Genotype by Prenatal Environment Interaction for Postnatal Growth of Nelore Beef Cattle Raised under Tropical Grazing Conditions

The prenatal environment is recognized as crucial for the postnatal performance in cattle. In tropical regions, pregnant beef cows commonly experience nutritional restriction during the second half of the gestation period. Thus, the present study was designed to analyze the genotype by prenatal environment interaction (G × Epn) and to identify genomic regions associated with the level and response in growth and reproduction-related traits of beef cattle to changes in the prenatal environment. A reaction norm model was applied to data from two Nelore herds using the solutions of contemporary groups for birth weight as a descriptor variable of the gestational environment quality. A better gestational environment favored weights until weaning, scrotal circumference at yearling, and days to first calving of the offspring. The G × Epn was strong enough to result in heterogeneity of variance components and genetic parameters in addition to reranking of estimated breeding values and SNPs effects. Several genomic regions associated with the level of performance and specific responses of the animals to variations in the gestational environment were revealed, which harbor QTLs and can be exploited for selection purposes. Therefore, genetic evaluation models considering G × Epn and special management and nutrition care for pregnant cows are recommended.

Genetic architecture of a composite beef cattle population

Composite breeds are widely used in the beef industry. Composites allow producers to combine desirable traits from the progenitor breeds and simplify herd management, without repeated crossbreeding and maintenance of purebreds. In this study, genomic information was used to evaluate the genetic composition and characteristics of a three-breed beef cattle composite. This composite population referred to as Composite Gene Combination (CGC) consisted of 50% Red Angus, 25% Charolais, 25% Tarentaise. A total of 248 animals were used in this study CGC (n=79), Red Angus (n=61), Charolais (n=79) and Tarentaise (n=29). All animals were genotyped with 777k HD panel. Principal component and ADMIXTURE analyses were carried out to evaluate the genetic structure of CGC animals. The ADMIXTURE revealed the proportion of Tarentaise increased to approximately 57% while Charolais decreased to approximately 5%, and Red Angus decreased to 38% across generations. To evaluate these changes in the genomic composition across different breeds and in CGC across generations runs of homozygosity (ROH) were conducted. This analysis showed Red Angus to have the highest total length of ROH segments per animal with a mean of 349.92 Mb and lowest in CGC with a mean of 141.10 Mb. Furthermore, it showed the formation of new haplotypes in CGC around the sixth generation. Selection signatures were evaluated through Fst and HapFlk analyses. Several selection sweeps in CGC were identified especially in chromosomes 5 and 14 which have previously been reported to be associated with coat color and growth traits. The study supports our previous findings that progenitor combinations are not stable over generations and that either direct or natural selection plays a role in modifying the progenitor proportions. Furthermore, the results showed that Tarentaise contributed useful attributes to the composite in a cool semi-arid environment and suggests a re-exploration of this breed's role may be warranted.

Genetics and nutrition impacts on herd productivity in the Northern Australian beef cattle production cycle

Genetics and nutrition drive herd productivity due to significant impacts on all components of the beef cattle production cycle. In northern Australia, the beef production system is largely extensive and relies heavily on tropical cattle grazing low quality, phosphorus-deficient pastures with seasonal variations in nutritive value. The existing feedlots are predominantly grain-based; providing high-energy rations, faster turn-off and finishing of backgrounded cattle to meet market specifications. This review focusses on the beef cattle production cycle components of maternal nutrition, foetal development, bull fertility, post-natal to weaning, backgrounding, feedlotting, rumen microbes and carcass quality as influenced by genetics and nutrition. This student-driven review identified the following knowledge gaps in the published literature on northern Australian beef cattle production cycle: 1. Long-term benefits and effects of maternal supplementation to alter foetal enzymes on the performance and productivity of beef cattle; 2. Exogenous fibrolytic enzymes to increase nutrient availability from the cell wall and better utilisation of fibrous and phosphorus deficient pasture feedbase during backgrounding; 3. Supplementation with novel encapsulated calcium butyrate and probiotics to stimulate the early development of rumen papillae and enhance early weaning of calves; 4. The use of single nucleotide polymorphisms as genetic markers for the early selection of tropical beef cattle for carcass and meat eating quality traits prior to feedlotting; The review concludes by recommending future research in whole genome sequencing to target specific genes associated with meat quality characteristics in order to explore the development of breeds with superior genes more suited to the North Australian beef industry. Further research into diverse nutritional strategies of phosphorus supplementation and fortifying tropically adapted grasses with protein-rich legumes and forages for backgrounding and supplementing lot-fed beef cattle with omega-3 oil of plant origin will ensure sustainable production of beef with a healthy composition, tenderness, taste and eating quality.

