Review: Genetic mutations affecting bull fertility

Cattle are a well-suited "model organism" to study the genetic underpinnings of variation in male reproductive performance. The adoption of artificial insemination and genomic prediction in many cattle breeds provide access to microarray-derived genotypes and repeated measurements for semen quality and insemination success in several thousand bulls. Similar-sized mapping cohorts with phenotypes for male fertility are not available for most other species precluding powerful association testing. The repeated measurements of the artificial insemination bulls' semen quality enable the differentiation between transient and biologically relevant trait fluctuations, and thus, are an ideal source of phenotypes for variance components estimation and genome-wide association testing. Genome-wide case-control association testing involving bulls with either aberrant sperm quality or low insemination success revealed several causal recessive loss-of-function alleles underpinning monogenic reproductive disorders. These variants are routinely monitored with customised genotyping arrays in the male selection candidates to avoid the use of subfertile or infertile bulls for artificial insemination and natural service. Genome-wide association studies with quantitative measurements of semen quality and insemination success revealed quantitative trait loci for male fertility, but the underlying causal variants remain largely unknown. Moreover, these loci explain only a small part of the heritability of male fertility. Integrating genome-wide association studies with gene expression and other omics data from male reproductive tissues is required for the fine-mapping of candidate causal variants underlying variation in male reproductive performance in cattle.

Genetic polymorphisms within the ETAA1 gene associated with growth traits in Chinese sheep breeds

Ewing tumor-associated antigen 1 (ETAA1) is an important candidate gene for fat deposition in sheep. This study aimed to investigate the indel variations in the ETAA1 gene and their associations with growth traits in the 1619 sheep. The polymorphism information content of this indel ranged from 0.308 to 0.375, with medium genetic diversity (0.25 ≤ polymorphism information content ≤ 0.5). The correlation analysis showed that an 8-bp insertion within the ETAA1 gene was significantly associated with growth traits in Luxi Blackhead sheep (LXBH), Lanzhou fat-tailed sheep, Hu sheep, Tong sheep, and Tan sheep (p < 0.05). Furthermore, the ETAA1 gene was significantly associated with several growth traits (p < 0.01), such as chest width and paunch girth of LXBH, Tong, and Tan rams. It was significantly related to the body morphometric traits of LXBH, Lanzhou fat-tailed sheep, Hu, Tong, and Tan ewes. In conclusion, the detected 8-bp indel within the ETAA1 gene was confirmed in sheep, significantly affecting the growth traits, and might be a potential DNA marker for the selection of high-quality individuals in marker-assisted selection for sheep breeding.

Use of insemination data for joint evaluation of male and female fertility in predominantly seasonal-calving dairy herds

Conception in dairy cattle is influenced by the fertility of the cow and the bull and their interaction. Despite genetic selection for female fertility in many countries, selection for male fertility is largely not practiced. The primary objective of this study was to quantify variation in male and female fertility using insemination data from predominantly seasonal-calving herds. Nonreturn rate (NRR) was derived by coding each insemination as successful (1) or failed (0) based on a minimum of at least 25 d. The NRR was treated as a trait of the bull with semen (male fertility) and the cow that is mated (female fertility). The data (805,463 cows that mated to 5,776 bulls) were used to estimate parameters using either models that only included bulls with mating data or models that fitted the genetic and permanent environmental (PE) effects of bulls and cows simultaneously. We also evaluated whether fitting genetic and PE effects of bulls as one term is better for ranking bulls based on NRR compared with a model that ignored genetic effect. The age of cows that were mated, age of the bulls with semen data, season of mating, breed of cow that mated, inbreeding of cows and bulls, and days from calving to mating date were found to have a significant effect on NRR. Only about 3% of the total variance was explained by the random effects in the model, despite fitting the genetic and PE effects of the bull and cow. The 2 components of fertility (male and fertility) were not correlated. The heritability of male fertility was low (0.001 to 0.008), and that of female fertility was also low (~0.016). The highest heritability estimate for male fertility was obtained from the model that fitted the additive genetic relationship matrix and PE component of the bull as one term. When this model was used to calculate bull solutions, the difference between bulls with at least 100 inseminations was up to 19.2% units (-9.6 to 9.6%). Bull solutions from this model were compared with bull solutions that were predicted fitting bull effects ignoring pedigree. Bull solutions that were obtained considering pedigree had (1) the highest accuracy of prediction when early insemination was used to predict yet-to-be observed insemination data of bulls, and (2) improved model stability (i.e., a higher correlation between bull solutions from 2 randomly split herds) compared with the model which fitted bull with no pedigree. For practical purposes, the model that fitted genetic and PE effect as one term can provide more accurate semen fertility values for bulls than the model without genetic effect. To conclude, insemination data from predominantly seasonal-calving herds can be used to quantify variability between bulls for male fertility, which makes their ranking on NRR feasible. Potentially this information can be used for monitoring bulls and can supplement efforts to improve herd fertility by avoiding or minimizing the use of semen from subfertile bulls.

