Omics approaches to understand impact of heat stress on semen quality and fertility in bovines

Recent surge in global climate change poses unprecedented challenges to traditional livestock breeding methods. In tropical countries, where large bovines are vital source of meat and milk, the escalating global warming significantly impact their productivity. Central to this challenge is the resilient ability of the animals, which directly influences the productivity. Artificial insemination (AI) programs, a cornerstone in modern livestock production, have also been severely hampered by climate change-induced heat stress, affecting the quality semen production. This stress not only affects the blood biochemical profiles of the animals but also their testicular physiology, leading to the issues such as low-quality semen with compromised freezability and fertility. Researchers have identified specific markers, including single nucleotide polymorphisms (SNPs), copy number variations (CNV), and epigenetic signatures like histone modifications, DNA methylation, and noncoding RNAs, influencing the semen quality in livestock species. Furthermore, the issue of heat stress has been addressed in a very precise way, and biomarkers have been identified, which can be integrated into the breeding programme to keep up the sire summary. Transcriptomic studies have further illuminated the temporal expression patterns of genes related to sperm quality during heat stress, pinpointing candidate genes for further exploration. This review comprehensively summarizes the progress made in understanding the intricacies of sperm biology in bovines, with a specific focus on cattle and buffalo delving into a spectrum of changes, from biochemical shifts to profound cellular alterations, including genomic, transcriptomic, and epigenetic modifications.

Genome-wide association studies and functional annotation of pre-weaning calf mortality and reproductive traits in Nellore cattle from experimental selection lines

BACKGROUND

Reproductive efficiency is crucial for the long-term economic sustainability of beef cattle production. Pregnancy loss and stillbirth are complex reproductive traits that do not yet have their genomic background fully understood, especially in zebu breeds (Bos taurus indicus). Hence, this study aimed to perform a genome-wide association study (GWAS) and functional annotation for conception success (CS), pregnancy loss (PL), stillbirth (SB), and pre-weaning calf mortality (PWM) in Nellore cattle. In this study, 3,728 cows with 17,094 reproductive records and 11,785 calves were evaluated. A total of 3,351 genotyped animals and 383,739 SNP markers were considered for GWAS analyses. SNP effects were estimated using the weighted single-step GWAS (WssGWAS), which considered two iterations. The top ten genomic windows with the highest contribution to the additive genetic variance of the traits were selected for gene annotation. Candidate genes were then analyzed for Gene Ontology terms (GO) and metabolic pathways.

RESULTS

The top ten genomic windows that explained the largest proportion of the direct additive genetic variance ([Formula: see text]) for CS, PL, SB, and PWM accounted for 17.03% (overlapping with 79 genes), 16.76% (57 genes), 11.71% (73 genes), and 12.03% (65 genes) of the total [Formula: see text], respectively. For CS, significant GO terms included Somitogenesis (GO:0001756), Somite Development (GO:0061053), and Chromosome Segregation (GO:0007059). Considering PL, the processes annotated were the Regulation of Hormone Secretion (GO:0046883), and Hormone Transport (GO:0009914), along with the Glucagon Signaling Pathway (bta04922). Embryonic Development (GO:0045995), and Cerebellum Development (GO:0021549) were the main biological processes found in the gene enrichment analysis for SB. For PWM, the Regulation of Glucose metabolic processes (GO:0010906), Zinc Ion Homeostasis (GO:0055069), Lactation (GO:0007595), and Regulation of Insulin Secretion (GO:0050796) were the most significant GO terms observed.

CONCLUSIONS

These findings provide valuable information on genomic regions, candidate genes, biological processes, and metabolic pathways that may significantly influence the expression of complex reproductive traits in Nellore cattle, offering potential contributions to breeding strategies and future genomic selection strategies.

Identification of candidate SNPs associated with embryo mortality and fertility traits in lactating Holstein cows

Introduction: Targeted single nucleotide polymorphisms (SNPs) have been used in genomic prediction methodologies to enhance the accuracy of associated genetic transmitting abilities in Holstein cows. The objective of this study was to identify and validate SNPs associated with fertility traits impacting early embryo mortality. Methods: The mRNA sequencing data from day 16 normal (n = 9) and embryo mortality (n = 6) conceptuses from lactating multiparous Holstein cows were used to detect SNPs. The selection of specific genes with SNPs as preliminary candidates was based on associations with reproductive and fertility traits. Validation of candidate SNPs and genotype-to-phenotype analyses were conducted in a separate cohort of lactating primiparous Holstein cows (n = 500). After genotyping, candidate SNPs were filtered using a quality control pipeline via PLINK software. Continuous numeric and binary models from reproductive traits were evaluated using the mixed procedure for a generalized linear model-one way ANOVA or logistic regression, respectively. Results: Sixty-nine candidate SNPs were initially identified, but only 23 passed quality control procedures. Ultimately, the study incorporated 466 observations for statistical analysis after excluding animals with missing genotypes or phenotypes. Significant (p <0.05) associations with fertility traits were identified in seven of the 23 SNPs: DSC2 (cows with the A allele were older at first calving); SREBF1 and UBD (cows with the T or G alleles took longer to conceive); DECR1 and FASN (cows with the C allele were less likely to become pregnant at first artificial insemination); SREBF1 and BOLA-DMB (cows with the T allele were less likely to be pregnant at 150 days in milk). It was also determined that two candidate SNPs within the DSC2 gene were tag SNPs. Only DSC2 SNPs had an important allele substitution effect in cows with the G allele, which had a decreased age at first calving by 10 days. Discussion: Candidate SNPs found in this study could be used to develop genetic selection tools to improve fertility traits in dairy production systems.

Genomic insights into key genes and QTLs involved in cattle reproduction

From an economic standpoint, reproductive characteristics are fundamental for sustainable production, particularly for monotocous livestock like cattle. A longer inter-calving interval is indicative of low reproductive capacity. This issue changes the dynamics of current and future lactations since it necessitates more inseminations, veterinary care, and hormone interventions. Various reproductive phenotypes, including ovulation, mating, fertility, pregnancy, embryonic growth, and calving-related traits, are observed in dairy cattle, and these traits have been associated with several QTLs. Calving ease, age at puberty, scrotal circumference, and inseminations per conception have been associated with 4437, 10623, 10498, and 2476 Quantitative Trait Loci (QTLs), respectively. This data offers valuable insights into enhancing and comprehending reproductive traits in livestock breeding. Studying QTLs associated with reproductive traits has far-reaching implications across various fields, from agriculture and animal husbandry to human health, evolutionary biology, and conservation. It provides the foundation for informed breeding practices, advances in biotechnology, and a deeper understanding of the genetic underpinnings of reproduction.

