Goat sperm associated antigen 17 protein gene (SPAG17): Small and large fragment genetic variation detection, association analysis, and mRNA expression in gonads

Novel homozygous SPAG17 variants cause human male infertility through multiple morphological abnormalities of spermatozoal flagella related to axonemal microtubule doublets

ABSTRACT

Male infertility can result from impaired sperm motility caused by multiple morphological abnormalities of the flagella (MMAF). Distinct projections encircling the central microtubules of the spermatozoal axoneme play pivotal roles in flagellar bending and spermatozoal movement. Mammalian sperm-associated antigen 17 ( SPAG17 ) encodes a conserved axonemal protein of cilia and flagella, forming part of the C1a projection of the central apparatus, with functions related to ciliary/flagellar motility, skeletal growth, and male fertility. This study investigated two novel homozygous SPAG17 mutations (M1: NM_206996.2, c.829+1G>T, p.Asp212_Glu276del; and M2: c.2120del, p.Leu707*) identified in four infertile patients from two consanguineous Pakistani families. These patients displayed the MMAF phenotype confirmed by Papanicolaou staining and scanning electron microscopy assays of spermatozoa. Quantitative real-time polymerase chain reaction (PCR) of patients' spermatozoa also revealed a significant decrease in SPAG17 mRNA expression, and immunofluorescence staining showed the absence of SPAG17 protein signals along the flagella. However, no apparent ciliary-related symptoms or skeletal malformations were observed in the chest X-rays of any of the patients. Transmission electron microscopy of axoneme cross-sections from the patients showed incomplete C1a projection and a higher frequency of missing microtubule doublets 1 and 9 compared with those from fertile controls. Immunofluorescence staining and Western blot analyses of spermatogenesis-associated protein 17 (SPATA17), a component of the C1a projection, and sperm-associated antigen 6 (SPAG6), a marker of the spring layer, revealed disrupted expression of both proteins in the patients' spermatozoa. Altogether, these findings demonstrated that SPAG17 maintains the integrity of spermatozoal flagellar axoneme, expanding the phenotypic spectrum of SPAG17 mutations in humans.

Potential Candidate Genes Associated with Litter Size in Goats: A Review

This review examines genetic markers associated with litter size in goats, a key reproductive trait impacting productivity in small ruminant farming. Goats play a vital socioeconomic role in both low- and high-income regions; however, their productivity remains limited due to low reproductive efficiency. Litter size, influenced by multiple genes and environmental factors, directly affects farm profitability and sustainability by increasing the output per breeding cycle. Recent advancements in genetic research have identified key genes and pathways associated with reproductive traits, including gonadotropin-releasing hormone (GnRH), inhibin (INHAA), Kit ligand (KITLG), protein phosphatase 3 catalytic subunit alpha (PPP3CA), prolactin receptor (PRLR), POU domain class 1 transcription factor 1 (POU1F1), anti-Müllerian hormone (AMH), bone morphogenetic proteins (BMP), growth differentiation factor 9 (GDF9), and KISS1 and suppressor of mothers against decapentaplegic (SMAD) family genes, among others. These genes regulate crucial physiological processes such as folliculogenesis, hormone synthesis, and ovulation. Genome-wide association studies (GWASs) and transcriptomic analyses have pinpointed specific genes linked to increased litter size, highlighting their potential in selective breeding programs. By incorporating genomic data, breeding strategies can achieve higher selection accuracy, accelerate genetic gains, and improve reproductive efficiency. This review emphasizes the importance of genetic markers in optimizing litter size and promoting sustainable productivity in goat farming.

Analysis of goat PPP6C mRNA profile, detection of genetic variations, and their associations with litter size

