Puberty is a complex physiological event by which animals mature into an adult capable of sexual reproduction. In order to enhance our understanding of the genes and regulatory pathways and networks involved in puberty, we characterized the transcriptome of five reproductive tissues (i.e. hypothalamus, pituitary gland, ovary, uterus, and endometrium) as well as tissues known to be relevant to growth and metabolism needed to achieve puberty (i.e., longissimus dorsi muscle, adipose, and liver). These tissues were collected from pre- and post-pubertal Brangus heifers (3/8 Brahman; Bos indicus x 5/8 Angus; Bos taurus) derived from a population of cattle used to identify quantitative trait loci associated with fertility traits (i.e., age of first observed corpus luteum (ACL), first service conception (FSC), and heifer pregnancy (HPG)). In order to exploit the power of complementary omics analyses, pre- and post-puberty co-expression gene networks were constructed by combining the results from genome-wide association studies (GWAS), RNA-Seq, and bovine transcription factors. Eight tissues among pre-pubertal and post-pubertal Brangus heifers revealed 1,515 differentially expressed and 943 tissue-specific genes within the 17,832 genes confirmed by RNA-Seq analysis. The hypothalamus experienced the most notable up-regulation of genes via puberty (i.e., 204 out of 275 genes). Combining the results of GWAS and RNA-Seq, we identified 25 loci containing a single nucleotide polymorphism (SNP) associated with ACL, FSC, and (or) HPG. Seventeen of these SNP were within a gene and 13 of the genes were expressed in uterus or endometrium. Multi-tissue omics analyses revealed 2,450 co-expressed genes relative to puberty. The pre-pubertal network had 372,861 connections whereas the post-pubertal network had 328,357 connections. A sub-network from this process revealed key transcriptional regulators (i.e., PITX2, FOXA1, DACH2, PROP1, SIX6, etc.). Results from these multi-tissue omics analyses improve understanding of the number of genes and their complex interactions for puberty in cattle.

Measures of heifer fertility are economically relevant traits for beef production systems and knowledge of candidate genes could be incorporated into future genomic selection strategies. Ten traits related to growth and fertility were measured in 890 Brangus heifers (3/8 Brahman × 5/8 Angus, from 67 sires). These traits were: BW and hip height adjusted to 205 and 365 d of age, postweaning ADG, yearling assessment of carcass traits (i.e., back fat thickness, intramuscular fat, and LM area), as well as heifer pregnancy and first service conception (FSC). These fertility traits were collected from controlled breeding seasons initiated with estrous synchronization and AI targeting heifers to calve by 24 mo of age. The BovineSNP50 BeadChip was used to ascertain 53,692 SNP genotypes for ∼802 heifers. Associations of genotypes and phenotypes were performed and SNP effects were estimated for each trait. Minimally associated SNP (P < 0.05) and their effects across the 10 traits formed the basis for an association weight matrix and its derived gene network related to FSC (57.3% success and heritability = 0.06 ± 0.05). These analyses yielded 1,555 important SNP, which inferred genes linked by 113,873 correlations within a network. Specifically, 1,386 SNP were nodes and the 5,132 strongest correlations (|r| ≥ 0.90) were edges. The network was filtered with genes queried from a transcriptome resource created from deep sequencing of RNA (i.e., RNA-Seq) from the hypothalamus of a prepubertal and a postpubertal Brangus heifer. The remaining hypothalamic-influenced network contained 978 genes connected by 2,560 edges or predicted gene interactions. This hypothalamic gene network was enriched with genes involved in axon guidance, which is a pathway known to influence pulsatile release of LHRH. There were 5 transcription factors with 21 or more connections: ZMAT3, STAT6, RFX4, PLAGL1, and NR6A1 for FSC. The SNP that identified these genes were intragenic and were on chromosomes 1, 5, 9, and 11. Chromosome 5 harbored both STAT6 and RFX4. The large number of interactions and genes observed with network analyses of multiple sources of genomic data (i.e., GWAS and RNA-Seq) support the concept of FSC being a polygenic trait.

