Genome-Wide Association Analyses of Fertility Traits in Beef Heifers

Beef Cattle Genome Project: Advances in Genome Sequencing, Assembly, and Functional Genes Discovery

Beef is a major global source of protein, playing an essential role in the human diet. The worldwide production and consumption of beef continue to rise, reflecting a significant trend. However, despite the critical importance of beef cattle resources in agriculture, the diversity of cattle breeds faces severe challenges, with many breeds at risk of extinction. The initiation of the Beef Cattle Genome Project is crucial. By constructing a high-precision functional annotation map of their genome, it becomes possible to analyze the genetic mechanisms underlying important traits in beef cattle, laying a solid foundation for breeding more efficient and productive cattle breeds. This review details advances in genome sequencing and assembly technologies, iterative upgrades of the beef cattle reference genome, and its application in pan-genome research. Additionally, it summarizes relevant studies on the discovery of functional genes associated with key traits in beef cattle, such as growth, meat quality, reproduction, polled traits, disease resistance, and environmental adaptability. Finally, the review explores the potential of telomere-to-telomere (T2T) genome assembly, structural variations (SVs), and multi-omics techniques in future beef cattle genetic breeding. These advancements collectively offer promising avenues for enhancing beef cattle breeding and improving genetic traits.

Puberty classifications in beef heifers are moderately to highly heritable and associated with candidate genes related to cyclicity and timing of puberty

Introduction: Pubertal attainment is critical to reproductive longevity in heifers. Previously, four heifer pubertal classifications were identified according to attainment of blood plasma progesterone concentrations > 1 ng/ml: 1) Early; 2) Typical; 3) Start-Stop; and 4) Non-Cycling. Early and Typical heifers initiated and maintained cyclicity, Start-Stop started and then stopped cyclicity and Non-Cycling never initiated cyclicity. Start-Stop heifers segregated into Start-Stop-Discontinuous (SSD) or Start-Stop-Start (SSS), with SSD having similar phenotypes to Non-Cycling and SSS to Typical heifers. We hypothesized that these pubertal classifications are heritable, and loci associated with pubertal classifications could be identified by genome wide association studies (GWAS). Methods: Heifers (n = 532; 2017 - 2022) genotyped on the Illumina Bovine SNP50 v2 or GGP Bovine 100K SNP panels were used for variant component estimation and GWAS. Heritability was estimated using a univariate Bayesian animal model. Results: When considering pubertal classifications: Early, Typical, SSS, SSD, and Non-Cycling, pubertal class was moderately heritable (0.38 ± 0.08). However, when heifers who initiated and maintained cyclicity were compared to those that did not cycle (Early+Typical vs. SSD+Non-Cycling) heritability was greater (0.59 ± 0.19). A GWAS did not identify single nucleotide polymorphisms (SNPs) significantly associated with pubertal classifications, indicating puberty is a polygenic trait. A candidate gene approach was used, which fitted SNPs within or nearby a set of 71 candidate genes previously associated with puberty, PCOS, cyclicity, regulation of hormone secretion, signal transduction, and methylation. Eight genes/regions were associated with pubertal classifications, and twenty-two genes/regions were associated with whether puberty was attained during the trial. Additionally, whole genome sequencing (WGS) data on 33 heifers were aligned to the reference genome (ARS-UCD1.2) to identify variants in FSHR, a gene critical to pubertal attainment. Fisher's exact test determined if FSHR SNPs segregated by pubertal classification. Two FSHR SNPs that were not on the bovine SNP panel were selected for additional genotyping and analysis, and one was associated with pubertal classifications and whether they cycled during the trial. Discussion: In summary, these pubertal classifications are moderately to highly heritable and polygenic. Consequently, genomic tools to inform selection/management of replacement heifers would be useful if informed by SNPs associated with cyclicity and early pubertal attainment.

