Genomic study and Medical Subject Headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers

Selection signatures detection in Nelore, Gir, and Red Sindhi cattle breeds

Technological advances in genomics and bioinformatics made it possible to study the genetic structure of breeds and understand genome changes caused by selection over generations. Our objective was to evaluate selection signatures (SS) in Nelore, Gir, and Red Sindhi cattle from Brazil and the Asian continent to identify divergent variants due to the history of formation and selection of populations, with a focus on the SS of animals from Brazil. Extended haplotype homozygosities between populations (XP-EHH), the ratio of site-specific extended haplotype homozygosity between populations (Rsb), and the allelic fixation index (Fst) were used to detect SS. Considering a window size of 50-kb, a non-sliding window approach was used to define SS regions. A total of 62, 57, and 72 genes were co-located within SS regions for Nelore, Gir, and Red Sindhi, respectively, and used to perform functional analyses per breed. Most genes were associated with productive and reproductive traits, while others were related to thermotolerance, the immune system, temperament, and coat color. The identified SS demonstrate how animal breeding programs shape the genetic makeup of these breeds to meet production system requirements, given that animals from Brazil and the Asian continent have undergone different selection processes. The identification of genes related to thermotolerance, temperament, and the immune system suggests specific alleles have enabled animals to adapt to environmental conditions and selection criteria in Brazil. Understanding SS can support breeding strategies for Nelore, Gir, and Red Sindhi cattle, contributing to enhanced resistance, adaptation, and productivity to meet food production demands.

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.

Assessment of Genomic Diversity and Selective Pressures in Crossbred Dairy Cattle of Pakistan

Improving the low productivity levels of native cattle breeds in smallholder farming systems is a pressing concern in Pakistan. Crossbreeding high milk-yielding holstein friesian (HF) breed with the adaptability and heat tolerance of Sahiwal cattle has resulted in offspring that are well-suited to local conditions and exhibit improved milk yield. The exploration of how desirable traits in crossbred dairy cattle are selected has not yet been investigated. This study aims to provide the first overview of the selective pressures on the genome of crossbred dairy cattle in Pakistan. A total of eighty-one crossbred, thirty-two HF and twenty-four Sahiwal cattle were genotyped, and additional SNP genotype data for HF and Sahiwal were collected from a public database to equate the sample size in each group. Within-breed selection signatures in crossbreds were investigated using the integrated haplotype score. Crossbreds were also compared to each of their parental breeds to discover between-population signatures of selection using two approaches: cross-population extended haplotype homozygosity and fixation index. We identified several overlapping genes associated with production, immunity, and adaptation traits, including U6, TMEM41B, B4GALT7, 5S_rRNA, RBM27, POU4F3, NSD1, PRELID1, RGS14, SLC34A1, TMED9, B4GALT7, OR2AK3, OR2T16, OR2T60, OR2L3, and CTNNA1. Our results suggest that regions responsible for milk traits have generally experienced stronger selective pressure than others.

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.

Genome-wide association and functional annotation analysis for the calving interval in Nellore cattle

Calving interval (CI) measures the number of days between two consecutive calves of the same cow, and previous studies based on phenotype and pedigree data reported low heritability for this trait. However, the genetic architecture of CI in the Nellore breed was not evaluated based on genomic data. Thus, this study aimed to estimate the heritability based on genomic data and carry out a genome-wide association study (GWAS) for CI in the Nellore breed, using 12,599 pedigree records, 5078 CI records, and 3818 animals genotyped with 50k SNPchip panel. Both quality control and GWAS were performed in BLUPF90 family packages, which use the single-step genomic best linear unbiased predictor (ssGBLUP) method. The average CI was 427.6 days, with a standard deviation of 106.9 and a total range of 270-730 days. The heritability estimate was 0.04 ± 0.04. The p-values of GWAS analysis resulted in a genomic inflation factor (lambda) of 1.08. The only significant SNP (rs136725686) at the genome-wide level (p-value = 1.53E-06) was located on BTA13. Other 19 SNPs were significant at the chromosome-wide level, distributed on BTA1, 2, 3, 6, 10, 13, 14, 17, 18, 22, and 26. Functional annotation analysis found thirty-six protein-coding genes, including genes related to cell cycle (RAD21, BCAR3), oocyte function (LHX8, CLPX, UTP23), immune system (TXK, TEC, NFATC2), endocrine function (LRRFIP2, GPR158), estrous cycle (SLC38A7), and female fertility (CCK, LYZL4, TRAK1, FOXP1, STAC). Therefore, CI is a complex trait with small heritability in Nellore cattle, and various biological processes may be involved with the genetic architecture of CI in Nellore cattle.