QTLs and Candidate Genes Associated with Semen Traits in Merino Sheep

Ram semen traits play a significant role in conception outcomes, which in turn may influence reproductive efficiency and the overall productivity and profitability of sheep enterprises. Since hundreds of ewes may be inseminated from a single ejaculate, it is important to evaluate semen quality prior to use in sheep breeding programs. Given that semen traits have been found to be heritable, genetic variation likely contributes to the variability observed in these traits. Identifying such genetic variants could provide novel insights into the molecular mechanisms underlying variability in semen traits. Therefore, this study aimed to identify quantitative trait loci (QTLs) associated with semen traits in Merino sheep. A genome-wide association study (GWAS) was undertaken using 4506 semen collection records from 246 Merino rams collected between January 2002 and May 2021. The R package RepeatABEL was used to perform a GWAS for semen volume, gross motility, concentration, and percent post-thaw motility. A total of 35 QTLs, located on 16 Ovis aries autosomes (OARs), were significantly associated with either of the four semen traits in this study. A total of 89, 95, 33, and 73 candidate genes were identified, via modified Bonferroni, within the QTLs significantly associated with volume, gross motility, concentration, and percent post-thaw motility, respectively. Among the candidate genes identified, SORD, SH2B1, and NT5E have been previously described to significantly influence spermatogenesis, spermatozoal motility, and high percent post-thaw motility, respectively. Several candidate genes identified could potentially influence ram semen traits based on existing evidence in the literature. As such, validation of these putative candidates may offer the potential to develop future strategies to improve sheep reproductive efficiency. Furthermore, Merino ram semen traits are lowly heritable (0.071-0.139), and thus may be improved by selective breeding.

Assessing genomic diversity and signatures of selection in Pinan cattle using whole-genome sequencing data

BACKGROUND

Crossbreeding is an important way to improve production beef cattle performance. Pinan cattle is a new hybrid cattle obtained from crossing Piedmontese bulls with Nanyang cows. After more than 30 years of cross-breeding, Pinan cattle show a variety of excellent characteristics, including fast growth, early onset of puberty, and good meat quality. In this study, we analyzed the genetic diversity, population structure, and genomic region under the selection of Pinan cattle based on whole-genome sequencing data of 30 Pinan cattle and 169 published cattle genomic data worldwide.  RESULTS: Estimating ancestry composition analysis showed that the composition proportions for our Pinan cattle were mainly Piedmontese and a small amount of Nanyang cattle. The analyses of nucleotide diversity and linkage disequilibrium decay indicated that the genomic diversity of Pinan cattle was higher than that of European cattle and lower than that of Chinese indigenous cattle. De-correlated composite of multiple selection signals, which combines four different statistics including θπ, CLR, F_ST, and XP-EHH, was computed to detect the signatures of selection in the Pinan cattle genome. A total of 83 genes were identified, affecting many economically important traits. Functional annotation revealed that these selected genes were related to immune (BOLA-DQA2, BOLA-DQB, LSM14A, SEC13, and NAALADL2), growth traits (CYP4A11, RPL26, and MYH10), embryo development (REV3L, NT5E, CDX2, KDM6B, and ADAMTS9), hornless traits (C1H21orf62), and climate adaptation (ANTXR2).

CONCLUSION

In this paper, we elucidated the genomic characteristics, ancestry composition, and selective signals related to important economic traits in Pinan cattle. These results will provide the basis for further genetic improvement of Pinan cattle and reference for other hybrid cattle related studies.

Actions of CSF2 and DKK1 on bovine embryo development and pregnancy outcomes are affected by composition of embryo culture medium

Procedures for in vitro embryo production in cattle have not been optimized. In the current experiment, we utilized a 3 × 3 factorial design to test whether the proportion of embryos becoming blastocysts in culture and the pregnancy rate after embryo transfer are affected by type of serum in the medium [no serum; 3% (v/v) KnockOut Serum Replacement (SR); 3% (v/v) fetal bovine serum (FBS)] and addition of specific embryokines [vehicle; 10 ng/mL colony stimulating factor 2 (CSF2); 100 ng/mL dickkopf related protein 1 (DKK1)] at day 5 of culture. Embryos were produced using abattoir-derived ovaries and Y-sorted semen from two Angus sires. The percent of putative zygotes and cleaved embryos becoming blastocysts was improved by SR and FBS. Pregnancy rate at day 30 was determined for 1426 Nelore recipients and calving rate for 266 recipients. In the absence of CSF2 or DKK1, pregnancy rates were lower for embryos cultured with SR or FBS. CSF2 and DKK1 reduced pregnancy rate for embryos cultured without serum but had no detrimental effect in the SR or FBS groups. Indeed, CSF2 blocked the negative effect of FBS on pregnancy rate. Data on birth weights were available for 67 bull calves. There were no effects of treatment. The sire used to produce embryos had significant and large effects on development to the blastocyst stage, pregnancy rate at day 30, calving rate and pregnancy loss between day 30 and calving. Results indicate that (1) SR and FBS can improve embryonic development in vitro while also compromising competence of embryos to survive after transfer, (2) actions of CSF2 and DKK1 depend upon other characteristics of the embryo production system, and (3) sire can have a large effect on embryonic development before and after transfer.

