A SNP in intron 8 of CD46 causes a novel transcript associated with mastitis in Holsteins

Polymorphism within the GATA binding protein 4 gene is significantly associated with goat litter size

GATA binding protein 4 (GATA4) is a typical transcription binding factor, and its main functions include regulating the proliferation, differentiation and apoptosis of ovarian granulosa cells, promoting spermatogenesis and sex differentiation, implying that this gene have possibly roles in animal reproduction. This study aims to detect five potential insertion/deletions (indels) of the GATA4 gene in 606 healthy unrelated Shaanbei white cashmere (SBWC) goats and analyze its association with the litter size. The electrophoresis and DNA sequencing identified two polymorphic indels (e.g., P4-Del-8bp and P5-Ins-9bp indel). Then T-test analysis showed that P4-Del-8bp was significantly correlated with litter size (p = 0.022) because of two different genotypes detected, e.g., insertion-deletion (ID) and deletion-deletion (DD), and the average litter size of individuals with DD genotype goats was higher than that of others. However, there was no correlation between P5-Ins-9bp and lambing of goats. Chi-square (X2) test found that the distribution of and P4-Del-8bp genotypes (X2 = 6.475, p = 0.011) was significantly different between single and multiple-lamb groups, while P5-Ins-9bp (X2 = 0.030, p = 0.862) was not. Therefore, these findings revealed that P4-Del-8bp polymorphism of goat GATA4 gene was a potential molecular marker significantly associated with litter size, which can be used for the marker-assisted selection (MAS) breeding to improve goat industry.

The Hoof Color of Australian White Sheep Is Associated with Genetic Variation of the MITF Gene

Studying the characteristics of mammalian hoof colors is important for genetic improvements in animals. A deeper black hoof color is the standard for breeding purebred Australian White (AUW) sheep and this phenotype could be used as a phenotypic marker of purebred animals. We conducted a genome-wide association study (GWAS) analysis using restriction site associated DNA sequencing (RAD-seq) data from 577 Australian White sheep (black hoof color = 283, grey hoof color = 106, amber hoof color = 186) and performed association analysis utilizing the mixed linear model in EMMAX. The results of GWAS demonstrated that a specific single-nucleotide polymorphism (SNP; g. 33097911G>A) in intron 14 of the microphthalmia-associated transcription factor (MITF) gene was significantly associated with the hoof color in AUW sheep (p = 9.40 × 10-36). The MITF gene plays a key role in the development, differentiation, and functional regulation of melanocytes. Furthermore, the association between this locus and hoof color was validated in a cohort of 212 individuals (black hoof color = 122, grey hoof color = 38, amber hoof color = 52). The results indicated that the hoof color of AUW sheep with GG, AG, and AA genotypes tended to be black, grey, and amber, respectively. This study provided novel insights into hoof color genetics in AUW sheep, enhancing our comprehension of the genetic mechanisms underlying the diverse range of hoof colors. Our results agree with previous studies and provide molecular markers for marker-assisted selection for hoof color in sheep.

Polymorphism in neutrophil cytosolic factor 4 (NCF4) of dairy cows had mastitis in previous lactations, and the relationship with the respiratory burst

Nicotinamide adenine dinucleotide phosphate oxidase (NADPH oxidase), as a key factor in innate immunity, consists of several components, one of them is p40phox which is encoded by neutrophil cytosolic factor 4 (NCF4). Respiratory burst and reactive oxygen species (ROS) production are antimicrobial mechanisms associated with NADPH oxidase. This study evaluated the effects of g.18174 A > G and g.18270C > T single-nucleotide polymorphisms (SNP) in NCF4 on bovine mastitis and the respiratory burst capacity of neutrophils. SNPs of 160 dairy cattle were determined using a novel PCR-RFLP protocol by employing restriction enzymes, MboI and FokI. Also, the flow cytometry measured respiratory burst in 82 blood samples. Our results indicated that only g.18174 A > G SNP reduced the respiratory burst capacity. However, both SNPs were not significantly correlated with clinical mastitis. We concluded that g.18174 A > G decreases the function of NADPH oxidase. However, both SNPs were not significantly correlated with clinical mastitis.

Genetic polymorphisms in immune- and inflammation-associated genes and their association with bovine mastitis resistance/susceptibility

Bovine mastitis, the inflammation of the mammary gland, is a contagious disease characterized by chemical and physical changes in milk and pathological changes in udder tissues. Depressed immunity and higher expression of inflammatory cytokines with an elevated milk somatic cell count can be observed during mastitis in dairy cattle. The use of somatic cell count (SCC) and somatic cell score (SCS) as correlated traits in the indirect selection of animals against mastitis resistance is in progress globally. Traditional breeding for mastitis resistance seems difficult because of the low heritability (0.10-0.16) of SCC/SCS and clinical mastitis. Thus, genetic-marker-selective breeding to improve host genetics has attracted considerable attention worldwide. Moreover, genomic selection has been found to be an effective and fast method of screening for dairy cattle that are genetically resistant and susceptible to mastitis at a very early age. The current review discusses and summarizes the candidate gene approach using polymorphisms in immune- and inflammation-linked genes (CD4, CD14, CD46, TRAPPC9, JAK2, Tf, Lf, TLRs, CXCL8, CXCR1, CXCR2, C4A, C5, MASP2, MBL1, MBL2, LBP, NCF1, NCF4, MASP2, A2M, and CLU, etc.) and their related signaling pathways (Staphylococcus aureus infection signaling, Toll-like receptor signaling, NF-kappa B signaling pathway, Cytokine-cytokine receptor, and Complement and coagulation cascades, etc.) associated with mastitis resistance and susceptibility phenotypic traits (IL-6, interferon-gamma (IFN-γ), IL17, IL8, SCS, and SCC) in dairy cattle.