The Protein Phosphatase 6 Catalytic Subunit (PPP6C) is evolutionarily a conserved gene in eukaryotes known to play a significant role in mammalian reproduction. This study aimed to investigate expression patterns of PPP6C and explore its association with litter size in Shaanbei white cashmere (SBWC) goats. Initially, we determined the mRNA expression levels of PPP6C in both male and female goats across multiple tissues. The results showed that PPP6C mRNA was expressed in multiple tissues, with higher levels in the testis and fallopian tubes, suggesting its involvement in goat reproduction. Additionally, we identified a novel 19 bp InDel within the PPP6C gene in a population of 1030 SBWC goats, which exhibited polymorphism. Statistical analysis revealed a significant association between the19 bp InDel mutation and litter size (P < 0.05). Subsequent, bioinformatics analysis, including linkage disequilibrium (LD) block and selective scanning, highlighted the linkage tendency among most InDel loci did not stand out within B-8 block, there were still some InDel loci linked to the 19 bp within a relatively narrow region. Furthermore, comparative analysis with Bezoars, these selective signals all indicated that this gene was under higher selection pressure, implying that the 19 bp InDel locus within the PPP6C is potentially associated with domesticated traits, particularly in relation to litter size. The results of the present study suggest that the PPP6C is a vital candidate gene affecting prolificacy in goats, with implications for selective breeding programs for goat breeds.

Three novel simple sequence repeats (SSRs) identified by MALDI-TOF-MS method were associated with backfat in pig

Backfat trait is an important economic trait and highly heritable, but difficult to evaluate. Thus, it is of great significance to explore optimal backfat thickness of pigs by using marker-assisted selection (MAS) to speed up its breeding process and improve economic efficiency. This study aimed to investigate the relationship between genetic variations (e.g., SSRs) and backfat of Qinghai Bamei pigs using MALDI-TOF Mass Spectrometry (MALDI-TOF-MS). Herein, five alternative SSR loci (namely V1, V2, V3, V4 and V5) were selected for subsequent detection. The results suggested that 3 (141-, 143- and 145-), 3 (128-, 130- and 132-), 2 (160- and 162-), 2 (136- and 139-) and 3 (170-, 184- and 192-) alleles of V1, V2, V3, V4 and V5 were found, respectively. Subsequent analysis showed that there was linkage equilibrium among five SSRs and Hap19 (13.1%) (141-/132-/160-/139-/192-) had the highest haplotype frequency. Among these five SSR loci, V1, V2 and V3 loci were significantly associated to the backfat of Qinghai Bamei sows. These findings enriched the study of SSRs in Qinghai Bamei pigs, and (AC)n (Chr15:85485851-85485995), (AC)n (Chr10:52724583-52724713) and (TG)n (Chr4:90732644-90732802) could be utilized as the candidate locus for MAS in pig industry.HIGHLIGHTSFive novel SSR loci was identified in pigs through MALDI-TOF MS.V1, V2 and V3 loci was were significantly associated to the backfat of pigs.

Goat Pleomorphic Adenoma Gene 1 (PLAG1): mRNA Expression, CNV Detection and Associations with Growth Traits

The pleomorphic adenoma gene 1 (PLAG1) gene, as the major gene responsible for growth, plays a vital role in myogenesis. Meanwhile, the relationship between copy number variation (CNV) of this gene and growth traits in goats remains unclear. Therefore, this study investigated four aspects: bioinformatics analysis, mRNA expression (n = 6), CNV detection (n = 224), and association analysis. The findings indicated that the gene had a large number of conserved motifs, and the gene expression level was higher in fetal goats than in adult goats. Three CNV loci were selected from the database, among which CNV1 was located in the bidirectional promoter region and was associated with goat growth traits. CNV analysis showed that CNV2 and CNV3 of the PLAG1 gene were associated with growth traits such as body weight, heart girth, height at hip cross, and hip width (p < 0.05), with CNV1 loss genotype being the superior genotype, and CNV2 and CNV3 median and gain genotypes of being superior genotypes. This finding further confirms that the PLAG1 gene is the dominant gene for growth traits, which will serve as theoretical guidance for goat breeding.

Goat SMAD family member 1 (SMAD1): mRNA expression, genetic variants, and their associations with litter size

SMAD family member 1 (SMAD1) is phosphorylated and activated by the BMP receptors, which help regulate ovulation rate, cell growth, apoptosis, and development. Previously, the genome-wide association study revealed that it has been associated with fecundity in sheep. However, its effect on litter size has not been investigated in goats. Therefore, this study aimed to determine the level of SMAD1 mRNA expression in various tissues and to identify its polymorphisms and their association with litter size in Shaanbei white cashmere goat (SBWC). As a result, RT-qPCR analysis showed that SMAD1 was expressed in various tissues in female SBWC goats, including the ovary (P < 0.05). Importantly, the mRNA expression level in the ovaries of mothers of multi-lambs had a higher level than the mothers of single lambs (P < 0.05). Moreover, two InDels (18-bp and 7-bp) in intron 1 of SMAD1 were polymorphic among ten potential loci. Both 18-bp and 7-bp InDels were significantly correlated with litter size (P = 0.014) and (P = 0.0001), respectively. As shown by the chi-squared test, genotypic distributions of 18-bp and 7-bp were significantly distinct between single-lamb (P = 0.02) and multi-lamb mothers (P = 0.002). Our findings confirm that two InDels in SMAD1 were significantly associated with litter size and suggest that they could be used to improve fertility traits in goat breeding strategies.