Harnessing Genomics and Transcriptomics Approaches to Improve Female Fertility in Beef Cattle-A Review

Female fertility is the foundation of the cow-calf industry, impacting both efficiency and profitability. Reproductive failure is the primary reason why beef cows are sold in the U.S. and the cause of an estimated annual gross loss of USD 2.8 billion. In this review, we discuss the status of the genomics, transcriptomics, and systems genomics approaches currently applied to female fertility and the tools available to cow-calf producers to maximize genetic progress. We highlight the opportunities and limitations associated with using genomic and transcriptomic approaches to discover genes and regulatory mechanisms related to beef fertility. Considering the complex nature of fertility, significant advances in precision breeding will rely on holistic, multidisciplinary approaches to further advance our ability to understand, predict, and improve reproductive performance. While these technologies have advanced our knowledge, the next step is to translate research findings from bench to on-farm applications.

A multi-omics analysis identifies molecular features associated with fertility in heifers (Bos taurus)

Infertility or subfertility is a critical barrier to sustainable cattle production, including in heifers. The development of heifers that do not produce a calf within an optimum window of time is a critical factor for the profitability and sustainability of the cattle industry. In parallel, heifers are an excellent biomedical model for understanding the underlying etiology of infertility because well-nourished heifers can still be infertile, mostly because of inherent physiological and genetic causes. Using a high-density single nucleotide polymorphism (SNP) chip, we collected genotypic data, which were analyzed using an association analysis in PLINK with Fisher's exact test. We also produced quantitative transcriptome data and proteome data. Transcriptome data were analyzed using the quasi-likelihood test followed by the Wald's test, and the likelihood test and proteome data were analyzed using a generalized mixed model and Student's t-test. We identified two SNPs significantly associated with heifer fertility (rs110918927, chr12: 85648422, P = 6.7 × 10-7; and rs109366560, chr11:37666527, P = 2.6 × 10-5). We identified two genes with differential transcript abundance (eFDR ≤ 0.002) between the two groups (Fertile and Sub-Fertile): Adipocyte Plasma Membrane Associated Protein (APMAP, 1.16 greater abundance in the Fertile group) and Dynein Axonemal Intermediate Chain 7 (DNAI7, 1.23 greater abundance in the Sub-Fertile group). Our analysis revealed that the protein Alpha-ketoglutarate-dependent dioxygenase FTO was more abundant in the plasma collected from Fertile heifers relative to their Sub-Fertile counterparts (FDR < 0.05). Lastly, an integrative analysis of the three datasets identified a series of molecular features (SNPs, gene transcripts, and proteins) that discriminated 21 out of 22 heifers correctly based on their fertility category. Our multi-omics analyses confirm the complex nature of female fertility. Very importantly, our results also highlight differences in the molecular profile of heifers associated with fertility that transcend the constraints of breed-specific genetic background.

