Genomic scan for quantitative trait loci of chemical and physical body composition and deposition on pig chromosome X including the pseudoautosomal region of males

To understand the genetic control of economically important traits in pigs a large number of studies have investigated QTL that contribute to variation in these traits e.g. [1-4]. Most QTL have been identified on autosomes with only a few on the sex chromosomes. One reason may be that the role of sex chromosomes in the genomic regulation of these traits is less important. Another reason may come from the fact that, until recently, software modelling more appropriately the specific features of sex chromosomes was not available. Indeed, the mammalian X chromosome is considerably larger than the Y chromosome and carries more genes [5,6]. For example, 1 250 genes are known on the human X chromosome but only 147 on the Y chromosome [7]. As a result, female cells, which carry two copies of the X chromosome, contain twice as many X-linked genes than males. Mammals have developed a mechanism to balance the dosage of the X chromosome genes between sexes, called the dosage compensation phenomenon [8,9]. Furthermore, chromosomes X and Y only share a small homologous region called the pseudoautosomal region [10].Because QTL mapping software taking into account the specific X chromosome features was not available, most studies have adopted a regression based approach analyzing males and females separately, which decreases the power of QTL detection e.g. [11,1,12]. Recently, Perez-Enciso et al. [13] have developed software combining a mixed model methodology and a maximum likelihood approach, which can model the specific X chromosome features in a QTL analysis.Therefore, the aim of the present study was to investigate QTL on pig chromosome X (SSCX) for chemical and physical body composition and deposition using a methodology, which accurately takes into account the features associated with this chromosome.This study was based on data recorded from a three-generation full-sib design, developed from a cross between seven unrelated Pietrain grandsires, all heterozygous (Nn) at the r