Effect of calfhood nutrition on metabolic hormones, gonadotropins, and estradiol concentrations and on reproductive organ development in beef heifer calves

This study examined the effect of plane of nutrition on the endocrinological regulation of the hypothalamic-pituitary-ovarian (HPO) axis in beef heifer calves during a critical sexual developmental window early in calf hood. Forty Holstein-Friesian × Angus heifers (mean age 19 d, SEM = 0.63) were assigned to a high (HI; ADG 1.2 kg) or moderate (MOD; ADG 0.50 kg) nutritional level from 3 to 21 wk of life. Intake was recorded using an electronic calf feeding system, BW was recorded weekly, and blood samples were collected on the week of age 5, 10, 15, and 20 for metabolite, reproductive, and metabolic hormone determination. At 19 wk of age, on sequential days, an 8-h window bleed was carried out for luteinizing hormone (LH), follicle-stimulating hormone (FSH), and estradiol analysis. To characterize anterior pituitary gland function, an intravenous GnRH challenge was conducted (19 wk of age). Blood was collected via a jugular catheter every 15 min for 135 min for the analysis of LH, FSH, and estradiol. Calves were subsequently euthanized at 21 wk of age; the anterior pituitary, metabolic organs, and reproductive tract were weighed, and ovarian surface follicular numbers and oocytes recovered were recorded. Mean ADG was 1.18 and 0.50 kg for HI and MOD, respectively, resulting in a 76.6-kg difference in BW (P < 0.001). Blood insulin, glucose, and IGF-1 concentrations were greater (P < 0.001) for HI compared with MOD. There was a diet × time interaction for leptin (P < 0.01); concentrations were greater in HI compared with MOD at 20 wk of age with no difference between treatments before this. Dietary treatment did not alter the concentrations of adiponectin or anti-mullerian hormone. There was a diet × time interaction for FSH, whereby MOD had greater concentrations than HI at 10, 15, and 20, but not at 5 wk of age. Over the duration of an 8-h window bleed (19 wk of age), serum concentrations of LH, LH pulse frequency, and LH pulse amplitude were unaffected by treatment, whereas FSH (0.23 vs. 0.43 ng/mL) and estradiol (0.53 vs. 0.38 ng/mL) concentrations were less than and greater, respectively, for HI than MOD (P < 0.05). Likewise, following a GnRH challenge, the area under the curve analysis revealed greater (P < 0.01) estradiol and lesser (P < 0.01) FSH concentrations in calves on the HI relative to MOD diet, whereas concentrations of LH were unaffected (P = 0.26) between treatments. Ovarian surface follicle numbers were greater (P < 0.05) in HI compared with MOD. Total reproductive tract, uterus, and ovarian tissue expressed relative to BW were greater (P < 0.05) for HI compared with MOD. In conclusion, enhanced nutrition in early calfhood advances the ontogeny development of the HPO axis.