Goat SNX29: mRNA expression, InDel and CNV detection, and their associations with litter size

The sorting nexin 29 (SNX29) gene, a member of the SNX family, is associated with material transport and lipid metabolism. Previous studies have shown that lipid metabolism affects reproductive function in animals. Thus, we hypothesized there is a correlation between the SNX29 gene and reproductive trait. To date, studies on the relationship between the SNX29 gene and reproductive traits are limited. Therefore, the purpose of this study was to examine the polymorphism in the SNX29 gene and its correlation with litter size. Herein, the mRNA expression levels of SNX29 were assayed in various goat tissue. Surprisingly, we found that SNX29 was highly expressed in the corpus luteum, large and small follicles. This result led us to suggest that the SNX29 gene has a critical role in reproduction. We further detected potential polymorphisms in Shaanbei white cashmere (SBWC) goats, including insertion/deletion (InDel, n = 2,057) and copy number variation (CNV, n = 1,402), which were related to fertility. The 17 bp deletion (n = 1004) and the 20 bp deletion (n = 1,053) within the SNX29 gene were discovered to be significantly associated with litter size (P < 0.05), and individuals the ID genotype of P1-Del-17 bp and the DD genotype of P2-Del-20bp had larger litter size. Additionally, the four CNV loci had significant correlations with litter size (P < 0.01) in our detected population. In CNV5, individuals with the median genotype were superior compared to those with loss or gain genotype in term of litter size, and in other three CNVs showed better reproductive trait in the gain genotype. Briefly, these findings suggest that SNX29 could be used as a candidate gene for litter size in goat breeding through marker-assisted selection (MAS).

Are Copy Number Variations within the FecB Gene Significantly Associated with Morphometric Traits in Goats?

The Booroola fecundity (FecB) gene is a major fertility-related gene first identified in Booroola sheep. Numerous studies have investigated whether the FecB gene is a major fecundity gene in goats or whether there are other genes that play a critical role in goat fertility. Nevertheless, little attention has been paid to the role of the FecB gene in the body morphometric traits of goats, despite the positive relationship discerned between litter size and growth. We identified five copy number variations (CNVs) within the FecB gene in 641 goats, including 318 Shaanbei white cashmere (SBWC) goats, 203 Guizhou Heima (GZHM) goats, and 120 Nubian goats, which exhibited different distributions among these populations. Our results revealed that these five CNVs were significantly associated with goat morphometric traits (p < 0.05). The normal type of CNV3 was the dominant type and displayed superior phenotypes in both litter size and morphometric traits, making it an effective marker for goat breeding. Consequently, LD blocks in the region of 10 Mb upstream and downstream from FecB and potential transcription factors (TFs) that could bind with the CNVs were analyzed via bioinformatics. Although no significant LD block was detected, our results illustrated that these CNVs could bind to growth-related TFs and indirectly affect the growth development of the goats. We identified potential markers to promote litter size and growth, and we offer a theoretical foundation for further breeding work.

Genetic Variations and mRNA Expression of Goat DNAH1 and Their Associations with Litter Size

Dynein Axonemal Heavy Chain 1 (DNAH1) encodes proteins which provide structural support for the physiological function and motor structure of spermatozoa (hereafter referred to as sperm) and ova. This study found that three single nucleotide polymorphisms (SNPs), the 27-bp insertion/deletion (InDel) mutations and three exonic copy number variations (CNVs) within DNAH1 were significantly associated with litter size of Shaanbei white cashmere goats (n = 1101). Goats with the wildtypes of these three SNPs had higher litter sizes than other carriers (p < 0.05). II genotype of the 27-bp InDel had the highest litter size compared with ID carriers (p = 0.000022). The gain genotype had the largest litter sizes compared with the loss or medium carriers for the three CNV mutations (p < 0.01). Individuals with the AA-TT-CC-II-M1-M2-M3 and AA-TT-CC-II-G1-G2-M3 combination genotypes had larger litter sizes compared with the other genotypes. This study also showed the DNAH1 expression in mothers of multiple kids was higher than mothers of single kids. These three SNPs, the 27-bp InDel and three CNVs in DNAH1 could be used as molecular markers for the selection of goat reproductive traits.

