Generation and characterization of a 12,000-rad radiation hybrid panel for fine mapping in pig

Abstract

We have constructed a 12,000-rad porcine whole-genome radiation hybrid panel to complement the first generation 7,000-rad panel (IMpRH) and allow higher resolution mapping studies both in specific areas of interest and on the whole genome. We analyzed 243 hybrid clones on the basis of their marker retention frequency to produce a final panel of 90 hybrid clones with an average retention frequency of 35.4%. The resolution of this 12,000-rad panel (IMNpRH2) was compared to the resolution of the 7,000-rad panel (IMpRH) by constructing framework maps in the 2.4-Mb region of porcine chromosome 15 containing the acid meat RN gene. In this region, two-point analysis was used to estimate RH distances and demonstrates their reliability with the estimation of physical distances. This study demonstrates that the 12,000-rad panel constitutes a powerful tool for constructing high-resolution maps. Indeed, the resolution of IMNpRH2 (12–14 kb/cR_12,000) is two to three times more than that of IMpRH (35–37 kb/cR_7,000). As expected, the increase in the radiation dose allows an increase of the mapping resolution in terms of kb/cR with the same suppleness of use for mapping experiments. In addition the RH map constructed in the region investigated proved to be more homogeneous on IMNpRH2 than on IMpRH.

Swine Genome Sequencing Consortium (SGSC): a strategic roadmap for sequencing the pig genome

“…To date, >3000 mapped loci are catalogued for the pig genome (http://www.thearkdb.org). Recently, whole-genome radiation hybrid (WG-RH) panels (7500 and 12 500 rad) have been generated for swine (Hawken et al, 1999;Yerle et al, 2002), resulting in yet another rapid increase in the number of expressed sequences being mapped, facilitating comparative mapping with other species (Rinke et al, 2002). The swine genomics community has also acquired access to resources such as bacterial artificial chromosome (BAC) libraries (Fahrenkrug et al, 2001;Anderson et al, 2000) that provide approximately 35× coverage of the swine genome.…”

Molecular characterization, chromosome mapping, and expression profile of porcine CDC16

“…Primers, corresponding to exon 4 and 5 and intron 4 of pig CDC16, were designed (Table 1). A 743 bp PCR product for CDC16 was used to type SCHP and IMpRH panel (Yerle et al, 1999(Yerle et al, , 2001). The PCR products were visualized on 2% agarose gel stained with ethidium bromide.…”

Minimizing a QTL region for intramuscular fat content by characterizing the porcine Phosphodiesterase 4B (PDE4B) gene

“…Primer sets were designed for PDE4B using sequences analyzed in this study, and PDE4B and two microsatellite markers, S0121 and SW1881, were typed using the IMNpRH212,000rad panel (22). With the scoring results of these three markers and 15 genes previously scored, a new RH map was constructed using the RHMAXLINK program (23) (Fig.…”