Physiology and Endocrinology Symposium: How single nucleotide polymorphism chips will advance our knowledge of factors controlling puberty and aid in selecting replacement beef females

Advances in our understanding of the estrous cycle and applications for improving targeted reproductive management in livestock

The scientific discipline of endocrinology has been invaluable to our understanding of the estrous cycle. In the second half of the twentieth century the development of immunoassay technologies provided a rapid and sensitive method to quantify circulating concentrations of reproductive hormones and relate them to stage of the estrous cycle and physiological status of the animal. Ovarian ultrasonography provided the ability to track the growth and regression of ovarian structures within the same animal across the estrous cycle in real time and, in combination with hormonal profiling, accurately identify mechanisms regulating the estrous cycle and early pregnancy. Before this, the best technique had been serial collections with each animal being a single endpoint. The availability of continuous data such as daily hormone concentrations and daily follicular measurements within animals led to the improvement of methods to synchronize estrus in each of the species. Unfortunately, the use of radio-immunoassays has been declining for two decades. While enzyme-linked immunosorbent assays have been developed for many endocrine, paracrine, and autocrine factors, their primary market is human medicine and rodent models of human health, leaving those available for livestock species economically infeasible. Automated sensors such as accelerometers apply the knowledge attained through decades of endocrinology and ultrasonography studies to identify females in estrus and measure parameters of the estrous cycle that are related to fertility. The ability of automated sensors to centralize and assimilate large amounts of behavioral and physiological data from numerous animals will enhance targeted reproductive management in livestock production systems.

Selecting oocyte donors based on anti-Müllerian hormone (AMH) concentrations: A critical analysis of using cutoff values as exclusion criterion for an in vitro embryo production program in Gir cattle

The aims of this study were to determine anti-müllerian hormone (AMH) cutoff values for selecting Gir (Bos taurus indicus) oocyte donors and estimate the impact of using AMH concentrations as a selection criterion. In Exp. 1, Gir heifers (n=120) were sampled for AMH analysis and submitted to ovum pick-up and in vitro embryo production (OPU-IVEP). AMH cutoff values were calculated using ROC analysis or, alternatively, by the successive exclusion of heifers with the lowest AMH values. The correlations between AMH and OPU-IVEP outcomes were significant (P<0.001), though low or moderate (r= 0.34-0.52). We estimated an improvement (P<0.05) after the use of AMH cutoff values to select donors of +15.3% for total oocyes, +19.4% for viable COC, and +23.4% for blastocysts. This selection pressure, however, led to the exclusion of 32.8%, 37.9%, and 50.0% of the initial potential donors, respectively. In Exp. 2, we analyzed data from OPU-IVEP sessions of 658 Gir donors with known genomic values for predicted transmitting ability for milk (GPTAm) and age at first calving (GPTAafc). The selection based on the number of oocytes recovered had no effect (P>0.05) on the average GPTAm nor GPTAafc values of the remaining donors. In summary, plasma AMH ≥700 pg/mL is a cutoff value that can be used to select Gir heifers with a greater potential as oocyte donors. Nevertheless, this selection leads to the exclusion of up to 50% of potential donors. Finally, exclusion of poor responders had no effect on mean genomic estimates for milk production or age at first calving in the selected subset of donors.

Developmental programming of the ovarian reserve in livestock

Mammalian females are born with a finite number of follicles in their ovaries that is referred to as the ovarian reserve. There is a large amount of variation between females in the number of antral follicles that they are born with, but this number is positively correlated to size of the ovarian reserve, has a strong repeatability within a female, and a moderate heritability. Although the heritability is moderate, numerous external factors including health, nutrition, ambient temperature, and litter size influence the size and function of the ovarian reserve throughout life. Depletion of the ovarian reserve contributes to reproductive senescence, and genetic and epigenetic factors can lead to a more rapid decline in follicle numbers in some females than others. The relationship of the size of the ovarian reserve to development of the reproductive tract and fertility is generally positive, although some studies report antagonistic associations of these traits. It seems likely that management decisions and environmental factors that result in epigenetic modifications to the genome throughout life may cause variability in the function of ovarian genes that influence fecundity and fertility, leading to differences in reproductive longevity among females born with ovarian reserves of similar size. This review summarizes our current understanding of factors influencing size of the ovarian reserve in cattle, sheep, and pigs and the relationship of the ovarian reserve to reproductive tract development and fertility. It provides strategies to apply this knowledge to improve diagnostics for better assessment of fertility and reproductive longevity in female livestock.