Identification of Y-SNPs within ovine MSY region and their association with testicular size

The screening of genomic variations within the male-specific region of the mammalian Y chromosome (MSY) is one of the most effective ways to investigate paternal evolutionary history and identify molecular markers related to male fertility. The current study was to identify single nucleotide polymorphisms (SNPs) within single-copy genes of the ovine MSY, and confirm whether they are associated with testicular size. A total of 21 Y-specific gene fragments were successfully amplified to screen Y-SNPs in 956 rams across nine sheep breeds. Three Y-SNPs, including SRY16: g.88 A > G in South African Mutton Merino sheep, ZFY16: g.146 C > T in Suffolk and South African Mutton Merino sheep, and EIF2S3Y2: g.77 C > G in Hu and Tan sheep, were identified using DNA-pooled sequencing and PCR restriction fragment length polymorphism (PCR-RFLP) methods. The investigation of the global distribution for three Y-SNPs showed that the C allele of ZFY16: g.146 C > T co-segregated with haplogroup y-HC, and the C/G allele of EIF2S3Y2: g.77 C > G co-segregated with haplogroup y-HA/y-HB1 in Hu sheep according to data mining from a previous study. In addition, association analysis revealed that ZFY16: g.146 C > T had a significant effect on yearling scrotal circumference in Suffolk sheep, and EIF2S3Y2: g.77 C > G was significantly associated with testicular and epididymis weight in Hu sheep (P ≤ 0.05). The current study concluded that Y-SNPs were associated with testicular size in specific sheep, which provides valuable candidate makers for selecting elite rams at an early age.

New Insights on Nucleotide Sequence Variants and mRNA Levels of Candidate Genes Assessing Resistance/Susceptibility to Mastitis in Holstein and Montbéliarde Dairy Cows

A major factor in the propagation of an infectious disease is host genetics. In this study, 180 dairy cows (90 of each breed: Holstein and Montbéliarde) were used. Each breed's tested dairy cows were divided into two groups of comparable size (45 cows each), mastitis-free and mastitis-affected groups. Each cow's jugular vein was punctured to obtain blood samples for DNA and RNA extraction. In the examined Holstein and Montbéliarde dairy cows, single nucleotide polymorphisms (SNPs) related with mastitis resistance/susceptibility were found in the RASGRP1, NFkB, CHL1, MARCH3, PDGFD, MAST3, EPS15L1, C1QTNF3, CD46, COX18, NEURL1, PPIE, and PTX3 genes. Chi-square analysis of identified SNPs revealed a significant difference in gene frequency between mastitic and healthy cows. Except for CHL1, mastitic dairy cows of two breeds had considerably higher mRNA levels of the examined genes than did healthy ones. Marker-assisted selection and monitoring of dairy cows' susceptibility to mastitis may be accomplished through the use of discovered SNPs and changes in the gene expression profile of the studied genes. These findings also point to a possible method for reducing mastitis in dairy cows through selective breeding of animals using genetic markers linked to an animal's ability to resist infection.

Genetic polymorphisms of TRAPPC9 and CD4 genes and their association with milk production and mastitis resistance phenotypic traits in Chinese Holstein

The present study was designed to evaluate the association of polymorphisms in bovine trafficking protein particle complex subunit 9 (TRAPPC9) and cluster of differentiation 4 (CD4) genes with milk production and mastitis resistance phenotypic traits in a different cattle population. Three single nucleotide polymorphisms (SNPs) (SNP1 Position: Chr14:2484891, SNP2 (rs110017379), SNP3 Position: Chr14:2525852) in bovine TRAPPC9 and one SNP (Position: Chr5:104010752) in CD4 were screened through Chinese Cow's SNPs Chip-I (CCSC-I) and genotyped in a population of 312 Chinese Holsteins (156: Mastitis, 156: Healthy). The results were analyzed using the general linear model in SAS 9.4. Our analysis revealed that milk protein percentage, somatic cell count (SCC), somatic cell score (SCS), serum cytokines interleukin 6 (IL-6) and interferon-gamma (IFN-γ) were significantly (P < 0.05) associated with at least one or more identified SNPs of TRAPPC9 and CD4 genes. Furthermore, the expression status of SNPs in CD4 and TRAPPC9 genes were verified through RT-qPCR. The expression analysis showed that genotypes GG in SNP3 of TRAPPC9 and TT genotype in SNP4 of CD4 showed higher expression level compared to other genotypes. The GG genotype in SNP2 and TT genotype in SNP3 of TRAPPC9 were associated with higher bovine milk SCC and lower IL6. Altogether, our findings suggested that the SNPs of TRAPPC9 and CD4 genes could be useful genetic markers in selection for milk protein improvement and mastitis resistance phenotypic traits in dairy cattle. The CCSC-I used in current study is proposed to be validate in different and large population of dairy cattle not only in China but also in other countries. Moreover, our analyses recommended that besides SCC and SCS, the association of genetic markers could also be considered with the serum cytokines (IL-6, IFN-γ) while selecting genetically mastitis resistance dairy cattle.

Characterization of peripheral white blood cells transcriptome to unravel the regulatory signatures of bovine subclinical mastitis resistance

Subclinical bovine mastitis is a pathogenic infection of the breast characterized by a marked decrease in milk production and quality. As it has no obvious clinical symptoms, diagnosis and treatment are challenging. Therefore, searching for biomarkers in cows’ peripheral white blood cells is valuable for preventing and treating subclinical mastitis. Thus, in this study, the transcriptome of peripheral blood from healthy and subclinical mastitis cows was characterized to find the regulatory signatures of bovine subclinical mastitis using RNA-seq. A total of 287 differentially expressed genes (DEGs) and 70 differentially expressed lncRNAs (DELs) were detected, and 37 DELs were documented near known Quantitative Trait Loci (QTL) associated with the mastitis of cows. Bioinformatic analysis indicated that lncRNAs MSTRG25101.2, MSTRG.56327.1, and MSTRG.18968.1, which are adjacent to the SCS QTL and SCC QTL, may be candidate lncRNAs that influence the pathogenesis of mastitis in cows by up-regulating the expression of genes TLR4, NOD2, CXCL8, and OAS2. Moreover, the alternative splicing (AS) pattern of transcriptional sequence differences between healthy cows and subclinical mastitis cows suggested a molecular mechanism of mastitis resistance and susceptibility. A total of 2,212 differential alternative splicing (DAS) events, corresponding to 1,621 unique DAS genes, were identified in both groups and significantly enriched in immune and inflammatory pathways. Of these, 29 DAS genes were subject to regulation by 32 alternative splicing SNPs, showing diverse and specific splicing patterns and events. It is hypothesized that the PIK3C2B and PPRPF8 splice variants associated with AS SNPs (rs42705933 and rs133847062) may be risk factors for susceptibility to bovine subclinical mastitis. Altogether, these key blood markers associated with resistance to subclinical mastitis and SNPs associated with alternative splicing of genes provide the basis for genetic breeding for resistance to subclinical mastitis in cows.