Genome-wide association study identifies genomic regions associated with key reproductive traits in Korean Hanwoo cows

BACKGROUND

Conducting genome-wide association studies (GWAS) for reproductive traits in Hanwoo cattle, including age at first calving (AFC), calving interval (CI), gestation length (GL), and number of artificial inseminations per conception (NAIPC), is of paramount significance. These analyses provided a thorough exploration of the genetic basis of these traits, facilitating the identification of key markers for targeted trait improvement. Breeders can optimize their selection strategies, leading to more efficient and sustainable breeding programs, by incorporating genetic insights. This impact extends beyond individual traits and contributes to the overall productivity and profitability of the Hanwoo beef cattle industry. Ultimately, GWAS is essential in ensuring the long-term genetic resilience and adaptability of Hanwoo cattle populations. The primary goal of this study was to identify significant single nucleotide polymorphisms (SNPs) or quantitative trait loci (QTLs) associated with the studied reproductive traits and subsequently map the underlying genes that hold promise for trait improvement.

RESULTS

A genome-wide association study of reproductive traits identified 68 significant single nucleotide polymorphisms (SNPs) distributed across 29 Bos taurus autosomes (BTA). Among them, BTA14 exhibited the highest number of identified SNPs (25), whereas BTA6, BTA7, BTA8, BTA10, BTA13, BTA17, and BTA20 exhibited 8, 5, 5, 3, 8, 2, and 12 significant SNPs, respectively. Annotation of candidate genes within a 500 kb region surrounding the significant SNPs led to the identification of ten candidate genes relevant to age at first calving. These genes were: FANCG, UNC13B, TESK1, TLN1, and CREB3 on BTA8; FAM110B, UBXN2B, SDCBP, and TOX on BTA14; and MAP3K1 on BTA20. Additionally, APBA3, TCF12, and ZFR2, located on BTA7 and BTA10, were associated with the calving interval; PAX1, SGCD, and HAND1, located on BTA7 and BTA13, were linked to gestation length; and RBM47, UBE2K, and GPX8, located on BTA6 and BTA20, were linked to the number of artificial inseminations per conception in Hanwoo cows.

CONCLUSIONS

The findings of this study enhance our knowledge of the genetic factors that influence reproductive traits in Hanwoo cattle populations and provide a foundation for future breeding strategies focused on improving desirable traits in beef cattle. This research offers new evidence and insights into the genetic variants and genome regions associated with reproductive traits and contributes valuable information to guide future efforts in cattle breeding.

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.

Mapping Expression Quantitative Trait Loci Targeting Candidate Genes for Pregnancy in Beef Cows

Despite collective efforts to understand the complex regulation of reproductive traits, no causative genes and/or mutations have been reported yet. By integrating genomics and transcriptomics data, potential regulatory mechanisms may be unveiled, providing opportunities to dissect the genetic factors governing fertility. Herein, we identified regulatory variants from RNA-Seq data associated with gene expression regulation in the uterine luminal epithelial cells of beef cows. We identified 4676 cis and 7682 trans eQTLs (expression quantitative trait loci) affecting the expression of 1120 and 2503 genes, respectively (FDR < 0.05). These variants affected the expression of transcription factor coding genes (71 cis and 193 trans eQTLs) and genes previously reported as differentially expressed between pregnant and nonpregnant cows. Functional over-representation analysis highlighted pathways related to metabolism, immune response, and hormone signaling (estrogen and GnRH) affected by eQTL-regulated genes (p-value ≤ 0.01). Furthermore, eQTLs were enriched in QTL regions for 13 reproduction-related traits from the CattleQTLdb (FDR ≤ 0.05). Our study provides novel insights into the genetic basis of reproductive processes in cattle. The underlying causal mechanisms modulating the expression of uterine genes warrant further investigation.