Genome-wide assessment and mapping of inbreeding depression identifies candidate genes associated with semen traits in Holstein bulls

BACKGROUND

The reduction in phenotypic performance of a population due to mating between close relatives is called inbreeding depression. The genetic background of inbreeding depression for semen traits is poorly understood. Thus, the objectives were to estimate the effect of inbreeding and to identify genomic regions underlying inbreeding depression of semen traits including ejaculate volume (EV), sperm concentration (SC), and sperm motility (SM). The dataset comprised ~ 330 K semen records from ~ 1.5 K Holstein bulls genotyped with 50 K single nucleotide polymorphism (SNP) BeadChip. Genomic inbreeding coefficients were estimated using runs of homozygosity (i.e., F_ROH > 1 Mb) and excess of SNP homozygosity (F_SNP). The effect of inbreeding was estimated by regressing phenotypes of semen traits on inbreeding coefficients. Associated variants with inbreeding depression were also detected by regressing phenotypes on ROH state of the variants.

RESULTS

Significant inbreeding depression was observed for SC and SM (p < 0.01). A 1% increase in F_ROH reduced SM and SC by 0.28% and 0.42% of the population mean, respectively. By splitting F_ROH into different lengths, we found significant reduction in SC and SM due to longer ROH, which is indicative of more recent inbreeding. A genome-wide association study revealed two signals positioned on BTA 8 associated with inbreeding depression of SC (p < 0.00001; FDR < 0.02). Three candidate genes of GALNTL6, HMGB2, and ADAM29, located in these regions, have established and conserved connections with reproduction and/or male fertility. Moreover, six genomic regions on BTA 3, 9, 21 and 28 were associated with SM (p < 0.0001; FDR < 0.08). These genomic regions contained genes including PRMT6, SCAPER, EDC3, and LIN28B with established connections to spermatogenesis or fertility.

CONCLUSIONS

Inbreeding depression adversely affects SC and SM, with evidence that longer ROH, or more recent inbreeding, being especially detrimental. There are genomic regions associated with semen traits that seems to be especially sensitive to homozygosity, and evidence to support some from other studies. Breeding companies may wish to consider avoiding homozygosity in these regions for potential artificial insemination sires.

Genome-wide association and genotype by environment interactions for growth traits in U.S. Red Angus cattle

Background

Genotypic information produced from single nucleotide polymorphism (SNP) arrays has routinely been used to identify genomic regions associated with complex traits in beef and dairy cattle. Herein, we assembled a dataset consisting of 15,815 Red Angus beef cattle distributed across the continental U.S. and a union set of 836,118 imputed SNPs to conduct genome-wide association analyses (GWAA) for growth traits using univariate linear mixed models (LMM); including birth weight, weaning weight, and yearling weight. Genomic relationship matrix heritability estimates were produced for all growth traits, and genotype-by-environment (GxE) interactions were investigated.

Results

Moderate to high heritabilities with small standard errors were estimated for birth weight (0.51 ± 0.01), weaning weight (0.25 ± 0.01), and yearling weight (0.42 ± 0.01). GWAA revealed 12 pleiotropic QTL (BTA6, BTA14, BTA20) influencing Red Angus birth weight, weaning weight, and yearling weight which met a nominal significance threshold (P ≤ 1e-05) for polygenic traits using 836K imputed SNPs. Moreover, positional candidate genes associated with Red Angus growth traits in this study (i.e., LCORL, LOC782905, NCAPG, HERC6, FAM184B, SLIT2, MMRN1, KCNIP4, CCSER1, GRID2, ARRDC3, PLAG1, IMPAD1, NSMAF, PENK, LOC112449660, MOS, SH3PXD2B, STC2, CPEB4) were also previously associated with feed efficiency, growth, and carcass traits in beef cattle. Collectively, 14 significant GxE interactions were also detected, but were less consistent among the investigated traits at a nominal significance threshold (P ≤ 1e-05); with one pleiotropic GxE interaction detected on BTA28 (24 Mb) for Red Angus weaning weight and yearling weight.

Conclusions

Sixteen well-supported QTL regions detected from the GWAA and GxE GWAA for growth traits (birth weight, weaning weight, yearling weight) in U.S. Red Angus cattle were found to be pleiotropic. Twelve of these pleiotropic QTL were also identified in previous studies focusing on feed efficiency and growth traits in multiple beef breeds and/or their composites. In agreement with other beef cattle GxE studies our results implicate the role of vasodilation, metabolism, and the nervous system in the genetic sensitivity to environmental stress.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08667-6.