Of rodents and ruminants: a comparison of small noncoding RNA requirements in mouse and bovine reproduction

Ruminants are major producers of meat and milk, thus managing their reproductive potential is a key element in cost-effective, safe, and efficient food production. Of particular concern, defects in male germ cells and female germ cells may lead to significantly reduced live births relative to fertilization. However, the underlying molecular drivers of these defects are unclear. Small noncoding RNAs, such as piRNAs and miRNAs, are known to be important regulators of germ-cell physiology in mouse (the best-studied mammalian model organism) and emerging evidence suggests that this is also the case in a range of ruminant species, in particular bovine. Similarities exist between mouse and bovids, especially in the case of meiotic and postmeiotic male germ cells. However, fundamental differences in small RNA abundance and metabolism between these species have been observed in the female germ cell, differences that likely have profound impacts on their physiology. Further, parentally derived small noncoding RNAs are known to influence early embryos and significant species-specific differences in germ-cell born small noncoding RNAs have been observed. These findings demonstrate the mouse to be an imperfect model for understanding germ-cell small noncoding RNA biology in ruminants and highlight the need to increase research efforts in this underappreciated aspect of animal reproduction.

Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility

Cattle are ideally suited to investigate the genetics of male reproduction, because semen quality and fertility are recorded for all ejaculates of artificial insemination bulls. We analysed 26,090 ejaculates of 794 Brown Swiss bulls to assess ejaculate volume, sperm concentration, sperm motility, sperm head and tail anomalies and insemination success. The heritability of the six semen traits was between 0 and 0.26. Genome-wide association testing on 607,511 SNPs revealed a QTL on bovine chromosome 6 that was associated with sperm motility (P = 2.5 x 10⁻²⁷), head (P = 2.0 x 10⁻⁴⁴) and tail anomalies (P = 7.2 x 10⁻⁴⁹) and insemination success (P = 9.9 x 10⁻¹³). The QTL harbors a recessive allele that compromises semen quality and male fertility. We replicated the effect of the QTL on fertility (P = 7.1 x 10⁻³²) in an independent cohort of 2481 Brown Swiss bulls. The analysis of whole-genome sequencing data revealed that a synonymous variant (BTA6:58373887C>T, rs474302732) in WDR19 encoding WD repeat-containing protein 19 was in linkage disequilibrium with the fertility-associated haplotype. WD repeat-containing protein 19 is a constituent of the intraflagellar transport complex that is essential for the physiological function of motile cilia and flagella. Bioinformatic and transcription analyses revealed that the BTA6:58373887 T-allele activates a cryptic exonic splice site that eliminates three evolutionarily conserved amino acids from WDR19. Western blot analysis demonstrated that the BTA6:58373887 T-allele decreases protein expression. We make the remarkable observation that, in spite of negative effects on semen quality and bull fertility, the BTA6:58373887 T-allele has a frequency of 24% in the Brown Swiss population. Our findings are the first to uncover a variant that is associated with quantitative variation in semen quality and male fertility in cattle.

