Genetic Features of Reproductive Traits in Bovine and Buffalo: Lessons From Bovine to Buffalo

Integration of ssGWAS and ROH analyses for uncovering genetic variants associated with reproduction traits in Large White pigs

The low heritability of reproduction traits such as total number born (TNB), number born alive (NBA) and adjusted litter weight until 21 days at weaning (ALW) poses a challenge for genetic improvement. In this study, we aimed to identify genetic variants that influence these traits and evaluate the accuracy of genomic selection (GS) using these variants as genomic features. We performed single-step genome-wide association studies (ssGWAS) on 17 823 Large White (LW) pigs, of which 2770 were genotyped by 50K single nucleotide polymorphism (SNP) chips. Additionally, we analyzed runs of homozygosity (ROH) in the population and tested their effects on the traits. The genomic feature best linear unbiased prediction (GFBLUP) was then carried out in an independent population of 350 LW pigs using identified trait-related SNP subsets as genomic features. As a result, our findings identified five, one and four SNP windows that explaining more than 1% of genetic variance for ALW, TNB, and NBA, respectively and discovered 358 hotspots and nine ROH islands. The ROH SSC1:21814570-27186456 and SSC11:7220366-14276394 were found to be significantly associated with ALW and NBA, respectively. We assessed the genomic estimated breeding value accuracy through 20 replicates of five-fold cross-validation. Our findings demonstrate that GFBLUP, incorporating SNPs located in effective ROH (p-value < 0.05) as genomic features, might enhance GS accuracy for ALW compared with GBLUP. Additionally, using SNPs explaining more than 0.1% of the genetic variance in ssGWAS for NBA as genomic features might improve the GS accuracy, too. However, it is important to note that the incorporation of inappropriate genomic features can significantly reduce GS accuracy. In conclusion, our findings provide valuable insights into the genetic mechanisms of reproductive traits in pigs and suggest that the ssGWAS and ROH have the potential to enhance the accuracy of GS for reproductive traits in LW pigs.

Genomic analysis of genotype-environment interaction in age at first calving of Murrah buffaloes

Age at first calving (AFC) is a measure of sexual maturity associated with the start of productive life of dairy animals. Additionally, a lower AFC reduces the generation interval and early culling of females. However, AFC has low heritability, making it a trait highly influenced by environmental factors. In this scenario, one way to improve the reproductive performance of buffalo cows is to select robust animals according to estimated breeding value (EBV) using models that include genotype-environment interaction (GEI) with the application of reaction norm models (RNMs). This can be achieved by understanding the genomic basis related to GEI of AFC. Thus, in this study, we aimed to predict EBV considering GEI via the RNM and identify candidate genes related to this component in dairy buffaloes through genome-wide association studies (GWAS). We used 1795 AFC records from three Murrah buffalo herds and formed environmental gradients (EGs) from contemporary group solutions obtained from genetic analysis of 270-day cumulative milk yield. Heritability estimates ranged from 0.15 to 0.39 along the EG. GWAS of the RNM slope parameter identified important genomic regions. The genomic window that explained the highest percentage of genetic variance of the slope (0.67%) was located on BBU1. After functional analysis, five candidate genes were detected, involved in two biological processes. The results suggested the existence of a GEI for AFC in Murrah buffaloes, with reclassification of animals when different environmental conditions were considered. The inclusion of genomic information increased the accuracy of breeding values for the intercept and slope of the reaction norm. GWAS analysis suggested that important genes associated with the AFC reaction norm slope were possibly also involved in biological processes related to lipid metabolism and immunity.

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.

