Genome‐wide linkage and QTL mapping in porcine F₂ families generated from Pietrain, Meishan and Wild Boar crosses

Abstract

Summary Three informative pig F2 families based on European Wild Boar (W), Meishan (M) and Pietrain (P) crosses have been used for genome‐wide linkage and quantitative trait loci (QTL) analysis. Altogether 129 microsatellites, 56 type I loci and 46 trait definitions (specific to growth, fattening, fat deposition, muscling, meat quality, stress resistance and body conformation) were included in the study. In the linkage maps of M × P, W × P and W × M families, average spacing of markers were 18.4, 19.7 and 18.8 cM, the numbers of informative meioses were 582, 534 and 625, and the total lengths of autosomes measured were 27.3, 26.0 and 26.2 Morgan units, respectively. Maternal maps were on average 1.3 times longer than paternal maps. QTLs contributing more than 3% of F2 phenotypic variance could be identified at p < 0.05 chromosome‐wide level. Differences in the numbers and positions of QTLs were observed between families. Genome‐wide significant QTL effects were mapped for growth and fattening traits on eight chromosomes (1, 2, 4, 13, 14, 17, 18 and X), for fat deposition traits on seven chromosomes (1, 2, 3, 4, 6, 7 and X), for muscling traits on 11 chromosomes (1, 2, 3, 4, 6, 7, 8, 12, 14, 15 and X), for meat quality and stress resistance traits on seven chromosomes (2, 3, 6, 13, 16, 18 and X), and QTLs for body‐conformation traits were detected on 14 chromosomes. Closely correlated traits showed similar QTL profiles within families. Major QTL effects for meat quality and stress resistance traits were found on SSC6 in the interval RYR1‐A1BG in the W × P and M × P families, and could be attributed to segregation of the RYR1 allele T derived from Pietrain, whereas no effect in the corresponding SSC6 interval was found in family W × M, where Wild Boar and Meishan both contributed the RYR1 allele C. QTL positions were mostly similar in two of the three families for body conformation traits and for growth, fattening, fat deposition and muscling traits, especially on SSC4 (interval SW1073‐NGFB). QTLs with large effects were also mapped on SSC7 in the major histocompatibility complex (MHC) (interval CYP21A2‐S0102) and affected body length, weight of head and many other traits. The identification of DNA variants in genes causative for the QTLs requires further fine mapping of QTL intervals and a positional cloning. However, for these subsequent steps, the genome‐wide QTL mapping in F2 families represents an essential starting point and is therefore significant for animal breeding.

Mapping of quantitative trait loci and confirmation of the FAT1 region on chromosome 4 in an F2 population of pigs

“…Alleles inherited from the naturalized Brazilian Piau breed were responsible for the decreased muscling traits. Geldermann et al (2003) observed the presence of QTL for HW and BSW at position 115 cM on SSC4 in a cross between wild boar and Pietrain pigs; the QTL for HW and BSW were responsible for 5.2% and 8.3% of the phenotypic variation, respectively. Possibly, these QTL are the same.…”

Mapping QTL for growth and muscling traits in three connected porcine F&lt;sub&gt;2&lt;/sub&gt; crosses

“…In conclusion, in this study the three connected F 2 -designs of Geldermann et al (2003) were analysed jointly for muscling and growth traits using a multi-allele multi-QTL model. A large number of QTL was found compared to the separate analysis of crosses (see Geldermann et al 2003).…”

“…the same W boar was used to generate the W × P and the W × M cross. A detailed description of the design can be found in Geldermann et al (2003). The F 2 -individuals were phenotyped for numerous traits.…”

“…However, it has frequently been shown that a combined analysis of QTL experiments boosts the statistical power substantially (Walling et al 2000, Bennewitz et al 2003. The three F 2 -designs established by Geldermann et al (2003) are especially well suited for a joint analysis, because not only same founder breeds, but also same founder animals were used to set up the designs. Rückert & Bennewitz (2010) proposed a model adapted from plant breeding for analysis of connected F 2 -experiments and showed the benefit of a joint analysis of these three designs.…”

“…Stratz et al (2012) mapped QTL for meat quality traits considering main and pairwise epistatic effects. The aim of the present study was to map QTL for growth and muscling traits in the three F 2 -designs from Geldermann et al (2003) using the approach of Rückert & Bennewitz (2010).…”