In cattle farming, artificial insemination is the most common method of breeding. To ensure high fertilization rates, ejaculate quality and insemination success are closely monitored in artificial insemination bulls. We analyse semen quality, insemination success and microarray-called genotypes at more than 600,000 genome-wide SNP markers of 794 bulls to identify a recessive allele that compromises semen quality. We take advantage of whole-genome sequencing to pinpoint a variant in the coding sequence of WDR19 encoding WD repeat-containing protein 19 that activates a novel exonic splice site. Our results indicate that cryptic splicing in WDR19 is associated with reduced male reproductive performance. This is the first report of a variant that contributes to quantitative variation in bovine semen quality.

Detection of a 4 bp Mutation in the 3'UTR Region of Goat Sox9 Gene and Its Effect on the Growth Traits

Simple Summary

The sex determining region Y (SRY)-type high mobility group (HMG) box 9 (Sox9) gene is critically important in the formation and development of cartilage and is considered the “main regulator” of chondrogenesis. Additionally, a large number of studies have shown that mutations in a single allele of human Sox9 can lead to campomelic dysplasia syndrome. Therefore, the mutations of Sox9 have been the subject of increasing interest among researchers. However, no studies to date have examined the association between Sox9 gene variants and growth traits in goats. Here, we detected a 4 bp indel in the 3′Untranslated Regions (3′UTR) region of Sox9 in Shaanbei white cashmere (SBWC) goats (n = 1109) and studied the association between this indel and growth traits. The 4 bp indel of Sox9 was significantly associated with body length, heart girth, hip width, and all body measurement indexes (p < 0.05) in SBWC goats. Thus, this deletion could be used as an effective molecular marker for maximizing the growth traits of goats in breeding programs.

Abstract

The SRY-type HMG box 9 (Sox9) gene plays an important role in chondrocyte development as well as changes in hypertrophic chondrocytes, indicating that Sox9 can regulate growth in animals. However, no studies to date have examined the correlation between variations in Sox9 and growth traits in goats. Here, we found a 4 bp indel in the 3′UTR of Sox9 and verified its association with growth traits in Shaanbei white cashmere goats (n = 1109). The frequencies of two genotypes (ID and II) were 0.397 and 0.603, respectively, and polymorphic information content (PIC) values showed that the indel had a medium PIC (PIC > 0.25). The 4 bp indel was significantly correlated with body length (p = 0.006), heart girth (p = 0.001), and hip width (p = 4.37 × 10 ⁻⁴). Notably, individuals with the ID genotype had significantly superior phenotypic traits compared with individuals bearing the II genotype. Hence, we speculated that the 4 bp indel is an important mutation affecting growth traits in goat, and may serve as an effective DNA molecular marker for marker-assisted selection in goat breeding programs.

Goat CMTM2: mRNA expression profiles of different alternative spliced variants and associations analyses with growth traits

CKLF like MARVEL transmembrane domain containing 2 (CMTM2) plays crucial roles in spermiogenesis, skeletogenous, growth, and development through PI3K/Akt and other pathways. The purpose of this study was to explore the expression profile and variation of different spliced CMTM2 gene in Shaanbei white cashmere goats, as well as to find the relationships between a CMTM2 promoter region 14 bp genetic variant and growth traits in 1366 Shaanbei white cashmere goats. In this study, we identified alternative CMTM2 splicing and detected the effects of the spliced variants on mRNA expression levels in tissues. Meanwhile, an unreported spliced variant of CMTM2 in goat was identified using in CDS cloning and RT-PCR, namely, CMTM2-AS2. Compared with the normal transcript (CMTM2-AS1), the novel variant had the higher expression level in muscle and liver tissues, indicating that it plays an effective role in growth traits. Furthermore, a 14 bp deletion was detected within CMTM2 promoter region, and the different genotypes were significantly associated with growth traits (e.g., body length, circumference of cannon bone) in the large group of 1366 individuals in Shaanbei white cashmere goats. We found that the body length of the individuals with II (n = 571) genotype had better phenotypes than those with DD (n = 118) and ID (n = 650) genotypes. These results have direct guiding significance for goat breeding in the future and provide a new idea for studying the characteristics and functions of CMTM2 gene in goats.