Exploring the ovine sperm transcriptome by RNAseq techniques. I Effect of seasonal conditions on transcripts abundance

Understanding the cell molecular changes occurring as a results of climatic circumstances is crucial in the current days in which climate change and global warming are one of the most serious challenges that living organisms have to face. Sperm are one of the mammals’ cells most sensitive to heat, therefore evaluating the impact of seasonal changes in terms of its transcriptional activity can contribute to elucidate how these cells cope with heat stress events. We sequenced the total sperm RNA from 64 ejaculates, 28 collected in summer and 36 collected in autumn, from 40 Manchega rams. A highly rich transcriptome (11,896 different transcripts) with 90 protein coding genes that exceed an average number of 5000 counts were found. Comparing transcriptome in the summer and autumn ejaculates, 236 significant differential abundance genes were assessed, most of them (228) downregulated. The main functions that these genes are related to sexual reproduction and negative regulation of protein metabolic processes and kinase activity. Sperm response to heat stress supposes a drastic decrease of the transcriptional activity, and the upregulation of only a few genes related with the basic functions to maintain the organisms’ homeostasis and surviving. Rams’ spermatozoids carry remnant mRNAs which are retrospectively indicators of events occurring along the spermatogenesis process, including abiotic factors such as environmental temperature.

Identification of important genomic footprints using eight different selection signature statistics in domestic cattle breeds

In the present study, the population genomic data of different cattle breeds were explored to decipher the genomic regions affected due to selective events and reflected in the productive, reproductive, thermo-tolerance, and health-related traits. To find out these genomic deviations due to selective sweeps, we used eight different statistical tools (Tajima's D, Fu & Li's D*, CLR, ROH, iHS, F_ST, FLK, and hapFLK) on seven indigenous and five exotic cattle breeds. We further performed composite analysis by comparing their covariance matrix. Several candidate genes were found to be related to milk production (ADARB, WDR70, and CA8), reproductive (PARN, FAM134B2, and ZBTB20), and health-related traits (SP110, CXCL2, CLXCL3, CXCL5, IRF8, and MYOM1). The outcome of this investigation provides a basis for detecting selective sweeps that explain the genetic variation of traits. They may possess functional importance for multiple cattle breeds in different subcontinents. However, further studies are required to improve the findings using high-density arrays or whole-genome sequencing with higher resolution and greater sample sizes.

Genetic and Genomic Analyses of Service Sire Effect on Female Reproductive Traits in Holstein Cattle

Fertility and reproductive performance are key drivers of dairy farm profitability. Hence, reproduction traits have been included in a large majority of worldwide dairy cattle selection indexes. The reproductive traits are lowly heritable but can be improved through direct genetic selection. However, most scientific studies and dairy cattle breeding programs have focused solely on the genetic effects of the dam (GED) on reproductive performance and, therefore, ignored the contribution of the service sire in the phenotypic outcomes. This study aimed to investigate the service sire effects on female reproductive traits in Holstein cattle from a genomic perspective. Genetic parameter estimation and genome-wide association studies (GWAS) were performed for the genetic effect of service sire (GESS) on conception rate (CR), 56-day non-return rate (NRR56), calving ease (CE), stillbirth (SB), and gestation length (GL). Our findings indicate that the additive genetic effects of both sire and dam contribute to the phenotypic variance of reproductive traits measured in females (0.0196 vs. 0.0109, 0.0237 vs. 0.0133, 0.0040 vs. 0.0289, 0.0782 vs. 0.0083, and 0.1024 vs. 0.1020 for GESS and GED heritability estimates for CR, NRR56, CE, SB, and GL, respectively), and these two genetic effects are positively correlated for SB (0.1394) and GL (0.7871). Interestingly, the breeding values for GESS on insemination success traits (CR and NRR56) are unfavorably and significantly correlated with some production, health, and type breeding values (ranging from -0.449 to 0.274), while the GESS values on calving traits (CE, SB, and GL) are usually favorably associated with those traits (ranging from -0.493 to 0.313). One hundred sixty-two significant single-nucleotide polymorphisms (SNPs) and their surrounding protein-coding genes were identified as significantly associated with GESS and GED, respectively. Six genes overlapped between GESS and GED for calving traits and 10 genes overlapped between GESS for success traits and calving traits. Our findings indicate the importance of considering the GESS when genetically evaluating the female reproductive traits in Holstein cattle.

Genome-wide association studies for growth-related traits in a crossbreed pig population

Growth-related traits are important economic traits in the pig industry that directly influence pork production efficiency. To detect quantitative trait loci and candidate genes affecting growth traits, genome-wide association studies were performed for backfat thickness (BF) and loin muscle depth (LMD) in 370 Chuying-black pigs using Illumina PorcineSNP50 BeadChip array. We totally identified 14 BF-associated SNPs, which included 11 genome-wide SNPs (P < 1.39E-06) and 3 chromosome-wide suggestive SNPs (P < 2.79E-05) and for LMD, 9 SNPs surpassed the genome-wide significant threshold (P < 1.39E-06). These SNPs explained 30.33 and 27.51% phenotypic variance for BF and LMD respectively. Furthermore, 14 and 9 genes nearest to the significant SNPs were selected to be candidate genes, including MAGED1, GPHN, CCSER1, and GUCY2D for BF and PARM1, COL18A1, HSF5, and SCML2 genes for LMD. One significant SNP, which explained 6.07% of phenotypic variance for BF, mapped to a pleiotropic quantitative trait locus with a 494-kb interval. Together, the SNPs and candidate genes identified in this study will advance our understanding of the complex genetic architecture of BF and LMD traits, and they will also provide important clues for future implementation of a genomic selection program in Chuying-black pigs.

Genome-wide association studies for sperm traits in Assaf sheep breed

Sperm quality traits routinely collected by artificial insemination (AI) center for rams progeny test are related with the capacity to produce sperm doses for AI and, in more or less grade, with males' fertility. Low-quality ejaculates are unuseful to perform AI sperm doses, which suppose high economic loses for the AI center. Moreover, sperm quality traits have low heritability values which make traditional genetic selection little efficient to its improvement. In this work, a genome-wide association study (GWAS) was conducted by using sperm quality traits data and 50 K Affymetrix custom chip genotypes of 429 rams of Assaf breed from OVIGEN AI centre. Furthermore, 47 of these rams were also genotyped with the Illumina HD Ovine BeadChip, and therefore HD genotypes were imputed for all rams with phenotype data. Previous to the GWAS, a linear regression model was fitted including sperm traits as dependent variables; the flock of origin, date of sperm collection, and jump number as fixed effects; rams age at collection in months as covariate; and ram permanent effect as random. Pseudo-phenotypes obtained from this model were used as input for GWAS. Associations at the chromosome-wise level (FDR 10%) of 76 single-nucleotide polymorphisms (SNPs) in 4 chromosomes for ejaculate concentration (CON), 20 SNPs in 3 chromosomes for ejaculate volume (VOL), 32 SNPs in 1 chromosome for ejaculate number of spermatozoa (SPZ), and 23 SNPs for spermatozoa mass motility (MOT) in 17 chromosomes were found. Only SNPs associated with MOT overcame the genome-wide significance level. Some candidate genes for sperm traits variability were SLC9C1 (OAR1), TSN (OAR2), and FUT10 (OAR26) for MOT;. DOCK2, CPLANE1, SPEF2, and RAI14 (OAR16) for CON; SCAPER and PSMA4 (OAR18) for VOL; and PARM1 and LOC101110593 (OAR6) for SPZ. SNPs associated with sperm traits were not found to be correlated with milk production genetic variation; however, the high frequencies of some SNPs with negative effect over sperm traits found in animals at the top milk yield estimated breeding values (EBVs) ranking would allow to exert some selective presure to improve rams sperm performances. Effects and frequencies of some of the SNPs detected over sperm quality traits make these variants good candidates to be used in marker-assisted selection to improve sperm characteristics of Assaf rams and AI center efficiency to produce sperm doses.

