Reproductive traits are related to economic efficiency and productivity of cattle systems. Age at first calving (AFC) and occurrence of early pregnancy (OP) are used in beef breeding programs in order to anticipate the reproductive life. The measure (r²) of linkage disequilibrium (LD) is used in genome wide association studies to detect genetic markers and genes affecting quantitative traits (QTL). The aim of this study was to determine the extent of LD in the genome of Nellore cattle, and examine associations between single nucleotide polymorphisms (SNP) and AFC and OP, using a panel of high-density SNPs. Data from 1.182 Nellore born in 2007 and 2008, belonging to Agropecuária Jacarezinho were used. A total of 13 contemporary groups (CG) consisting of farm, season and year of birth, with an average of 90 animals per CG were formed. For genomic-wide association, SNPs with minor allele frequency (MAF) below 0.05, and animals with Call Rate below 0.90 were excluded, totaling 431,885 SNPs. For the statistics analyses, a linear model was used for IPP and a threshold model was used for OP. To estimate the significance of the associations, for both traits, the model included the classificatory fixed effects of GC and SNPs (0,1, and 2). To estimate the allelic substitution effect, the same model was used, considering the SNP effects as covariable. The Bonferroni correction was applied to adjust the limit of significance (1.16 x10-7). The average r ² for all autosomes was 0.18 at a distance of 4.8 kb and the average MAF was 0.25 ± 0.13. The LD decreased as the distance between markers increased: 0.35 (1 kb) to 0.12 (100 kb). Eleven significant associations were detected in seven different chromosomes (BTA1, BTA4, BTA6, BTA11, BTA17, BTA21, and BTA22). Among these, seven SNPs were associated with AFC and four were linked to the OP. Three SNPs were significant for both traits (BTA1, BTA21, and BTA22). Chromosome BTA21 showed two SNPs associated with OP. A total of 19 chromosomes showed potential QTL regions for AFC and OP. The most evident peaks of significant SNPs, that may suggest potential QTL regions, were located on chromosomes BTA4, BTA6, BTA8, BTA17, and BTA19. The identification of SNPs associated with AFC and OP may contribute to selection of animals with greater sexual precocity.
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