Investigation of Copy Number Variations (CNVs) of the Goat PPP3CA Gene and Their Effect on Litter Size and Semen Quality

Simple Summary

PPP3CA is one of the candidate genes for goat reproduction, but no studies have been carried out yet. Therefore, the purpose of this study was to determine the associations between copy number variations in the goat PPP3CA gene and litter size and semen quality in goats, including Shaanbei white cashmere goats (SBWC) (n = 353) and Guizhou Heima (GZHM) goats (n = 64). Based on the association analysis, the results showed that only CNV1 (copy number variation 1) and CNV2 (copy number variation 2) were distinctly related to the first-birth litter size in female goats (p = 7.6802 × 10⁻¹¹; p = 5.0895 × 10⁻⁹), and they were also significantly associated with the semen quality of SBWC goats (p < 0.05). These findings prove that the PPP3CA gene plays an important role in reproduction traits in goats.

Abstract

Copy number variations (CNVs) have many forms of variation structure, and they play an important role in the research of variety diversity, biological evolution and disease correlation. Since CNVs have a greater impact on gene regulation and expression, more studies are being finalized on CNVs in important livestock and poultry species. The protein phosphatase 3 catalytic subunit alpha (PPP3CA) is a key candidate gene involved in the goat fecundity trait, and has important effects on precocious puberty, estrogen signal transduction pathways and oocyte meiosis. Additionally, PPP3CA also has a dephosphorylation effect in the process of spermatogonial stem cell meiosis and spermatogenesis. So far, there is no research on the relationship between the copy number variations of the PPP3CA gene and reproduction traits. Therefore, the purpose of this study was to determine the association between copy number variations in the goat PPP3CA gene and litter size and semen quality in Shaanbei white cashmere goats (SBWC) (n = 353) and Guizhou Heima goats (n = 64). Based on the association analysis, the results showed that only CNV1 and CNV2 within the PPP3CA gene were distinctly related to the first-birth litter size in female goats (p = 7.6802 × 10⁻¹¹; p = 5.0895 × 10⁻⁹, respectively) and they were also significantly associated with the semen quality of SBWC goats (p < 0.05). In addition, individuals with Loss genotypes demonstrated better phenotypic performance compared to those with other types. Therefore, CNV1 and CNV2 of the PPP3CA gene are potentially useful for breeding, as they are linked to important goat reproduction traits.

Screen of small fragment mutations within the sheep thyroid stimulating hormone receptor gene associated with litter size

The thyroid stimulating hormone receptor (TSHR), a glycoprotein hormone receptor, plays an important role in metabolic regulation and photoperiod control in the time of reproduction in birds and mammals. Previous genome-wide association studies revealed that the TSHR gene was related to reproduction and its function was identified in female reproduction, but rare studies reported the polymorphism of TSHR gene. However, the molecular mutations of the TSHR gene in sheep have not been reported so far. Herein, we explored potential polymorphisms of the sheep TSHR gene, and a 29 bp nucleotide sequence variant (rs1089565492) was identified in the AUW sheep. There were three genotypes of the 29 bp variant locus detected which named 'II' 'DD' and 'ID' been identified. Association analysis results showed the 29 bp variant was significantly associated with the litter size of the AUW sheep (p < 0.05). This finding suggests that the 29 bp nucleotide sequence variant within TSHR gene could be a candidate marker of reproduction traits for sheep breeding improving through the marker-assisted selection (MAS).