Effects of maternal antral follicle count in Bos taurus indicus cattle on the genetic merit of male offspring and antral follicle count of female offspring

This study evaluated the effects of antral follicle count (AFC) in female cattle on offspring characteristics. Recently calved multiparous Bos indicus cows (Nelore; n = 222) were evaluated using ultrasonography on random days of their estrous cycle to determine the AFC and were classified into "low" (≤15 follicles), "intermediate" (≥16 and ≤ 29 follicles), and "high" (≥30 follicles) AFC groups. Weight and scrotal circumference (SC) of male offspring from these cows (n = 127) were determined from 20 to 27 months, and the data were added to a genetic evaluation program (economic total genetic merit, MGTe and TOP value) that uses the kinship matrix to evaluate the genetic relationship between animals. The AFC of female offspring from these cows (n = 95) was evaluated to analyze the relationship between the AFC of mothers and daughters. The effects of maternal AFC on the genetic merit of male and female offspring were analyzed using GLIMMIX and GLM, respectively. Correlations were assessed using the Pearson's coefficient. Male offspring of cows with high AFC had superior MGTe (P = 0.005) and TOP values (P = 0.01) than those from cows with low AFC. Additionally, the AFC of mothers was positively correlated with MGTe (R = 0.33; P < 0.0001) and negatively correlated with TOP values (R = -0.32; P < 0.0001). The SC (P = 0.01), but not body weight of the offspring (P = 0.46) was affected by maternal AFC. The daughters' AFC were correlated (R = 0.29; P = 0.004) with mothers' AFC and were influenced by maternal (P = 0.05) but not paternal (P = 0.77) effect. In conclusion, cows with high AFC produced males with greater MGTe, superior TOP values and higher SC. Maternal AFC did not influence the weight of male offspring but was correlated with the AFC of daughters.

The ovarian follicle of ruminants: the path from conceptus to adult

This review resulted from an international workshop and presents a consensus view of critical advances over the past decade in our understanding of follicle function in ruminants. The major concepts covered include: (1) the value of major genes; (2) the dynamics of fetal ovarian development and its sensitivity to nutritional and environmental influences; (3) the concept of an ovarian follicle reserve, aligned with the rise of anti-Müllerian hormone as a controller of ovarian processes; (4) renewed recognition of the diverse and important roles of theca cells; (5) the importance of follicular fluid as a microenvironment that determines oocyte quality; (6) the 'adipokinome' as a key concept linking metabolic inputs with follicle development; and (7) the contribution of follicle development to the success of conception. These concepts are important because, in sheep and cattle, ovulation rate is tightly regulated and, as the primary determinant of litter size, it is a major component of reproductive efficiency and therefore productivity. Nowadays, reproductive efficiency is also a target for improving the 'methane efficiency' of livestock enterprises, increasing the need to understand the processes of ovarian development and folliculogenesis, while avoiding detrimental trade-offs as greater performance is sought.

Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: II: carcass merit traits

BACKGROUND

Genome wide association studies (GWAS) were conducted on 7,853,211 imputed whole genome sequence variants in a population of 3354 to 3984 animals from multiple beef cattle breeds for five carcass merit traits including hot carcass weight (HCW), average backfat thickness (AFAT), rib eye area (REA), lean meat yield (LMY) and carcass marbling score (CMAR). Based on the GWAS results, genetic architectures of the carcass merit traits in beef cattle were elucidated.

RESULTS

The distributions of DNA variant allele substitution effects approximated a bell-shaped distribution for all the traits while the distribution of additive genetic variances explained by single DNA variants conformed to a scaled inverse chi-squared distribution to a greater extent. At a threshold of P-value < 10-5, 51, 33, 46, 40, and 38 lead DNA variants on multiple chromosomes were significantly associated with HCW, AFAT, REA, LMY, and CMAR, respectively. In addition, lead DNA variants with potentially large pleiotropic effects on HCW, AFAT, REA, and LMY were found on chromosome 6. On average, missense variants, 3'UTR variants, 5'UTR variants, and other regulatory region variants exhibited larger allele substitution effects on the traits in comparison to other functional classes. The amounts of additive genetic variance explained per DNA variant were smaller for intergenic and intron variants on all the traits whereas synonymous variants, missense variants, 3'UTR variants, 5'UTR variants, downstream and upstream gene variants, and other regulatory region variants captured a greater amount of additive genetic variance per sequence variant for one or more carcass merit traits investigated. In total, 26 enriched cellular and molecular functions were identified with lipid metabolisms, small molecular biochemistry, and carbohydrate metabolism being the most significant for the carcass merit traits.

