Impact of STAT5A-CNVs on growth traits in Chinese beef cattle breeds.

CNVs, which are a type of structural variation, make a substantial impact on diverse characteristics in multiple species. Q-PCR and data association analysis were used for STAT5A gene copy in this study. This study aimed to investigate the copy number variation (CNV) of the STAT5A gene in seven Chinese cattle breeds, namely Qinchuan cattle, Xianan cattle, Yunling cattle, Ji'an cattle, Jiaxian Red cattle, Qaidam cattle, and Guyuan yellow cattle. Blood samples were collected for CNV typing, and the correlation between CNV type and growth traits was analyzed using SPSS 23.0 software and ANOVA. The findings revealed variations in the distribution of different copy number types among the different cattle breeds. Furthermore, association analysis demonstrated a positive impact of CNV in the STAT5A gene on cattle growth: in the JX, individuals with duplication types exhibited superior performance in terms of rump length (P < 0.05). Conversely, normal GY cattle demonstrated better body height and abdomen circumference (P < 0.05), while QD cattle exhibited a significant correlation between weight and body length with normal individuals (P < 0.05). Moreover, QC bovine duplication individuals outperformed other types, with copy number variation significantly associated with chest depth, chest width, and body length (P < 0.05). The results validate the correlation between copy number variation (CNV) of the STAT5A gene and growth characteristics in five different cattle breeds, providing a reliable benchmark for the purpose of cattle breeding.

mRNA sequencing provides new insights into the pathogenesis of Hirschsprung's disease in mice.

PURPOSE: The aim of this study is to use RNA sequencing and RT-qPCR to identify the main susceptibility genes linked to the occurrence and development of Hirschsprung disease in the colonic tissues of EDNRBm1yzcm and wild mice. METHODS: RNA was extracted from colon tissues of 3 mutant homozygous mice and 3 wild mice. RNA degradation, contamination concentration, and integrity were then measured. The extracted RNA was then sequenced using the Illumina platform. The obtained sequence data are filtered to ensure data quality and compared to the reference genome for further analysis. DESeq2 was used for gene expression analysis of the raw data. In addition, graphene oxide enrichment analysis and RT-qPCR validation were also performed. RESULTS: This study identified 8354 differentially expressed genes in EDNRBm1yzcm and wild mouse colon tissues by RNA sequencing, including 4346 upregulated genes and 4005 downregulated genes. Correspondingly, the results of RT-qPCR analysis showed good correlation with the transcriptome data. In addition, GO and KEGG enrichment results suggested that there were 8103 terms and 320 pathways in all DEGs. When P < 0.05, 1081 GO terms and 320 KEGG pathways reached a significant level. Finally, through the existing studies and the enrichment results of differentially expressed genes, it was determined that axon guidance and the focal adhesion pathway may be closely related to the occurrence of HSCR. CONCLUSIONS: This study analyzed and identified the differential genes in colonic tissues between EDNRBm1yzcm mice and wild mice, which provided new insight for further mining the potential pathogenic genes of Hirschsprung's disease.

Genomic analysis reveals a KIT-related chromosomal translocation associated with the white coat phenotype in yak.

White coat pigmentation is a striking phenotype of many domesticated species and has various genetic controls. The Tianzhu White yak, an indigenous breed with a complete white coat, has fascinated Tibetans for centuries. However, the genetic basis of this trait remains unknown. Here, we conducted population genomics analysis and genome-wide association study based on the whole-genome sequencing data of 38 white and 59 non-white-coated yak. The results revealed the presence of KIT-linked Cs alleles characterized by the translocations between chromosomes 6 and 29 in all-white yak. Furthermore, structural variations showed additional duplications of the Cs alleles in white yak compared with colour-sidedness cattle. Interestingly, the Cs alleles associated with the white coat phenotype in yak were found to have introgressed from taurine cattle. Our findings unveil the shared genetic control of the white coat phenotype and its evolution in closely related bovine species.

Insertion/deletions within the bovine FoxO1 gene and their association analysis with growth traits in three Chinese cattle breeds.

