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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 #384905

Research Project: Improving Lifetime Productivity in Swine

Location: Livestock Bio-Systems

Title: GBLUP-GWAS identifies candidate genes and polymorphisms for age at puberty in gilts

item WIJESENA, HIRUNI - Orise Fellow
item Nonneman, Danny - Dan
item Snelling, Warren
item Rohrer, Gary
item Keel, Brittney
item Lents, Clay

Submitted to: International Society for Animal Genetics Conference
Publication Type: Abstract Only
Publication Acceptance Date: 6/3/2021
Publication Date: 7/26/2021
Citation: Wijesena, H.R., Nonneman, D.J., Snelling, W.M., Rohrer, G.A., Keel, B.N., Lents, C.A. 2021. GBLUP-GWAS identifies candidate genes and polymorphisms for age at puberty in gilts. In proceedings: International Society for Animal Genetics Conference, July 26-30, 2021. Virtual. p. 111. Abstract P320.

Interpretive Summary:

Technical Abstract: Age at puberty is the earliest known indicator for sow reproductive longevity. Gilts that reach puberty earlier have a greater probability of having more lifetime litters. Identifying genetic variants associated with age at puberty will facilitate genomic prediction for other related sow fertility traits expressed later in life. Gilts with puberty records and imputed genotypes for 71,634 SNP (n = 4,986) were used in a genomic BLUP (GBLUP) based genome-wide association (GWAS) for age at puberty. Twenty-one genome-wide significant SNP located in SSC1, SSC2, SSC9, and SSC14 were identified explaining 3.7% of the phenotypic variation of age at puberty. Some loci confirmed associations previously identified for age at puberty in gilts. Several genes within QTL regions (GMFB, EWSR1, MEF2C, SOSTDC1, AHR) were differentially expressed in ovaries of gilts with delayed puberty. The QTL on SSC9 (83.5 to 86.5 Mb) was characterized by long range LD (r2 = 0.75 to 0.99) and estimated effects for significant SNP on SSC9 ranged from -1.14 to 1.35 days (P < 0.001). AHR located within this locus is a ligand activated transcription factor that regulates expression of CYP1A genes necessary for estrogen metabolism. AHR activation negatively affects ovarian function and association of AHR variants with age at puberty was previously reported in this population. The SNP with the largest effect on age at puberty on SSC2 (ALGA0116099; 82.7 Mb; P < 0.0001) had an estimated -1.8 day allelic substitution effect. ANKRA2 located upstream of this SNP (~50Kb) acts as a corepressor for AHR by binding to C-terminus of AHRR, suggesting it is involved in mediating negative effects of AHR on puberty. Other genes with known effects on ovarian follicular development (BMP4; SSC1), gonadotropin secretion (FOXD1; SSC2), and pregnancy (LIF; SSC14) were identified within QTL regions. Transcriptomic data confirmed the presence of several polymorphisms in these genes, including two missense SNP in ANKRA2, that could act as potential functional variants affecting age at puberty.