CONCLUSIONS

The GWAS results have shown that the carcass merit traits are controlled by a few DNA variants with large effects and many DNA variants with small effects. Nucleotide polymorphisms in regulatory, synonymous, and missense functional classes have relatively larger impacts per sequence variant on the variation of carcass merit traits. The genetic architecture as revealed by the GWAS will improve our understanding on genetic controls of carcass merit traits in beef cattle.

Brangus cows have ovarian reserve parameters more like Brahman than Angus cows

Bos indicus females have more surface antral follicles than Bos taurus females; however, histological studies demonstrated no difference in total number of primordial follicles between these two biological types of cattle. Primordial follicle density in the ovary was less in Nelore ovaries compared to Angus ovaries, but no studies have examined the primordial follicle density in Bos indicus cross-bred females. It, therefore, was hypothesized that primordial follicle density in the ovary would decrease as percentage Bos indicus increased. Ovaries were collected from cross-bred Angus (n = 32, no Bos indicus influence), Brangus (n = 15), or Brahman (n = 9) cows and prepared for histological evaluation. There was no difference in total number of primordial follicles per ovary between breeds (P > 0.10). When numbers of primordial follicles were expressed on a per gram of ovarian tissue basis, there were fewer primordial follicles per gram of ovarian tissue in Brangus and Brahman cows than in Angus cows (P < 0.05). Brangus cows did not differ from Brahman cows in primordial follicle density (P > 0.10). Differences in primordial follicle density could indicate differences in capacity of ovarian stroma to produce factors necessary for oogonial proliferation and primordial follicle formation among breeds. Identifying these factors could improve the aprroach for culturing pre-antral follicles of cattle. Furthermore, these results explain why ultrasonographic antral follicle counts may need to be adjusted to a greater threshold to predict size of the ovarian reserve and determine ovarian reserve related reproductive traits in Bos indicus females.

BEEF SPECIES-RUMINANT NUTRITION CACTUS BEEF SYMPOSIUM: Influence of management decisions during heifer development on enhancing reproductive success and cow longevity1

Profitability of beef cattle producers can be directly tied to the productive lifespan of a cow. Management decisions influencing heifer nutrition and reproduction play a key role in establishing heifer fertility and longevity. Altering feeding strategies to utilize compensatory growth has been reported to have a positive influence on fertility during the first breeding season; however, there are discrepancies in the literature as to the impact this strategy may have on the proportion of heifers attaining puberty prior to entering their first breeding season. Ultimately, this may affect lifetime productivity as heifers born early in the calving season produce more kilograms of weaned calf over their first 6 calves, as well as, remain in the herd longer than those animals born later in the calving season. Thus, incorporation of reproductive technologies to identify fertile animals or aid in improving conception earlier in the breeding season may improve heifer reproductive performance and longevity. Reproductive tract scores have been utilized to identify animals which are more reproductively mature, increasing the likelihood of successful artificial insemination. Antral follicle counts (AFC), which predict the number of follicles in the ovarian reserve, have not only been reported to have a moderate to high heritability, but have also been used to identify animals with greater reproductive potential. Beef heifers classified as high AFC have greater pregnancy rates and longevity than low AFC heifers. Additionally, maternal diet may play a role in influencing reproductive success and ultimately cow longevity. Improving maternal plane of nutrition has been reported to increase female offspring pregnancy rates. Overall, recent research has provided producers with a variety of methods to optimize animal performance while enhancing reproductive success and longevity to ensure profitability.