Genetic parameters for reproductive traits in the Italian Mediterranean buffalo using milk yield as a correlated trait

Until now, the genetic evaluation of the Italian Mediterranean Buffalo has been mainly focused on production traits. However, female fertility affects the efficiency of the dairy industry as it is essential to maintain the profitability of dairy farms. Indeed, the estimation of its genetic component is crucial for its improvement. In this study, 3 measures of buffalo's fertility were analyzed: the age at first calving (AFC), the interval between first and second calving (CIV1), and the interval between second and successive calvings (CIV2_12). Milk yield at 270 d (MY270) was used as a correlated trait. First, genetic parameters were estimated using 7,915 buffalo cows with first calving from 1991 to 2018, then breeding values were calculated from 236,087 buffalo cows. Genetic parameters were estimated by Bayesian inference fitting a multiple-trait animal model using the GIBBS1F90 program, and BLUPF90 was used for estimation of breeding value. The heritability and repeatability estimates of fertility traits were low. The genetic correlations among fertility traits ranged from 0.10 (AFC-CIV1) to 0.92 (CIV1-CIV2_12). Genetic correlation between MY270 and fertility traits was unfavorable, ranging from 0.23 to 0.48. The results from this study can be used as a basis for the future genetic improvement of fertility traits in the Italian Mediterranean Buffaloes.

Upgrading the fixed-time artificial insemination (FTAI) protocol in Romanian buffaloes

The present study describes the challenges of assisted reproduction in Romanian buffaloes while increasing the efficacy of artificial insemination by choosing the most suitable method. The modified fixed-time artificial insemination (FTAI) protocol with sexed semen was used to increase the conception rate. This study included a total of 80 buffalo heifers that received ovarian stimulation using the OvSynch protocol. Two groups (n = 40), namely, a control group, in which the classic FTAI method was performed, and an experimental group, in which deep intrauterine AI was performed in cows that had developed a dominant follicle (US+UcFTAI), were randomly selected. The conception rate (CR) was 63.6% in the experimental group, which was statistically higher (P < 0.05) than the control group (30%). The ultrasound examination indicated that, using the OvSynch protocol, 82.5% (33 out of 40) of buffaloes developed a dominant follicle (DF) while the distribution between the warm and cold seasons was 75 and 90%, respectively. The CR was 60% during the hot season and 66.6% during the cold season. At calving, 92.5% female fetuses were born. The improved FTAI method in this study enhanced the results by reducing the waste of sexed semen and maximizing the response to OvSynch, making it a recommendation for practitioners. This study presents preliminary results and highlights that genetic progress is difficult to achieve. A systematic approach is needed in order to choose the most suitable biotechnological method for each farm.

Molecular Characteristics and Polymorphisms of Buffalo (Bubalus bubalis) ABCG2 Gene and Its Role in Milk Fat Synthesis

The ATP-binding cassette subfamily G member 2 (ABCG2) serves crucial roles in secreting riboflavin and biotin vitamins into the milk of cattle, mice, and humans, as well as in the transportation of xenotoxic and cytostatic drugs across the plasma membrane. However, the specific role of the ABCG2 gene in water buffaloes (Bubalus bubalis), especially its effect on milk fat synthesis in buffalo mammary epithelial cells (BuMECs), remains inadequately understood. In this study, the full-length CDS of the buffalo ABCG2 gene was isolated and identified from the mammary gland in buffaloes. A bioinformatics analysis showed a high degree of similarity in the transcriptional region, motifs, and conservative domains of the buffalo ABCG2 with those observed in other Bovidae species. The functional role of buffalo ABCG2 was associated with the transportation of solutes across lipid bilayers within cell membranes. Among the 11 buffalo tissues detected, the expression levels of ABCG2 were the highest in the liver and brain, followed by the mammary gland, adipose tissue, heart, and kidney. Notably, its expression in the mammary gland was significantly higher during peak lactation than during non-lactation. The ABCG2 gene was identified with five SNPs in river buffaloes, while it was monomorphic in swamp buffaloes. Functional experiments revealed that ABCG2 increased the triglyceride (TAG) content by affecting the expression of liposynthesis-related genes in BuMECs. The results of this study underscore the pivotal role of the ABCG2 gene in influencing the milk fat synthesis in BuMECs.