Detection of mRNA Expression and Copy Number Variations Within the Goat Fec B Gene Associated With Litter Size

The Booroola fecundity (Fec ^B ) gene, as the first major fecundity gene identified in Booroola sheep, has attracted careful attention. So far, previous research have uncovered the Fec^B mutation (Q249R) as the main mutation by virtue of which sheep exhibits multiple lambing phenomena. This mutation is now being intensively studied and widely used. However, such effect of the Fec^B mutation has not been applied to goats, and similar types of the Fec ^B gene in goats still need to be studied. Thus, the current study attempted to verify potential mutations in the goat Fec ^B gene as well as investigate their functions related to fecundity. First, Fec ^B expression was investigated in six different goat tissues, and we found that Fec ^B expression was highest in the mammary gland, followed by the ovary. Next, the influence of the Fec ^B gene was analyzed from a new perspective, where five potential copy number variations (CNVs) (CNV1-5) within the Fec ^B gene were identified for the first time, and then their effects on litter size were measured. Our results point out that CNV3 (P = 3.44E-4) and CNV5 (P = 0.034) could significantly influence the litter size of goats. Identically, the combination genotype of CNV3 and CNV5 which consisted of their dominant genotypes was also significantly associated with goat litter size (P = 7.80E-5). Hence, CNV3 and CNV5 could serve as potential DNA molecular markers applied to DNA editing and DNA microarray. Additionally, the abovementioned study has laid a theoretical foundation for the detection of potential fertility-related quantitative trait loci within the goat Fec ^B gene.

Goat AKAP12: Indel Mutation Detection, Association Analysis With Litter Size and Alternative Splicing Variant Expression

A-kinase anchoring protein 12 (AKAP12) plays key roles in male germ cells and female ovarian granulosa cells, whereas its influence on livestock litter size remains unclear. Herein we detected the genetic variants of AKAP12 gene and their effects on litter size as well as alternative splicing variants expression in Shaanbei white cashmere (SBWC) goats, aiming at exploring theoretical basis for goat molecular breeding. We identified two Insertion/deletions (Indels) (7- and 13-bp) within the AKAP12 gene. Statistical analyses demonstrated that the 13-bp indel mutation in the 3′ UTR was significantly associated with litter size (n = 1,019), and the carriers with DD genotypes presented lower litter sizes compared with other carriers (P < 0.01). Bioinformatics analysis predicted that this 13-bp deletion sequence could bind to the seed region of miR-181, which has been documented to suppress porcine reproductive and respiratory syndrome virus (PRRSV) infection by targeting PRRSV receptor CD163 and affect the pig litter size. Therefore, luciferase assay for this 13-bp indel binding with miRNA-181 was performed, and the luciferase activity of pcDNA-miR-181-13bp-Deletion-allele vector was significantly lower than that of the pcDNA-miR-181-13bp-Insertion-allele vector (P < 0.05), suggesting the reduced binding capability with miR-181 in DD genotype. Given that alternative spliced variants and their expression considerably account for the Indel genetic effects on phenotypic traits, we therefore detected the expression of the alternative spliced variants in different tissues and identified that AKAP12-AS2 exhibited the highest expression levels in testis tissues. Interestingly, the AKAP12-AS2 expression levels of homozygote DD carriers were significantly lower than that of individuals with heterozygote ID, in both testis and ovarian tissues (P < 0.05), which is consistent with the effect of the 13-bp deletion on the reduced litter size. Taken together, our results here suggest that this 13-bp indel mutation within goat AKAP12 might be utilized as a novel molecular marker for improving litter size in goat breeding.

The mRNA expression profile of the goat prion protein testis-specific (PRNT) gene and its associations with litter size

The goat PRNT gene was initially identified as a testis-specific gene with a role in spermatogenesis. In this study, we used quantitative real-time PCR (qPCR) to first determine the mRNA expression profile of this gene in different goat tissues. Surprisingly, we found that PRNT was expressed not only in the testis but also in nine other tissues in goats. Moreover, PRNT was weakly expressed in the testis, while its expression was strongest in the ovary. These results, combined with those of other studies, led us to hypothesize that the goat PRNT gene has a role in both male and female reproduction. We further used direct DNA sequencing to detect potential SNPs within this gene in Shaanbei whit cashmere (SBWC) rams and ewes, and identified three SNPs within the PRNT gene, namely, c.-58C > T, c.71A > G (p.Alanine24Valine), and c.102C > T (synonymous). In rams, c.-58C > T and c.102C > T were strongly linked with each other (D' = 1.000, r² = 0.504), whereas no significant association (P > 0.05) was found between the three SNPs and semen quality, which was consistent with the low expression of the PRNT gene in the testis. Interestingly, in ewes (n = 502), c.-58C > T and c.71A > G were also strongly linked with each other (D' = 0.973, r² = 0.537). Additionally, the c.71A > G locus, especially the AA genotype, had a significant influence on litter size (P = 0.006), consistent with the high PRNT expression in the ovary. Combined, the results of the expression profiling and analysis of the association between the SNPs and reproductive traits showed that two strongly linked nucleotide sequence variants within PRNT were significantly associated with goat litter size. These findings provide potential DNA markers for use in the marker-assisted selection (MAS) of goats with high-fertility traits.