Analysis of single nucleotide polymorphisms related to heifer fertility in Hanwoo (Korean cattle)

Genome-wide association studies (GWAS) have accelerated the identification of functional trait loci in cattle and identified single nucleotide polymorphisms (SNPs) in candidate genes associated with fertility and production traits in high milk yield dairy cattle. The fertility of Hanwoo (Korean native beef cattle) has declined after the adaptation of a selection program for high quantity and quality meat. However, there are few GWAS studies of fertility in beef cattle. We performed a genome-wide association study of 40 Korean native beef cattle heifers with imputed 770 K genotype and identified 12 significant SNPs within seven regions on three chromosomes (BTA 8, BTA 16 and BTA 24) associated with services per conception (SPC). Five SNPs were located in the ABCA1, BRINP3 and ESRRG genes, which are involved in early embryo development. In addition, 27 proximal genes were identified within 1 Mb of the candidate SNPs, which are involved in muscle cell differentiation and muscle structure development. However, we did not find any previously reported SNPs related to fertility in Holstein cows. Taken together, we identified SNPs associated with SPC and their proximal genes using gene-based analysis and the candidates were different from SNPs associated with subfertility of dairy cattle.

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses—calculation of fixation index (F_ST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals—were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp, BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds.

Genome-Wide Association Study and Pathway Analysis for Female Fertility Traits in Iranian Holstein Cattle

Female fertility is an important trait that contributes to cow’s profitability and it can be improved by genomic information. The objective of this study was to detect genomic regions and variants affecting fertility traits in Iranian Holstein cattle. A data set comprised of female fertility records and 3,452,730 pedigree information from Iranian Holstein cattle were used to predict the breeding values, which were then employed to estimate the de-regressed proofs (DRP) of genotyped animals. A total of 878 animals with DRP records and 54k SNP markers were utilized in the genome-wide association study (GWAS). The GWAS was performed using a linear regression model with SNP genotype as a linear covariate. The results showed that an SNP on BTA19, ARS-BFGL-NGS-33473, was the most significant SNP associated with days from calving to first service. In total, [69] significant SNPs were located within 27 candidate genes. Novel potential candidate genes include OSTN, DPP6, EphA5, CADPS2, Rfc1, ADGRB3, Myo3a, C10H14orf93, KIAA1217, RBPJL, SLC18A2, GARNL3, NCALD, ASPH, ASIC2, OR3A1, CHRNB4, CACNA2D2, DLGAP1, GRIN2A and ME3. These genes are involved in different pathways relevant to female fertility and other characteristics in mammals. Gene set enrichment analysis showed that thirteen GO terms had significant overrepresentation of genes statistically associated with female fertility traits. The results of network analysis identified CCNB1 gene as a hub gene in the progesterone-mediated oocyte maturation pathway, significantly associated with age at first calving. The candidate genes identified in this study can be utilized in genomic tests to improve reproductive performance in Holstein cattle.

Prospects for gene introgression or gene editing as a strategy for reduction of the impact of heat stress on production and reproduction in cattle

In cattle, genetic variation exists in regulation of body temperature and stabilization of cellular function during heat stress. There are opportunities to reduce the impact of heat stress on cattle production by identifying the causative mutations responsible for genetic variation in thermotolerance and transferring specific alleles that confer thermotolerance to breeds not adapted to hot climates. An example of a mutation conferring superior ability to regulate body temperature is the group of frame-sift mutations in the prolactin receptor gene (PRLR) that lead to a truncated receptor and development of cattle with a short, sleek hair coat. Slick mutations in PRLR have been found in several extant breeds derived from criollo cattle. The slick mutation in Senepol cattle has been introgressed into dairy cattle in Puerto Rico, Florida and New Zealand. An example of a mutation that confers cellular protection against elevated body temperature is a deletion mutation in the promoter region of a heat shock protein 70 gene called HSPA1L. Inheritance of the mutation results in amplification of the transcriptional response of HSPA1L to heat shock and increased cell survival. The case of PRLR provides a promising example of the efficacy of the genetic approach outlined in this paper. Identification of other mutations conferring thermotolerance at the whole-animal or cellular level will lead to additional opportunities for using genetic solutions to reduce the impact of heat stress.

Whole-genome sequence analysis reveals candidate genomic footprints and genes associated with reproductive traits in Thoroughbred horse

The primary objective of most horse breeding operations was to maximize reproductive efficiency and minimize the cost of producing live foals. Here, we compared individual horses from the Thoroughbred population (n = 17), known as a horse breed with poor reproductive performance, with other six horse populations (n = 28), to detect genomic signatures of positive selection underlying of reproductive traits. A number of protein-coding genes with significant (p-value <.01) higher F_ST values (616 genes) and a lower value for nucleotide diversity (π) (310 genes) were identified. The results of our study revealed some candidate genes such as IGFBP2, IGFBP5, GDF9, BRINP3 and GRID1 are possibly associated with functions influencing reproductive traits. These genes may have been under selection due to their essential roles in reproduction performance in horses. The candidate selected genes identified in this work should be of great interest for future research into genetic architecture of traits relevant to horse breeding programmes.