Genetic analysis for semen quality traits in buffalo bulls

This study was attempted to estimate the genetic parameters of semen quality traits in buffalo bulls. The study data consisted of 10975 ejaculates from 45 Murrah buffalo bulls (aged 24-72 months) used for breeding program during year 2010 to 2020. Semen quality traits (ejaculate volume, concentration of sperm, mass activity, initial and post-thaw motility, number of sperms per ejaculate, motile sperm number and discard rates) were studied. It was observed that average ejaculate volume was 2.82 ± 1.45 mL with mean concentration of 1040.12 ± 523.26 million/mL. Higher heritability was observed for number of sperms per ejaculate, number of motile sperm and sperm concentration. Significant phenotypic correlation was obtained between volume and number of sperms per ejaculate as well as volume and number of motile sperms. Likewise, significant phenotypic correlation was evident between sperm concentration with sperm number per ejaculate. Highest phenotypic correlation was obtained between sperm count per ejaculate and motile sperm count. Estimated genetic trends showed significant change in volume and motile sperm number. In conclusion, this study ascertains that genetic parameters of semen traits can be considered during the selection of buffalo bulls in breeding program.

Exploring molecular dynamic indicators associated with reproductive performance of Bos indicus cattle in blood plasma samples through data-independent acquisition mass spectrometry

Improving reproductive performance of cattle is of paramount importance for sustainable dairy farming. Poor reproduction performance (RP) hinders the genetic improvement of important Bos indicus cattle breeds. It is well known that incorporation of molecular information along with conventional breeding method is far better than use of conventional method alone for the genetic improvement of reproductive performance traits in cattle. Therefore, the present study sought to investigate the plasma proteome of the Deoni cows in cyclical (n = 6) and pregnant (n = 6) reproductive phases with varying reproductive performance (high and low). High-throughput data independent acquisition (DIA) based proteomics was performed to understand corresponding proteome. We identified a total of 430 plasma proteins. Among cyclic cows, twenty proteins were differentially regulated in low RP as compared to high RP. BARD1 and AFP proteins were observed upregulated in cyclical cows whose upregulation reported to affect reproductive performance in cattle. Among the pregnant cows, thirty-five proteins were differentially regulated, including the downregulation of FGL2 and ZNFX1 that modulates the maternal immune response mechanism which is required for successful implantation of the embryo. Also, proteins such as AHSG, CLU and SERPINA6 were upregulated in the pregnant cows whose upregulation reported to reduced reproductive performance. The results of this study will be helpful in establishing a framework for future research on the aspect of improving reproductive performance in Bos indicus cattle breeds. SIGNIFICANCE: The Indian subcontinent is the center of domestication for Bos indicus cattle breeds and they are known for their disease resistance, heat tolerance, ability to survive in low input regime and harsh climatic conditions. In recent times, population of many important Bos indicus breeds including Deoni cattle is declining due to various factors, especially due to reproductive performance. Traditional breeding methods are not sufficient enough to understand and improve the reproductive performance traits in important Bos indicus cattle breeds. Proteomics approach is a promising technology to understand the complex biological factors which leads to poor reproductive performance in cattle. The present study utilized DIA based LC- MS/MS analysis to identify the plasma proteins associated with reproductive performance in cyclical and pregnant cows. This study if improved further, can be used to develop potential protein markers associated with reproductive performance which is useful for the selection and genetic improvement of important Bos indicus breeds.

Genetic improvement of economic traits in Murrah buffalo using significant SNPs from genome-wide association study