Selection for bull fertility: a review

Fertility is a critically important factor in cattle production because it directly relates to the ability to produce the offspring necessary to offset costs in production systems. Female fertility has received much attention and has been enhanced through assisted reproductive technologies, as well as genetic selection; however, improving bull fertility has been largely ignored. Improvements in bull reproductive performance are necessary to optimize the efficiency of cattle production. Selection and management to improve bull fertility not only have the potential to increase conception rates but also have the capacity to improve other economically relevant production traits. Bull fertility has reportedly been genetically correlated with traits such as average daily gain, heifer pregnancy, and calving interval. Published studies show that bull fertility traits are low to moderately heritable, indicating that improvements in bull fertility can be realized through selection. Although female fertility has continued to progress according to increasing conception rates, the reported correlation between male and female fertility is low, indicating that male fertility cannot be improved by selection for female fertility. Correlations between several bull fertility traits, such as concentration, number of spermatozoa, motility, and number of spermatozoa abnormalities, vary among studies. Using male fertility traits in selection indices would provide producers with more advanced selection tools. The objective of this review was to discuss current beef bull fertility measurements and to discuss the future of genetic evaluation of beef bull fertility and potential genetic improvement strategies.

One 16 bp insertion/deletion (indel) within the KDM6A gene revealing strong associations with growth traits in goat

Lysine demethylase 6A (KDM6A), as a candidate gene associated with skeletal dysplasia and the differentiation of osteogenesis, might affect the growth traits in animals. In the previous study (Cui et al., 2018), one 16 bp intronic insertion/deletion (NW_017189516.1: g.138, 431_138,446delAATGTATAGCTTAAAA) within the KDM6A gene significantly influenced KDM6A gene expression. The objective of this work was to investigate the association between this 16 bp indel and growth-related traits in Shaanbei White Cashmere goat (SWCG). Association analyses showed the 16 bp indel was related to growth traits strongly (body height, chest depth, height across the hip, body length and chest circumference) in SWCG population (n = 1953, P < 0.05). Insertion/insertion (II) genotype individuals (n = 1502) had the best growth traits, by comparison of those of insertion/deletion (ID) (n = 410) and the deletion/deletion (DD) genotypes (n = 41). Particularly, the body weight of II genotype individuals were significantly higher than ID and DD genotypes (P < 0.01). Besides, the remarkable influence of this indel on traits might cause by the change of MEF2 binding site. These findings hinted that the 16 bp deletion mutation in KDM6A gene, which was significantly associated with growth-related traits, could be assigned to an effective molecular marker for growth traits in goat breeding.

Gene polymorphisms in PROP1 associated with growth traits in sheep

The PROP paired-like homeobox 1 (PROP1) gene encodes a protein that regulates growth and development in mammals. Possessing DNA-binding and transcriptional activation abilities, PROP1 is able to control the expression of crucial anterior pituitary hormones including growth hormone, thyroid-stimulating hormone, and prolactin. The objective of this study was to identify genetic variation in ovine PROP1 in 670 New Zealand Romney sheep. Three single nucleotide polymorphisms (SNPs) were detected, two of which located in intron 1 were novel (c.109+40 T>C and c.109+207C>T), whilst the one located in exon 1 (c.45A>G) had been previously reported. These SNPs were arranged into three haplotypic variants - A₁, B₁ and C₁. At each locus, all three genotypes were observed with frequencies in accordance with the Hardy-Weinberg Equilibrium. Association analysis revealed that the variant GG, CC and CC genotypes for c.45A>G, c.109+40 T>C and c.109+207C>T respectively were significantly associated with higher lamb tailing and weaning weights, and growth rate-to-weaning. The A₁ haplotype had a positive effect on tailing weight, weaning weight and growth rate, while the B₁ haplotype impacted growth traits negatively. These findings suggest that variations in ovine PROP1 could serve as potential genetic markers for use in marker-assisted selection and the breeding for animals with superior growth traits.