A transcriptomic analysis of skeletal muscle tissues reveals promising candidate genes and pathways accountable for different daily weight gain in Hanwoo cattle

Cattle traits like average daily weight gain (ADG) greatly impact profitability. Selecting based on ADG considering genetic variability can lead to economic and genetic advancements in cattle breeding. This study aimed to unravel genetic influences on ADG variation in Hanwoo cattle at the skeletal muscle transcriptomic level. RNA sequencing was conducted on longissimus dorsi (LD), semimembranosus (SB), and psoas major (PM) muscles of 14 steers assigned to same feed, grouped by low (≤ 0.71 kg) and high (≥ 0.77 kg) ADG. At P ≤ 0.05 and log2fold > 1.5, the distinct pattern of gene expression was identified with 184, 172, and 210 differentially expressed genes in LD, SB, and PM muscles, respectively. Tissue-specific responses to ADG variation were evident, with myogenesis and differentiation associated JAK-STAT signaling pathway and prolactin signaling pathways enriched in LD and SB muscles, while adipogenesis-related PPAR signaling pathways were enriched in PM muscle. Key hub genes (AXIN2, CDKN1A, MYC, PTGS2, FZD5, SPP1) were upregulated and functionally significant in muscle growth and differentiation. Notably, DPP6, CDKN1A, and FZD5 emerged as possible candidate genes linked to ADG variation. These findings enhance our understanding of genetic factors behind ADG variation in Hanwoo cattle, illuminating skeletal muscle mechanisms influencing ADG.

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 computational framework for improving genetic variants identification from 5,061 sheep sequencing data

BACKGROUND

Pan-genomics is a recently emerging strategy that can be utilized to provide a more comprehensive characterization of genetic variation. Joint calling is routinely used to combine identified variants across multiple related samples. However, the improvement of variants identification using the mutual support information from multiple samples remains quite limited for population-scale genotyping.

RESULTS

In this study, we developed a computational framework for joint calling genetic variants from 5,061 sheep by incorporating the sequencing error and optimizing mutual support information from multiple samples' data. The variants were accurately identified from multiple samples by using four steps: (1) Probabilities of variants from two widely used algorithms, GATK and Freebayes, were calculated by Poisson model incorporating base sequencing error potential; (2) The variants with high mapping quality or consistently identified from at least two samples by GATK and Freebayes were used to construct the raw high-confidence identification (rHID) variants database; (3) The high confidence variants identified in single sample were ordered by probability value and controlled by false discovery rate (FDR) using rHID database; (4) To avoid the elimination of potentially true variants from rHID database, the variants that failed FDR were reexamined to rescued potential true variants and ensured high accurate identification variants. The results indicated that the percent of concordant SNPs and Indels from Freebayes and GATK after our new method were significantly improved 12%-32% compared with raw variants and advantageously found low frequency variants of individual sheep involved several traits including nipples number (GPC5), scrapie pathology (PAPSS2), seasonal reproduction and litter size (GRM1), coat color (RAB27A), and lentivirus susceptibility (TMEM154).

CONCLUSION

The new method used the computational strategy to reduce the number of false positives, and simultaneously improve the identification of genetic variants. This strategy did not incur any extra cost by using any additional samples or sequencing data information and advantageously identified rare variants which can be important for practical applications of animal breeding.

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.

Molecular markers for thermo-tolerance are associated with reproductive and physiological traits in Pelibuey ewes raised in a semiarid environment

Pelibuey sheep exhibit reproductive activity through the year, but warm weather lowers their fertility and demonstrates physiological limitations of environmental heat stress. Single nucleotide polymorphisms (SNPs) associated with heat stress tolerance in sheep have been reported previously. The objective was to validate the association of seven thermo-tolerance SNP markers with reproductive and physiological traits in Pelibuey ewes raised in a semiarid region. Pelibuey ewes were assigned to a cool (January 1st^.- March 31st^.; n = 101) or warm (April 1st^.- August 31st^.; n = 104) experimental group. All ewes were exposed to fertile rams and assessed for pregnancy diagnosis 90 days later; lambing day was reported at birth. These data served to calculate the reproductive traits of services per conception, prolificacy, days to estrus, days to conception, conception rate and lambing rate. Rectal temperature, rump/leg skin temperature and respiratory rate were measured and reported as physiological traits. Blood samples were collected and processed to extract DNA, which was genotyped using the TaqMan allelic discrimination method and qPCR. A mixed effects statistical model was used to validate associations between SNP genotypes and phenotypic traits. The SNPs rs421873172, rs417581105 and rs407804467 were confirmed as markers associated with reproductive and physiological traits (P < 0.05), and these SNPs were in the genes PAM, STAT1 and FBXO11, respectively. Interestingly, these SNP markers resulted as predictors for the evaluated traits but only in ewes from the warm group, which indicated their association with heat-stress tolerance. An additive SNP effect was confirmed with the highest contribution (P < 0.01) of the SNP rs417581105 for the evaluated traits. Reproductive performance improved (P < 0.05) and physiological parameters decreased in ewes carrying favorable SNP genotypes. In conclusion, three thermo-tolerance SNP markers were associated with improved reproductive and physiological traits in a prospective population of heat-stressed ewes raised in a semiarid environment.