Short variation of the sheep PDGFD gene is correlated with litter size

Platelet-derived growth factor (PDGF) family, exert plays a key role in embryonic development, cell proliferation, cell migration, angiogenesis and reproduction. Related studies about GWAS analyses have found that PDGFD significantly affected deposition of tail fat in sheep, but there are no studies on reproduction in animals. In this study, three breed of sheep were used to find insertion/deletion (indel) fragment polymorphism of PDGFD which including Australian white (AUW) sheep (Meat type, n = 932), Guiqian semi-fine wool (GSFW) sheep (wool type, n = 60) and East Friensian milk (EFM) sheep (dairy type, n = 60). Only a 18-bp variation was polymorphic in the study AUW sheep population and the genotypes of different sheep breed are also specific. Moreover, the association analysis indicated that this variant was associated with litter size of AUW sheep in the first parity (p < 0.05). The litter size of II genotype was significantly lower than other genotypes in the first parity (p < 0.05). We also revealed that the PDGFD gene was relatively conservative in eight species, PDGFD mRNA expression in 832 sheep samples implying this gene was related to reproduction traits. Hence, these finding demonstrated the one-cause multipotency of PDGFD gene. Collectively, these results suggest that this indel can be used as an effective marker for sheep breeding.

Whole-genome resequencing to investigate the determinants of the multi-lumbar vertebrae trait in sheep

Multi-lumbar vertebrae trait is a beneficial mutation that can significantly improve livestock meat production. However, the genetic basis of the multi-lumbar vertebrae in sheep is still unclear. Here, we analysed the number of lumbar vertebrae of Duolang sheep and found three different traits of lumbar vertebrae number. Compared with the normal sheep, the length and weight of animal carcass from the multi-lumbar vertebrae sheep increased by 2.21 cm and 0.78 kg, respectively. We performed high-throughput genome resequencing on multi-lumbar vertebrae (n = 18) and normal (n = 11) Duolang sheep and obtained a total of more than 528.87 GB data. We found that the most significantly selective region were located in the 49.68-49.74 MB of chromosome 4 by selective-sweep analysis. We annotated this region and found that it contains SFRP4 which is known to regulate bone development. We further used the PCR-SSCP technology to detect the single nucleotide polymorphism (SNP) of the putative candidate SFRP4 and found that the two SNPs (rs600370085:C > T and rs415133338: A > G) of this gene were significantly associated with the multi-lumbar vertebrae of Duolang sheep. Our study indicates that the SFRP4 may be a potential major gene that affects the number of lumbar vertebrae in Duolang sheep, and has the potential to be utilized for sheep breeding in the future.

Population validation of reproductive gene mutation loci and association with the litter size in Nubian goat

Litter size is an important component trait of doe reproduction. By improving it, production efficiency and economic benefits can be significantly provided. Genetic marker-assisted selection (MAS) based on proven molecular indicators could enhance the efficacy of goat selection, as well as litter size trait. Many molecular markers have been identified that they can be used to improve litter size in different goat breeds. However, the presence and value of these markers vary among goat breeds. In the present study, we used the reported loci on other breeds of goat as candidate loci to detect whether these loci appear in this Nubian goat population; then we proceed to genotype and detect surrounding loci (50 bp) by multiplex PCR and sequencing technology. As a result, 69 mutations (59 SNPs and 10 indels) were screened out from 23 candidate genes in Nubian goat population, 12 loci were significantly associated with the litter size of first-parity individuals; 5 loci were significantly associated with the litter size of second-parity individuals; 3 loci were significantly associated with the litter size of third-parity individuals. In addition, five loci were significantly associated with the average litter size. The additive effect value of KITLG: g.18047318 G>A in first parity, KITLG: g.18152042G>A in third parity, KISS-1: g.1341674 C>G in first parity, and GHR: g.32134187G>A in second parity exceed more than 0.40, and the preponderant alleles are G, C, A and G, respectively. Further, linkage disequilibrium analysis of 21 mutation loci shows that 3 haplotype blocks are formed, and the litter size of combination type AACC in KISS-1 gene and AAGG in KITLG gene are significantly lower than that of other combinations genotype in first parity (P<0.05). These findings can provide effective candidate DNA markers for selecting superior individuals in Nubian goat breeding.

Genome Wide Prediction, Mapping and Development of Genomic Resources of Mastitis Associated Genes in Water Buffalo