Proteomics Recapitulates Ovarian Proteins Relevant to Puberty and Fertility in Brahman Heifers (Bos indicus L.)

High fertility and early puberty in Bos indicus heifers are desirable and genetically correlated traits in beef production. The hypothalamus-pituitary-ovarian (HPO) axis synthesizes steroid hormones, which contribute to the shift from the pre-pubertal state into the post-pubertal state and influence subsequent fertility. Understanding variations in abundance of proteins that govern steroid synthesis and ovarian signaling pathways remains crucial to understanding puberty and fertility. We used whole ovaries of six pre-pubertal and six post-pubertal Brahman heifers to conduct differential abundance analyses of protein profiles between the two physiological states. Extracted proteins were digested into peptides followed by identification and quantification with massspectrometry (MS) by sequential window acquisition of all instances of theoretical fragment ion mass spectrometry (SWATH-MS). MS and statistical analysis identified 566 significantly differentially abundant (DA) proteins (adjusted p < 0.05), which were then analyzed for gene ontology and pathway enrichment. Our data indicated an up-regulation of steroidogenic proteins contributing to progesterone synthesis at luteal phase post-puberty. Proteins related to progesterone signaling, TGF-β, retinoic acid, extracellular matrix, cytoskeleton, and pleiotrophin signaling were DA in this study. The DA proteins probably relate to the formation and function of the corpus luteum, which is only present after ovulation, post-puberty. Some DA proteins might also be related to granulosa cells signaling, which regulates oocyte maturation or arrest in ovaries prior to ovulation. Ten DA proteins were coded by genes previously associated with reproductive traits according to the animal quantitative trait loci (QTL) database. In conclusion, the DA proteins and their pathways were related to ovarian activity in Bos indicus cattle. The genes that code for these proteins may explain some known QTLs and could be targeted in future genetic studies.

Influences of sire conception rate on pregnancy establishment in dairy cattle

Establishment of pregnancy in cattle is complex and encompasses ovulation, fertilization, blastocyst formation and growth into an elongated conceptus, pregnancy recognition signaling, and development of the embryo and placenta. The objective here was to investigate sire influences on pregnancy establishment in cattle. First, 10 Holstein bulls were classified as high or low fertility based on their sire conception rate (SCR) value. In a field trial, pregnancy at first timed insemination was not different between high and low SCR bulls. Next, 5 of the 10 sires were phenotyped using in vitro and in vivo embryo production. There was no effect of SCR classification on in vitro embryo cleavage rate, but low SCR sires produced fewer day 8 blastocysts. In superovulated heifers, high SCR bulls produced a lower percentage of unfertilized oocytes and fewer degenerated embryos compared to low SCR bulls. Recipient heifers received three to five in vivo produced embryos from either high or low SCR sires on day 7 postestrus. Day 16 conceptus recovery and length were not different between SCR groups, and the conceptus transcriptome was not appreciably different between high and low SCR sires. The reduced ability of embryos from low SCR bulls to establish pregnancy is multifactorial and encompasses sperm fertilizing ability, preimplantation embryonic development, and development of the embryo and placenta after conceptus elongation and pregnancy recognition. These studies highlight the importance of understanding genetic contributions of the sire to pregnancy establishment that is crucial to increase reproductive efficiency in dairy cattle.

Sex affects immunolabeling for histone 3 K27me3 in the trophectoderm of the bovine blastocyst but not labeling for histone 3 K18ac

The mammalian embryo displays sexual dimorphism in the preimplantation period. Moreover, competence of the embryo to develop is dependent on the sire from which the embryo is derived and can be modified by embryokines produced by the endometrium such as colony stimulating factor 2 (CSF2). The preimplantation period is characterized by large changes in epigenetic modifications of DNA and histones. It is possible, therefore, that effects of sex, sire, and embryo regulatory molecules are mediated by changes in epigenetic modifications. Here it was tested whether global levels of two histone modifications in the trophectoderm of the bovine blastocyst were affected by sex, sire, and CSF2. It was found that amounts of immunolabeled H3K27me3 were greater (P = 0.030) for male embryos than female embryos. Additionally, labeling for H3K27me3 and H3K18ac depended upon the bull from which embryos were derived. Although CSF2 reduced the proportion of embryos developing to the blastocyst, there was no effect of CSF2 on labeling for H3K27me3 or H3K18ac. Results indicate that the blastocyst trophoctoderm can be modified epigenetically by embryo sex and paternal inheritance through alterations in histone epigenetic marks.

Importance of prostate androgen-regulated mucin-like protein 1 in development of the bovine blastocyst

Background

Prostate androgen-regulated mucin-like protein 1 (PARM1) is a pro-proliferative and anti-apoptotic glycoprotein involved in the endoplasmic reticulum (ER) stress response. A single nucleotide polymorphism in the coding region of PARM1 has been associated with competence of bovine embryos to develop to the blastocyst stage. Here we tested the importance of PARM1 for development by evaluating consequences of reducing PARM1 mRNA abundance on embryonic development and differentiation, gene expression and resistance to ER stress.

Results

Knockdown of PARM1 using an anti-PARM1 GapmeR did not affect competence of embryos to develop into blastocysts but decreased the number of trophectoderm (TE) cells in the blastocyst and tended to increase the number of cells in the blastocyst inner cell mass (ICM). Treatment of embryos with anti-PARM1 GapmeR affected expression of 4 and 3 of 90 genes evaluated at the compact-morula and blastocyst stage of development at days 5.5 and 7.5 after fertilization, respectively. In morulae, treatment increased expression of DAB2, INADL, and STAT3 and decreased expression of CCR2. At the blastocyst stage, knockdown of PARM1 increased expression of PECAM and TEAD4 and decreased expression of CCR7. The potential role of PARM1 in ER stress response was determined by evaluating effects of knockdown of PARM1 on development of embryos after exposure to heat shock or tunicamycin and on expression of ATF6, DDIT3 and EIF2AK3 at the compact morula and blastocyst stages. Both heat shock and tunicamycin reduced the percent of embryos becoming a blastocyst but response was unaffected by PARM1 knockdown. Similarly, there was no effect of knockdown on steady-state amounts of ATF6, DDIT3 or EIF2AK3.

Conclusion

PARM1 participates in formation of TE and ICM cells in early embryonic development but there is no evidence for the role of PARM1 in the ER stress response.