Sustainable Intensification of Beef Production in the Tropics: The Role of Genetically Improving Sexual Precocity of Heifers

Simple Summary

Tropical pasture-based beef production systems play a vital role in global food security. The importance of promoting sustainable intensification of such systems has been debated worldwide. Demand for beef is growing together with concerns over the impact of its production on the environment. Implementing sustainable livestock intensification programs relies on animal genetic improvement. In tropical areas, the lack of sexual precocity is a bottleneck for cattle efficiency, directly impacting the sustainability of production systems. In the present review we present and discuss the state of the art of genetic evaluation for sexual precocity in Bos indicus beef cattle, covering the definition of measurable traits, genetic parameter estimates, genomic analyses, and a case study of selection for sexual precocity in Nellore breeding programs.

Abstract

Increasing productivity through continued animal genetic improvement is a crucial part of implementing sustainable livestock intensification programs. In Zebu cattle, the lack of sexual precocity is one of the main obstacles to improving beef production efficiency. Puberty-related traits are complex, but large-scale data sets from different “omics” have provided information on specific genes and biological processes with major effects on the expression of such traits, which can greatly increase animal genetic evaluation. In addition, genetic parameter estimates and genomic predictions involving sexual precocity indicator traits and productive, reproductive, and feed-efficiency related traits highlighted the feasibility and importance of direct selection for anticipating heifer reproductive life. Indeed, the case study of selection for sexual precocity in Nellore breeding programs presented here show that, in 12 years of selection for female early precocity and improved management practices, the phenotypic means of age at first calving showed a strong decreasing trend, changing from nearly 34 to less than 28 months, with a genetic trend of almost −2 days/year. In this period, the percentage of early pregnancy in the herds changed from around 10% to more than 60%, showing that the genetic improvement of heifer’s sexual precocity allows optimizing the productive cycle by reducing the number of unproductive animals in the herd. It has a direct impact on sustainability by better use of resources. Genomic selection breeding programs accounting for genotype by environment interaction represent promising tools for accelerating genetic progress for sexual precocity in tropical beef cattle.

Taurine and Indicine Haplotype Representation in Advanced Generation Individuals From Three American Breeds

Development of the American Breeds of beef cattle began in the 1920s as breeders and U. S. Experiment Station researchers began to create Bos taurus taurus × Bos taurus indicus hybrids using Brahman as the B. t. indicus source. By 1954, U.S. Breed Associations had been formed for Brangus (5/8 Angus × 3/8 Brahman), Beefmaster (½ Brahman × ¼ Shorthorn × ¼ Hereford), and Santa Gertrudis (5/8 Shorthorn × 3/8 Brahman). While these breeds were developed using mating designs expected to create base generation animals with the required genome contributions from progenitor breeds, each association has now registered advanced generation animals in which selection or drift may have caused the realized genome compositions to differ from initial expected proportions. The availability of high-density SNP genotypes for 9,161 Brangus, 3,762 Beefmaster, and 1,942 Santa Gertrudis animals allowed us to compare the realized genomic architectures of breed members to the base generation expectations. We used RFMix to estimate local ancestry and identify genomic regions in which the proportion of Brahman ancestry differed significantly from a priori expectations. For all three breeds, lower than expected levels of Brahman composition were found genome-wide, particularly in early-generation animals where we demonstrate that selection on beef production traits was likely responsible for the taurine enrichment. Using a proxy for generation number, we also contrasted the genomes of early- and advanced-generation animals and found that the indicine composition of the genome has increased with generation number likely due to selection on adaptive traits. Many of the most-highly differentiated genomic regions were breed specific, suggesting that differences in breeding objectives and selection intensities exist between the breeds. Global ancestry estimation is commonly performed in admixed animals to control for stratification in association studies. However, local ancestry estimation provides the opportunity to investigate the evolution of specific chromosomal segments and estimate haplotype effects on trait variation in admixed individuals. Investigating the genomic architecture of the American Breeds not only allows the estimation of indicine and taurine genome proportions genome-wide, but also the locations within the genome where either taurine or indicine alleles confer a selective advantage.