Sexual precocity and productivity of beef cattle female under grazing conditions

In view of the importance of female reproductive traits as a key profit indicator in beef-cattle production systems, the objective of the present study was to explore the relationships between female sexual precocity and potential predictive traits of easy and early measurement, related to the productive and reproductive efficiency. Heifers born in 2011 and 2012 (n = 132) from five genetic groups (Angus, Hereford, Angus-Hereford, Hereford-Angus and Argentine Creole) in 2 years (Trial 1 and Trial 2) under grazing conditions were evaluated. After weaning, the presence of corpus luteum, liveweight, body condition score, hip height, rump fat thickness and rib fat thickness were recorded every 28 days, and Longissimus muscle area at 15 months of age. Also, to evaluate the relationships between age at puberty and the subsequent production efficiency, the annual records of 895 cows (217 Angus, 253 Hereford, 125 Creole, 116 Angus-Hereford and 184 Hereford-Angus) born between 1986 and 2009 were studied to estimate the average annual productivity of cows, and its components of (Co)variance, heritability and breeding values. Nutritional conditions immediately after weaning were determinants in reaching puberty. The univariate animal model for average annual productivity showed a heritability of 0.14 ± 0.05. Regression multiple and covariance analyses revealed that the rib fat thickness at 450 days of age was a good predictor of age at puberty, but lose some relevance as early selection criterion. Finally, it is important for future studies to analyse in more detail the existence of critical thresholds of fat deposition for the onset of reproductive activity.

Maternal age influences the number of primordial follicles in the ovaries of yearling Angus heifers

The number of antral follicles detectable by ultrasonography in heifers is influenced by age of the dam, because daughters of primiparous cows have fewer antral follicles than daughters of mature cows. We, therefore, hypothesized that heifers with primiparous dams would have fewer primordial follicles in their ovaries than heifers born to mature (4+ y) cows. Angus heifers (n = 464) were submitted for ultrasonographic evaluation of antral follicle number at 325, 355, and 385 d of age. Ovaries were collected from a random subset of heifers (n = 79) and processed for histological evaluation to determine number of primordial follicles. A greater percentage of heifers with primiparous dams had a corpus luteum at first ultrasonographic examination; however, a greater percentage of heifers with multiparous dams had ovulated by the start of breeding (P <  0.01). Heifers with primiparous dams had fewer antral follicles detectable by ultrasonography (P <  0.01). Heifers with primparous dams had fewer surface antral follicles on their ovaries (P <  0.01), and the number of primordial follicles per histological section was less for heifers with primiparous dams (P =  0.02). These data indicate that the lesser number of antral follicles detectable by ultrasonography in heifers with primparous dams is due to less ovarian follicle reserves. Selecting replacement heifers from mature dams may result in daughters with greater fertility and reproductive longevity; however, further research is necessary to determine if interactions between size of the ovarian follicle reserve and age at puberty influence fertility and reproductive longevity in replacement heifers.

Relationships between numbers of antral follicles and postpartum interval in Brahman females

To determine relationships of ovarian antral follicle count (AFC) on d 28 postpartum with postpartum interval (PPI) and AFC on d 8 post-estrus, three-dimensional ultrasonography was performed on multiparous (n = 47) and primiparous (n = 20) Brahman cows on d 28 postpartum and on d 8 post-estrus. Follicles were evaluated to determine numbers of total, small (≤17 mm³), medium (17 mm³-67 mm³), and large follicles (≥67 mm³) on each ovary. Estrus was detected using vasectomized, penile-deviated bulls fitted with chin-ball markers during the AI period and with tail paint during the natural service period. Cows with AFC ≥ ½ SD above the mean were classified as high, those within ½ SD of the mean were classified as intermediate, and those ≥ ½ SD below the mean were classified as low. Classes of AFC for total follicles included low (L ≤ 73), intermediate (74 ≤ I ≤ 112), and high (H ≥ 113). Classes of AFC for small follicles included low (L ≤ 55), intermediate (56 ≤ I ≤ 87), and high (H ≥ 88). Classes of AFC for medium follicles included low (L ≤ 13), intermediate (14 ≤ I ≤ 23), and high (H ≥ 24). Classes of AFC for large follicles included low (L ≤ 2), intermediate (3 ≤ I ≤ 4), and high (H ≥ 5). Cows with PPI ≥ ½ SD above the mean were classified as long, those within ½ SD of the mean were classified as intermediate, and those ≥ ½ SD below the mean were classified as short. Classes of PPI included short (S ≤ 47 d), intermediate (48 d ≤ I ≤ 75 d), and long (L ≥ 76 d). The PROC MIXED procedure of SAS was used to analyze potential differences among classes of AFC and PPI. The PROC REG procedure of SAS was used to analyze relationships between AFC and PPI and between AFC on d 28 postpartum and on d 8 post-estrus. The PPI differed among classes of total (P < 0.01; L = 76.2 ± 6.0, I = 61.7 ± 4.5, H = 43.8 ± 6.5), small (P < 0.01; L = 74.3 ± 5.6, I = 64.6 ± 4.8, H = 42.9 ± 5.9), and medium AFC (P = 0.04; L = 72.3 ± 5.9, I = 59.3 ± 5.8, H = 52.1 ± 5.8). The PPI did not differ among classes of large AFC (P = 0.81). As total AFC on d 28 postpartum increased, PPI decreased (P < 0.01, Adj.R² = 0.13). Total AFC on d 8 post-estrus was positively associated with total AFC on d 28 postpartum (P < 0.01, Adj.R² = 0.66). These results suggest that: a) populations of total, small, and medium follicles in the postpartum period predict PPI in Brahman females and b) total AFC in Brahman females are consistent.