Water buffalo (Bubalus bubalis) are an important animal resource that contributes milk, meat, leather, dairy products, and power for plowing and transport. However, mastitis, a bacterial disease affecting milk production and reproduction efficiency, is most prevalent in populations having intensive selection for higher milk yield, especially where the inbreeding level is also high. Climate change and poor hygiene management practices further complicate the issue. The management of this disease faces major challenges, like antibiotic resistance, maximum residue level, horizontal gene transfer, and limited success in resistance breeding. Bovine mastitis genome wide association studies have had limited success due to breed differences, sample sizes, and minor allele frequency, lowering the power to detect the diseases associated with SNPs. In this work, we focused on the application of targeted gene panels (TGPs) in screening for candidate gene association analysis, and how this approach overcomes the limitation of genome wide association studies. This work will facilitate the targeted sequencing of buffalo genomic regions with high depth coverage required to mine the extremely rare variants potentially associated with buffalo mastitis. Although the whole genome assembly of water buffalo is available, neither mastitis genes are predicted nor TGP in the form of web-genomic resources are available for future variant mining and association studies. Out of the 129 mastitis associated genes of cattle, 101 were completely mapped on the buffalo genome to make TGP. This further helped in identifying rare variants in water buffalo. Eighty-five genes were validated in the buffalo gene expression atlas, with the RNA-Seq data of 50 tissues. The functions of 97 genes were predicted, revealing 225 pathways. The mastitis proteins were used for protein-protein interaction network analysis to obtain additional cross-talking proteins. A total of 1,306 SNPs and 152 indels were identified from 101 genes. Water Buffalo-MSTdb was developed with 3-tier architecture to retrieve mastitis associated genes having genomic coordinates with chromosomal details for TGP sequencing for mining of minor alleles for further association studies. Lastly, a web-genomic resource was made available to mine variants of targeted gene panels in buffalo for mastitis resistance breeding in an endeavor to ensure improved productivity and the reproductive efficiency of water buffalo.

Influence of Genetic Variance on Biomarker Levels After Occupational Exposure to 1,6-Hexamethylene Diisocyanate Monomer and 1,6-Hexamethylene Diisocyanate Isocyanurate

We evaluated the impact of genetic variance on biomarker levels in a population of workers in the automotive repair and refinishing industry who were exposed to respiratory sensitizers 1,6-hexamethylene diisocyanate (HDI) monomer and one of its trimers, HDI isocyanurate. The exposures and respective urine and plasma biomarkers 1,6-diaminohexane (HDA) and trisaminohexyl isocyanurate (TAHI) were measured in 33 workers; and genome-wide microarrays (Affymetrix 6.0) were used to genotype the workers' single-nucleotide polymorphisms (SNPs). Linear mixed model analyses have indicated that interindividual variations in both inhalation and skin exposures influenced these biomarker levels. Using exposure values as covariates and a false discovery rate < 0.10 to assess statistical significance, we observed that seven SNPs were associated with HDA in plasma, five were associated with HDA in urine, none reached significance for TAHI in plasma, and eight were associated with TAHI levels in urine. The different genotypes for the 20 significant SNPs accounted for 4- to 16-fold changes observed in biomarker levels. Associated gene functions include transcription regulation, calcium ion transport, vascular morphogenesis, and transforming growth factor beta signaling pathway, which may impact toxicokinetics indirectly by altering inflammation levels. Additionally, in an expanded analysis using a minor allele cutoff of 0.05 instead of 0.10, there were biomarker-associated SNPs within three genes that have been associated with isocyanate-induced asthma: ALK, DOCK2, and LHPP. We demonstrate that genetic variance impacts the biomarker levels in workers exposed to HDI monomer and HDI isocyanurate and that genetics can be used to refine exposure predictions in small cohorts when quantitative personal exposure and biomarker measurements are included in the models.

The role of O-polysaccharide chain and complement resistance of Escherichia coli in mammary virulence

Mastitis, inflammation of the mammary gland, is a common disease of dairy animals. The disease is caused by bacterial infection ascending through the teat canal and mammary pathogenic Escherichia coli (MPEC) are common etiology. In the first phase of infection, virulence mechanisms, designated as niche factors, enable MPEC bacteria to resist innate antimicrobial mechanisms, replicate in milk, and to colonize the mammary gland. Next, massive replication of colonizing bacteria culminates in a large biomass of microbe-associated molecular patterns (MAMPs) recognized by pattern recognition receptors (PRRs) such as toll-like receptors (TLRs) mediating inflammatory signaling in mammary alveolar epithelial cells (MAEs) and macrophages. Bacterial lipopolysaccharides (LPSs), the prototypical class of MAMPs are sufficient to elicit mammary inflammation mediated by TLR4 signaling and activation of nuclear factor kB (NF-kB), the master regulator of inflammation. Using in vivo mastitis model, in low and high complements mice, and in vitro NF-kB luminescence reporter system in MAEs, we have found that the smooth configuration of LPS O-polysaccharides in MPEC enables the colonizing organisms to evade the host immune response by reducing inflammatory response and conferring resistance to complement. Screening a collection of MPEC field strains, we also found that all strains were complement resistant and 94% (45/48) were smooth. These results indicate that the structure of LPS O-polysaccharides chain is important for the pathogenesis of MPEC mastitis and provides protection against complement-mediated killing. Furthermore, we demonstrate a role for complement, a key component of innate immunity, in host-microbe interactions of the mammary gland.

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.

Isolated perfused udder model for transcriptome analysis in response to Streptococcus agalactiae

This study aimed to evaluate the transcriptional changes occurring in isolated perfused mammary alveolar tissue in response to inoculation with S. agalactiae and to identify the most affected biological functions and pathways after 3 h. Four udders taken at slaughter from cows with healthy mammary gland were perfused ex situ with warmed and gassed Tyrode's solution. Mammary alveolar tissue samples were taken from the left fore and rear quarters (IQ-inoculated quarters) before inoculation (hour 0) and at 3 h post inoculation (hpi) and at the same times from control right fore and rear quarters (not inoculated: NIQ). A total of 1756 differentially expressed genes (DEGs) were identified between IQ and NIQ at 3 hpi using edgeR package. Within this set of DEGs, 952 were up regulated and mainly involved with innate immune response and inflammatory response, e.g., CD14, CCL5, TLR2, IL-8, SAA3, as well as in transcriptional regulation such as FOS, STAT3 and NFKBIA. Genes down-regulated (804) included those involved with lipid synthesis e.g., APOC2, SCD, FABP3 and FABP4. The most affected pathways were chemokine signaling, Wnt signaling and complement and coagulation cascades, which likely reflects the early stage response of mammary tissue to S. agalactiae infection. No significant gene expression changes were detected by RNA-Seq in the others contrasts. Real time-PCR confirmed the increase in mRNA abundance of immune-related genes: TLR2, TLR4, IL-1β, and IL-10 at 3 hpi between IQ and NIQ. The expression profiles of Casp1 and Bax for any contrasts were unaffected whereas Bcl2 was increased in IQ, which suggests no induction of apoptosis during the first hours after infection. Results provided novel information regarding the early functional pathways and gene network that orchestrate innate immune responses to S. agalactiae infection. This knowledge could contribute to new strategies to enhance resistance to this disease, such as genomic selection.