The functional genetic architecture of egg-laying and live-bearing reproduction in common lizards

All amniotes reproduce either by egg-laying (oviparity), which is ancestral to vertebrates or by live-bearing (viviparity), which has evolved many times independently. However, the genetic basis of these parity modes has never been resolved and, consequently, its convergence across evolutionary scales is currently unknown. Here, we leveraged natural hybridizations between oviparous and viviparous common lizards (Zootoca vivipara) to describe the functional genes and genetic architecture of parity mode and its key traits, eggshell and gestation length, and compared our findings across vertebrates. In these lizards, parity trait genes were associated with progesterone-binding functions and enriched for tissue remodelling and immune system pathways. Viviparity involved more genes and complex gene networks than did oviparity. Angiogenesis, vascular endothelial growth and adrenoreceptor pathways were enriched in the viviparous female reproductive tissue, while pathways for transforming growth factor were enriched in the oviparous. Natural selection on these parity mode genes was evident genome-wide. Our comparison to seven independent origins of viviparity in mammals, squamates and fish showed that genes active in pregnancy were related to immunity, tissue remodelling and blood vessel generation. Therefore, our results suggest that pre-established regulatory networks are repeatedly recruited for viviparity and that these are shared at deep evolutionary scales.

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.

Rewiring of gene expression in circulating white blood cells is associated with pregnancy outcome in heifers (Bos taurus)

Infertility is a challenging phenomenon in cattle that reduces the sustainability of beef production worldwide. Here, we tested the hypothesis that gene expression profiles of protein-coding genes expressed in peripheral white blood cells (PWBCs), and circulating micro RNAs in plasma, are associated with female fertility, measured by pregnancy outcome. We drew blood samples from 17 heifers on the day of artificial insemination and analyzed transcript abundance for 10,496 genes in PWBCs and 290 circulating micro RNAs. The females were later classified as pregnant to artificial insemination, pregnant to natural breeding or not pregnant. We identified 1860 genes producing significant differential coexpression (eFDR < 0.002) based on pregnancy outcome. Additionally, 237 micro RNAs and 2274 genes in PWBCs presented differential coexpression based on pregnancy outcome. Furthermore, using a machine learning prediction algorithm we detected a subset of genes whose abundance could be used for blind categorization of pregnancy outcome. Our results provide strong evidence that transcript abundance in circulating white blood cells is associated with fertility in heifers.

Beef heifer fertility: importance of management practices and technological advancements

The development of replacement heifers is at the core of cow-calf beef production systems. In 2020, the USDA, National Agricultural Statistics Service reported 5.771 million beef heifers, 500 pounds and over, are under development for cow replacement. A compilation of data from several studies indicate that between 85% and 95% of these heifers will become pregnant in their first breeding season. Several thousands of heifers being raised for replacement may not deliver a calf on their first breeding season and result in economic losses to cow-calf producers. Many management procedures have been developed to maximize the reproductive potential of beef heifers. Such approaches include, but are not limited to the following: nutritional management for controlled weight gain, identification of reproductive maturity by physiological and morphological indicators, and the implementation of an estrous synchronization program. The implementation of management strategies has important positive impact(s) on the reproductive efficiency of heifers. There are limitations, however, because some heifers deemed ready to enter their first breeding season do not become pregnant. In parallel, genetic selection for fertility-related traits in beef heifers have not promoted major genetic gains on this particular area, most likely due to low heritability of female fertility traits in cattle. Technologies such as antral follicle counting, DNA genotyping and RNA profiling are being investigated as a means to aid in the identification of heifers of low fertility potential. To date, many polymorphisms have been associated with heifer fertility, but no DNA markers have been identified across herds. Antral follicle count is an indication of the ovarian reserve and is an indicator of the reproductive health of a heifer. We have been working on the identification of transcriptome profiles in heifers associated with pregnancy outcome. Our current investigations integrating protein-coding transcript abundance and artificial intelligence have identified the potential for bloodborne transcript abundance to be used as indicators of fertility potential in beef heifers. In summary, there is an ongoing pressure for reducing costs and increasing efficiency in cow-calf production systems, and new technologies can help reduce the long-standing limitations in beef heifer fertility.

