Animal Science Department


Date of this Version

January 2004


Published in 2004 Nebraska Swine Report, compiled by Duane Reese; University of Nebraska Cooperative Extension EC 04-219-A. Prepared by the staff in Animal Science and cooperating Departments for use in Extension, Teaching and Research programs. Cooperative Extension Division, Agricultural Research Division, Institute of Agriculture and Natural Resources, University of Nebraska–Lincoln.


The Nebraska Index Line is reproductively superior to its contemporary control, producing approximately four pigs more per litter. However, the genes or quantitative trait loci (QTL) that cause these differences are unknown. A previous study with an F2 resource population created by crossing the NE Index and Control lines identified one QTL affecting ovulation rate, one QTL affecting number of fully formed fetuses, one QTL affecting number of pigs born alive, two QTL affecting number of stillborn pigs, five QTL affecting nipple number, and six QTL affecting age at puberty. However, individual birth weight and weaning weight had not been included in the analyses. In addition, improved statistical models with greater power to identify QTL and test for additional kinds of gene action have been developed. The objective of this experiment was to apply these more powerful models to the data from the F2 resource population to identify additional chromosomal regions that contain genes that affect reproduction and early growth. Using standard statistical techniques identical to those used in the previous analyses, evidence was found for QTL (P < 0.10) affecting birth weight on chromosomes (C) 8 and 12. Additive effects of the C8 and C12 alleles inherited from the control line were -20 + 17 g and -59 + 19 g, and dominance effects were 85 + 31 g and -73 + 37 g, respectively. No QTL were detected for weaning weight. While fitting the largest QTL for the respective trait as a background effect to increase the statistical power, additional QTL affecting number of stillborn pigs on C12, fully formed pigs on C6, and ovulation rate on C15 and C8 were identified. No additional QTL were detected for number born alive, nipple number, age at puberty, or birth weight. Statistical procedures to test for imprinting or parent-of-origin effects were then used. Imprinting is a genetic phenomena in which an allele is expressed when inherited from one parent, but is not expressed when inherited from the other parent. Paternal imprinting describes the situation when an allele is expressed only when it is inherited from the father, whereas maternal imprinting occurs when the allele is expressed only when inherited from the mother. Partial imprinting occurred for a gene on C18 affecting number born alive (P < 0.05) and for a gene on C3 affecting age at puberty (P < 0.05). Evidence existed for paternal imprinting of a gene on C10 affecting nipple number and for maternal imprinting of a gene on C1 affecting birth weight and a gene on C4 affecting weaning weight (P < 0.10). Knowledge of imprinting could be used to more effectively develop the parental lines used to produce F1 females. Selection within maternal sire lines should increase the frequency of beneficial paternally and partially imprinted QTL affecting litter size, nipple number, and age at puberty. Selection within sire lines should also increase the frequency of beneficial maternally imprinted QTL affecting birth and weaning weight in grand-progeny. Selection within maternal dam lines should increase the frequency of beneficial maternally imprinted QTL affecting litter size, age at puberty, birth and weaning weights. F1 gilts produced from the crossing of these two lines should produce larger litters, have greater number of nipples, reach puberty sooner and produce heavier pigs at birth and weaning.