Fertility traits such as age at puberty are economically important for meat production system. Occurrence of early pregnancy (OPP) is considered a good indicator of age at puberty and can be used as selection criteria. The search for causal mutations in candidate genes can helpful to improve the accuracy of genomic prediction if used to design low-density chips. The objective of this study was to identify polymorphism in candidate genes associated with puberty in heifers. DNA sequences were obtained from 380 Nellore heifers from exons sequencing of PPP3CA and FABP4 genes through MiSeq® equipment (Illumina, Inc.). From these sequences were found two SNP in the region of PPP3CA gene and 13 variations in the gene FABP4. Among these 15 variations 12 were SNP and one was a deletion, and this deletion was detected in all samples sequenced, which leads us to conclude that this may be a variation between Nellore and Hereford. One haplotype consisting of four SNP located in the FABP4 and nine SNP, that were analyzed separately, had not a significant effect at the p <0.05 on OPP characteristic. Also were analyzed RNA sequences from Brangus heifers in 62 candidate genes associated with puberty with the aim to discovery SNP in these regions. Were detected 1157 SNP in the region of 46 gene. These SNP were compared with SNP detected from RNA sequences from four breeds, Angus, Brahma, Nellore and Holstein. One hundred and seventy-two SNP were matched in all breeds. From Brangus RNA sequences were also detected 160 new transcripts in the region of 42 candidate genes and five genes not annotated that overlap the region of candidate genes. Detection of new transcripts and genes is essential to enrich the bovine genome annotation. The mutations detected can be used for the customization of low density chips and future genomics selection strategies.