A novel indel within goat casein alpha S1 gene is significantly associated with litter size

The ruminant casein gene family (CSNs, link as CSN1S1-CSN2-CSN1S2-CSN3) is characterized by diverse variations and has been extensively studied for ruminant milk traits, however, studies on insertion/deletion (indel) mutations within this gene family and their effects on prolificacy are extremely limited. This study aimed to detect possible novel indels within CSNs in an indigenous Chinese goat breed-Shaanbei White Cashmere goat (SBWC, n = 3047) and four other Chinese goat breeds (n = 1136) with varied litter size rates (105%-283%) and different estrus types (seasonal vs. perennial), as well as exploring the association between these potential indels and litter size. Only one novel 11-bp indel within the CSN1S1 gene was found. The association analyses uncovered that this novel indel was related to the first-birth litter size of SBWC population (n = 2690) (P < 1.0 E-8). Individuals with the II genotype (n = 676) had the best litter size when compared with those ID genotype (n = 1098) and DD genotype (n = 916) individuals. Animals with the II genotype were found to have higher relative expression level of CSN1S1 gene in the ovary (P < 0.01). Besides, Chi-square tests for different litter size and estrous cycle breeds showed that perennial-estrus breeds and multi-kids breeds had higher "I" allelic frequencies and "II" genotypic frequencies. These findings suggest the 11-bp indel within the CSN1S1 gene is significantly associated with reproduction traits and can be an effective molecular marker for litter size of goat breeding.

Review: Genomics of bull fertility

Fertility is one of the most economically important traits in both beef and dairy cattle production; however, only female fertility is typically subjected to selection. Male and female fertility have only a small positive genetic correlation which is likely due to the existence of a relatively small number of genetic variants within each breed that cause embryonic and developmental losses. Genomic tools have been developed that allow the identification of lethal recessive loci based upon marker haplotypes. Selection against haplotypes harbouring lethal alleles in conjunction with selection to improve female fertility will result in an improvement in male fertility. Genomic selection has resulted in a two to fourfold increase in the rate of genetic improvement of most dairy traits in US Holstein cattle, including female fertility. Considering the rapidly increasing rate of adoption of high-throughput single nucleotide polymorphism genotyping in both the US dairy and beef industries, genomic selection should be the most effective of all currently available approaches to improve male fertility. However, male fertility phenotypes are not routinely recorded in natural service mating systems and when artificial insemination is used, semen doses may be titrated to lower post-thaw progressively motile sperm numbers for high-merit and high-demand bulls. Standardization of sperm dosages across bull studs for semen distributed from young bulls would allow the capture of sire conception rate phenotypes for young bulls that could be used to generate predictions of genetic merit for male fertility in both males and females. These data would allow genomic selection to be implemented for male fertility in addition to female fertility within the US dairy industry. While the rate of use of artificial insemination is much lower within the US beef industry, the adoption of sexed semen in the dairy industry has allowed dairy herds to select cows from which heifer replacements are produced and cows that are used to produce terminal crossbred bull calves sired by beef breed bulls. Capture of sire conception rate phenotypes in dairy herds utilizing sexed semen will contribute data enabling genomic selection for male fertility in beef cattle breeds. As the commercial sector of the beef industry increasingly adopts fixed-time artificial insemination, sire conception rate phenotypes can be captured to facilitate the development of estimates of genetic merit for male fertility within US beef breeds.

Whole-genome scan reveals significant non-additive effects for sire conception rate in Holstein cattle

Background

Service sire has a considerable impact on reproductive success in dairy cattle. Most gene mapping studies for bull fertility have focused on additive effects, while non-additive effects have been largely ignored. The main goal of this study was to assess the relevance of non-additive effects on Sire Conception Rate (SCR) in Holstein dairy cattle. The analysis included 7.5 k Holstein bulls with both SCR records and 57.8 k single nucleotide polymorphism (SNP) markers spanning the entire genome.