Genome-wide analysis of mammary gland shows modulation of transcriptome landscape with alternative splice variants in Staphylococcus aureus mastitis in mice

Epidemiological mapping shows Staphylococcus aureus to be the leading mastitis causing pathogen in India with diverse genetic lineages circulating in the dairy cattle population. We previously reported that endemic clonal strains of S. aureus isolated from subclinical mastitis lead to specific alteration of epigenetic modulators resulting in deviating immune response in intramammary infection mouse model. However, the extent of transcriptome modulation and associated alternative splicing in S. aureus mastitis is poorly understood. Hence, to gain a deeper insight of the extent of modulation of transcriptome landscape, we expanded the study here using high throughput, paired-end RNA sequencing analysis of the mouse mammary gland inoculated with three strains of S. aureus (SA1, SA2, and SA3) possessing specific genotype, virulence and enterotoxin traits. Overall, we detected 35,878 transcripts in S. aureus inoculated mammary gland, 23% more than those annotated in the reference genome. Expression of 20,756 transcripts was > 1 fragment per kilobase of transcript per million mapped fragments and 25.95% of multi-exonic genes were alternatively spliced. We noted Alternative Splicing (AS) events for > 100 immune-related genes. S. aureus infection quantitatively altered AS events in mice mammary gland. Collectively, the majority of differentially expressed significant genes clustered into immune-associated, cell adhesion and metabolic process categories. We observed AS events for 379 transcripts of genes putatively encoding several splicing associated proteins and transcription factors besides inflammatory mediators. The present analysis provides new insights into global transcriptome landscape and AS events in host-defense related genes in response to S. aureus intramammary infection, suggesting the need for studies focusing on multi-target and/or network therapeutics approach to combat mastitis.

Genome-Wide SNPs and InDels Characteristics of Three Chinese Cattle Breeds

Simple Summary

Whole-genome resequencing is an important tool to reveal the in-depth genomic characteristics of a genome. Adaptability traits are key to the survival of the south Chinese zebu cattle. However, the potential genetic information behind these remarkable traits still remains uncertain and needs to be addressed. In the current study, we utilized a total of 15 local south Chinese cattle samples (Leiqiong (LQ), Wannan (WN), Wenshan (WS)) from one of our previous studies mapped to the old reference genome (Btau_5.0.1) and remapped them to the latest reference genome (ARS-UCD1.2) to explore potential single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) responsible for some important immune related traits. The present study emphasizes and illustrates the genetic diversity, extending our previous study. The InDel annotation show that WS cattle had more enriched genes associated with immune functions than the other two breeds. Our findings provide valuable resources for further investigation of the functions of SNP- and InDels-related genes and help to determine the molecular basis of adaptive mutations in Chinese zebu cattle.

Abstract

We report genome characterization of three native Chinese cattle breeds discovering ~34.3 M SNPs and ~3.8 M InDels using whole genome resequencing. On average, 10.4 M SNPs were shared amongst the three cattle breeds, whereas, 3.0 M, 4.9 M and 5.8 M were specific to LQ, WN and WS breeds, respectively. Gene ontology (GO)analysis revealed four immune response-related GO terms were over represented in all samples, while two immune signaling pathways were significantly over-represented in WS cattle. Altogether, we found immune related genes (PGLYRP2, ROMO1, FYB2, CD46, TSC1) in the three cattle breeds. Our study provides insights into the genetic basis of Chinese indicine adaptation to the tropic and subtropical environment, and provides a valuable resource for further investigations of genetic characteristics of the three breeds.

Derived Polymorphic Amplified Cleaved Sequence (dPACS): A Novel PCR-RFLP Procedure for Detecting Known Single Nucleotide and Deletion-Insertion Polymorphisms

Most methods developed for detecting known single nucleotide polymorphisms (SNP) and deletion-insertion polymorphisms (DIP) are dependent on sequence conservation around the SNP/DIP and are therefore not suitable for application to heterogeneous organisms. Here we describe a novel, versatile and simple PCR-RFLP procedure baptised 'derived Polymorphic Amplified Cleaved Sequence' (dPACS) for genotyping individual samples. The notable advantage of the method is that it employs a pair of primers that cover the entire fragment to be amplified except for one or few diagnostic bases around the SNP/DIP being investigated. As such, it provides greater opportunities to introduce mismatches in one or both of the 35-55 bp primers for creating a restriction site that unambiguously differentiates wild from mutant sequences following PCR-RFLP and horizontal MetaPhorTM gel electrophoresis. Selection of effective restriction enzymes and primers is aided by the newly developed dPACS 1.0 software. The highly transferable dPACS procedure is exemplified here with the positive detection (in up to 24 grass and broadleaf species tested) of wild type proline106 of 5-enolpyruvylshikimate-3-phosphate synthase and its serine, threonine and alanine variants that confer resistance to glyphosate, and serine264 and isoleucine2041 which are key target-site determinants for weed sensitivities to some photosystem II and acetyl-CoA carboxylase inhibiting herbicides, respectively.

Two Insertion/Deletion Variants within SPAG17 Gene Are Associated with Goat Body Measurement Traits

Simple Summary

Sperm-associated antigen 17 (SPAG17) is a reproduction and skeletal development related gene. This study aimed to identify crucial insertion-deletion (indel) variations, which influence the body measurement traits of goats. Two intronic indels (14 bp and 17 bp indels) were identified by sequencing. In Shaanbei white cashmere goat (SBWC), the different genotypes of the 14 bp indel were markedly associated with goat body height, chest width, body length, and chest depth. The genotypes of the 17 bp indel were significantly associated with body height and chest width. The different combined genotypes were significantly associated with body height and chest width of SBWC and ten traits of Hainan black goat. These results suggested that the 14 and 17 bp indels within SPAG17 can be used in goat growth related traits marker-assisted selection breeding, especially body height.

