Indel mutations within the bovine HSD17B3 gene are significantly associated with ovary morphological traits and mature follicle number

Exploration of the Polymorphism Distribution of Bovine HMGA2 Gene in Worldwide Breeds and Its Associations with Ovarian Traits

The high-mobility group AT-hook 2(HMGA2) gene has been widely studied in the context of cancer and animal growth. However, recently, several studies have uncovered its critical role in cell proliferation. A genome-wide association study (GWAS) further suggests that the HMGA2 gene is a candidate gene in fertility, indicating its connection not only to growth traits but also to reproduction, specifically ovarian traits. Thus, this study aimed to analyze the distribution of the HMGA2 gene in 54 bovine breeds worldwide, identify important short fragment variants (indels), and investigate the relationship between HMGA2 and ovarian development. The dataset included genotypic information from a bovine population of 634 individuals (n = 634). After genotyping and analyzing four selected loci, we found that one out of four loci, rs133750033 (P4-D22-bp), was polymorphic. Our results also reveal that this indel of HMGA2 is significantly associated with certain ovarian traits (p < 0.05). Specifically, it has connection with ovarian length (p = 0.004) and ovarian height (p = 0.026) during diestrus. Additionally, we discovered a higher expression of the HMGA2 gene in Asian cattle breeds. In summary, this study suggests that HMGA2 has the potential to serve as an animal fertility testing marker gene. Moreover, these findings contribute to a more promising outlook for the bovine industry.

Bovine FRAS1: mRNA Expression Profile, Genetic Variations, and Significant Correlations with Ovarian Morphological Traits, Mature Follicle, and Corpus Luteum

The amelioration of bovine fertility caused by a multi-factorial problem has always been a hot topic, among which the detection of available target genes is the most crucial. It was hypothesized that the Fraser extracellular matrix complex subunit 1 (FRAS1) gene detected by GWAS is involved in physiological activities such as ovarian development. Herein, unilateral ovaries from 2111 cows were used to examine the mRNA expression profile and polymorphisms of bovine FRAS1 and their associations with fertility-related characteristics. Firstly, it was confirmed that FRAS1 gene transcripts are expressed in various bovine tissues. Then, among five potential insertion-deletion (indel) loci, the 20 bp (named P3-D20-bp) and 15 bp (P4-D15-bp) deletion mutations were confirmed to be polymorphic with linkage equilibrium. Secondly, the P3-D20-bp polymorphism was significantly associated with ovarian weight and corpus luteum diameter in the metaestrus phase and ovarian length in the dioestrum stage. Additionally, both ovarian length and mature follicle diameter in metaestrus are significantly correlated with different genotypes of P4-D15-bp. Thirdly, the transcriptional expression of the FRAS1 gene in groups with a minimum value of ovarian weight or volume was significantly higher than the expression in groups with a maximum value. Instead of that, the more corpus luteum and mature follicles there are, the higher the transcription expression of the FRAS1 gene is. Furthermore, FRAS1 expression in cows with a heterozygous genotype (ID) of P3-D20-bp was significantly higher than others. Eventually, P3-D20-bp deletion could disturb the binding efficiency of WT1-I and Sox2 to FRAS1 sequence according to binding prediction, indicating that mutation may affect gene expression and traits by influencing the binding of transcription factors. Overall, the polymorphisms of P3-D20-bp and P4-D15-bp of the bovine FRAS1 gene significantly correlated to follicle or ovarian traits that could be applied in optimizing female fertility in cow MAS breeding programs.

A 14-bp deletion in bovine EPAS1 gene is associated with carcass traits

EPAS1 (Endothelial PAS Domain Protein 1) gene is well-known for its function in plateau hypoxia adaptability. It encodes HIF-2α, which involved in the induction of genes regulated by oxygen and then affects multiple physiological processes such as angiogenesis and energy metabolism. All of these indicate it may affect the development of animals. In this study, a 14-bp deletion in EPAS1 gene was uncovered in Shandong black cattle population (n = 502). Two genotypes (II and ID) were found and the frequency of the homozygous II genotype is higher than the heterozygous ID genotype. This population is consisted with HWE (p > 0.05). And more importantly, the 14-bp deletion was associated with outside flat (p = 0.003), brisket (p = 0.001), and knuckle (p = 0.032). These findings suggested that the 14-bp deletion is significantly associated with carcass traits, which could be served as a molecular marker applied to cow breeding.

