Peanut or groundnut (Arachis hypogaea L.) is widely used as a source of edible oil and protein. It is cultivated mainly in tropical, subtropical and warm regions around the world. It is also the second most important seed legume of the world following soybean, with a total global production of 36.46 million tons, ranking among the top fi ve oilseeds cultivated in the world (FAO 2009). China, India and the US have been the leading producers of peanut for decades and consume approximately 65% of the world´s production (Gunstone 2011). Despite the importance of peanut, progress in peanut breeding, genetics and genomics still lag far behind that of major crops. This is in large part because of the relatively few researchers involved in this crop, the low fi nancial resources allocated to fundamental study as well as the complex genome of peanut (allotetraploidy, large genome size of 2,800 Mb; Temsch et al. 2000). Peanut is an economically important food crop worldwide, and thus its quality has become increasingly important and received more attention from the food industry and consumers, while growers are more interested on high-yielding varieties for higher income. Peanut well known for its allergens, is affected by a wide range of diseases such as those caused by Aspergillus, leaf fungi, nematodes and also various abiotic environmental stresses including drought. These constraints have led to yield loss as well as quality deterioration, e.g., allergenicity and afl atoxin contamination (Li et al. 2000; Holbrook et al. 2003; Ratnaparkhe et al. 2011). Peanut is morphologically diverse, however, many agronomical traits are diffi cult to select by conventional breeding, as they are quantitatively inherited. For this reason, it is quite hard to diminish the rate of adverse reactions and to enhance resistance to abiotic and biotic stresses through conventional breeding systems. The application of genomic tools in the breeding programs would greatly facilitate the genetic enhancement of cultivated peanut in a relatively rapid way (Livingstone et al. 2005; Varshney et al. 2009; Knoll et al. 2011). Unfortunately, understanding the genetic mechanism underlying complex traits in peanut is hindered by the fact that peanut possesses a narrow genetic diversity and its genome has not yet been sequenced and transcriptome resources are still limited (Pandey et al. 2011).