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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #359182

Research Project: Identifying Genomic Solutions to Improve Efficiency of Swine Production

Location: Genetics and Animal Breeding

Title: Fine mapping of QTL associated with age at puberty in gilts using a novel Affymetrix SNP (SowPro90)

item WIJESENA, HIRUNI - University Of Nebraska
item Nonneman, Danny - Dan
item Keel, Brittney
item RIETHOVEN, JEAN - University Of Nebraska
item Rohrer, Gary
item KACHMAN, STEPHEN - University Of Nebraska
item CIOBANU, DANIEL - University Of Nebraska

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 12/4/2018
Publication Date: 1/16/2019
Citation: Wijesena, H.R., Nonneman, D.J., Keel, B.N., Riethoven, J.J., Rohrer, G.A., Kachman, S.D., Ciobanu, D.C. 2019. Fine mapping of QTL associated with age at puberty in gilts using a novel Affymetrix SNP (SowPro90) [abstract]. In: Plant and Animal Genome Conference Proceedings XXVII, 12-16 January 2019, San Diego, CA. pg. 116. PE0404. Available:

Interpretive Summary:

Technical Abstract: Age at puberty (AP) is the earliest indicator of sow fertility. Identification of the pleotropic sources that influence phenotypic variation of AP and other fertility traits has the potential to improve genomic predictions for traits expressed late in life such as sow reproductive longevity. Novel genetic variants identified by transcriptomic and genomic sequencing and genome-wide associations were integrated into “SowPro90”, a custom Affymetrix SNP array. This array includes SNPs located in genes overlapping major QTL for AP, SNPs located in other fertility related genes, and potential loss of function SNPs identified in the UNL and USMARC populations. UNL animals representing the extremes of the distribution for genomic prediction values for AP (early, n=154; late, n=129) were genotyped with the SowPro90 to fine map functional polymorphisms associated with the trait. Two of the major QTL (SSC2, 13.3Mb and SSC9, 96.1Mb) previously identified in the UNL population were oversaturated with SNPs located in flanking regions of the top SNP (±250kb). In SSC2, a SNP located in the proximal promoter of the UBE2L6 (SSC2, 13.3Mb; F=13.39) was associated with the largest effect, exceeding the effect of the original top SNP (DIAS0004771; F=6.98). In SSC9, the original SNP (ALGA0115279) still had the largest effect and is located in the first intron of SEMA3A (SSC9, 96.1Mb; F=23.47). The proportion of the phenotypic variance explained by these SNPs is relatively small, however, UBE2L6 is known to catalyze the binding of ISG15, a marker for pregnancy, and SEMA3A is involved in the neuronal control of AP.