Exploring the Impact of Insertion/Deletion in FTO and PLIN1 Genes on Morphometric Traits in Sheep

This study aimed to identify InDels from the FTO and PLIN1 genes and to analyze their association with morphometric traits in Hu sheep (HS), Dupor sheep (DS), and Small Tail Han sheep (STHS). The FTO and PLIN1 genes were genotyped using the insertion/deletion (InDel) method. A one-way ANOVA with SPSS 26.0 software (IBM Corp, Armonk, NY, USA) was used to assess the effect of the InDel FTO and PLIN1 genes on morphometric traits. The results revealed significant associations between certain InDels and the morphometric traits in different breeds of sheep. Specifically, FTO-2 was significantly associated with cannon circumference (CaC) in HS rams and body height (BoH) in HS ewes (p < 0.05). FTO-2 was also significantly associated with chest width (ChW), CaC, head length (HeL), and coccyx length (CoL) in the STHS breed (p < 0.05). FTO-3 showed significant associations with BoH in HS rams and BoH, back height (BaH), ChW, and chest depth (ChD) in HS ewes (p < 0.05). FTO-3 was also significantly associated with ChW in the DS and STHS breeds (p < 0.05). FTO-5 was significantly associated with body weight (BoW) in the DS breed and BoH in the STHS breed (p < 0.05). Furthermore, PLIN1 was significantly related to BoW in the DS breed and was significantly associated with CoL and forehead width (FoW) in the STHS breed (p < 0.05). In conclusion, the study suggested that InDels in the FTO and PLIN1 genes could provide practical information to improve morphometric traits in sheep breeding.

A novel indel within the bovine SEPT7 gene is associated with ovary length

The ovary can generate oocytes and secrete female hormones and thus is of great significance to animal fertility. In turn, the functioning of this organ has an effect on the profit margins of the livestock breeding industry. As the development-regulating gene and target gene of miR-202, SEPT7 might play an important role in ovarian growth. Therefore, we hypothesized that SEPT7 is related to ovarian traits owing to the regulation of gonad-specific miR-202. To further investigate the connection between bovine SEPT7 and ovarian development, we analyzed data from 408 samples. After genotyping and analyzing three selected loci, we found that two out of the three loci (L1 and L5) were polymorphic, of which the minimum allelic frequencies were 0.417 (L1) and 0.094 (L5). Moreover, one novel indel L1 of SEPT7 was associated with ovarian length (p < 0.05). More specifically, individuals with II and ID genotypes have longer ovaries than those with the DD genotype. Our work shows that SEPT7 can be selected as a testing marker gene for animal fertility. Our findings contribute to improving the prospects of the cattle industry and the wider use of genetic techniques in breeding.

Diversity of Mitochondrial DNA Haplogroups and Their Association with Bovine Antral Follicle Count

Maternal origins based on the bovine mitochondrial D-loop region are proven to have two main origins: Bos taurus and Bos indicus. To examine the association between the maternal origins of bovine and reproductive traits, the complete mitochondrial D-loop region sequences from 501 Chinese Holstein cows and 94 individuals of other breeds were analyzed. Based on the results obtained from the haplotype analysis, 260 SNPs (single nucleotide polymorphism), 32 indels (insertion/deletion), and 219 haplotypes were identified. Moreover, the nucleotide diversity (π) and haplotype diversity (Hd) were 0.024 ± 0.001 and 0.9794 ± 0.003, respectively, indicating the abundance of genetic resources in Chinese Holstein cows. The results of the median-joining network analysis showed two haplogroups (HG, including HG1 and HG2) that diverged in genetic distance. Furthermore, the two haplogroups were significantly (p < 0.05) correlated with the antral follicle (diameter ≥ 8 mm) count, and HG1 individuals had more antral follicles than HG2 individuals, suggesting that these different genetic variants between HG1 and HG2 correlate with reproductive traits. The construction of a neighbor-joining phylogenetic tree and principal component analysis also revealed two main clades (HG1 and HG2) with different maternal origins: Bos indicus and Bos taurus, respectively. Therefore, HG1 originating from the maternal ancestors of Bos indicus may have a greater reproductive performance, and potential genetic variants discovered may promote the breeding process in the cattle industry.

Genetic variations of bovine PCOS-related DENND1A gene identified in GWAS significantly affect female reproductive traits

Genome-wide association studies (GWAS) have identified DENND1A as a potential candidate gene linked to the fertility-related phenotypes in dairy cows. However, to date, no studies have examined the association of the DENND1A insertion/deletions (indels) to bovine fertility on a large scale. Herein, two indel sites, including P4-del-26-bp and P8-ins-15-bp were identified in 1064 Holstein cows. The values of the minor allelic frequency (MAF) ranged between 0.471 (deletion) and 0.230 (deletion), respectively, and combined four different haplotypes by analyzing the haplotype combination. It is noteworthy that P4-del-26-bp is associated with the ovarian width (P = 0.0004) and corpus luteum diameter (P = 0.004). Meanwhile, P8-ins-15-bp was found to have a significant association with the ovarian width (P = 0.020), ovarian weight (P = 0.004), the number of mature follicles (P = 0.020), and diameter of the mature follicles (P = 0.016). Furthermore, the combinatorial analysis showed that the two indel combined-genotypes were significantly related to several reproductive traits (ovarian width, ovarian weight, etc.). Collectively, our findings indicated that these two novel indels and their combinations are correlated with the reproductive traits, and hence, they can serve in the marker-assisted selection (MAS) in cattle breeding. Nevertheless, further functional experiments are needed for understanding the mechanisms of these indels in cattle reproduction in a better way.