Genotype by environment interaction in response to cold stress in a composite beef cattle breed

Extreme weather conditions such as cold stress influence the productivity and survivability of beef cattle raised on pasture. The objective of this study was to identify and evaluate the extent of the impact of genotype by environment interaction due to cold stress on birth weight (BW) and weaning weight (WW) in a composite beef cattle population. The effect of cold stress was modelled as the accumulation of total cold load (TCL) calculated using the Comprehensive Climate Index units, considering three TCL classes defined based on temperature: less than -5°C (TCL5), -15°C (TCL15) and -25°C (TCL25). A total of 4221 and 4217 records for BW and WW, respectively, were used from a composite beef cattle population (50% Red Angus, 25% Charolais and 25% Tarentaise) between 2002 and 2015. For both BW and WW, a univariate model (ignoring cold stress) and a reaction norm model were implemented. As cold load increased, the direct heritability slightly increased in both BW and WW for TCL5 class; however, this heritability remained consistent across the cold load of TCL25 class. In contrast, the maternal heritability of BW was constant with cold load increase in all TCL classes, although a slight increase of maternal heritability was observed for TCL5 and TCL15. The direct and maternal genetic correlation for BW and maternal genetic correlation for WW across different cold loads between all TCL classes were high (r > 0.99), whereas the lowest direct genetic correlations observed for WW were 0.88 for TCL5 and 0.85 for TCL15. The Spearman rank correlation between the estimated breeding value of top bulls (n = 79) using univariate and reaction norm models across TCL classes showed some re-ranking in direct and maternal effects for both BW and WW particularly for TCL5 and TCL15. In general, cold stress did not have a big impact on direct and maternal genetic effects of BW and WW.

Multigenerational Effects

Environmental influences resulting in epigenetic mediation of gene expression can affect multiple generations via direct effect (first generation); direct or maternally mediated effects on the fetus (second generation), or gonadal cell lines of the fetus (third generation) when pregnant animals are exposed to the stimuli; and through generational inheritance. The cumulative effects are rapid changes in phenotypic characteristics of the population when compared with rate of phenotypic change from genetic selection. With extensive data collection, significant potential exists to propagate desired characteristics in the livestock industry through epigenetic pathways.

Developmental and reproductive characteristics of beef heifers classified by number of estrous cycles experienced by start of first breeding

A retrospective analysis was conducted to evaluate the effect of number of estrous cycles exhibited before breeding on growth and reproductive performance of replacement beef heifers fed ad-libitum or restricted by 20% less than ad-libitum during postweaning development over a 9-yr period. Progesterone concentration in blood samples collected at 9- to 11-d intervals were used to assign heifers into groups by number of estrous cycles exhibited before the start of breeding: 0 (nonpubertal; n = 395), 1 (n = 205), 2 (n = 211), 3 (n = 116), or >3 (n = 249). Heifers (P < 0.01) in the 0 cycle group were born 6 d later than the 1, 2, or 3 cycle groups, which were born 4 d later (P < 0.01) than the >3 cycle group. Weight of heifers at birth decreased (P < 0.05) as the number of cycles increased. Weaning weight and ultrasound measures of loin area and fat thickness over the loin at 1 yr age increased as the number of cycles increased (P < 0.01). Postwean weight gain, hip height at 1 yr age, and weights from the start of breeding through precalving increased with cycle numbers in a quadratic fashion (P < 0.02) and were greater (P < 0.05) in ad-libitum than restricted-fed heifers. Pregnancy rate in the 0 cycle group was lower (84%; P < 0.05) than the 1 (90%) or >3 (94%) estrous cycles groups and tended to differ (P < 0.1) from the 2 (88%) and 3 (89%) estrous cycle groups. Interval from the start of breeding to calving was 3 to 5 d longer (P < 0.05) for the 0 cycle group (300 ± 1 d) than other groups. Proportion of heifers calving in the first 21 d was less (P < 0.05) in the 0 or 1 cycle groups than other groups. Pregnancy rates of 2-yr-old cows (n = 898) were lowest (P < 0.05) for the 0 (73%) and 2 (79%) estrous cycle groups than the 1 (85%), 3 (90%), or >3 (92%) estrous cycle groups. Restricted level of feeding during postweaning development resulted in greater (P < 0.05) proportion of heifers in 0 cycle group and lower (P < 0.05) proportion in >3 cycle group, but reproductive performance was not influenced (P > 0.1) by level of feeding or interaction of feeding and estrous cycle grouping. In summary, date of birth and rate of physical maturation (weight, height, and fat deposition) were associated with timing of puberty. Pregnancy rate was greater in heifers that exhibited estrus before the start of breeding, but did not improve from having more than one estrous cycle. Proportion conceiving early was greater for heifers having two or more cycles before breeding.

