| Research summary for genomic research in swine |
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1 - Research Summaries
2 - Research summary for genomic research in swine |
Research summary for genomic research in swine
Gary Rohrer, Dan Nonneman and Brad Freking
USDA,
With changing consumer preferences and market demands for meat products in the last few decades, livestock producers frequently need to quickly change selection targets and strategies to remain competitive. Traditional selection methods generally take several generations of selective breeding before substantial improvements are realized in the herd. Therefore, many theoretical studies have been done over the past few decades to incorporate molecular genetic information in selection programs. This requires the development and validation of genetic markers that are predictive of traits targeted for selection. The first step to developing markers with predictive value is to scan the genome for locations that are significantly associated with performance traits of economic interest. This scan is often conducted in a structured population developed from a cross of breeds that are divergent for the traits of interest. The next step is to re-evaluate the genomic region in a separate set of animals to verify that associations exist. The first resource populations were developed to maximize the number of important traits that could be studied in one population. Therefore some of the first populations included Meishan pigs as they were quite different from US pigs for most production traits, specifically, growth rate, body composition and a number of reproduction related measurements. Later, resource populations were developed with commercially relevant breeds.
Development of QTL discovery populations
The Meishan/White composite population
The Meishan/White composite population developed at USMARC was initially a backcross population that was then mated to produce a F3 generation that was ? Meishan and ? White composite. The animals were then crossed with a new White composite reducing the Meishan influence to only ? in the F5 generation (Rohrer et al., 1999). This closed population was maintained until the F13 generation when it was terminated. Genome-wide scans to identify quantitative trait loci (QTL) were conducted in the F2-F4 generations (total number of animals was about 2,000), while subsequent generations are being maintained to validate and fine-map QTL (about 2,500 additional animals).
Numerous genomic regions associated with economically important traits have been discovered in this population. Growth rate QTL were discovered on chromosome 1 and 7 (Rohrer, 2000) and fat deposition QTL on chromosomes 1, 7 and X (Rohrer & Keele, 1998a; Rohrer & Keele, 1998b) Regions associated with female reproductive traits were found on chromosomes 1, 3, 8 and 10 while a region on the X chromosome affected testes size in boars.Subsequent generations of this population have been used to determine biological mechanisms that may be involved with identified QTL or to validate the presence of QTL. Boars from many different generations have been used to validate the presence of a QTL on the X chromosome that affects testes size and serum
A commercial Duroc-Landrace population
The Duroc breed was found to possess the best pork palatability traits by a study conducted by the National Pork Producer's Council and Landrace were frequently poorest for most pork quality traits. Therefore, an F2 population was developed by a local producer to identify QTL for carcass composition and pork palatability traits (380 animals slaughtered). As this was a terminal population, the QTL discovered in this population need to be validated in other populations.
Several unique genomic regions were found to be associated with intramuscular fat deposition, taste panel tenderness, loin-eye area and other meat quality traits (Rohrer et al., 2006).
Unique selection lines for component traits of litter size
A four-breed composite with equal contributions from Chester White, Landrace, Large White, and
Commercial Duroc-Landrace-Yorkshire population
A composite population whose performance is similar to current
Development of porcine Expressed Sequence Tags (ESTs)
A limitation for livestock genomic research has been the lack of gene sequence data available and a well-developed comparative map. To address this limitation in the pig, four normalized cDNA libraries were developed from a variety of pooled tissues primarily relating to embryonic development and reproduction. The concept and value behind the use of normalized pooled tissue libraries was addressed in Fahrenkrug et al. (2002). Sequencing of individual gene fragments was done at USMARC, the data processed by our bioinformatics team and deposited into the public sequence database (http://www.ncbi.nlm.nih.gov/). Sequencing of these libraries has been completed, resulting in 198,000 sequence reads incorporated into the current porcine gene index (http://www.tigr.org/tdb/ssgi/) which contains over 600,000 sequences. USMARC has generated about one-third of all publicly available ESTs for the pig in the world. These data have a significant worldwide impact on research efforts in the pig by facilitating studies in gene expression and efforts to screen populations for important genetic variation.
Development of a porcine comparative map and SNP markers
About 60% of all publicly available mapped microsatellite markers were developed and first characterized by the group at USMARC. The first microsatellite-based linkage map for any livestock species was published in 1994 and that map with nearly 400 microsatellite markers (Rohrer et al., 1994) is more comprehensive than any other swine group has produced to date. In 1996 the map was updated with the addition of 600 more microsatellite markers (Rohrer et al, 1996) and the current map contains over 3,000 markers (http://www.marc.usda.gov/).
Identification of specific genes influencing phenotypic variation in swine would be more efficient using high-resolution comparative maps with human and mouse. We have positioned over 1,200 gene-based loci on the swine comparative map using single nucleotide polymorphisms (
Fine-mapping QTL
Several regions on pig chromosomes have been identified that affect reproductive traits including ovulation rate (Campbell et al., 2003), uterine capacity and age at puberty. In order to identify the genes affecting these traits, efforts were made to further develop comparative maps with human and pigs (Kim et al, 2004; Nonneman & Rohrer, 2004, Mousel et al, 2006). Candidate genes were sequenced for variation and markers developed for association with phenotypic traits in the resource populations. SNPs were identified that are significantly associated with age of puberty, ovulation rate, nipple number and testis size in the White composite/Meishan resource population (Nonneman et al, 2005; Nonneman et al, 2006). Future studies will rely on extended pedigrees of commercially-relevant populations in order to effectively and efficiently identify genes affecting economically important traits.
References
Campbell EM, Nonneman D, and Rohrer GA. 2003. Fine mapping a quantitative trait locus affecting ovulation rate in swine on chromosome 8. J Anim Sci. 81:1706-1714.
Fahrenkrug SC, Smith TP, Freking BA, Cho J, White J, Vallet J,
Ford JJ,
Kim JG, Rohrer GA, Vallet JL, Christenson RK, and Nonneman D. 2004. Addition of 14 anchored loci to the porcine chromosome 8 comparative map. Anim Genet. 35:474-476.
Leymaster K. A., and R. K. Christenson. 2000. Direct and correlated responses to selection for ovulation rate or uterine capacity in swine. J. Anim. Sci. 78(Suppl. 1):68. (Abstr.)
Mousel MR, Nonneman DJ, and Rohrer GA. 2006. Rearranged gene order between pig and human in a quantitative trait loci region on SSC3. Anim Genet. 37:403-6.
Nonneman D, and
Nonneman D,
Nonneman DJ, Wise TH, Ford JJ, Kuehn LA, Rohrer GA. 2006. Characterization of the aldo-keto reductase 1C gene cluster on pig chromosome 10: possible associations with reproductive traits.
Rohrer GA, Ford JJ,
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