Electronic supplementary material

The online version of this article (10.1186/s12861-019-0195-7) contains supplementary material, which is available to authorized users.

Interactions of human chorionic gonadotropin with genotype and parity on fertility responses of lactating dairy cows

Fertility-promoting effects of treatment of lactating dairy cattle with human chorionic gonadotropin (hCG) after artificial insemination (AI) have been variable. Here, we tested whether fertility response to hCG in lactating Holstein cows interacts with genotype and parity. Primiparous (n = 538) and multiparous (n = 613) cows were treated with hCG (3,300 IU) or vehicle 5 d after AI. Pregnancy was diagnosed on d 32 and 60 after AI. A subset of cows (n = 593-701) was genotyped for 4 single nucleotide polymorphisms (SNP) previously associated with fertility. Treatment with hCG increased progesterone concentration on d 12 after AI regardless of genotype or parity. Pregnancy per AI was improved by hCG in primiparous cows but not in multiparous cows. Moreover, hCG treatment interacted with a SNP in coenzyme Q9 (COQ9) to affect fertility. Fertility of cows treated with vehicle was greatest for the AA allele, whereas fertility was lowest for the same genotype among cows treated with hCG. Pregnancy per AI was also affected by genotype for heat shock protein A1-like (HSPA1L) and progesterone receptor (PGR), but no interactions were observed with treatment. Genotype for a SNP in prostate androgen-regulated mucin-like protein 1 (PARM1) was not associated with fertility. Overall, results show that variation in response to hCG treatment on fertility depends on parity and interacts with a SNP in COQ9.

Functional haplotypes of ARID4A affect promoter activity and semen quality of bulls

The AT-rich interaction domain 4 A (ARID4A) has an important role in regulating Sertoli cell function and male fertility. Its molecular mechanisms, however, remain largely unknown. In this study, two single nucleotide polymorphisms (SNPs) (g.53 G > T, ss 1966531596, and g.826 G > A, rs 210809648) were identified in the promoter region of ARID4A in 215 Chinese Holstein bulls using polymerase chain reaction (PCR)-restriction fragment length polymorphism and created restriction site-PCR. Results revealed that bulls with g.53 G > T-GG and g.826 G > A-G G genotype exhibited higher sperm deformity rate than those with g.53 G > T-TT and g.826 G > A-AA genotype (P <  0.01). Furthermore, three haplotypes (H1 (GG), H3 (TG), H4 (TA)) and six haplotype combinations (H1H1, H1H3, H1H4, H3H3, H3H4, H4H4) were obtained. The bulls with H4H4 exhibited lower sperm deformity rate than those with H1H1 and H1H3 (P <  0.05). In addition, results of bioinformatics analysis revealed that ARID4A has two promoters and that two SNPs of ARID4A are located in transcription factor binding sites. Compared with g.53 G > T-G and g.826 G > A-G allele, there was a greater fluorescence intensity in g.53 G > T-T and g.826 G > A-A allele by transient transfection in MLTC-1 cells and the luciferase report assay. qRT-PCR indicated the ARID4A expression was greater in bull spermatozoa with H4H4 haplotype combination than those with H1H1 haplotype combination (P < 0.05). Results of the present study indicate that g.53 G > T and g.826 G > A are functional mutations that are involved in regulation of ARID4A gene expression by affecting promoter activity and thus semen quality of Chinese Holstein bulls.

Comparative expression profile of microRNAs and piRNAs in three ruminant species testes using next-generation sequencing

microRNA (miRNA) and piwi-interacting RNA (piRNA) are two classes small non-coding regulatory RNAs that play crucial roles in multiple biological processes such as spermatogenesis. However, there are no published studies on conjoint analysis of miRNA and piRNA profiles among cattle, yak and their interspecies (the dzo) using sequencing technology. Next-generation sequencing technology was used to profile miRNAs and piRNAs among those three ruminants to elucidate their functions. A total of 119, 14 and six differentially expressed miRNAs were obtained in cattle vs. dzo, cattle vs. yak and yak vs. dzo comparison groups, while there were 873, 1,065 and 1,158 differentially expressed piRNAs in those three comparison groups. The expression of three miRNAs was validated in the three ruminants, and the results suggested that the miRNA expression profiles data could represent actual miRNA expression levels. Moreover, the putative targets of differentially expressed miRNAs were predicted by their own genome, it is worth to note that both the cattle and yak genome were used for dzo, then the targets were subjected to GO enrichment and KEGG pathway analysis, revealing the likely roles for these differentially expressed miRNAs in spermatogenesis. In conclusion, this study provided a useful resource for further elucidation of the miRNAs and piRNAs regulatory roles in spermatogenesis. It may also facilitate the development of therapeutic strategies for dzo reproduction research.

Review: Sperm-oocyte interactions and their implications for bull fertility, with emphasis on the ubiquitin-proteasome system

Fertilization is an intricate cascade of events that irreversibly alter the participating male and female gamete and ultimately lead to the union of paternal and maternal genomes in the zygote. Fertilization starts with sperm capacitation within the oviductal sperm reservoir, followed by gamete recognition, sperm-zona pellucida interactions and sperm-oolemma adhesion and fusion, followed by sperm incorporation, oocyte activation, pronuclear development and embryo cleavage. At fertilization, bull spermatozoon loses its acrosome and plasma membrane components and contributes chromosomes, centriole, perinuclear theca proteins and regulatory RNAs to the zygote. While also incorporated in oocyte cytoplasm, structures of the sperm tail, including mitochondrial sheath, axoneme, fibrous sheath and outer dense fibers are degraded and recycled. The ability of some of these sperm contributed components to give rise to functional zygotic structures and properly induce embryonic development may vary between bulls, bearing on their reproductive performance, and on the fitness, health, fertility and production traits of their offspring. Proper functioning, recycling and remodeling of gamete structures at fertilization is aided by the ubiquitin-proteasome system (UPS), the universal substrate-specific protein recycling pathway present in bovine and other mammalian oocytes and spermatozoa. This review is focused on the aspects of UPS relevant to bovine fertilization and bull fertility.