Polymorphisms in TOX and NCOA2 genes and their associations with reproductive traits in cattle

Reproductive traits are an important component of the economic selection index for beef cattle in the tropics. Phenotypic expression of these traits occurs late because they are measured when the animals reach reproductive age. Association studies using high-density markers have been conducted to identify genes that influence certain traits. The identification of causal mutations in these genes permits the inclusion of these single nucleotide polymorphisms (SNPs) in customised DNA chips to increase efficiency and validity. Therefore, the aim of the present study was to detect causal mutations in the TOX and NCOA2 genes, previously identified by genome-wide association studies of zebu cattle. DNA was extracted from 385 Nellore females and polymorphisms were investigated by polymerase chain reaction sequencing. Five polymorphisms were detected in the NCOA2 gene and four in the TOX gene that were associated with reproductive traits. Analysis of variance showed that SNP 1718 in the NCOA2 gene was significant for early pregnancy probability (P=0.02) and age at first calving (P=0.03), and SNP 2038 in the same gene was significant for days to calving (P=0.03). Studies investigating polymorphisms in other regions of the gene and in other genes should be conducted to identify causal mutations.

Factors affecting puberty in replacement beef heifers

Puberty is defined as when ovulation is accompanied by visual signs of estrus and subsequent normal luteal function. Age at puberty is an important trait in relation to reproductive success, productive life span, and profitability in beef operations. Although puberty and initiation of normal estrous cycles are complex events that require maturation of the hypothalamic-pituitary-ovarian axis, it has been well documented that nutrition, age, and genetics are regulators of age at puberty. However, their role is mainly as regulators of the endocrine maturation that must occur for sustained ovarian cyclicity to be initiated. Increased growth rate between 4 and 7 months of age is apparently sufficient to induce early puberty, and this increased growth rate decreased the negative feedback of estradiol on LH secretion during the prepubertal period. As puberty approaches, a progressive decrease in the negative feedback of estradiol on GnRH secretion allows increased pulse frequency of LH, thus stimulating follicular growth and increased estradiol production. In addition, expression of estrogen receptors in the anterior hypothalamus and ventromedial nucleus is negatively correlated with LH pulse frequency. Although a significant number of genes and pathways are involved in neuromaturation for the initiation of normal estrous cycles, the inhibitory effects of neuropeptide Y on GnRH/LH release appear to decrease, and the stimulatory effect of melanocyte-stimulating hormone alpha on GnRH appears to increase as puberty approaches. Thus, a thorough understanding of the metabolic and neuroendocrine changes that occur to initiate normal estrous cycles is needed to facilitate management of the important reproductive event.

Genome-wide association for heifer reproduction and calf performance traits in beef cattle

The aim of this study was to identify SNP markers that associate with variation in beef heifer reproduction and performance of their calves. A genome-wide association study was performed by means of the generalized quasi-likelihood score (GQLS) method using heifer genotypes from the BovineSNP50 BeadChip and estimated breeding values for pre-breeding body weight (PBW), pregnancy rate (PR), calving difficulty (CD), age at first calving (AFC), calf birth weight (BWT), calf weaning weight (WWT), and calf pre-weaning average daily gain (ADG). Data consisted of 785 replacement heifers from three Canadian research herds, namely Brandon Research Centre, Brandon, Manitoba, University of Alberta Roy Berg Kinsella Ranch, Kinsella, Alberta, and Lacombe Research Centre, Lacombe, Alberta. After applying a false discovery rate correction at a 5% significance level, a total of 4, 3, 3, 9, 6, 2, and 1 SNPs were significantly associated with PBW, PR, CD, AFC, BWT, WWT, and ADG, respectively. These SNPs were located on chromosomes 1, 5-7, 9, 13-16, 19-21, 24, 25, and 27-29. Chromosomes 1, 5, and 24 had SNPs with pleiotropic effects. New significant SNPs that impact functional traits were detected, many of which have not been previously reported. The results of this study support quantitative genetic studies related to the inheritance of these traits, and provides new knowledge regarding beef cattle quantitative trait loci effects. The identification of these SNPs provides a starting point to identify genes affecting heifer reproduction traits and performance of their calves (BWT, WWT, and ADG). They also contribute to a better understanding of the biology underlying these traits and will be potentially useful in marker- and genome-assisted selection and management.

