Characterization of 24 porcine (dA-dC)n-(dT-dG)n microsatellites: genotyping of unrelated animals from four breeds and linkage studies

Abstract

Twenty-four PCR primer pairs were designed for the detection of porcine microsatellites. Polymorphism was investigated in 76 unrelated animals from four different breeds: Duroc, Landrace, Hampshire, and Yorkshire. Compared with human microsatellites, a general lower heterozygosity was detected; however, for each microsatellite a significant variation between breeds in number of alleles and heterozygosity was seen. Mean heterozygosity was found to be significantly higher (P < 0.01%) in the Yorkshire breed than in the other three breeds. Linkage analyses with the CEPH linkage packet were performed in a backcross family comprising 45 animals, of which 43 had informative meioses. Ten of the microsatellites could be assigned to six different linkage groups, demonstrating that linkage mapping with microsatellites can be carried out with great efficiency in a relatively small number of animals. Four of the linkage groups represent Chromosomes (Chrs) 4, 6, 7, and 8 respectively, while two linkage groups are unassigned.

Genetic diversity of eleven European pig breeds

“…The panel of markers used in this trial exhibited a very high polymorphism, confirming an early study of microsatellite polymorphisms in 4 major pig breeds by [10] and the study on Belgian pig breeds of [29]. There are also good indications that null alleles were at a low frequency in the samples investigated.…”

“…This level of polymorphism is similar to the values so far reported for microsatellites in European pig and cattle breeds, e.g. by [10], [29] and [16], but below the values observed in human or chimpanzee populations where the expected heterozygosity ranges from 0.7 to 0.9 [11]. This level of polymorphism when compared to the corresponding effective sizes of the breeds, ranging from 13 to over 30 000 (Tab.…”

Microsatellite-based characterization of Southern African domestic pigs (<i>Sus scrofa domestica</i>)

“…A panel of 39 microsatellite loci distributed throughout the genome and identified as part of the Pig Genome Project was used in this study. The markers used (with chromosome position) were: S0073 (4), SW35 (4), S0298 (16), SW1134 (5), SW1851 (1), SW2456 (X/Y), SW2514 (2), SW983 (9), S0120 (18), SW2 (5), SW1557 (14), SW378 (5), SW761 (14), SW2008 (11), SW995 (5), SW352 (7), SW472 (7), SW949 (X/Y), S0004 (15), S0165 (3), S0217 (4), SW225 (13), SW1041 (10), SW21 (9), SW2404 (4), S0035 (6), S0006 (16), SW749 (9), SW2410 (8), SW940 (9), S0295 (9), SW839 (4), SW2406 (6), SW2419 (6), SW316 (6), S0121 (7), SW322 (6), S0385 (11) and SW2443 (2) (Fredholm et al, 1993;Ellegren et al, 1994;Hoyheim et al, 1994;McQueen et al, 1994;Robic et al, 1994;Rohrer et al, 1994;Groenen et al, 1995;Alexander et al, 1996;Rohrer et al, 1996;Lopez-Corrales et al, 1999).…”

A comprehensive map of the porcine genome.

“…Only 3.8% of intervals are greater than the maximum (10 cM) desired for human mapping (Ott and Donis-Keller 1994). Sufficient informative markers are available to conduct a genome scan at intervals of 20 cM in diverse resource populations, but additional markers will likely be needed to identify QTL within purebred swine populations where marker heterozygosities will be lower (Fredholm et al 1993;Rohrer et al 1994b). Regional marker density is sufficient to support positional cloning, but strategies to develop markers in deficient regions need to be implemented.…”