Abstract

Sperm-associated antigen 17 (SPAG17) gene encodes a multifunctional cytoplasmic protein, which influences not only reproduction but also skeletal development related body measurement traits, especially body height. Thus, this study aimed to identify crucial insertion-deletion (indel) variations, which influence the body measurement traits of goats in large goat populations (n = 1725). As a result, two intronic indels (14 bp and 17 bp indel) were identified by sequencing. For the two indel loci, the distributions of genotypes and alleles were significantly different between the Shaanbei white cashmere goat (SBWC) and the Hainan black goat (HNBG). In SBWC goats, the different genotypes of the 14 bp indel were markedly associated with goat body height, chest width, body length and chest depth. The genotypes of the 17 bp indel were significantly related to body height and chest width. At the two loci, for all seven analyzed traits of SBWC goat, the growth data of DD homozygotes were the worst, which means that the 14 bp insertion and the 17 bp deletion were beneficial and detrimental variations, respectively. Moreover, the combined genotypes were significantly related to body height and chest width of SBWC goats and ten traits of HNBG. These results suggested that the 14 and 17 bp indels within SPAG17 can be used in goat growth related traits marker-assisted selection breeding, especially body height.

Production of an aberrant splice variant of CCL5 is not caused by genetic mutation in the mammary glands of mastitis‑infected Holstein cows

Genetic mutations, including single nucleotide polymorphisms (SNPs), result in aberrant alternatively splicing of gene and involves in susceptibility of inflammatory diseases, including bovine mastitis. C‑C motif chemokine ligand 5 (CCL5) is an immune‑associated gene, but its alternative splicing (AS) mechanism of gene expression has not yet been understood. The present study identified the splice variant of CCL5 and the compared differential expression of various transcripts between healthy and mastitic mammary gland tissue from cows. A novel transcript lacking exon 2 with a deletion of 112 bp (referred to as CCL5‑AS) was identified in the mammary gland. The expression of CCL5‑AS was lower compared with CCL5‑reference in the healthy and mastitic mammary tissues. A total of two novel SNPs (g.1647 C>T and g.1804 G>A) were identified in exon 2 of CCL5. Using the splicing mini‑gene reporter assay in bovine mammary epithelial cells (MAC‑T) and 293T cells, it was confirmed that the production of CCL5‑AS was not caused by the two SNPs. The present findings suggested that alternative splicing is one of the mechanisms of CCL5 expression regulation and is involved in mastitis infection, but that genetic mutation was not responsible for the generation of the abnormal transcript of CCL5 in cows.

Functional reassessment of PAX6 single nucleotide variants by in vitro splicing assay

Nucleotide variants that disrupt normal splicing might be the cause of a large number of diseases. Nevertheless, because of the complexity of splicing regulation, it is not always possible to accurately predict the effect of nucleotide sequence changes on splicing events and mRNA structure. Thereby, a number of newly identified nucleotide variants are falsely classified as VUS (a variant of uncertain significance). In the present study we used the minigene assay to analyze the functional consequences of six intronic (c.142-5T>G, c.142-14C>G, c.142-64A>C, c.141+4A>G, c.1032+ 6T>G, c.682+4delA), one missense (c.140A>G) and one synonymous (c.174C>T) variants in the PAX6 gene found in patients with congenital aniridia. We revealed that all except one (c.142-64A>C) variants lead to the disruption of normal splicing patterns resulting in premature termination codon formation followed by mRNA degradation through the nonsense mediated decay pathway. This produces a null allele of the PAX6 gene. That allowed us to reclassify the analyzed variants as loss-of-function and to establish their functional role.

DNA methylation rather than single nucleotide polymorphisms regulates the production of an aberrant splice variant of IL6R in mastitic cows

Interleukin-6 receptor-alpha (IL6R) interacts with IL6 and forms a ligand-receptor complex, which can stimulate various cellular responses, such as cell proliferation, cell differentiation, and activation of inflammatory processes. Both genetic mutation and epigenetic modification regulate gene transcription. We identified a novel splice variant of bovine IL6R, designated as IL6R-TV, which is characterized by the skipping of exon 2 of the NCBI-referenced IL6R gene (IL6R-reference). The expression levels of IL6R-TV and IL6R-reference transcripts were lower in normal mammary gland tissues. These transcripts play a potential role during inflammatory infection. We also detected two putative functional SNPs (g.19711 T > C and g.19731 G > C) located within the upstream 100 bp of exon 2. These SNPs formed two haplotypes (T-G and C-C). Two mutant pSPL3 exon-trapping plasmids (pSPL3-T-G and pSPL3-C-C) were transferred into the bovine mammary epithelial cells (MAC-T) and human embryonic kidney 293 T cells (HEK293T) to investigate the relationship between the two SNPs and the aberrant splicing of IL6R. DNA methylation levels of the alternatively spliced exon in normal and mastitis-infected mammary gland tissues were quantified through nested bisulfate sequencing PCR (BSP) and cloning sequencing. We found that DNA methylation regulated IL6R transcription. The DNA methylation level was high in mastitis-infected mammary gland tissues and stimulated IL6R expression, thereby promoting the inclusion of the alternatively spliced exon. The upregulated expression of the two transcripts was due to DNA methylation modification rather than genetic mutations.

Idiopathic male infertility in the Han population in China is affected by polymorphism in the VDAC2 gene

BACKGROUND

It has been proved that human voltage-dependent anion channel 2 (VDAC2) plays a significant role in sperm function and male fertility. This study was primarily aimed at exploring whether VDAC2 is a risk factor for idiopathic male infertility.