Non-synonymous mutations mapped to chromosome X associated with andrological and growth traits in beef cattle

Background

Previous genome-wide association analyses identified QTL regions in the X chromosome for percentage of normal sperm and scrotal circumference in Brahman and Tropical Composite cattle. These traits are important to be studied because they are indicators of male fertility and are correlated with female sexual precocity and reproductive longevity. The aim was to investigate candidate genes in these regions and to identify putative causative mutations that influence these traits. In addition, we tested the identified mutations for female fertility and growth traits.

Results

Using a combination of bioinformatics and molecular assay technology, twelve non-synonymous SNPs in eleven genes were genotyped in a cattle population. Three and nine SNPs explained more than 1% of the additive genetic variance for percentage of normal sperm and scrotal circumference, respectively. The SNPs that had a major influence in percentage of normal sperm were mapped to LOC100138021 and TAF7L genes; and in TEX11 and AR genes for scrotal circumference. One SNP in TEX11 was explained ~13% of the additive genetic variance for scrotal circumference at 12 months. The tested SNP were also associated with weight measurements, but not with female fertility traits.

Conclusions

The strong association of SNPs located in X chromosome genes with male fertility traits validates the QTL. The implicated genes became good candidates to be used for genetic evaluation, without detrimentally influencing female fertility traits.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1595-0) contains supplementary material, which is available to authorized users.

Comparison of breeding value prediction for two traits in a Nellore-Angus crossbred population using different Bayesian modeling methodologies

The objectives of this study were to 1) compare four models for breeding value prediction using genomic or pedigree information and 2) evaluate the impact of fixed effects that account for family structure. Comparisons were made in a Nellore-Angus population comprising F₂, F₃ and half-siblings to embryo transfer F₂ calves with records for overall temperament at weaning (TEMP; n = 769) and Warner-Bratzler shear force (WBSF; n = 387). After quality control, there were 34,913 whole genome SNP markers remaining. Bayesian methods employed were BayesB (π̃ = 0.995 or 0.997 for WBSF or TEMP, respectively) and BayesC (π = 0 and π̃), where π̃ is the ideal proportion of markers not included. Direct genomic values (DGV) from single trait Bayesian analyses were compared to conventional pedigree-based animal model breeding values. Numerically, BayesC procedures (using π̃) had the highest accuracy of all models for WBSF and TEMP (ρ̂_gĝ = 0.843 and 0.923, respectively), but BayesB had the least bias (regression of performance on prediction closest to 1, β̂_y,x = 2.886 and 1.755, respectively). Accounting for family structure decreased accuracy and increased bias in prediction of DGV indicating a detrimental impact when used in these prediction methods that simultaneously fit many markers.

Identification of genomic regions associated with feed efficiency in Nelore cattle

Background

Feed efficiency is jointly determined by productivity and feed requirements, both of which are economically relevant traits in beef cattle production systems. The objective of this study was to identify genes/QTLs associated with components of feed efficiency in Nelore cattle using Illumina BovineHD BeadChip (770 k SNP) genotypes from 593 Nelore steers. The traits analyzed included: average daily gain (ADG), dry matter intake (DMI), feed-conversion ratio (FCR), feed efficiency (FE), residual feed intake (RFI), maintenance efficiency (ME), efficiency of gain (EG), partial efficiency of growth (PEG) and relative growth rate (RGR). The Bayes B analysis was completed with Gensel software parameterized to fit fewer markers than animals. Genomic windows containing all the SNP loci in each 1 Mb that accounted for more than 1.0% of genetic variance were considered as QTL region. Candidate genes within windows that explained more than 1% of genetic variance were selected by putative function based on DAVID and Gene Ontology.

