Guiry et al. BMC Genomics 2010, 11:211 http://www.biomedcentral.com/1471-2164/11/211 Background Alternative reproduction tactics (ARTs) enable fish to exploit a wide spectrum of resources and to respond to conditions such as an imbalance of sexes in the population [1]. The opportunity for ARTs in fishes arises largely as a consequence of external fertilisation. Access to eggs for fertilisation can be by adult males or alternatively by pre- cociously mature parr variously described as ‘satellite males’ or ‘sneakers’ [2,3]. The mature parr succeed mainly through speed or through being inconspicuous to adult males who might otherwise drive them off. The approach taken by an individual fish is believed to depend on the balance of energetic cost against reproductive payoff. The energetic cost of adult male reproduction in salmon is very high and few adults return to reproduce a second time [4,5]. However, the payoff is also high because an adult male can dominate an egg-laying female and almost all offspring are sired by that male. The energetic cost for a juvenile male (precocious male) may be much less but only a small number of eggs may be fertilised by that male. The decision to mature precociously or remain imma- ture for another winter has been modelled as a threshold trait [6,7]. A threshold level which takes into account parameters such as growth rate, body size and condition must be reached before the parr can mature. Both genetic [8] and environmental factors [9], which include social structure, are believed to play a part in attaining this threshold. For example, where environmental factors have been largely excluded by removing wild fish to a hatchery, the proportion of mature parr offspring was related to the source river of the parents suggesting involvement of a genetic component [10]. However, an environmental component was intimated by a study that showed tributaries of a single river had size thresholds for precocity that depended on the altitude of the tribu- tary [11]. Precocity levels of 20% have been reported in Scotland [12] though levels as high as 65% have been reported for more southerly rivers [13] possibly as a result of the warmer waters and faster growth of the fish. In cultured salmonids levels of precocity can vary depending on the genetic stock but high levels lead to reduced productivity and can present a health risk to the fish population through the negative effect of testosterone on immune function [14]. In the wild, fish that fortuitously find a better food source may grow faster and become socially dominant. Hatchery-reared fish are well fed yet growth and social hierarchy are still factors that influence the choice to mature precociously or undergo the parr- smolt transformation. In Ireland, wild Atlantic salmon generally remain in fresh water until the parr-smolt trans- formation at year 2+ or later [15]. They feed heavily in the marine environment for one year (grilse) or several years (multi-sea winter; MSW) before returning to their native Page 2 of 18 streams to spawn. In the hatchery environment the major- ity of salmon parr are expected to smolt at year 1+: popu- lations generally show a bimodal growth distribution in the previous autumn (year 0+) with larger fish preparing to smolt while the minor group of smaller fish will smolt a year later [16]. The juvenile male parr has three possible life trajec- tories: it can remain immature, it can undergo the parr- smolt transformation, or it can mature precociously prior to the parr-smolt transformation. Precocious parr are more likely to be those juvenile parr that have grown rapidly; they then transfer their energies into gonad development at the expense of bodily growth. At some point the balance will change when the immature parr out-grow the sexually mature parr and the social structure may again change [5]. The brain-pituitary-gonad (BPG) axis is the key regu- lator of sexual maturation. Neuron stimulation of the brain leads to stimulation of the pituitary through gona- dotropin releasing hormone (GnRH) which releases rele- vant hormones, such as follicle stimulating hormone (FSH) and luteinising hormone (LH) into the blood plasma for transport to the effector tissue. In the testes LH induces the production of testosterone which then affects various aspects of male physiology, secondary sexual characteristics and behaviour. In this study our goal was to develop a comprehensive picture of gene expression in the gonad and brain in precocious males, and compare mature parr testes to adult testes. How- ever, in an extension to this study, we also aimed to develop resources and investigate interactions between sexual maturation and the parr-smolt transformation. There are now several genomic resources available to the Atlantic salmon research community. The Canadian GRASP project [17], the Norwegian Salmon Genome Project http://www.salmongenome.no and the EU SAL- GENE project http://www.salmongenome.no/cgi-bin/ sgp.cgi all have provided large numbers of cDNA sequences for the DNA databases. We have developed a new Atlantic salmon cDNA microarray that is specifi- cally targeted at sexual maturation and the parr-smolt transformation: this is the first description of this array. The focus was on generating single tissue libraries of key transition stages from subtracted salmon cDNA libraries: we have observed that novel regulated genes are more likely to be represented in these subtracted libraries between two conditions than in single condi- tion cDNA libraries [18]. Adult maturation differs from precocious maturation in a number of important aspects; adult fish mature in fresh water after a sustained period of growth at sea having undergone the parr-smolt transformation either one or several years earlier. We have therefore also