RESULTS

We determined a significantly increased risk of idiopathic infertility with abnormal semen parameters in association with the variant rs2804535 and a decreased risk of idiopathic infertility with abnormal semen parameters in association with the variant rs11001334. However, among subjects with normal semen parameters, no significant differences could be found in these genotypes. Moreover, we could not find any differences in the variants rs7896741 and rs1259503, which showed no risk of male infertility, whether normal or abnormal.

MATERIALS AND METHODS

All of the experimental subjects, including 523 men who cannot conceive children and 277 fertile controls, underwent complete historical and physical examinations. Each participant donated an ejaculate for semen analysis and 5 ml of peripheral blood for genomic DNA extraction. A computer-assisted semen analysis system was used for the semen analysis. Four single-nucleotide polymorphisms were identified and analyzed using TaqMan SNP Genotyping Assays.

CONCLUSIONS

The result shows that the relationships between different variants in the VDAC2 gene and male fertility differ, and the individuals who carry those variants may have a decreased or increased risk of abnormal semen parameters associated with male infertility.

Splicing-related single nucleotide polymorphism of RAB, member of RAS oncogene family like 2B (RABL2B) jeopardises semen quality in Chinese Holstein bulls

RAB, member of RAS oncogene family like 2B (RABL2B) is a member of a poorly characterised clade of the RAS GTPase superfamily, which plays an essential role in male fertility, sperm intraflagellar transport and tail assembly. In the present study, we identified a novel RABL2B splice variant in bovine testis and spermatozoa. This splice variant, designated RABL2B-TV, is characterised by exon 2 skipping. Moreover, a single nucleotide polymorphism (SNP), namely c.125G>A, was found within the exonic splicing enhancer (ESE) motif, indicating that the SNP caused the production of the RABL2B-TV aberrant splice variant. This was demonstrated by constructing a pSPL3 exon capturing vector with different genotypes and transfecting these vectors into murine Leydig tumour cell line (MLTC-1) cells. Expression of the RABL2B-TV transcript was lower in semen from high- versus low-performance bulls. Association analysis showed that sperm deformity rate was significantly lower in Chinese Holstein bulls with the GG or GA genotype than in bulls with the AA genotype (P < 0.05). In addition, initial sperm motility was significantly higher in individuals with the GG or GA genotype than in individuals with the AA genotype (P < 0.05). The findings of the present study suggest that the difference in semen quality in bulls with different RABL2B genotypes is generated via an alternative splicing mechanism caused by a functional SNP within the ESE motif.

Deciphering Transcriptome and Complex Alternative Splicing Transcripts in Mammary Gland Tissues from Cows Naturally Infected with Staphylococcus aureus Mastitis

Alternative splicing (AS) contributes to the complexity of the mammalian proteome and plays an important role in diseases, including infectious diseases. The differential AS patterns of these transcript sequences between the healthy (HS3A) and mastitic (HS8A) cows naturally infected by Staphylococcus aureus were compared to understand the molecular mechanisms underlying mastitis resistance and susceptibility. In this study, using the Illumina paired-end RNA sequencing method, 1352 differentially expressed genes (DEGs) with higher than twofold changes were found in the HS3A and HS8A mammary gland tissues. Gene ontology and KEGG pathway analyses revealed that the cytokine–cytokine receptor interaction pathway is the most significantly enriched pathway. Approximately 16k annotated unigenes were respectively identified in two libraries, based on the bovine Bos taurus UMD3.1 sequence assembly and search. A total of 52.62% and 51.24% annotated unigenes were alternatively spliced in term of exon skipping, intron retention, alternative 5′ splicing and alternative 3ʹ splicing. Additionally, 1,317 AS unigenes were HS3A-specific, whereas 1,093 AS unigenes were HS8A-specific. Some immune-related genes, such as ITGB6, MYD88, ADA, ACKR1, and TNFRSF1B, and their potential relationships with mastitis were highlighted. From Chromosome 2, 4, 6, 7, 10, 13, 14, 17, and 20, 3.66% (HS3A) and 5.4% (HS8A) novel transcripts, which harbor known quantitative trait locus associated with clinical mastitis, were identified. Many DEGs in the healthy and mastitic mammary glands are involved in immune, defense, and inflammation responses. These DEGs, which exhibit diverse and specific splicing patterns and events, can endow dairy cattle with the potential complex genetic resistance against mastitis.

Effects of SNPs and alternative splicing within HGF gene on its expression patterns in Qinchuan cattle

Background

Identification of genetic variants, including SNPs (Single Nucleotide Polymorphisms), CNVs (Copy Number Variations) and alternative splicing, within functional genes has received increasing attention in animal science research. HGF (Hepatocyte Growth Factor) is a very important growth factor that works as a mitogen or a morphogen during tissue growth, development and regeneration. However, to date, the functions of genetic variants within the bovine HGF gene, particularly their effects on mRNA expression, have not been determined well.

Results

The present study aimed to perform association analysis between genetic variants and mRNA expression for the bovine HGF gene in Qinchuan cattle using various strategies, including PCR-RFLP (Restriction Fragment Length Polymorphism), qPCR (Quantitative Real-time quantitative PCR), TA cloning, DNA sequencing and bioinformatics analysis. A total of five SNPs were identified and only SV1 locus significantly affected HGF mRNA expression in fetal skeletal muscle (P < 0.05). Heterozygous genotype individuals showed significantly higher HGF expression (P < 0.05), which was significantly greater in the “CTCCAGGGTT” combined genotype than that in the “CCCCGGGGTT” combined genotype (P < 0.05). In addition, two alternative splicing variations, HGF-W and HGF-M, were identified, which resulted from alternative 3′ splice sites of exon 5, and HGF-W showed higher mRNA levels than HGF-M in all tissues.

Conclusion

In summary, genetic variations within the HGF gene affected mRNA expression. These findings provide new insight into the molecular characteristics and functions of bovine HGF.