Results

The importance of non-additive effects was evaluated using an efficient two-step mixed model-based approach. Four genomic regions located on chromosomes BTA8, BTA9, BTA13 and BTA17 showed marked dominance and/or recessive effects. Most of these regions harbor genes, such as ADAM28, DNAJA1, TBC1D20, SPO11, PIWIL3 and TMEM119, that are directly implicated in testis development, male germ line maintenance, and sperm maturation.

Conclusions

This study provides further evidence for the relevance of non-additive effects in fitness-related traits, such as male fertility. In addition, these findings may point out new strategies for improving service sire fertility in dairy cattle via marker-assisted selection.

Genome-wide association study of conformation and milk yield in mixed-breed dairy goats

Identification of genetic markers that affect economically important traits is of high value from a biological point of view, enabling the targeting of candidate genes and providing practical benefits for the industry such as wide-scale genomic selection. This study is one of the first to investigate the genetic background of economically important traits in dairy goats using the caprine 50K single nucleotide polymorphism (SNP) chip. The aim of the project was to perform a genome-wide association study for milk yield and conformation of udder, teat, and feet and legs. A total of 137,235 milk yield records on 4,563 goats each scored for 10 conformation traits were available. Out of these, 2,381 goats were genotyped with the Illumina Caprine 50K BeadChip (Illumina Inc., San Diego, CA). A range of pseudo-phenotypes were used including deregressed breeding values and pseudo-estimated breeding values. Genome-wide association studies were performed using the multi-locus mixed model (MLMM) algorithm implemented in SNP & Variation Suite v7.7.8 (Golden Helix Inc., Bozeman, MT). A genome-wise significant [-log₁₀(P-value) > 5.95] SNP for milk yield was identified on chromosome 19, with additional chromosome-wise significant (-log₁₀(P-value) > 4.46] SNP on chromosomes 4, 8, 14, and 29. Three genome-wise significant SNP for conformation of udder attachment, udder depth, and front legs were identified on chromosome 19, and chromosome-wise SNP were found on chromosomes 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 23, and 27. The proportion of variance explained by the significant SNP was between 0.4 and 7.0% for milk yield and between 0.1 and 13.8% for conformation traits. This study is the first attempt to identify SNP associated with milk yield and conformation in dairy goats. Two genome-wise significant SNP for milk yield and 3 SNP for conformation of udder attachment, udder depth, and front legs were found. Our results suggest that conformation traits have a polygenic background because, for most of them, we did not identify any quantitative trait loci with major effect.

Unravelling the genomic architecture of bull fertility in Holstein cattle

BACKGROUND

Fertility is considered an important economic trait in dairy cattle. Most studies have investigated cow fertility while bull fertility has received much less consideration. The main objective of this study was to perform a comprehensive genomic analysis in order to unravel the genomic architecture underlying sire fertility in Holstein dairy cattle. The analysis included the application of alternative genome-wide association mapping approaches and the subsequent use of diverse gene set enrichment tools.

RESULTS

The association analyses identified at least eight genomic regions strongly associated with bull fertility. Most of these regions harbor genes, such as KAT8, CKB, TDRD9 and IGF1R, with functions related to sperm biology, including sperm development, motility and sperm-egg interaction. Moreover, the gene set analyses revealed many significant functional terms, including fertilization, sperm motility, calcium channel regulation, and SNARE proteins. Most of these terms are directly implicated in sperm physiology and male fertility.

CONCLUSIONS

This study contributes to the identification of genetic variants and biological processes underlying sire fertility. These findings can provide opportunities for improving bull fertility via marker-assisted selection.

A frameshift mutation in ARMC3 is associated with a tail stump sperm defect in Swedish Red (Bos taurus) cattle

BACKGROUND

Artificial insemination is widely used in many cattle breeding programs. Semen samples of breeding bulls are collected and closely examined immediately after collection at artificial insemination centers. Only ejaculates without anomalous findings are retained for artificial insemination. Although morphological aberrations of the spermatozoa are a frequent reason for discarding ejaculates, the genetic determinants underlying poor semen quality are scarcely understood.