GWAS helps to identify QTL and candidate genes of specific traits. Buffalo breeding has primarily focused on milk production, but its negative correlation with reproduction traits resulted in unfavorable decline of reproductive performance among buffaloes. A genome wide scan was performed on a total of 120 Murrah buffaloes genotyped by ddRAD sequencing for 13 traits related to female fertility, production, and growth. The identified 25 significant single nucleotide polymorphisms (SNPs) (P <1×10⁶) are associated with age at first calving (AFC), age at first service (AFS), period from calving to 1^st Artifical Insemination (AI), service period (SP) and 6 month body weight (6M). Fifteen genetic variants overlapped with different QTL regions of reported studies. Among the associated loci, outstanding candidate genes for fertility, including AQP1, TRNAE-CUC, NRIP1, CPNE4, and VOPP1, have effect in different fertility traits. AQP1 gene is expressed in ovulatory phase and various stages of pregnancy. TRNAE-CUC gene is associated with AFC and number . of calvings after 4 years of age. Glycogen content-associated gene CPNE4 regulates muscle glycogen and is upregulated during early pregnancy. NRIP1 generegulates ovulation, corpus luteum at pregnancy, and mammary gland development. The objective is to identify potential genomic regions and genetic variants associated with economic traits and to select the most significant SNP which have positive effect on all the traits.

miRNA expression profiles of peripheral white blood cells from beef heifers with varying reproductive potential

Reproductive performance is the most critical factor affecting production efficiency in the cow-calf industry. Heifers with low reproductive efficiency may fail to become pregnant during the breeding season or maintain a pregnancy. The cause of reproductive failure often remains unknown, and the non-pregnant heifers are not identified until several weeks after the breeding season. Therefore, improving heifer fertility utilizing genomic information has become increasingly important. One approach is using microRNAs (miRNA) in the maternal blood that play an important role in regulating the target genes underlying pregnancy success and thereby in selecting reproductively efficient heifers. Therefore, the current study hypothesized that miRNA expression profiles from peripheral white blood cells (PWBC) at weaning could predict the future reproductive outcome of beef heifers. To this end, we measured the miRNA profiles using small RNA-sequencing in Angus-Simmental crossbred heifers sampled at weaning and retrospectively classified as fertile (FH, n = 7) or subfertile (SFH, n = 7). In addition to differentially expressed miRNAs (DEMIs), their target genes were predicted from TargetScan. The PWBC gene expression from the same heifers were retrieved and co-expression networks were constructed between DEMIs and their target genes. We identified 16 differentially expressed miRNAs between the groups (p-value ≤0.05 and absolute (log2 fold change ≥0.05)). Interestingly, based on a strong negative correlation identified from miRNA-gene network analysis with PCIT (partial correlation and information theory), we identified miRNA-target genes in the SFH group. Additionally, TargetScan predictions and differential expression analysis identified bta-miR-1839 with ESR1 , bta-miR-92b with KLF4 and KAT2B, bta-miR-2419-5p with LILRA4, bta-miR-1260b with UBE2E1, SKAP2 and CLEC4D, and bta-let-7a-5p with GATM, MXD1 as miRNA-gene targets. The miRNA-target gene pairs in the FH group are over-represented for MAPK, ErbB, HIF-1, FoxO, p53, mTOR, T-cell receptor, insulin and GnRH signaling pathways, while those in the SFH group include cell cycle, p53 signaling pathway and apoptosis. Some miRNAs, miRNA-target genes and regulated pathways identified in this study have a potential role in fertility; other targets are identified as novel and need to be validated in a bigger cohort that could help to predict the future reproductive outcomes of beef heifers.

Review: Early and late determinants of puberty in ruminants and the role of nutrition