Genome-wide association study for stayability measures in Nellore-Angus crossbred cows

Beef cow stayability is a complex, economically important trait often used as an indicator of a cow's potential lifetime productivity. Stayability is defined as capability of a cow to maintain a perfect record up to 6 yr of age. This age is commonly cited as a financial break-even point, where initial costs of cow development and maintenance are recovered by her cumulative net income from yearly calf receipts. Later-maturing Bos indicus-Bos taurus crossbred cows may experience reproductive difficulty early in life but have a high potential for a long reproductive life span. It was the objective of this study to identify genetic variants associated with measures of beef cow stayability. A population of B. indicus-B. taurus crossbred cows (n = 305) from central Texas was used. Phenotypes for various measures of stayability to 6 yr of age were produced by artificially imposing five different culling criteria on data from the population. Cows were scored either as a 1 (indicating a perfect record through 6 yr) or a 0 (indicating failure at or before 6 yr), under each criterion. Genome-wide association studies (GWAS) were conducted for each criterion using univariate procedures and prefitting the fixed effect of cow contemporary group. SNP associations for two criteria surpassed the false discovery threshold of 0.15, when a cow was scored as 0 upon her first failure to wean a calf, regardless of reason, through 6 yr (criterion 2), and when a cow was scored as 0 upon her first failure to give birth to a calf, through 6 yr (criterion 3). Associated SNP were found on bovine chromosomes (BTA) 1, 2, 5, 9, 18, and 21 for criterion 2 and on BTA 1, 5, 11, 15, and 24 for criterion 3. A critical region on BTA 5: 43-50 Mb was identified for each criterion. Due to the similarities to prior work, the tendency for B. indicus cattle to experience reproductive difficulties early in life, and due to the large proportion of cows that left the herd at an early age under these criteria, these results suggest that the associations are likely driven by an early life trait such as age at puberty or rate of heifer development.

Genotype × prenatal and post-weaning nutritional environment interaction in a composite beef cattle breed using reaction norms and a multi-trait model

Environmental effects have been shown to influence several economically important traits in beef cattle. In this study, genotype × nutritional environment interaction has been evaluated in a composite beef cattle breed (50% Red Angus, 25% Charolais, 25% Tarentaise). Four nutritional environments (marginal-restricted [MARG-RES], marginal-control [MARG-CTRL], adequate-restricted [ADEQ-RES], and adequate-control [ADEQ-CTRL]) were created based on two levels of winter supplement provided to dams grazing winter range during gestation (MARG and ADEQ) and two levels of input to offspring during post-weaning development (RES and CTRL). Genetic parameters of average daily gain (ADG) during the 140-d post-wean trial, yearling weight (YW), and ultrasound measurement of fat depth (FAT) at the 12th rib and intramuscular fat percentage (IMF) of 3,020 individuals in the four environments were estimated. The heritabilities estimated using a single trait mixed linear model were: ADG: 0.21, 0.23, 0.19 and 0.21; YW: 0.27, 0.33, 0.20 and 0.26; FAT: 0.30, 0.29, 0.29, 0.55; IMF: 0.45, 0.51, 0.33, 0.53 for MARG-RES, ADEQ-RES, MARG-CTRL and ADEQ-CTRL, respectively. The extent of genotype × environment interaction was modeled using two separate methods: reaction norms and multi-trait models. The genetic correlations were estimated using a multi-trait model for ADG, YW, FAT and IMF. Growth traits (ADG, YW) and FAT showed correlations less than 0.80 across the four different environments indicating genotype by environment interaction. For example, genetic correlation for ADG between MARG-CTRL and MARG-RES was 0.65 and 0.73 between ADEQ-RES and MARG-RES. In this example, the former genetic correlation corresponds to differences in post-weaning nutritional environment, and the later represents a nutritional difference imposed on dams (i.e., prenatal environment), potentially mediated via fetal programming. The reaction norm model results were in concordance with the multi-trait model, genotype by environment interaction had a higher effect on traits with a lower heritability.