FOXO1 (FKHR) gene, as a transcription factor, plays a vital role in animal growth and development, participating in many biological processes. The aim of this study was to ascertain Insertion/deletions (Indels) polymorphism within bovine FoxO1 gene in 679 Chinese adult cows and associate them with stature traits. Two Indels (named as Indel-3 and Indel-4, recorded as rs383545622 and rs525318770 in NCBI, respectively) were successfully genotyped by the Once PCR method, which was reliable, rapid and cost effective for simultaneous detection of two or more Indels. Indel-3 and Indel-4 were located at the second intron. All four different haplotypes (H1: D3D4, H2: I3D4, H3: D3I4, H4: I3I4) could be identified, and the D (del-) allele, DD (del-/del-) genotype and D3D4 haplotype retained the highest frequency. However, individuals with DI (D3I3, D4I4 or H1H4/H2H3 genotype) showed significantly better phenotypic traits than those with the other genotypes in Nanyang cattle, showing a hybrid vigor. The results implied that this DI genotype can be applied to early selective breeding to improve the productivity of Nanyang cattle. Our results suggested that these two Indels within the bovine FoxO1 gene might be used as genetic markers for marker-assisted selection (MAS) in cattle breeding and genetics.

A SNP of the COX4I2 gene associated with environmental adaptation in Chinese cattle.

COX4I2 is an isoform of cytochrome C oxidase subunit IV (COX4), which plays an important role in mitochondrial oxidative phosphorylation. This gene affects heat production and thus affects thermoregulatory capacity in mammals. A splice region variant (rs109072064, NC_037340.1:g.61202988C > T) was identified in COX4I2 by using Ensembl, which transforms the amino acid arginine into cysteine in XP_005214921.1. In this study, we sought to determine the relationship between the mutant locus and the environment in which the cattle are located. We verified that mRNA (XM_005214864.4), which translated XP_005214921.1, is expressed in bovine muscle, fat, heart, liver, kidney, lung and testis tissues. The g.61202988C > T variant was then genotyped in 569 individuals of 34 cattle breeds. Compared with the CC genotype, southern cattle carried more the CT and TT genotypes. Furthermore, the association results carried out that the frequencies of genotypes (CC, CT, TT) and the value of climate parameters (mean annual temperature (T), relative humidity (RH) and temperature humidity index (THI)) were significantly correlated (P < 0.01). Hence, we speculated that the g.61202988C > T variant of COX4I2 gene was associated with the environmental adaptation trait in Chinese cattle and the locus may be considered as a molecular marker for Chinese cattle breeding.

CircRNA Profiling Reveals an Abundant circBDP1 that Regulates Bovine Fat Development by Sponging miR-181b/miR-204 Targeting Sirt1/TRARG1.

The proliferation and differentiation of preadipocytes is an important factor determining bovine fat development, which is closely related to the feed conversion ratio, carcass traits, and beef quality. The purpose of this study was to identify the effects of candidate circRNA and miRNA on the proliferation and differentiation of bovine preadipocytes in order to provide basic materials for molecular breeding in cattle. circRNA sequencing was performed on bovine adipocyte samples at different differentiation time points, and a total of 1830 differentially expressed circRNAs were identified. Among them, circBDP1, derived from the bovine BDP1 gene, has potential binding sites for miR-204 (known as a regulator of bovine fat development) and miR-181b, which gives us a hint that circBDP1 may regulate bovine fat development by adsorbing miR-204 and miR-181b. Here, our results revealed that circBDP1 overexpression promoted the proliferation and differentiation of bovine preadipocytes. The miRNA profile of bovine adipocytes at different differentiation time points was also analyzed using the small RNA sequencing method, and a total of 89 differentially expressed miRNAs were identified, including miR-204 and miR-181b. As expected, dual-luciferase reporter results showed that circBDP1 competitively adsorbed miR-181b and miR-204. Overexpression and interference of miR-181b in bovine preadipocytes and 3T3-L1 showed that miR-181b promoted the proliferation and differentiation of preadipocytes. Further results displayed that miR-181b and miR-204 simultaneously targeted the SIRT1 gene, and miR-204 also targeted the 3' UTR region of the TRARG1 gene. In summary, this study found that miR-181b and miR-204 were involved in fat development by targeting SIRT1 and TRARG1. The results of this study will lay a foundation for the research of fat development and beef cattle industry.

SNP within the bovine ASB-3 gene and their association analysis with stature traits in three Chinese cattle breeds.

ASB-3 is one of the 18 members of ASB gene family. As a special negative regulation factor of TNF-R2, ASB-3 inhibits the signal transduction of JNK-TNF-R2 and JNK-STAT signaling pathway by TNF-R2 protein. In this study, the genetic polymorphisms of ASB-3 were detected in total of 637 from Qinchuan, Jinnan and Xianan cattle using the sequence of mixed DNA pool, Tetra-primer ARMS-PCR and PCR-RFLP methods. Four mutation sites were detected including the g.C41255T, g.G74754A, and g.T75438C were synonymous mutation, whereas the g.C115213T was missense mutation (Pro > Ser). The associated analysis of four polymorphic loci of ASB-3 gene respectively with growth traits in the three cattle breeds. The result showed that SNP1 site was significantly related with Qinchuan cattle height and TT was the dominant genotype; SNP2 had a significant relationship with body length of Xianan cattle and cross department height of Qinchuan cattle, AA was the dominant genotype; SNP3 was significantly related to cross height of Xianan cattle, TT was the dominant genotype; SNP4 site was significantly correlated with body height of Xianan cattle and cross height of Jinnan cattle. Genotype combinations were only significantly correlated with the hucklebone width in the adult Qinchuan cattle. The combination genotype CTAGCTCC was outperformed other combination genotypes of Qinchuan cattle. The results showed that ASB-3 could be an important candidate gene and the four SNPs in ASB-3 can be used for molecular marker-assisted selection of four beef cattle breeds.