This article reviews the scientific literature on puberty with a focus on ruminants and draws inference, where appropriate, from recent findings in transgenic mouse models and human pathology. Early genetic determinants of puberty have been discovered in humans suffering from hypogonadotropic hypogonadism or central precocious puberty. Transgenic mouse models selected on the basis of the causative defective genes helped in discovering the cellular and molecular mechanisms involved. Most of the genes found are involved in the development of neuroendocrine networks during embryo development and early postnatal life. Notwithstanding that the development of neuroendocrine networks takes place early in puberty, a delay or acceleration in the development of Gonadotropin Releasing Hormone (GnRH) neurons has an impact on puberty onset inducing a delay or an advance, respectively. Among the genes discovered in humans and laboratory models, only a few of them displayed polymorphisms associated with advanced sexual maturity, but also marbling, growth traits and callipygian conformation. This could be related to the fact that rather than puberty onset, most research monitored sexual maturity. Sexual maturity occurs after puberty onset and involves factors regulating the maturation of gonads and in the expression of sexual behaviour. The association with growth and metabolic traits is not surprising since nutrition is the major environmental factor that will act on late genetic determinants of puberty onset. However, a recent hypothesis emerged suggesting that it is the postnatal activation of the GnRH neuronal network that induces the acceleration of growth and weight gain. Hence, nutritional factors need the activation of GnRH neurons first before acting on late genetic determinants. Moreover, nutritional factors can also affect the epigenetic landscape of parental gamete's genome with the consequence of specific methylation of genes involved in GnRH neuron development in the embryo. Season is another important regulator of puberty onset in seasonal small ruminants and appears to involve the same mechanisms that are involved in seasonal transition in adults. The social environment is also an underestimated factor affecting puberty onset in domestic ruminants, most research studies focused on olfactory cues, but the genetic basis has not heretofore been adequately tackled by the scientific community. Additionally, there is some evidence to suggest transgenerational effects exist, in that nutritional and social cues to which parents were exposed, could affect the epigenetic landscape of parental gametes resulting in the epigenetic regulation of early genetic determinants of puberty onset in their offspring.

Genetic parameters for various semen production and quality traits and indicators of male and female reproductive performance in Nellore cattle

BACKGROUND

Given the economic relevance of fertility and reproductive traits for the beef cattle industry, investigating their genetic background and developing effective breeding strategies are paramount. Considering their late and sex-dependent phenotypic expression, genomic information can contribute to speed up the rates of genetic progress per year. In this context, the main objectives of this study were to estimate variance components and genetic parameters, including heritability and genetic correlations, for fertility, female precocity, and semen production and quality (andrological attributes) traits in Nellore cattle incorporating genomic information.

RESULTS

The heritability estimates of semen quality traits were low-to-moderate, while moderate-to-high estimates were observed for semen morphological traits. The heritability of semen defects ranged from low (0.04 for minor semen defects) to moderate (0.30 for total semen defects). For seminal aspect (SMN_ASPC) and bull reproductive fitness (BULL_FIT), low (0.19) and high (0.69) heritabilities were observed, respectively. The heritability estimates for female reproductive traits ranged from 0.16 to 0.39 for rebreeding of precocious females (REBA) and probability of pregnancy at 14 months (PP14), respectively. Semen quality traits were highly genetically correlated among themselves. Moderate-to-high genetic correlations were observed between the ability to remain productive in the herd until four years of age (stayability; STAY) and the other reproductive traits, indicating that selection for female reproductive performance will indirectly contribute to increasing fertility rates. High genetic correlations between BULL_FIT and female reproductive traits related to precocity (REBA and PP14) and STAY were observed. The genetic correlations between semen quality and spermatic morphology with female reproductive traits ranged from -0.22 (REBA and scrotal circumference) to 0.48 (REBA and sperm vigor). In addition, the genetic correlations between REBA with semen quality traits ranged from -0.23 to 0.48, and with the spermatic morphology traits it ranged from -0.22 to 0.19.

CONCLUSIONS

All male and female fertility and reproduction traits evaluated are heritable and can be improved through direct genetic or genomic selection. Selection for better sperm quality will positively influence the fertility and precocity of Nellore females. The findings of this study will serve as background information for designing breeding programs for genetically improving semen production and quality and reproductive performance in Nellore cattle.