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The growth endocrine axis influences reproduction. The objectives of this study were to evaluate population genetic characteristics of SNP genotypes within genes of the GH-IGF axis in straightbred and crossbred Angus, Brahman, and Romosinuano heifers (n = 650) and to test the association of these genotypes with measures of reproduction. These objectives were achieved using 73 SNP within 7 genes on chromosome 5 and the pregnancy-associated plasma protein A2 (PAPP-A2) and GH-receptor genes, which map to chromosomes 16 and 20, respectively. The SNP were elucidated by resequencing conserved regions of each gene by using DNA from familial-unrelated cattle of a multibreed discovery population. A multiplex SNP assay yielded 59 biallelic SNP useful for evaluating genetic identity and distance. Specifically, the divergence of straightbred Brahman cattle was approximately 15.5% from 5 Bos taurus-influenced breed groups. In the straightbred groups used as a validation population, only 3 SNP had minor allele frequencies >10%. These SNP were in the genes PAPP-A2 (ss115492449-A/C and ss115492450-G/T within intron 10) and signal transducers and activators of transcription 2 (STAT2; ss252841035-A/G within the 5' untranslated region), and they met the conditions of Hardy-Weinberg equilibrium (P > 0.31). The other 56 SNP were useful for assigning each animal into ancestral clusters (n = 3 proportions) to account for population stratification in genotype to phenotype association analyses. The 2 SNP in the PAPP-A2 gene influenced (P < 0.05) traits indicative of first-calf heifer rebreeding (i.e., calving interval, days to calving, and pregnancy rate). A STAT2 SNP genotype (i.e., GG) × primary ancestral cluster interaction (P < 0.05) suggested heifers primarily of B. taurus ancestry had a reduction of approximately 16.4 ± 0.1% in calving interval and days to calving relative to heifers clustering primarily as Bos indicus ancestry. Even though additional research is needed to delineate the allelic variation attributed to genes of the GH-IGF axis, results of this study provide support for STAT2 and PAPP-A2 as potential candidate genes associated with first-calf heifer rebreeding traits.

Balancing growth and reproductive performance in beef cattle managed in desert environments is challenging. Our objectives were to 1) evaluate trends in growth and reproductive traits, and 2) assess associative relationships between growth characteristics and reproductive performance in a Brangus herd managed in a Chihuahuan Desert production system from 1972 to 2006. Data were from bull (n = 597) and heifer calves (n = 585; 1988 to 2006) and cows (n = 525; repeated records of cows, n = 2,611; 1972 to 2006). Variables describing the growth curve of each cow were estimated using a nonlinear logistic function (each cow needed 6 yr of data). Mixed-effect models and logistic regression were used to analyze trends across years in growth and reproductive traits (both continuous and categorical). For continuous traits of calves, a slight cubic response (P < 0.01) described the dynamics of birth weight, 205-d BW, and 365-d BW across years. For categorical traits of females, positive linear trends (P < 0.05) across years were observed in percent pregnant as yearlings, calved at 2 yr of age, and first-calf heifer rebreeding (slopes ranged from 0.007 to 0.014%/yr). Autumn cow BW increased gradually until 1997 (509 kg +/- 8.8) and then decreased gradually by 0.6 kg/yr, whereas pregnancy percentage decreased gradually until 1995 (78.4% +/- 1.0) and then increased slightly by 0.2%/yr. A quadratic effect best described the dynamics of these 2 variables across years (P < 0.01) as well as estimates describing the growth curve of each cow. Specifically, asymptotic BW and age increased (P < 0.05) from 1972 to 1983 and 1990, respectively. Asymptotic age then decreased by 27% from 1983 to 1996 (P < 0.05). The maturing rate index was negatively correlated with age at first calving and calving interval (r = -0.42 and -0.18, P < 0.01), which suggested that early-maturing cows had enhanced fertility in this environment and production system. In summary, minimal changes were observed in measures of growth in bulls and heifers in a Brangus herd managed in the Chihuahuan Desert. Opposing relationships were observed among measures of cow size and fertility; as growth curves shifted toward earlier maturity, measures of reproductive performance suggested that fertility improved.