Genomic prediction of continuous and binary fertility traits of females in a composite beef cattle breed

Reproduction efficiency is a major factor in the profitability of the beef cattle industry. Genomic selection (GS) is a promising tool that may improve the predictive accuracy and genetic gain of fertility traits. There is a wide range of traits used to measure fertility in dairy and beef cattle including continuous (days open), discrete (pregnancy status), and count (number of inseminations) responses. In this study, a joint analysis of age of puberty (AOP), age at first calving (AOC), and the heifer pregnancy status (HPS) was performed. Data used in this study consisted of records from 1,365 Composite Gene Combination (CGC; 50% Red Angus, 25% Charolais, 25% Tarentaise) first parity females born between 2002 and 2011. The pedigree file included 5,374 animals. A total of 3,902 animals were genotyped with different density SNP chips (3K to 50K SNP). Animals genotyped with low-density arrays were imputed to higher density (BovineSNP50 BeadChip) using FImpute. Data were analyzed using univariate and multivariate classical quantitative models (pedigree based) and univariate genomic approaches. For the latter, 3 different Bayesian methods (BayesA, BayesB, and BayesCπ) were implemented and compared. Estimates of heritabilities using univariate and multivariate analyses based on pedigree relationships ranged between 0.03 (for AOC) to 0.2 (AOP). Heritability of pregnancy status was 0.15 and 0.09 using the univariate and multivariate analyses, respectively. Genetic correlation between pregnancy status and the other 2 traits was low being 0.08 with age at puberty and -0.10 with age at first calving. Heritability estimates were slightly higher using genomic rather than average additive relationships. The accuracy of genomic prediction was similar across the 3 Bayesian methods with higher accuracies for age of puberty than the age at first calving likely due to the higher heritability of the former. The prediction of the binary pregnancy status measured using the area under the curve increased by 27% to 29% compared to a random classifier. Due to the small size of the data, all estimates have large posterior standard deviations and results should be interpreted with caution.

Developmental and reproductive characteristics of beef heifers classified by pubertal status at time of first breeding

