#08-012

Complete

Date Full Report Received

02/25/2010

Date Abstract Report Received

02/25/2010

Investigation

Institution:
Primary Investigator:

Sow longevity or sow productive life (SPL) is an important complex trait for total profitability of pig production. Proper gilt development and selection are important means to reduce the culling and death rates of breeding sows, and thus increase the economic profitability. Breeding for more structurally sound females is an imperative prerequisite to achieve greater SPL. Our earlier candidate gene studies have provided a list of promising genetic markers suitable for marker assisted selection in improving sow structural soundness traits. More recently, the completion of the swine whole genome sequencing project and development of a pig high density SNP (single nucleotide polymorphism) array which were coordinated by PI Rothschild and other researchers (http://www.pignet.eu/conferences/pig-genome-iii/) have made it more feasible and powerful to identify the many genetic markers associated with structural soundness and other sow longevity related traits on a genome-wide level.

In this study, a genome-wide association analysis (GWAS) was performed using Illumina’s pig 60K SNP BeadChip in which approximately 65,000 SNPs or genetic markers were used. The genotyped animals were 820 commercial females, which were scored/recorded for body composition, body conformation, overall leg action, and foot and leg structure.
Several sow longevity and reproduction related traits such as the total number of born (TNB) and number born alive (NBA) over first three parities, lifetime total number born (LTTNB) and life time number born alive (LTNBA) were also recorded. GWAS was done with 57,814 SNPs that met the designed quality control guidelines, and the calculation procedures were implemented using a Bayesian (statistical) approach (termed as ‘Bayes C’) that was originally developed for genomic selection. The SNP annotations and gene searches were performed using the latest sequence information (http://www.ensembl.org/Sus_scrofa/Info/Index).
A number of genes and interesting chromosomal regions were identified in this study, including some well-known candidate genes, genes located in the quantitative trait locus (QTL) regions that were previously reported and other novel genes with unclear or unknown biological functions. A total of 18 and 17 chromosomal regions were found to be associated with 10th backfat and loin muscle area, respectively. Some genes such as TCF21, BCL2, MC4R and CCBE1 (SSC1), ATP6V1H and OPRK1 (SSC4), CHCHD3 and WNT16 (SSC18) were associated with 10th rib backfat. The genes including IGF2 and IGHMMP2 (SSC2), AQP5 (SSC5), DLG1 and PAK2 (SSC13), FST and NDUSF4 (SSC16), BMP2 (SSC17) were associated with loin muscle area. For body conformation traits, the BMP2 gene was simultaneously associated with three body size traits. Interestingly, the beneficial BMP2 allele was the same for body length (longer) and body depth (deeper), while it was negatively associated with body width (narrower). PAPPA (SSC1) was associated with both body length and body depth. There were 15 candidate regions associated with overall leg action. The Hox family genes HOXA1, HOXA2 and HOXA3 (SSC18), TWIST1 and SP4 (SSC9), FHL3 (SSC6), GHR and FGF10 (SSC16) were the most possible candidate genes underlying overall leg action. Based on the functional annotation clustering analyses, a proportion of candidate genes could be classified into the categories related to bone and cartilage development (SOX9, LRCH1, FBN2, BSX1, COL4A3, COL4A4, etc), skeletal muscle development (MYOD1, MUSK, MYH1, MYH2, MYL9, MAP2K6 and MAP3K4) and the insulin pathway genes (PDX1, PTPN1, CFGFL, WISP2, etc).
In addition to above traits, several promising genes and chromosomal regions associated with reproduction performance traits over parities, LTTNB and LTNBA were identified. Some genes on chromosome 2 (e.g., SLC22A18, NADSY1) were associated with both LTTNB and LTNBA. Different chromosomal regions or different genes were found to be associated with reproduction traits of different parities. For instance, the regions on SSC2 at MEF2C gene, SSC13 at PTX3 gene and SSC15 at ITG6 and GDF8 genes were found to be associated with TNB and NBA in the first, second and third parities, respectively. This suggests that litter size in different parities could be considered as different traits instead of the same trait, because these traits might be influenced different genes and by the animal’s age and farm management effects.

This study is the first GWAS report on sow structural soundness and other important sow longevity related traits. The present findings provided a comprehensive list of candidate genes and chromosomal regions worth further exploring in the future. The verified genetic markers will greatly contribute to MAS programs to improve sow longevity in the pig industry.
Contact information:
Dr. Max Rothschild
Phone: (515) 294-6202
Email: mfrothsc@iastate.edu