Characteristics of candidate genes associated with embryonic development in the cow: Evidence for a role for WBP1 in development to the blastocyst stage

The goal was to gain understanding of how 12 genes containing SNP previously related to embryo competence to become a blastocyst (BRINP3, C1QB, HSPA1L, IRF9, MON1B, PARM1, PCCB, PMM2, SLC18A2, TBC1D24, TTLL3 and WBP1) participate in embryonic development. Gene expression was evaluated in matured oocytes and embryos. BRINP3 and C1QB were not detected at any stage. For most other genes, transcript abundance declined as the embryo developed to the blastocyst stage. Exceptions were for PARM1 and WBP1, where steady-state mRNA increased at the 9-16 cell stage. The SNP in WBP1 caused large differences in the predicted three-dimensional structure of the protein while the SNP in PARM1 caused smaller changes. The mutation in WBP1 causes an amino acid substitution located close to a P-P-X-Y motif involved in protein-protein interactions. Moreover, the observation that the reference allele varies between mammalian species indicates that the locus has not been conserved during mammalian evolution. Knockdown of mRNA for WBP1 decreased the percent of putative zygotes becoming blastocysts and reduced the number of trophectoderm cells and immunoreactive CDX2 in the resulting blastocysts. WBP1 is an important gene for embryonic development in the cow. Further research to identify how the SNP in WBP1 affects processes leading to differentiation of the embryo into TE and ICM lineages is warranted.

Association of single nucleotide polymorphisms in candidate genes previously related to genetic variation in fertility with phenotypic measurements of reproductive function in Holstein cows

Many genetic markers related to health or production traits are not evaluated in populations independent of the discovery population or related to phenotype. Here we evaluated 68 single nucleotide polymorphisms (SNP) in candidate genes previously associated with genetic merit for fertility and production traits for association with phenotypic measurements of fertility in a population of Holstein cows that was selected based on predicted transmitting ability (PTA) for daughter pregnancy rate (DPR; high, ≥1, n = 989; low, ≤ -1.0, n = 1,285). Cows with a high PTA for DPR had higher pregnancy rate at first service, fewer services per conception, and fewer days open than cows with a low PTA for DPR. Of the 68 SNP, 11 were associated with pregnancy rate at first service, 16 with services per conception, and 19 with days open. Single nucleotide polymorphisms in 12 genes (BDH2, BSP3, CAST, CD2, CD14, FUT1, FYB, GCNT3, HSD17B7, IBSP, OCLN, and PCCB) had significant associations with 2 fertility traits, and SNP in 4 genes (CSPP1, FCER1G, PMM2, and TBC1D24) had significant associations with each of the 3 traits. Results from this experiment were compared with results from 2 earlier studies in which the SNP were associated with genetic estimates of fertility. One study involved the same animals as used here, and the other study was of an independent population of bulls. A total of 13 SNP associated with 1 or more phenotypic estimates of fertility were directionally associated with genetic estimates of fertility in the same cow population. Moreover, 14 SNP associated with reproductive phenotype were directionally associated with genetic estimates of fertility in the bull population. Nine SNP (located in BCAS, BSP3, CAST, FUT1, HSD17B7, OCLN, PCCB, PMM2, and TBC1D24) had a directional association with fertility in all 3 studies. Examination of the function of the genes with SNP associated with reproduction in more than one study indicates the importance of steroid hormones and immune function as determinants of reproductive function. All but 1 of the 68 evaluated SNP were variable in 11 breeds besides Holstein, indicating the potential effects of these SNP on reproductive function across breeds of cattle.

Functional SNPs of INCENP Affect Semen Quality by Alternative Splicing Mode and Binding Affinity with the Target Bta-miR-378 in Chinese Holstein Bulls

Inner centromere protein (INCENP) plays an important role in mitosis and meiosis as the main member of chromosomal passenger protein complex (CPC). To investigate the functional markers of the INCENP gene associated with semen quality, the single nucleotide polymorphisms (SNPs) g.19970 A>G and g.34078 T>G were identified and analyzed. The new splice variant INCENP-TV is characterized by the deletion of exon 12. The g.19970 A>G in the exonic splicing enhancer (ESE) motif region results in an aberrant splice variant by constructing two minigene expression vectors using the pSPL3 exon capturing vector and transfecting vectors into MLTC-1 cells. INCENP-TV was more highly expressed than INCENP-reference in adult bull testes. The g.34078 T>G located in the binding region of bta-miR-378 could affect the expression of INCENP, which was verified by luciferase assay. To analyze comprehensively the correlation of SNPs with sperm quality, haplotype combinations constructed by g.19970 A>G and g.34078 T>G, as well as g.-692 C>T and g.-556 G>T reported in our previous studies, were analyzed. The bulls with H1H12 and H2H2 exhibited a higher ejaculate volume than those with H2H10 and H9H12, respectively (P < 0.05). Bulls with H11H11 and H2H10 exhibited higher initial sperm motility than those with H2H2 (P < 0.05). The expression levels of INCENP in bulls with H1H12 and H11H11 were significantly higher than those in bulls with H9H12 (P < 0.05), as determined by qRT-PCR. Findings suggest that g.19970 A>G and g.34078 T>G in INCENP both of which appear to change the molecular and biological characteristics of the mRNA transcribed from the locus may serve as a biomarkers of male bovine fertility by affecting alternative splicing mode and binding affinity with the target bta-miR-378.

Modification of embryonic resistance to heat shock in cattle by melatonin and genetic variation in HSPA1L