Litter Size of Sheep (Ovis aries): Inbreeding Depression and Homozygous Regions

Ovine litter size (LS) is an important trait showing variability within breeds. It remains largely unknown whether inbreeding depression on LS exists based on genomic homozygous regions, and whether the homozygous regions resulted from inbreeding are significantly associated with LS in sheep. We here reanalyze a set of single nucleotide polymorphism (SNP) chip of six breeds to characterize the patterns of runs of homozygosity (ROH), to evaluate inbreeding levels and inbreeding depressions on LS, and to identify candidate homozygous regions responsible for LS. Consequently, unique ROH patterns were observed among six sheep populations. Inbreeding depression on LS was only found in Hu sheep, where a significant reduction of 0.016, 0.02, and 0.02 per 1% elevated inbreeding FROH4-8, FROH>8 and the total inbreeding measure was observed, respectively. Nine significantly homozygous regions were found for LS in Hu sheep, where some promising genes for LS possibly via regulation of the development of oocytes (NGF, AKT1, and SYCP1), fertilization (SPAG17, MORC1, TDRD9, ZFYVE21, ADGRB3, and CKB), embryo implantation (PPP1R13B, INF2, and VANGL1) and development (DPPA2, DPPA4, CDCA4, CSDE1, and ADSSL1), and reproductive health (NRG3, BAG5, CKB, and XRCC3) were identified. These results from the present study would provide insights into the genetic management and complementary understandings of LS in sheep.

Deletion mutation within the goat PPP3CA gene identified by GWAS significantly affects litter size

The protein phosphatase 3 catalytic subunit α (PPP3CA) gene is a high reproduction traits candidate gene for goats as revealed by a genome-wide association study. The aim of this work was to explore the genetic variations of the goat PPP3CA as well as to evaluate the genetic effects on litter size. Three novel insertions/deletions (indels) within the goat PPP3CA were found and their minor allelic frequencies (MAF) were 0.105, 0.066, and 0.042, respectively. The results showed that only the 20bp indel polymorphism was significantly associated with litter size in Shaanbei white cashmere goats (P<0.05) and individuals with deletion/deletion (DD) genotypes demonstrated the junior phenotypes when compared with those with other genotypes. These findings suggested that the 20bp indel is a potential DNA marker for selecting superior individuals in marker-assisted selection for breeding concerning fecundity in goats.

Relationships between novel nucleotide variants within the colony-stimulating factor 1 receptor (CSF1R) gene and mastitis indicators in sheep

Colony-stimulating factor 1 receptor (CSF1R) plays an important role in the process of innate immunity and inflammation, thus it was hypothesized that the CSF1R gene might affect the occurrence of mammalian mastitis. The purpose of this study was to investigate the association between nucleotide variations of CSF1R gene and mastitis in Australian white sheep (AUWs). Two indel variants (Intron5-27 bp and Intron5-22 bp) within the CSF1R gene have been found in AUWs. The Chi-square test for different mastitis symptoms demonstrated that individuals without symptoms of mastitis had higher 'I' allele frequencies and 'II' genotype frequencies (p < 0.01). We found strong correlation between mastitis and lactation score through Pearson correlation analysis. Therefore, we also analyzed the relationship between the two indel loci and lactation, we found that the lactation ability of individuals with type II was stronger than that of DD genotype at the Intron5-22 bp (p < 0.05). Additionally, we found that the combined genotype of the two loci was significantly associated with mastitis (p < 0.01). These findings indicated that CSF1R mutations were significantly associated with mastitis, and could affect lactation performance, suggesting that two deletion sites could be used as the effective molecular markers against mastitis in sheep breeding.