacher Department of Biology, University of Leicester, Leicester LE1 7RH, UK [email protected] and [email protected] Chapter for: Plant biotechnology and agriculture: Prospects for the 21st century Editors: Arie Altman (Hebrew University of Jerusalem, Israel), Paul Michael Hasegawa (Purdue University, USA) Contents Genetics and genomics of crop domestication ........................................................................................................ 1 Key Words .......................................................................................................................................................... 1 1.1 Plants and Domestication ............................................................................................................................. 2 1.1.1 Scope ..................................................................................................................................................... 2 1.1.2 Domesticated crops ................................................................................................................................ 2 1.1.3 Weeds .................................................................................................................................................... 3 1.1.4 Invasive species ..................................................................................................................................... 4 1.1.5 Model species and crop sciences ........................................................................................................... 4 1.2 Understanding domestication processes ....................................................................................................... 5 1.2.1 Evidence of relatives and processes of early domestication .................................................................. 5 1.2.2 Genes of domestication .......................................................................................................................... 6 1.2.3 Genetic variation and domestication ................................................................................................. 6 1.2.4 Genetic control related to diversity and speciation ................................................................................ 7 1.2.5 Domestication of maize ......................................................................................................................... 7 1.2.6 Domestication of legumes ..................................................................................................................... 8 1.2.7 Yield traits ............................................................................................................................................. 9 1.3 Hybrid species and new polyploids in domestication ................................................................................... 9 1.4 Post-domestication selection ...................................................................................................................... 10 1.4.1 Modifications in crop characteristics ................................................................................................... 10 1.5 New domestication ..................................................................................................................................... 11 1.5.1 Domesticated species ........................................................................................................................... 11 1.5.2 Lost crops ............................................................................................................................................ 12 1.5.3 Trees and biofuels. ............................................................................................................................... 12 1.5.4 Genetics and breeding for new uses: ecosystem services .................................................................... 12 1.6 Features of domesticated genomes ............................................................................................................. 13 1.7 Superdomestication .................................................................................................................................... 13 1.8 Acknowledgements..................................................................................................................................... 15 1.9 Literature cited ............................................................................................................................................ 15 Legend to table ..................................................................................................................................................... 20 Key Words Crops, genomics, chromosomes, biodiversity, molecular markers, domestication SUMMARY/ABSTRACT Domesticated species or crop plants typically include only a fraction of the genetic diversity in their wild relatives, and have a range of genetically controlled features that were selected at the time of domestication such as lack of seed dispersal gigantism in the harvested parts, determinate and synchronized growth, increased harvest index and change in sweetness or bitterness. They were also adapted to agricultural practices and technology, lacking dormancy, being easy to propagate and grow, and carrying resistances to diseases and pests. Most of today’s major crops were cultivated at the start of agriculture and genetic Heslop-Harrison & Schwarzacher. May 4, 2011. Page 1. improvements have continued, although a number of species have been lost over subsequent millennia. Weeds species (and invasive plants) have been co-selected with crops, The genetic bases of the changes from wild ancestors are now well understood, and this research provides the basis for future improvements in crops for uses including food, feed, fuel and pharmaceuticals. The introduction of new crops, and the selection of crops for new uses such as ecosystem services is possible with better direction of the breeding. Superdomestication, involving definition of crop requirements and use of appropriate germplasm and technology to give crops with the required characters, has the potential to provide solutions to the challenges now facing agriculture and the environment. 1.1 Plants and Domestication 1.1.1 Scope In this review of genetics and genomics related to plant biotechnology and agriculture, we aim to consider the nature of species that are grown as crops and used by mankind, or otherwise associated with people. We will then overview aspects of the genetics and genome changes that have been associated with crop plants and their domestication from their wild relatives, before speculating about some of the new opportunities for plant biotechnology to meet the challenges faced in the 21st century. 1.1.2 Domesticated crops Domesticated crops are a subset of all plants. Domesticated species, whether plants or animals, can be considered as those that are grown by people for economic or other reasons, and that differ from their closest wild relatives. Domesticated species are reliant on human intervention for their reproduction, nutrition, health, planting and dispersal. They are harvested with the possibility that a different species will be planted in their place. Additional characters that are selected for under domestication include size of harvested parts, yield or yield stability, and quality for the use of the product. There are extensive genetic differences in all these characters between individuals within a species as well as between species, and multiple characters have been selected at the time of domestication, making the crop worthwhile to grow, then continuing over subsequent millennia by farmers, and by plant breeders more recently. Genomic techniques are allowing the underlying selection processes to be understood, exploited and refined for crop improvement, so genomic scientists can now understand and improve the efficiency 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 the invention of agriculture, but agriculture requires knowledge beyond genotypes that are suitable (Janick, 2005), involving the planting, growing, protection and harvest of the plants with the requirement for accurate timing of the various farming operations. Domesticated plants are grown by the human population to meet a range of needs which can be summarized by the six ‘F’s: food, feed, fuel, fibres (and chemicals), flowers and pharmaceuticals. Plants within each of these classes have substantial economic impact. Nevertheless, out of a total of 400,000 species of flowering 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 1,000 gymnosperms, and arguably none of the 15,000 ferns and allies, have been domesticated. New knowledge of genetics and improved techniques of Heslop-Harrison & Schwarzacher. May 4, 2011. Page 2. 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 (‘flowers’) plants, collected over the last millennia from the wild, and cultivated on a small
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