RESULTS

A tail stump sperm defect was observed in three bulls of the Swedish Red cattle breed. The spermatozoa of affected bulls were immotile because of severely disorganized tails indicating disturbed spermatogenesis. We genotyped three affected bulls and 18 unaffected male half-sibs at 46,035 SNPs and performed homozygosity mapping to map the fertility disorder to an 8.42 Mb interval on bovine chromosome 13. The analysis of whole-genome re-sequencing data of an affected bull and 300 unaffected animals from eleven cattle breeds other than Swedish Red revealed a 1 bp deletion (Chr13: 24,301,425 bp, ss1815612719) in the eleventh exon of the armadillo repeat containing 3-encoding gene (ARMC3) that was compatible with the supposed recessive mode of inheritance. The deletion is expected to alter the reading frame and to induce premature translation termination (p.A451fs26). The mutated protein is shortened by 401 amino acids (46 %) and lacks domains that are likely essential for normal protein function.

CONCLUSIONS

We report the phenotypic and genetic characterization of a sterilizing tail stump sperm defect in the Swedish Red cattle breed. Exploiting high-density genotypes and massive re-sequencing data enabled us to identify the most likely causal mutation for the fertility disorder in bovine ARMC3. Our results provide the basis for monitoring the mutated variant in the Swedish Red cattle population and for the early identification of infertile animals.

Identification of novel isoforms of dairy goat EEF1D and their mRNA expression characterization

Eukaryotic translation elongation factor 1 delta (EEF1D) gene encodes guanine nucleotide exchange protein eEF1Bδ, which participates in the eukaryotic protein synthesis, and plays important roles in regulating cell cycling and milk production. This study firstly focused on detecting the isoforms of dairy goat EEF1D gene and their mRNA expression characterization. Herein, two novel isoforms, EEF1Da and EEF1Dc, were identified in dairy goat. The entire coding sequences of EEF1Da and EEF1Dc isoforms were 843bp and 267bp in length, respectively. Goat EEF1Da had complete conserved domains of elongation factor 1 (EF1) family, and the evolution of goat EEF1Da isoform was agreed with the evolution of species. Expression pattern analysis of different isoforms revealed relatively ubiquitous expression of EEF1D and EEF1Da. While EEF1Dc only expressed in heart, lung, kidney, adipose and muscle. Combining with the analysis results of cloning, qRT-PCR and bioinformatics, EEF1Da is the major alternative splicing form of EEF1D gene. Interestingly, qRT-PCR result showed that the highest expression of EEF1D was in adipose, which is the major component of mammary. This result was consistent with the early research that EEF1D expressed highly in the mammary, which indicated that EEF1D played a potential key role in regulating adipose development and milk production. All these findings would provide a foundation for the further research of EEF1D gene and development of dairy goat industry.

Genetic tools to improve reproduction traits in dairy cattle

Fertility is a major concern in the dairy cattle industry and has been the subject of numerous studies over the past 20 years. Surprisingly, most of these studies focused on rough female phenotypes and, despite their important role in reproductive success, male- and embryo-related traits have been poorly investigated. In recent years, the rapid and important evolution of technologies in genetic research has led to the development of genomic selection. The generalisation of this method in combination with the achievements of the AI industry have led to the constitution of large databases of genotyping and sequencing data, as well as refined phenotypes and pedigree records. These resources offer unprecedented opportunities in terms of fundamental and applied research. Here we present five such examples with a focus on reproduction-related traits: (1) detection of quantitative trait loci (QTL) for male fertility and semen quality traits; (2) detection of QTL for refined phenotypes associated with female fertility; (3) identification of recessive embryonic lethal mutations by depletion of homozygous haplotypes; (4) identification of recessive embryonic lethal mutations by mining whole-genome sequencing data; and (5) the contribution of high-density single nucleotide polymorphism chips, whole-genome sequencing and imputation to increasing the power of QTL detection methods and to the identification of causal variants.

