Kishore Prayaga

Association weight matrix for the genetic dissection of puberty in beef cattle

We describe a systems biology approach for the genetic dissection of complex traits based on applying gene network theory to the results from genome-wide associations. The associations of single-nucleotide polymorphisms (SNP) that were individually associated with a primary phenotype of interest, age at puberty in our study, were explored across 22 related traits. Genomic regions were surveyed for genes harboring the selected SNP. As a result, an association weight matrix (AWM) was constructed with as many rows as genes and as many columns as traits. Each {i, j} cell value in the AWM corresponds to the z-score normalized additive effect of the ith gene (via its neighboring SNP) on the jth trait. Columnwise, the AWM recovered the genetic correlations estimated via pedigree-based restricted maximum-likelihood methods. Rowwise, a combination of hierarchical clustering, gene network, and pathway analyses identified genetic drivers that would have been missed by standard genome-wide association studies. Finally, the promoter regions of the AWM-predicted targets of three key transcription factors (TFs), estrogen-related receptor γ (ESRRG), Pal3 motif, bound by a PPAR-γ homodimer, IR3 sites (PPARG), and Prophet of Pit 1, PROP paired-like homeobox 1 (PROP1), were surveyed to identify binding sites corresponding to those TFs. Applied to our case, the AWM results recapitulate the known biology of puberty, captured experimentally validated binding sites, and identified candidate genes and gene–gene interactions for further investigation.

Genome-wide association studies of female reproduction in tropically adapted beef cattle

The genetics of reproduction is poorly understood because the heritabilities of traits currently recorded are low. To elucidate the genetics underlying reproduction in beef cattle, we performed a genome-wide association study using the bovine SNP50 chip in 2 tropically adapted beef cattle breeds, Brahman and Tropical Composite. Here we present the results for 3 female reproduction traits: 1) age at puberty, defined as age in days at first observed corpus luteum (CL) after frequent ovarian ultrasound scans (AGECL); 2) the postpartum anestrous interval, measured as the number of days from calving to first ovulation postpartum (first rebreeding interval, PPAI); and 3) the occurrence of the first postpartum ovulation before weaning in the first rebreeding period (PW), defined from PPAI. In addition, correlated traits such as BW, height, serum IGF1 concentration, condition score, and fatness were also examined. In the Brahman and Tropical Composite cattle, 169 [false positive rate (FPR) = 0.262] and 84 (FPR = 0.581) SNP, respectively, were significant (P < 0.001) for AGECL. In Brahman, 41% of these significant markers mapped to a single chromosomal region on BTA14. In Tropical Composites, 16% of these significant markers were located on BTA5. For PPAI, 66 (FPR = 0.67) and 113 (FPR = 0.432) SNP were significant (P < 0.001) in Brahman and Tropical Composite, respectively, whereas for PW, 68 (FPR = 0.64) and 113 (FPR = 0.432) SNP were significant (P < 0.01). In Tropical Composites, the largest concentration of PPAI markers were located on BTA5 [19% (PPAI) and 23% (PW)], and BTA16 [17% (PPAI) and 18% (PW)]. In Brahman cattle, the largest concentration of markers for postpartum anestrus was located on BTA3 (14% for PPAI and PW) and BTA14 (17% PPAI). Very few of the significant markers for female reproduction traits for the Brahman and Tropical Composite breeds were located in the same chromosomal regions. However, fatness and BW traits as well as serum IGF1 concentration were found to be associated with similar genome regions within and between breeds. Clusters of SNP associated with multiple traits were located on BTA14 in Brahman and BTA5 in Tropical Composites.

Transcription profiling provides insights into gene pathways involved in horn and scurs development in cattle

BackgroundTwo types of horns are evident in cattle - fixed horns attached to the skull and a variation called scurs, which refers to small loosely attached horns. Cattle lacking horns are referred to as polled. Although both the Poll and Scurs loci have been mapped to BTA1 and 19 respectively, the underlying genetic basis of these phenotypes is unknown, and so far, no candidate genes regulating these developmental processes have been described. This study is the first reported attempt at transcript profiling to identify genes and pathways contributing to horn and scurs development in Brahman cattle, relative to polled counterparts.ResultsExpression patterns in polled, horned and scurs tissues were obtained using the Agilent 44 k bovine array. The most notable feature when comparing transcriptional profiles of developing horn tissues against polled was the down regulation of genes coding for elements of the cadherin junction as well as those involved in epidermal development. We hypothesize this as a key event involved in keratinocyte migration and subsequent horn development. In the polled-scurs comparison, the most prevalent differentially expressed transcripts code for genes involved in extracellular matrix remodelling, which were up regulated in scurs tissues relative to polled.ConclusionFor this first time we describe networks of genes involved in horn and scurs development. Interestingly, we did not observe differential expression in any of the genes present on the fine mapped region of BTA1 known to contain the Poll locus.

Behavioral aspects of electronic bull separation and mate allocation in multiple-sire mating paddocks

Controlling spatial positioning of cattle through use of electronic collars could provide new ways to farm under extensive conditions. This study examined the potential for bulls to be controlled during mating using mild electric shocks delivered through radio-controlled collars. Eighteen Belmont Red bulls were fitted with collars containing the Global Positioning System and that were able to emit a mild electric shock (500 mW) at the top of the neck behind the poll. Eighteen Belmont Red cows were fitted with Global Positioning System collars only. The experiment was replicated 3 times in 3 paddocks. Each paddock contained 2 bulls and 1 cow in induced estrus. On d 1, the bulls were either assigned to the cow or not assigned to the cow, and on d 2, the assignments were reversed, and bulls received the other treatment using a new cow. Treatments were applied for 2 h on each day. The nonassigned bull received a mild electric shock on approach to either the cow or to a bull, whereas the assigned bull received a mild electric shock on approach to the other bull only. The electric shock was applied when the bulls were within approximately 10 m and moving toward the nonallowed animal. The electric shock was terminated when the animal responded by stopping movement toward the nonallowed animal. In the first 10 min, nonassigned bulls spent less time within 5 m of the cow (P = 0.03) than assigned bulls. Assigned bulls spent more time close to the cow during the entire 120 min on d 1 than on d 2 (P = 0.014). On d 1, the assigned bulls moved more toward the cow and the nonassigned bull than they did on d 2 (P = 0.02). Assigned bulls displayed more sexual behaviors than nonassigned bulls (P = 0.004). Nonassigned bulls were sometimes observed not to approach the cow despite a change in its location. This suggests that the bull associated the electric shock with the cow and not with the location in which it received the electric shock. Instances were observed in which the cow pursued the nonassigned bull, in which case the bull did not receive an electric shock, and this may reflect the preference of the cow. This study demonstrated that bulls can be separated and prevented from approaching a cow in estrus using a mild electric shock. However, mate allocation was not completely successful due to the potential for cow preference for certain bulls.