Genetic Parameters and Genome-Wide Association Studies for Anti-Müllerian Hormone Levels and Antral Follicle Populations Measured After Estrus Synchronization in Nellore Cattle

Reproductive efficiency plays a major role in the long-term sustainability of livestock industries and can be improved through genetic and genomic selection. This study aimed to estimate genetic parameters (heritability and genetic correlation) and identify genomic regions and candidate genes associated with anti-Müllerian hormone levels (AMH) and antral follicle populations measured after estrous synchronization (AFP) in Nellore cattle. The datasets included phenotypic records for 1099 and 289 Nellore females for AFP and AMH, respectively, high-density single nucleotide polymorphism (SNP) genotypes for 944 animals, and 4129 individuals in the pedigree. The heritability estimates for AMH and AFP were 0.28 ± 0.07 and 0.30 ± 0.09, and the traits were highly and positively genetically correlated (rG = 0.81 ± 0.02). These findings indicated that these traits can be improved through selective breeding, and substantial indirect genetic gains are expected by selecting for only one of the two traits. A total of 31 genomic regions were shown to be associated with AMH or AFP, and two genomic regions located on BTA1 (64.9-65.0 Mb and 109.1-109.2 Mb) overlapped between the traits. Various candidate genes were identified to be potentially linked to important biological processes such as ovulation, tissue remodeling, and the immune system. Our findings support the use of AMH and AFP as indicator traits to genetically improve fertility rates in Nellore cattle and identify better oocyte donors.

Genetic analysis of in-vitro embryo production traits in Dairy Gir cattle

The potential of dams as oocyte donors can be a selection criterion for animal breeding programs, but also an involuntary driver of the process. In both cases, it is important to determine genetic components influencing the outcome of in vitro embryo production (IVEP). The objective of the present study was to perform a detailed genetic analysis for in vitro embryo production traits in Dairy Gir cows. A dataset containing 11,450 records of ovum pick-up (OPU) and in vitro fertilization (IVF) procedures from 2684 Dairy Gir donors was evaluated. Analyzed traits were number (N_OV) and percentage (P_OV) of viable oocytes; number (N_GI) and percentage (P_GI) of grade I oocytes; number (N_EMB) and percentage (P_EMB) of viable embryos. All analyzes were performed using animal models by a Bayesian framework. Heritability estimates varied from 0.16 to 0.32 for count traits and from 0.01 to 0.06 for percentage traits. The proportion of the total variation represented by the additive genetic effect of sire (semen used in IVF) for N_EMB and P_EMB was 7% and 5% respectively. Associations between estimated breeding values from progeny tested bulls for IVEP traits, milk production, age at first calving and conformation traits were mainly low or close to zero. Results indicate that selection for IVEP traits is possible in Dairy Gir cattle and would not impair genetic progress for traits already considered as selection criteria. The N_OV seems to be a promising target trait. However, a selection index could help to avoid the use of sires with negative genetic merit for percentage traits, minimizing possible deterioration in the long term.

Fine mapping of genomic regions associated with female fertility in Nellore beef cattle based on sequence variants from segregating sires

BACKGROUND

Impaired fertility in cattle limits the efficiency of livestock production systems. Unraveling the genetic architecture of fertility traits would facilitate their improvement by selection. In this study, we characterized SNP chip haplotypes at QTL blocks then used whole-genome sequencing to fine map genomic regions associated with reproduction in a population of Nellore (Bos indicus) heifers.