Assessing Reproductive Performance to Establish Benchmarks for Small-Holder Beef Cattle Herds in South Africa

Smallholder beef cattle farms in South Africa have had low reproductive performance, which has been associated with management practices. Considering current farm management practices, a multi-stage selection study was conducted to assess reproductive performance as defined by pregnancy rate, fetal and calf losses, calving interval and days open to benchmark reproductive performance. Data were collected twice, in autumn (March−May) for pregnancy diagnosis and in spring (September−November) for monitoring of confirmed pregnancies. Overall, 3694 cow records from 40 smallholder herds were collected during 2018 and 2019 breeding seasons from five provinces. The preferred 25th quartile described target performance and GLIMMIX procedure determined associations between management practices and performance. Smallholder farms on average recorded 50% pregnancy rate and 12% fetal and calf losses with 304 and 608 days open and calving interval, respectively. The derived target benchmarks for pregnancy rate, fetal and calf losses, days open and calving intervals in smallholder farms were 54%, 1.4%, 152 and 425 days, respectively. Reproductive performance was associated with no knowledge of body condition scoring before breeding, culling of old and non-productive cows, record keeping and low bull to cow ratio (p < 0.05). The performance benchmarks implied that industry averages may be improved if sustainable management services are provided through extension and advisory services.

Genetic parameters and genome-wide association for milk production traits and somatic cell score in different lactation stages of Shanghai Holstein population

The aim of this study was to investigate the genetic parameters and genetic architectures of six milk production traits in the Shanghai Holstein population. The data used to estimate the genetic parameters consisted of 1,968,589 test-day records for 305,031 primiparous cows. Among the cows with phenotypes, 3,016 cows were genotyped with Illumina Bovine SNP50K BeadChip, GeneSeek Bovine 50K BeadChip, GeneSeek Bovine LD BeadChip v4, GeneSeek Bovine 150K BeadChip, or low-depth whole-genome sequencing. A genome-wide association study was performed to identify quantitative trait loci and genes associated with milk production traits in the Shanghai Holstein population using genotypes imputed to whole-genome sequences and both fixed and random model circulating probability unification and a mixed linear model with rMVP software. Estimated heritabilities (h2) varied from 0.04 to 0.14 for somatic cell score (SCS), 0.07 to 0.22 for fat percentage (FP), 0.09 to 0.27 for milk yield (MY), 0.06 to 0.23 for fat yield (FY), 0.09 to 0.26 for protein yield (PY), and 0.07 to 0.35 for protein percentage (PP), respectively. Within lactation, genetic correlations for SCS, FP, MY, FY, PY, and PP at different stages of lactation estimated in random regression model were ranged from -0.02 to 0.99, 0.18 to 0.99, 0.04 to 0.99, 0.04 to 0.99, 0.01 to 0.99, and 0.33 to 0.99, respectively. The genetic correlations were highest between adjacent DIM but decreased as DIM got further apart. Candidate genes included those related to production traits (DGAT1, MGST1, PTK2, and SCRIB), disease-related (LY6K, COL22A1, TECPR2, and PLCB1), heat stress–related (ITGA9, NDST4, TECPR2, and HSF1), and reproduction-related (7SK and DOCK2) genes. This study has shown that there are differences in the genetic mechanisms of milk production traits at different stages of lactation. Therefore, it is necessary to conduct research on milk production traits at different stages of lactation as different traits. Our results can also provide a theoretical basis for subsequent molecular breeding, especially for the novel genetic loci.

An Appropriate Genetic Approach for Improving Reproductive Traits in Crossbred Thai-Holstein Cattle under Heat Stress Conditions

Thailand is a tropical country affected by global climate change and has high temperatures and humidity that cause heat stress in livestock. A temperature−humidity index (THI) is required to assess and evaluate heat stress levels in livestock. One of the livestock types in Thailand experiencing heat stress due to extreme climate change is crossbred dairy cattle. Genetic evaluations of heat tolerance in dairy cattle have been carried out for reproductive traits. Heritability values for reproductive traits are generally low (<0.10) because environmental factors heavily influence them. Consequently, genetic improvement for these traits would be slow compared to production traits. Positive and negative genetic correlations were found between reproductive traits and reproductive traits and yield traits. Several selection methods for reproductive traits have been introduced, i.e., the traditional method, marker-assisted selection (MAS), and genomic selection (GS). GS is the most promising technique and provides accurate results with a high genetic gain. Single-step genomic BLUP (ssGBLUP) has higher accuracy than the multi-step equivalent for fertility traits or low-heritability traits.