Role of an SNP in Alternative Splicing of Bovine NCF4 and Mastitis Susceptibility

Neutrophil cytosolic factor 4 (NCF4) is component of the nicotinamide dinucleotide phosphate oxidase complex, a key factor in biochemical pathways and innate immune responses. In this study, splice variants and functional single-nucleotide polymorphism (SNP) of NCF4 were identified to determine the variability and association of the gene with susceptibility to bovine mastitis characterized by inflammation. A novel splice variant, designated as NCF4-TV and characterized by the retention of a 48 bp sequence in intron 9, was detected in the mammary gland tissues of infected cows. The expression of the NCF4-reference main transcript in the mastitic mammary tissues was higher than that in normal tissues. A novel SNP, g.18174 A>G, was also found in the retained 48 bp region of intron 9. To determine whether NCF4-TV could be due to the g.18174 A>G mutation, we constructed two mini-gene expression vectors with the wild-type or mutant NCF4 g.18174 A>G fragment. The vectors were then transiently transfected into 293T cells, and alternative splicing of NCF4 was analyzed by reverse transcription-PCR and sequencing. Mini-gene splicing assay demonstrated that the aberrantly spliced NCF4-TV with 48 bp retained fragment in intron 9 could be due to g.18174 A>G, which was associated with milk somatic count score and increased risk of mastitis infection in cows. NCF4 expression was also regulated by alternative splicing. This study proposes that NCF4 splice variants generated by functional SNP are important risk factors for mastitis susceptibility in dairy cows.

Tissue Factor Pathway Inhibitor-2 Gene Polymorphisms Associate With Coronary Atherosclerosis in Chinese Population

Tissue factor pathway inhibitor-2 (TFPI-2) may play critical roles in the pathogenesis of atherosclerosis. In this study, we aimed to investigate the association between TFPI-2 gene polymorphisms and coronary atherosclerosis.Four hundred and seven patients with coronary atherosclerosis and 306 individuals with normal coronary artery were enrolled in the present study. Nine single-nucleotide polymorphisms (SNPs) (rs3763473, rs59805398, rs60215632, rs59999573, rs59740167, rs34489123, rs4517, rs4264, and rs4271) were detected with polymerase chain reaction-direct sequencing method. Severity of coronary atherosclerosis was assessed by Gensini score. After the baseline investigation, patients with coronary atherosclerosis were followed up for incidence of cardiovascular events (CVEs).Eight SNPs were in accordance with the Hardy-Weinberg equilibrium, and 8 haplotypes were constructed based on rs59999573, rs59740167, and rs34489123 after linkage disequilibrium and haplotype analysis. Two SNPs (rs59805398 and rs34489123) and 5 haplotypes correlated with coronary atherosclerosis even after adjustment by Gensini score. At follow-up (median 53 months, range 1-60 months), 85 patients experienced CVE. However, there was no strong association between the gene polymorphisms and the occurrence of CVE.Tissue factor pathway inhibitor-2 gene polymorphisms were associated with coronary atherosclerosis in the Chinese population, suggesting that the information about TFPI-2 gene polymorphisms was useful for assessing the risk of developing coronary atherosclerosis, but there was not enough evidence showing it could predict occurrence of CVE.

Genetic analysis of clinical mastitis data for Holstein cattle in the Czech Republic

Abstract. Cases of mastitis were recorded from 22 812 lactations of 10 294 cows on seven farms in the Czech Republic from 2000 to 2012. The per cow number of clinical mastitis (CM) cases per lactation (CM1), number of days of CM per lactation (CM2), and CM considered as an all-or-none trait (CM3) with values of 0 (no CM case) or 1 (at least 1 CM case) were analyzed with linear animal models. Bivariate linear animal models were used for estimation of genetic correlations between CM traits and average lactation somatic cell score (SCS305), average 305-day milk (MY305), fat (FY305) and protein (PY305) yield, and interval between calving and first insemination (INT) and days open (DO). Factors included in the model of choice were parity, herd effect, year of calving, calving season, permanent environmental effect of the cow, and additive genetic effect of the cow. Estimated heritabilities for CM traits were in the range of 0.09 to 0.10. Genetic correlations of SCS305 with CM traits 1, 2, and 3 were 0.22 ± 0.062, 0.23 ± 0.064, and 0.29 ± 0.086, respectively; those of MY305 with the three CM traits were 0.80 ± 0.037, 0.79 ± 0.040, and 0.83 ± 0.038, respectively; those of INT with the three CM traits were 0.19 ± 0.087, 0.17 ± 0.089, and 0.26 ± 0.091, respectively; and those of DO with the three CM traits were 0.28 ± 0.089, 0.22 ± 0.091, and 0.27 ± 0.091, respectively. Knowledge of genetic parameters of mastitis incidence and assessment of the economic importance of the disease is necessary to design breeding programs to improve udder health.

Genetic mutations potentially cause two novel NCF1 splice variants up-regulated in the mammary gland, blood and neutrophil of cows infected by Escherichia coli

Neutrophil cytosolic factor 1 (NCF1) plays a crucial role in host defense against microbial pathogens. In this study, we investigated the potential alternative splicing patterns, expression and splice-relevant single nucleotide polymorphisms (SNPs) of the bovine NCF1 gene to increase insights into its potential role against bovine mastitis caused by Escherichia coli infection. Using RT-PCR and clone sequencing methods, we found two novel splice variants designed as NCF1-TV1 (retained intron 6) and NCF1-TV2 (retained part of intron 8), respectively, encoding two putative truncated proteins (239AA and 283AA). Two splice variants were drastically up-regulated in the mastitis-infected cows' mammary tissues, blood and neutrophils compared with these of healthy cows using real-time RT-PCR. Genomic sequencing analysis identified four novel SNPs g.10112 G>A, g.10766 T>C, SNPs g.12085 G>A and g.12430 T>C at the ends of intron 6 and intron 8 of NCF1. ESE motif predicted that the SNP (g.10766 T>C) might affect the binding with splicing-related factors and subsequently caused the production of aberrant splice variant NCF1-TV1, which is one of the potential reasons that the functional SNP was associated with increased milk somatic cell score in cow. Our results would help in better understanding the NCF1 gene function in the process against pathogen infection, and the effect of splicing-related SNP on the production of aberrant splice variant and careful functional characterization in dairy cattle.