METHODS

The dataset comprised of 1337 heifers genotyped using a GeneSeek® Genomic Profiler panel (74677 SNPs), representing the daughters from 78 sires. After performing marker quality control, 64800 SNPs were retained. Haplotypes carried by each sire at six previously identified QTL on BTAs 5, 14 and 18 for heifer pregnancy and BTAs 8, 11 and 22 for antral follicle count were constructed using findhap software. The significance of the contrasts between the effects of every two paternally-inherited haplotype alleles were used to identify sires that were heterozygous at each QTL. Whole-genome sequencing data localized to the haplotypes from six sires and 20 other ancestors were used to identify sequence variants that were concordant with the haplotype contrasts. Enrichment analyses were applied to these variants using KEGG and MeSH libraries.

RESULTS

A total of six (BTA 5), six (BTA 14) and five (BTA 18) sires were heterozygous for heifer pregnancy QTL whereas six (BTA 8), fourteen (BTA 11), and five (BTA 22) sires were heterozygous for number of antral follicles' QTL. Due to inadequate representation of many haplotype alleles in the sequenced animals, fine mapping analysis could only be reliably performed for the QTL on BTA 5 and 14, which had 641 and 3733 concordant candidate sequence variants, respectively. The KEGG "Circadian rhythm" and "Neurotrophin signaling pathway" were significantly associated with the genes in the QTL on BTA 5 whereas 32 MeSH terms were associated with the QTL on BTA 14. Among the concordant sequence variants, 0.2% and 0.3% were classified as missense variants for BTAs 5 and 14, respectively, highlighting the genes MTERF2, RTMB, ENSBTAG00000037306 (miRNA), ENSBTAG00000040351, PRKDC, and RGS20. The potential causal mutations found in the present study were associated with biological processes such as oocyte maturation, embryo development, placenta development and response to reproductive hormones.

CONCLUSIONS

The identification of heterozygous sires by positionally phasing SNP chip data and contrasting haplotype effects for previously detected QTL can be used for fine mapping to identify potential causal mutations and candidate genes. Genomic variants on genes MTERF2, RTBC, miRNA ENSBTAG00000037306, ENSBTAG00000040351, PRKDC, and RGS20, which are known to have influence on reproductive biological processes, were detected.

RAPID COMMUNICATION: Multi-breed validation study unraveled genomic regions associated with puberty traits segregating across tropically adapted breeds1

An efficient strategy to improve QTL detection power is performing across-breed validation studies. Variants segregating across breeds are expected to be in high linkage disequilibrium (LD) with causal mutations affecting economically important traits. The aim of this study was to validate, in a Tropical Composite cattle (TC) population, QTL associations identified for sexual precocity traits in a Nellore and Brahman meta-analysis genome-wide association study. In total, 2,816 TC, 8,001 Nellore, and 2,210 Brahman animals were available for the analysis. For that, genomic regions significantly associated with puberty traits in the meta-analysis study were validated for the following sexual precocity traits in TC: age at first corpus luteum (AGECL), first postpartum anestrus interval (PPAI), and scrotal circumference at 18 months of age (SC). We considered validated QTL those underpinned by significant markers from the Nellore and Brahman meta-analysis (P ≤ 10-4) that were also significant for a TC trait, i.e., presenting a P-value of ≤10-3 for AGECL, PPAI, or SC. We also considered as validated QTL those regions where significant markers in the reference population were at ±250 kb from significant markers in the validation population. Using this criteria, 49 SNP were validated for AGECL, 4 for PPAI, and 14 for SC, from which 5 were in common with AGECL, totaling 62 validated SNP for these traits and 30 candidate genes surrounding them. Considering just candidate genes closest to the top SNP of each chromosome, for AGECL 8 candidate genes were identified: COL8A1, PENK, ENSBTAG00000047425, BPNT1, ADAMTS17, CCHCR1, SUFU, and ENSBTAG00000046374. For PPAI, 3 genes emerged as candidates (PCBP3, KCNK10, and MRPS5), and for SC 8 candidate genes were identified (SNORA70, TRAC, ASS1, BPNT1, LRRK1, PKHD1, PTPRM, and ENSBTAG00000045690). Several candidate regions presented here were previously associated with puberty traits in cattle. The majority of emerging candidate genes are related to biological processes involved in reproductive events, such as maintenance of gestation, and some are known to be expressed in reproductive tissues. Our results suggested that some QTL controlling early puberty seem to be segregating across cattle breeds adapted to tropical conditions.