Results

Thirty-six QTL (1-Mb SNP window) were identified on chromosomes 1, 2, 3, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 18, 19, 20, 21, 22, 24, 25 and 26 (UMD 3.1). The amount of genetic variance explained by individual QTL windows for feed efficiency traits ranged from 0.5% to 9.07%. Some of these QTL minimally overlapped with previously reported feed efficiency QTL for Bos taurus. The QTL regions described in this study harbor genes with biological functions related to metabolic processes, lipid and protein metabolism, generation of energy and growth. Among the positional candidate genes selected for feed efficiency are: HRH4, ALDH7A1, APOA2, LIN7C, CXADR, ADAM12 and MAP7.

Conclusions

Some genomic regions and some positional candidate genes reported in this study have not been previously reported for feed efficiency traits in Bos indicus. Comparison with published results indicates that different QTLs and genes may be involved in the control of feed efficiency traits in this Nelore cattle population, as compared to Bos taurus cattle.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-014-0100-0) contains supplementary material, which is available to authorized users.

Criteria for selecting replacements at weaning, before breeding, and after breeding

At weaning, heifers should be considered for replacements based on their dam's previous performance; heifer calving date, age, and weight; and previous exposure to implants. Before breeding, heifers should be selected as replacements based on whether they have attained puberty (determined by a prebreeding examination), do not have abnormal pelvic areas, or fail to meet temperament standards. After breeding, heifers should be selected as replacements if they conceive early in the breeding season, are capable of achieving 85% of their mature weight by calving, and calve at a body condition of 5.5 to 6.0.

Incorporation of genetic technologies associated with applied reproductive technologies to enhance world food production

Animal breeding and reproductive physiology have been closely related throughout the history of animal production science. Artificial insemination provides the best method of increasing the influence of sires with superior genetics to improve production traits. Multiple ovulation embryo transfer (MOET) provides some ability to increase the genetic influence of the maternal line as well. The addition of genetic technologies to this paradigm allows for improved methods of selecting sires and dams carrying the best genes for production and yield of edible products and resistance to diseases and parasites. However, decreasing the number of influential parents within a population also increases the risk of propagating a recessive gene that could negatively impact the species (Reprod Domest Anim 44:792-796, 2009; BMC Genomics 11:337, 2010). Furthermore, antagonistic genotypic relationships between production traits and fertility (Anim Prod Sci 49:399-412, 2009; Anim Genet 43:442-446, 2012) suggest that care must be taken to ensure that increasing the frequency of genes with a positive influence on production does not negatively impact the fertility of the replacement females entering the herd.

Effect of age at puberty/conception date on cow longevity

Age at puberty is a critical trait, because pregnancy success during the breeding season is correlated with the percentage of heifers that reach puberty before or early in the breeding season. A negative genetic correlation between age at puberty and heifer pregnancy rate indicate that selection to decrease age at puberty would increase heifer pregnancy rates. Calving late has been reported to increase the chance of calving late or not calving the following year, and heifers need to wean 3 to 5 calves to pay for development costs. Therefore, puberty is important to the sustainability and profitability of beef operations.

Inferring quantitative trait pathways associated with bull fertility from a genome-wide association study

Whole-genome association studies typically focus on genetic markers with the strongest evidence of association. However, single markers often explain only a small component of the genetic variance and hence offer a limited understanding of the trait under study. As such, the objective of this study was to perform a pathway-based association analysis in Holstein dairy cattle in order to identify relevant pathways involved in bull fertility. The results of a single-marker association analysis, using 1,755 bulls with sire conception rate data and genotypes for 38,650 single nucleotide polymorphisms (SNPs), were used in this study. A total of 16,819 annotated genes, including 2,767 significantly associated with bull fertility, were used to interrogate a total of 662 Gene Ontology (GO) terms and 248 InterPro (IP) entries using a test of proportions based on the cumulative hypergeometric distribution. After multiple-testing correction, 20 GO categories and one IP entry showed significant overrepresentation of genes statistically associated with bull fertility. Several of these functional categories such as small GTPases mediated signal transduction, neurogenesis, calcium ion binding, and cytoskeleton are known to be involved in biological processes closely related to male fertility. These results could provide insight into the genetic architecture of this complex trait in dairy cattle. In addition, this study shows that quantitative trait pathways inferred from single-marker analyses could enhance our interpretations of the results of genome-wide association studies.

Association weight matrix: a network-based approach towards functional genome-wide association studies

In this chapter we describe the Association Weight Matrix (AWM), a novel procedure to exploit the results from genome-wide association studies (GWAS) and, in combination with network inference algorithms, generate gene networks with regulatory and functional significance. In simple terms, the AWM is a matrix with rows represented by genes and columns represented by phenotypes. Individual {i, j}th elements in the AWM correspond to the association of the SNP in the ith gene to the jth phenotype. While our main objective is to provide a recipe-like tutorial on how to build and use AWM, we also take the opportunity to briefly reason the logic behind each step in the process. To conclude, we discuss the impact on AWM of issues like the number of phenotypes under scrutiny, the density of the SNP chip and the choice of contrast upon which to infer the cause-effect regulatory interactions.