Estimation of the Genetic Components of (Co)variance and Preliminary Genome-Wide Association Study for Reproductive Efficiency in Retinta Beef Cattle

In this study, we analyzed the variation of reproductive efficiency, estimated as the deviation between the optimal and real parity number of females at each stage of the cow's life, in 12,554 cows belonging to the Retinta Spanish cattle breed, using classical repeatability and random regression models. The results of the analyses using repeatability model and the random regression model suggest that reproductive efficiency is not homogeneous throughout the cow's life. The h² estimate for this model was 0.30, while for the random regression model it increased across the parities, from 0.24 at the first calving to 0.51 at calving number 9. Additionally, we performed a preliminary genome-wide association study for this trait in a population of 252 Retinta cows genotyped using the Axiom Bovine Genotyping v3 Array. The results showed 5 SNPs significantly associated with reproductive efficiency, located in two genomic regions (BTA4 and BTA28). The functional analysis revealed the presence of 5 candidate genes located within these regions, which were previously involved in different aspects related to fertility in cattle and mice models. This new information could give us a better understanding of the genetic architecture of reproductive traits in this species, as well as allow us to accurately select more fertile cows.

Investigating anogenital distance and antral follicle count as novel markers of fertility within a herd of cows with positive or negative genetic merit for fertility traits

Using early-in-life markers of reproductive characteristics may enhance the speed and success of genetic improvement in fertility. We investigated 2 phenotypes that can be measured early in life and are moderately heritable to determine their association with traditional measures of reproductive success and genetic variation under a seasonal-calving, pasture-based system. Cows were bred to be divergent in the New Zealand Fertility Breeding Value, which estimates genetic merit for fertility. Cows consisted of 2 groups with an average positive (+5%) or negative (-5%) genetic merit for fertility traits and were expected to have large diversity in reproductive outcomes. Calves were genotyped at 41 ± 3.1 d of age (mean ± SD; n = 538), and antral follicle counts (AFC) were measured when they were postpubertal heifers before their first breeding (416 ± 15 d old; 92-d range; n = 520). The anogenital distance (AGD) was measured in 478 primiparous cows of this same population 50 to 60 d after the breeding start date when they were 881 ± 25 d old (145-d range). The AGD was shorter in animals with a positive genetic merit for fertility traits (based on parent averages). An indicator of herd reproductive success in a seasonal-calving system (recalving by 6 wk in lactation 2) was chosen for logistic regression with cross-validation, and if significant, a cut-off was calculated that categorized animals into groups. Both linear and quadratic regression was undertaken, and the model with the greatest sensitivity for detection of nonpregnant cows used. The AGD linear model was significant with a sensitivity of 64% and a specificity of 48%. This model resulted in a cut-off of 102 mm, which we used to classify cows as short (≤102 mm) or long (>102 mm) AGD animals. Primiparous cows with a short AGD were more likely to be pregnant within the first 3 and 6 wk of mating, and become pregnant as a primiparous cow, than those with a long AGD. The time from calving to conception was 20 d earlier in short AGD compared with long-AGD cows. None of the models tested for AFC were significant; therefore cows were categorized into 3 groups based on previous work in seasonal systems. However, associations between fertility phenotypes and AFC group were limited. Genomic regions of interest for AGD and AFC did not overlap, indicating phenotypes were genetically independent. Overall, AGD appears as a promising early marker of fertility in seasonal grazing systems.