The objectives were to test whether (1) melatonin blocks inhibition of embryonic development caused by heat shock at the zygote stage, and (2) the frequency of a thermoprotective allele for HSPA1L is increased in blastocysts formed from heat-shocked zygotes as compared with blastocysts from control zygotes. It was hypothesized that melatonin prevents effects of heat shock on development by reducing accumulation of reactive oxygen species (ROS) and that embryos inheriting the thermoprotective allele of HSPA1L would be more likely to survive heat shock. Effects of 1 µM melatonin on ROS were determined in experiments 1 and 2. Zygotes were cultured at 38.5 or 40°C for 3 h in the presence of CellROX reagent (ThermoFisher Scientific, Waltham, MA). Culture was in a low [5% (vol/vol)] oxygen (experiment 1) or low or high [21% (vol/vol)] oxygen environment (experiment 2). Heat shock and high oxygen increased ROS; melatonin decreased ROS. Development was assessed in experiments 3 and 4. In experiment 3, zygotes were cultured in low oxygen ± 1 µM melatonin and exposed to 38.5 or 40°C for 12 h (experiment 1) beginning 8 h after fertilization. Melatonin did not protect the embryo from heat shock. Experiment 4 was performed similarly except that temperature treatments (38.5 or 40°C, 24 h) were performed in a low or high oxygen environment (2×2 × 2 factorial design with temperature, melatonin, and oxygen concentration as main effects), and blastocysts were genotyped for a deletion (D) mutation (C→D) in the promoter region of HSPA1L associated with thermotolerance. Heat shock decreased percent of zygotes developing to the blastocyst stage independent of melatonin or oxygen concentration. Frequency of genotypes for HSPA1L was affected by oxygen concentration and temperature, with an increase in the D allele for blastocysts that developed in high oxygen and following heat shock. It was concluded that (1) lack of effect of melatonin or oxygen concentration on embryonic development means that the negative effects of heat shock on the zygote are not mediated by ROS, (2) previously reported effect of melatonin on fertility of heat-stressed cows might involve actions independent of the antioxidant properties of melatonin, and (3) the deletion mutation in the promoter of HSPA1L confers protection to the zygote from heat shock and high oxygen. Perhaps, embryonic survival during heat stress could be improved by selecting for thermotolerant genotypes.

Single nucleotide polymorphisms associated with thermoregulation in lactating dairy cows exposed to heat stress

Dairy cows with increased rectal temperature experience lower milk yield and fertility. Rectal temperature during heat stress is heritable, so genetic selection for body temperature regulation could reduce effects of heat stress on production. One aim of the study was to validate the relationship between genotype and heat tolerance for single nucleotide polymorphisms (SNPs) previously associated with resistance to heat stress. A second aim was to identify new SNPs associated with heat stress resistance. Thermotolerance was assessed in lactating Holsteins during the summer by measuring rectal temperature (a direct measurement of body temperature regulation; n = 435), respiration rate (an indirect measurement of body temperature regulation, n = 450) and sweating rate (the major evaporative cooling mechanism in cattle, n = 455). The association between genotype and thermotolerance was evaluated for 19 SNPs previously associated with rectal temperature from a genomewide analysis study (GWAS), four SNPs previously associated with change in milk yield during heat stress from GWAS, 2 candidate gene SNPs previously associated with rectal temperature and respiration rate during heat stress (ATPA1A and HSP70A) and 66 SNPs in genes previously shown to be associated with reproduction, production or health traits in Holsteins. For SNPs previously associated with heat tolerance, regions of BTA4, BTA6 and BTA24 were associated with rectal temperature; regions of BTA6 and BTA24 were associated with respiration rate; and regions of BTA5, BTA26 and BTA29 were associated with sweating rate. New SNPs were identified for rectal temperature (n = 12), respiration rate (n = 8) and sweating rate (n = 3) from among those previously associated with production, reproduction or health traits. The SNP that explained the most variation were PGR and ASL for rectal temperature, ACAT2 and HSD17B7 for respiration rate, and ARL6IP1 and SERPINE2 for sweating rate. ARL6IP1 was associated with all three thermotolerance traits. In conclusion, specific genetic markers responsible for genetic variation in thermoregulation during heat stress in Holsteins were identified. These markers may prove useful in genetic selection for heat tolerance in Holstein cattle.

Reproductive technologies and genomic selection in dairy cattle

Genomic tools are now available for most livestock species and are used routinely for genomic selection (GS) in cattle. One of the most important developments resulting from the introduction of genomic testing for dairy cattle is the application of reasonably priced low-density single nucleotide polymorphism technology in the selection of females. In this context, combining genome testing and reproductive biotechnologies in young heifers enables new strategies to generate replacement and elite females in a given period of time. Moreover, multiple markers have been detected in biopsies of preimplantation stage embryos, thus paving the way to develop new strategies based on preimplantation diagnosis and the genetic screening of embryos. Based on recent advances in GS, the present review focuses on new possibilities inherent in reproductive technologies used for commercial purposes and in genetic schemes, possible side effects and beneficial impacts on reproductive efficiency. A particular focus is on the different steps allowing embryo genotyping, including embryo micromanipulation, DNA production and quality assessment.

Association between an alternative promoter polymorphism and sperm deformity rate is due to modulation of the expression of KATNAL1 transcripts in Chinese Holstein bulls

Katanin p60 subunit A-like 1 (KATNAL1) is an ATPase that regulates Sertoli cell microtubule dynamics and sperm retention. We evaluated one novel splice variant and characterized the promoter and a functional single nucleotide polymorphism (SNP) of the bovine KATNAL1 gene to explore its expression pattern, possible regulatory mechanism and relationship with semen traits in Chinese Holstein bulls. A novel splice variant, KATNAL1 transcript variant 2 (KATNAL1-TV2) of the retained 68 bp in intron 2, was identified by RT-PCR and compared with KATNAL1 transcript variant 1 (KATNAL1-TV1, NM 001192918.1) in various tissues. Bioinformatics analyses predicted that KATNAL1 transcription was regulated by two promoters: P1 in KATNAL1-TV1 and P2 in KATNAL1-TV2. Results of qRT-PCR revealed that KATNAL1-TV1 had higher expression than did KATNAL1-TV2 in testes of adult bulls (P < 0.05). Promoter luciferase activity analysis suggested that the core sequences of P1 and P2 were mapped to the region of c.-575˜c.-180 and c.163-40˜c.333+59 respectively. One novel SNP (c.163-210T>C, ss836312085) located in intron 1 was found using sequence alignment. The SNP in P2 resulted in the presence of the DeltaE binding site, improving its basal promoter activity (P < 0.05); and we observed a greater sperm deformity rate in bulls with the genotype CC than in those with the genotype TT (P < 0.05), which indicated that different genotypes were associated with the bovine semen traits. Bioinformatics analysis of the KATNAL1 protein sequence predicted that the loss of the MIT domain in the KATNAL1-TV2 transcript resulted in protein dysfunction. These findings help us to understand that a functional SNP in P2 and subsequent triggering of expression diversity of KATNAL1 transcripts are likely to play an important role with regard to semen traits in bull breeding programs.