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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Livestock Bio-Systems » Research » Publications at this Location » Publication #285646
Title: A review of swine genome-wide association studies at USMARC

Author
item Schneider, James

Submitted to: Journal of Animal Science Supplement
Publication Type: Abstract Only
Publication Acceptance Date: 3/28/2012
Publication Date: 7/1/2012
Citation: Schneider, J.F. 2012. A review of swine genome-wide association studies at USMARC [abstract]. Journal of Animal Science Supplement. 90 (Supplement 3):675 (Abstract 690).

Interpretive Summary:

Technical Abstract: Reproductive efficiency has a great effect on the economic success of pork production. Traits including age at puberty (AP), ovulation rate, number born alive (NBA), and average piglet birth weight (ABW) contribute greatly to reproductive efficiency. To better understand the underlying genetics of reproductive efficiency, a series of GWAS were undertaken. Samples of DNA were collected and tested using the Illumina PorcineSNP60 BeadChip (Illumina Inc., San Diego, CA). The first analysis included total number born (TNB), NBA, number born dead (NBD), number still born, mummies, litter birth weight (LBW), and ABW taken from 1,152 first parity females. Chromosome and position assignments were based on Build 10. A total of 41,151 SNP were tested using a Bayesian approach. Beginning with the first 5 SNP on SSC1 and ending with the last 5 SNP on the SSCX, SNP were assigned to groups of 5 consecutive SNP by chromosome-position order and analyzed again using a Bayesian approach. These selected 5-SNP non-overlapping groups were defined as QTL. Of the available 8,814 QTL, 124 were found to be statistically significant (P < 0.01). Multiple testing was considered using the probability of false positives. QTL were found for litter traits on SSC1, SSC4, SSC6, SSC10, SSC11, SSC13,SSC14, SSC15, and SSC17. QTL were found for LBW and ABW on all chromosomes except SSC16 and SSCX. Several candidate genes have been identified that overlap QTL locations among TNB, NBA, NBD, and ABW. A second analysis measured AP on 752 gilts that showed estrous before 230 d of age. Chromosome and position assignments were made based on Build 10.2. Seventy-two QTL were found to be statistically significant (P < 0.01) and were found on all chromosomes except SSC17. One hundred fifty-seven gilts that failed to reach puberty were added to the data set and the 909 gilts were analyzed as a binomial trait. A similar number of QTL were found on all chromosomes except SSC11, SSC16, and SSC18. The results of these analyses demonstrate that opportunities exist to introduce QTL into genetic improvement programs designed to improve reproductive efficiency. Key Words: Bayes, GWAS, reproduction