Data collected for 10 or more years at the West Central Research and Extension Center, North Platte, NE ( = 1,104); the Gudmundsen Sandhills Laboratory, Whitman, NE ( = 1,333); and the USDA, ARS, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT ( = 1,176) were retrospectively analyzed to evaluate growth and reproductive performance of beef heifers classified by pubertal status before first breeding. Concentrations of progesterone in serum from 2 blood samples collected 9 to 11 d apart before the breeding season classified heifers as pubertal (progesterone ≥ 1.0 ng/mL in 1 or both samples) or nonpubertal (progesterone < 1.0 ng/mL in both samples). Average date of birth was earlier ( < 0.06) and proportion born in the first 21 d of the calving season was 10 to 20 percentage points greater for heifers that were pubertal at the start of breeding compared with heifers not pubertal by the start of breeding. Heifers that were pubertal by the start of breeding were 7 to 10 kg heavier ( < 0.01) and 1 cm taller ( < 0.01) at weaning than heifers not pubertal by the start of breeding. Differences in BW persisted through the start of breeding to pregnancy diagnosis. Heifers that achieved puberty by the start of breeding had greater ( < 0.05) feed intake and G:F during postweaning development and had greater ( < 0.01) LM area and fat thickness over the LM at approximately 1 yr of age compared with heifers not pubertal by the start of breeding. Heifers that achieved puberty before the start of breeding had greater ( < 0.01) ADG from birth to weaning but slower ( < 0.10) rates of gain from the start of breeding through pregnancy diagnosis. Pregnancy rate was greater ( < 0.01) for heifers that were pubertal at the start of breeding. In heifers that became pregnant, those that were pubertal before the start of breeding calved earlier ( < 0.01), with a greater ( < 0.01) percentage calving in the first 21 d of calving than heifers not pubertal at the start of breeding. Calves from heifers that achieved puberty before the start of breeding were heavier at weaning ( < 0.01) than calves from heifers that had not achieved puberty by the start of breeding. In summary, heifers that failed to achieve puberty by the start of breeding were less desirable for several traits evaluated. Based on these results, implementing feeding strategies to increase the proportion of heifers that achieve puberty before first breeding could result in propagation of undesirable characteristics.

TRIENNIAL LACTATION SYMPOSIUM/BOLFA: Plasticity of mammary development in the prepubertal bovine mammary gland

Although peripubertal mammary development represents only a small fraction of the total mass of mammary parenchyma present in the udder at the end of gestation and into lactation, there is increasing evidence that the tissue foundations created in early life can affect future mammary development and function. Studies on expression of estrogen and progesterone receptors seem to confirm the relevance of these steroids in prepubertal mammary development, but connections with other growth factors, hormones, and local tissue factors remain elusive. Enhanced preweaning feeding in the bovine appears to enhance the capacity of mammary tissue to response to mammogenic stimulation. This suggests the possibility that improved early nutrition might allow for creation of stem or progenitor cell populations to better support the massive ductal growth and lobulo-alveolar development during gestation. Increasing evidence that immune cells are involved in mammary development suggests there are unexpected and poorly understood connections between the immune system and mammary development. This is nearly unexplored in ruminants. Development of new tools to identify, isolate, and characterize cell populations within the developing bovine mammary gland offer the possibility of identifying and perhaps altering populations of mammary stem cells or selected progenitor cells to modulate mammary development and, possibly, mammary function.

Genomic prediction and genome-wide association analysis of female longevity in a composite beef cattle breed

Longevity is a highly important trait to the efficiency of beef cattle production. The objective of this study was to evaluate the genomic prediction of longevity and identify genomic regions associated with this trait. The data used in this study consisted of 547 Composite Gene Combination cows (1/2 Red Angus, 1/4 Charolais, 1/4 Tarentaise) born from 2002 to 2011 genotyped with Illumina BovineSNP50 BeadChip. Three models were used to assess genomic prediction: Bayes A, Bayes B and GBLUP using a genomic relationship matrix. To identify genomic regions associated with longevity 2 approaches were adopted: single marker genome wide association and Bayesian approach using GenSel software. The genomic prediction accuracy was low 0.28, 0.25, and 0.22 for Bayes A, Bayes B and GBLUP, respectively. The single-marker genome wide association study (GWAS)identified 5 loci with -value less than 0.05 after false discovery correction: UA-IFASA-7571 on chromosome 19 (58.03 Mb), ARS-BFGL-BAC-15059 on BTA 1 (28.8 Mb), ARS-BFGL-NGS-104159 on BTA3 (29.4 Mb), ARS-BFGL-NGS-32882 on BTA9 (104.07 Mb) and ARS-BFGL-NGS-32883 on BTA25 (33.77 Mb). The Bayesian GWAS yielded 4 genomic regions overlapping with the single marker GWAS results. The region with the highest percentage of genomic variance (3.73%) was detected on chromosome 19. Both GWAS approaches adopted in this study showed evidence for association with various chromosomal locations.