Short communication: Validation of 4 candidate causative trait variants in 2 cattle breeds using targeted sequence imputation

Most association studies for pinpointing trait-associated variants are performed within breed. The availability of sequence data from key ancestors of several cattle breeds now enables immediate assessment of the frequency of trait-associated variants in populations different from the mapping population and their imputation into large validation populations. The objective of this study was to validate the effects of 4 putatively causative variants on milk production traits, male fertility, and stature in German Fleckvieh and Holstein-Friesian animals using targeted sequence imputation. We used whole-genome sequence data of 456 animals to impute 4 missense mutations in DGAT1, GHR, PRLR, and PROP1 into 10,363 Fleckvieh and 8,812 Holstein animals. The accuracy of the imputed genotypes exceeded 95% for all variants. Association testing with imputed variants revealed consistent antagonistic effects of the DGAT1 p.A232K and GHR p.F279Y variants on milk yield and protein and fat contents, respectively, in both breeds. The allele frequency of both polymorphisms has changed considerably in the past 20 yr, indicating that they were targets of recent selection for milk production traits. The PRLR p.S18N variant was associated with yield traits in Fleckvieh but not in Holstein, suggesting that it may be in linkage disequilibrium with a mutation affecting yield traits rather than being causal. The reported effects of the PROP1 p.H173R variant on milk production, male fertility, and stature could not be confirmed. Our results demonstrate that population-wide imputation of candidate causal variants from sequence data is feasible, enabling their rapid validation in large independent populations.

A nonsense mutation in TMEM95 encoding a nondescript transmembrane protein causes idiopathic male subfertility in cattle

Genetic variants underlying reduced male reproductive performance have been identified in humans and model organisms, most of them compromising semen quality. Occasionally, male fertility is severely compromised although semen analysis remains without any apparent pathological findings (i.e., idiopathic subfertility). Artificial insemination (AI) in most cattle populations requires close examination of all ejaculates before insemination. Although anomalous ejaculates are rejected, insemination success varies considerably among AI bulls. In an attempt to identify genetic causes of such variation, we undertook a genome-wide association study (GWAS). Imputed genotypes of 652,856 SNPs were available for 7962 AI bulls of the Fleckvieh (FV) population. Male reproductive ability (MRA) was assessed based on 15.3 million artificial inseminations. The GWAS uncovered a strong association signal on bovine chromosome 19 (P = 4.08×10⁻⁵⁹). Subsequent autozygosity mapping revealed a common 1386 kb segment of extended homozygosity in 40 bulls with exceptionally poor reproductive performance. Only 1.7% of 35,671 inseminations with semen samples of those bulls were successful. None of the bulls with normal reproductive performance was homozygous, indicating recessive inheritance. Exploiting whole-genome re-sequencing data of 43 animals revealed a candidate causal nonsense mutation (rs378652941, c.483C>A, p.Cys161X) in the transmembrane protein 95 encoding gene TMEM95 which was subsequently validated in 1990 AI bulls. Immunohistochemical investigations evidenced that TMEM95 is located at the surface of spermatozoa of fertile animals whereas it is absent in spermatozoa of subfertile animals. These findings imply that integrity of TMEM95 is required for an undisturbed fertilisation. Our results demonstrate that deficiency of TMEM95 severely compromises male reproductive performance in cattle and reveal for the first time a phenotypic effect associated with genomic variation in TMEM95.

Impaired male fertility is a prevalent condition in many species and is often explained by aberrant semen quality. In some cases, male fertility is severely compromised although semen quality is without any apparent pathological findings (i.e., idiopathic male subfertility). The genetic mechanisms underlying idiopathic male subfertility often remain unexplained. In the present paper, we report a recessively inherited variant of idiopathic male subfertility in a cattle population. We use 650,000 genome-wide SNP markers genotyped in >7900 artificial insemination bulls to pinpoint the underlying genomic region. We take advantage of whole-genome re-sequencing data of 43 animals to identify a causal loss-of-function mutation in TMEM95 encoding a nondescript transmembrane protein. We demonstrate that transmembrane protein 95 is located at the plasma membrane of spermatozoa of fertile animals whereas it is absent in spermatozoa of subfertile animals. Our results indicate that integrity of transmembrane protein 95 is required for an undisturbed fertilisation. This is the first report to reveal a phenotypic effect associated with genomic variation in TMEM95 in any organism.