ABSTRACT
Coffee is one of the most economically important crops produced in about 80 tropical countries with an annual production of nearly 7 million tons of green beans (Musoli et al. 2009). It is the second most valuable commodity exported by developing countries with over 75 million people depending on it for their livelihood (Pendergrast 2009). Coffea (family Rubiaceae, subfamily Ixoroideae, and tribe Coffeeae) consists of 103 species distributed in Africa, Madagascar, the Comoros, and the Mascarene Islands (La Réunion and Mauritius) (Davis and Rakotonasolo 2008). Of these, three
10.1 Introduction .................................................................................................. 227 10.2 Diversity and Phylogeny ............................................................................... 229 10.3 Genome Analysis .......................................................................................... 231
10.3.1 Genome Size ..................................................................................... 232 10.3.2 Expressed Sequence Tags ................................................................. 232 10.3.3 Bacterial Arti›cial Chromosome Libraries ...................................... 233 10.3.4 Conserved Ortholog Set .................................................................... 233 10.3.5 Whole Genome Sequencing ............................................................. 233
10.4 Molecular Markers and Genetic Diversity ...................................................234 10.4.1 Isozymes and Allozymes ..................................................................234 10.4.2 Restriction Fragment Length Polymorphism ................................... 235 10.4.3 Random Ampli›ed Polymorphic DNA ............................................ 235 10.4.4 Ampli›ed Fragment Length Polymorphism ..................................... 236 10.4.5 Simple Sequence Repeats ................................................................. 236 10.4.6 Inter-Simple Sequence Repeat .......................................................... 237
10.5 Molecular Breeding ...................................................................................... 238 10.6 Genomics and Quality of Coffee ..................................................................240