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.

Across-breed validation study confirms and identifies new loci associated with sexual precocity in Brahman and Nellore cattle

The aim of this study was to identify candidate regions associated with sexual precocity in Bos indicus. Nellore and Brahman were set as validation and discovery populations, respectively. SNP selected in Brahman to validate in Nellore were from gene regions affecting reproductive traits (G1) and significant SNP (p ≤ 10^-3 ) from a meta-analysis (G2). In the validation population, early pregnancy (EP) and scrotal circumference (SC) were evaluated. To perform GWAS in validation population, we used regression and Bayes C. SNP with p ≤ 10^-3 in regression and Bayes factor ≥3 in Bayes C were deemed significant. Significant SNP (for EP or SC) or SNP in their ±250 Kb vicinity region, which were in at least one discovery set (G1 or G2), were considered validated. SNP identified in both G1 and G2 were considered candidate. For EP, 145 SNP were validated in G1 and 41 in G2, and for SC, these numbers were 14 and 2. For EP, 21 candidate SNP were detected (G1 and G2). For SC, no candidate SNP were identified. Validated SNP and their vicinity region were located close to quantitative trait loci or genes related to reproductive traits and were enriched in gene ontology terms related to reproductive success. These are therefore strong candidate regions for sexual precocity in Nellore and Brahman.

Multitrait meta-analysis identified genomic regions associated with sexual precocity in tropical beef cattle

Multitrait meta-analyses are a strategy to produce more accurate genome-wide association studies, especially for complex phenotypes. We carried out a meta-analysis study for traits related to sexual precocity in tropical beef cattle (Nellore and Brahman) aiming to identify important genomic regions affecting these traits. The traits included in the analyses were age at first calving (AFC), early pregnancy (EP), age at first corpus luteum (AGECL), first postpartum anoestrus interval (PPAI), and scrotal circumference (SC). The traits AFC, EP, and SCN were measured in Nellore cattle, while AGECL, PPAI, and SCB were measured in Brahman cattle. Meta-analysis resulted in 108 significant single-nucleotide polymorphisms (SNPs), at an empirical threshold P-value of 1.39 × 10-5 (false discovery rate [FDR] < 0.05). Within 0.5 Mb of the significant SNP, candidate genes were annotated and analyzed for functional enrichment. Most of the closest genes to the SNP with higher significance in each chromosome have been associated with important roles in reproductive function. They are TSC22D2, KLF7, ARHGAP29, 7SK, MAP3K5, TLE3, WDR5, TAF3, TMEM68, PPP1R15B, NR2F2, GALR1, SUFU, and KCNU1. We did not observe any significant SNP in BTA5, BTA12, BTA17, BTA18, BTA19, BTA20, BTA22, BTA23, BTA25, and BTA28. Although the majority of significant SNPs are in BTA14, it was identified significant associations in multiple chromosomes (19 out of 29 autosomes), which is consistent with the postulation that reproductive traits are complex polygenic phenotypes. Five proposed association regions harbor the majority of the significant SNP (76%) and were distributed over four chromosomes (P < 1.39 × 10-5, FDR < 0.05): BTA2 (5.55%) from 95 to 96 Mb, BTA4 (5.55%) from 94.1 to 94.8 Mb, BTA14 (59.26%) from 24 to 25 Mb and 29 to 30 Mb, and BTA21 (5.55%) from 6.7 Mb to 11.4 Mb. These regions harbored key genes related to reproductive function. Moreover, these genes were enriched for functional groups associated with immune response, maternal-fetal tolerance, pregnancy maintenance, embryo development, fertility, and response to stress. Further studies including other breeds and precocity traits could confirm the importance of these regions and identify new candidate regions for sexual precocity in beef cattle.

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.