Exploration of Genetic Variants within the Goat A-Kinase Anchoring Protein 12 (AKAP12) Gene and Their Effects on Growth Traits

Simple Summary

AKAP12, the family of A-kinase anchoring proteins (AKAPs), plays an important role in the regulation of growth and development. There have been no corresponding studies of the effect of the AKAP12 gene on growth traits in goats. In our previous study, 7 bp (intron 3) and 13 bp (3′UTR) indels within the AKAP12 gene significantly influenced AKAP12 gene expression. This study expected to identify the association between these two genetic variations and growth-related traits in 1405 Shaanbei white cashmere (SBWC) goats. The P1–7 bp indel locus was significantly correlated with height at hip cross (HHC; p < 0.05) and the P2–13 bp indel locus was associated with body weight, body length, chest depth, chest width, hip width, chest circumference and cannon (bone) circumference in SBWC goats (p < 0.05). These results prove that the AKAP12 gene plays an important role in the growth and development of goats.

Abstract

The A-kinase anchoring protein 12 gene (AKAP12) is a scaffold protein, which can target multiple signal transduction effectors, can promote mitosis and cytokinesis and plays an important role in the regulation of growth and development. In our previous study, P1–7 bp (intron 3) and P2–13 bp (3′UTR) indels within the AKAP12 gene significantly influenced AKAP12 gene expression. Therefore, this study aimed to identify the association between these two genetic variations and growth-related traits in Shaanbei white cashmere goats (SBWC) (n = 1405). Herein, we identified two non-linkage insertions/deletions (indels). Notably, we found that the P1–7 bp indel mutation was related to the height at hip cross (HHC; p < 0.05) and the P2–13 bp indel was associated with body weight, body length, chest depth, chest width, hip width, chest circumference and cannon (bone) circumference in SBWC goats (p < 0.05). Overall, the two indels’ mutations of AKAP12 affected growth traits in goats. Compared to the P1–7 bp indel, the P2–13 bp indel is more suitable for the breeding of goat growth traits.

Fertility-Associated Polymorphism within Bovine ITGβ5 and Its Significant Correlations with Ovarian and Luteal Traits

Simple Summary

The fertility of bovines is essential for cattle husbandry. ITGβ5, which is suggested to be closely related to fertility, is known to mediate cell adhesion and affect a variety of cellular activities. To investigate the relationship between the ITGβ5 gene and the fertility of bovines, 696 ovarian samples were collected and six potential indel (insertion/deletion) within ITGβ5 were analysed, from which a deletion mutation was found to be polymorphic. The genotype frequency and allele frequency of this locus in the investigated population were calculated and the population genetic parameters analyzed. In addition, this locus was found to be significantly correlated with ovarian width and corpus luteum diameter. Considering the importance of ovary and corpus luteum in reproduction, it is tempting to speculate the crucial effects of ITGβ5 on bovine fertility, which still need further validation. The results of our study might provide a theoretical basis for future breeding to enhance bovine reproduction.

Abstract

There is an urgent need to improve bovine fertility, and molecular marker-assisted selection (MAS) can accelerate this process. Genome-wide association studies suggest that Integrin β5 (ITGβ5) might affect fertility in bovines. As a member of the integrins family, ITGβ5 can bind to the extracellular matrix and mediate various cellular processes. In our study, primers spanning six potential insertion/deletion (indel) polymorphisms within the ITGβ5 gene were designed and 696 ovary samples from different individuals, the vast majority not in oestrum were collected for genetic variation detection. A deletion locus, rs522759246, namely P1-D_13-bp, was found to be polymorphic. The allele D frequency was 0.152 and the polymorphism information content (PIC) value was 0.224, indicating a low-degree PIC. This locus did not follow the Hardy–Weinberg equilibrium (p = 1.200E-23). Importantly, associations between P1-D_13-bp and ovarian morphological traits were established. Polymorphisms of this locus had significant correlations with ovarian width (p = 0.015). The corpus luteum is also linked to fertility and P1-D_13-bp was significantly correlated with corpus luteum diameter (p = 0.005). In conclusion, an indel mutation within the bovine ITGβ5 gene was identified, which was significantly associated with several ovarian and luteal traits.