Heritability and Bayesian genome-wide association study of first service conception and pregnancy in Brangus heifers

Brangus [3/8 Brahman (Bos indicus) × 5/8 Angus (Bos taurus); n ≈ 800] heifers from 67 sires were used to estimate heritability and conduct a genome-wide association study (GWAS) for 2 binary fertility traits: first service conception (FSC) and heifer pregnancy (HPG). Genotypes were from 53,692 loci on the BovineSNP50 (Infinium Bead Chips, Illumina, San Diego, CA). Yearling heifers were estrous synchronized, bred by AI, and then exposed to natural service breeding. Reproductive ultrasound and DNA-based parentage testing were used to determine if the heifer conceived by AI or natural service, and code for FSC and HPG traits. Success rates for FSC and HPG were 53.3% and 78.0% ± 0.01%, and corresponding heritability estimates were 0.18 ± 0.07 and 0.10 ± 0.06, respectively. The models used in obtaining these heritability estimates and GWAS included fixed effects of year (i.e., 2005 to 2007), birth location, calving season, age of dam, and contemporary group. In GWAS, simultaneous associations of 1 Mb SNP windows with phenotype were undertaken with Bayes C analyses using GenSel software. The 1 Mb windows contained 21.3 ± 1.1 SNP. Analyses fitted a mixture model that treated SNP effects as random, with an assumed fraction pi = 0.9995 having no effect on phenotype. The windows that accounted for 1.0% of genetic variance were considered as QTL associated with FSC or HPG. Eighteen QTL existed on 15 chromosomes for the 2 traits. On average, each QTL accounted for 2.43% ± 0.2% of the genetic variance. Chromosome 8 harbored 2 QTL for FSC and 1 for HPG; however, these regions did not overlap. Chromosomes 3, 15, 16, 19, 24, 26, 27, 29, and X included QTL only for FSC, whereas chromosomes 2, 4, 10, 13, and 20 contained QTL only for HPG. The multitude of QTL detected for FSC and HPG in this GWAS involving Brangus heifers exemplifies the complex regulation of variation in heifer fertility traits of low heritability.

Breeding and Genetics Symposium: building single nucleotide polymorphism-derived gene regulatory networks: Towards functional genomewide association studies

The advent of economically viable high-throughput genetic and genomic techniques has equipped animal geneticists with an unprecedented ability to generate massive amounts of molecular data. As a result, large lists of genes differentially expressed in many experimental conditions of interests have been reported and, likewise, the association of an ever growing number of DNA variants with phenotypes of importance is now a routine endeavor. Although these studies have greatly improved our understanding of the genetic basis of complex phenotypes, they have also revealed the difficulty in explaining more than a fraction of the genetic variance. Inspired by this data-rich and knowledge-poor dichotomy, systems biology aims at the formal integration of seemingly disparate datasets allowing for a holistic view where key properties of the systems emerge as an intuitive feature and enable the generation of testable hypotheses. Herein, we present 2 examples of integrating molecular data anchored in the power of gene network inference. The first example is concerned with the onset of puberty in Bos indicus-influenced cows bred in Australia. Using the results from genomewide association studies across a range of phenotypes, we developed what we termed an association weight matrix to generate a gene network underlying phenotypes of puberty in cattle. The network was mined for the minimal set of transcription factor genes whose predicted target spanned the majority of the topology of the entire network. The second example deals with piebald, a pigmentation phenotype in Merino sheep. Two networks were developed: a regulatory network and an epistatic network. The former is inferred based on promoter sequence analysis of differentially expressed genes. The epistatic network is built from 2-locus models among all pairwise associated polymorphisms. At the intersection between these 2 networks, we revealed a set of genes and gene-gene interactions of validated and de novo predicted relevance to the piebald phenotype. We argue that these new approaches are holistic and therefore more appropriate than traditional approaches for investigating genetic mechanisms underlying complex phenotypes of importance in livestock species.

Gene network analyses of first service conception in Brangus heifers: use of genome and trait associations, hypothalamic-transcriptome information, and transcription factors

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.