Pleomorphic adenoma gene 1 (PLAG1) promotes proliferation and inhibits apoptosis of bovine primary myoblasts through the PI3K-Akt signaling pathway.

Pleomorphic adenoma gene 1 (PLAG1) is a transcription factor involved in various cellular processes in organismal growth and development. However, its role in muscle function is unclear. This work investigated the roles of PLAG1 in muscle development and explored its regulatory mechanisms. The PLAG1 was proved to promote the proliferation of bovine primary myoblasts using the cell counting kit 8 (CCK-8) assay (P < 0.001), 5-ethynyl-2'-deoxyuridine (EdU) proliferation assay (P = 0.005), quantitative real-time polymerase chain reaction (qRT-PCR) (P = 0.028), western blot, and flow cytometry (P < 0.05), and to inhibit apoptosis of bovine primary myoblasts using qRT-PCR (P = 0.038), western blot, and flow cytometry (P < 0.001). Chromatin immunoprecipitation sequencing (ChIP-seq) and western blot showed PLAG1 upregulated phosphorylated (p)-PI3K, PI3K, p-Akt, Akt, Cyclin D1, and CDK2 and inhibited the expression of p21 and p27 to enhance myoblast proliferation, and increased expression of Bcl-2, and Bcl-xL to inhibit apoptosis. Additionally, PLAG1 was identified as a target of miR-1 using dual-luciferase assay (P < 0.001), qRT-PCR (P < 0.001), and western blot. Furthermore, miR-1 might be a potential mediator of the positive feedback regulation relationship between PLAG1 and the PI3K-Akt signaling pathway.

Pleomorphic adenoma gene 1 (PLAG1) is a critical candidate gene that affects bovine stature and height. Past studies have focused on correlations between PLAG1 and quantitative traits. However, few studies have focused on studying the function of PLAG1 at the cellular level. Here, we investigated the effects of PLAG1 on bovine primary myoblasts and found it promoted proliferation and inhibited the apoptosis of bovine primary myoblasts. In addition, our study demonstrated that the effects of PLAG1 on myoblast proliferation and apoptosis were through the PI3K-Akt signaling pathway. Further study suggested that there was a potential positive feedback regulation between PLAG1 and PI3K-Akt, and miR-1 acted as a key mediator. Our study provided a theoretical basis for further exploration.

The copy number variation of DMBT1 gene effects body traits in two Chinese cattle breeds.

Copy number variations (CNVs) belong to mutations in the genome level with loci in the region of genic or intergenic. It is through different effects (such as position effect and dose effect) that influence complex traits and diseases. Deleted in Malignant Brain Tumors 1 (DMBT1) gene is a member of the scavenger receptor cysteine-rich super family. In cattle, this gene has been associated with the susceptibility to bovine tuberculosis. In this study, a new CNV was found in DMBT1 gene of Chinese cattle breeds and tested in two different Chinese cattle breeds (Jiaxian red and Pinan) for frequency distribution analysis. Besides, the body size data such as body length, body height, chest girth, chest width, rump length, and rump girth for Jiaxian (JX) and Pinan (PN) cattle were collected and associated with the newly identified CNV. The CNV was significantly associated with the body length and chest girth of JX cattle, and the rump length of PN cattle (P < 0.05). Furthermore, the expression profile of the DMBT1 gene was tested in calves' tissues and the myoblasts differentiation. It was found that the DMBT1 gene expression was high in tuberculosis susceptible tissues (liver and lungs) at the calf stage and high in myoblast early differentiation. These tests were done using the qPCR method. As the result, the CNV of DMBT1 gene could be used as a candidate marker for bovine growth and health in marker-assisted selection (MAS) breeding.

Distribution and association study of PLAG1 gene between copy number variation and Chinese cattle populations.

Copy number variation mainly refers to the copy number change of DNA fragments from 1 to 5 Mb. The deletion, duplication, inversion and ectopic of these fragments are collectively referred to as CNV. Numerous studies have shown that transfer factors play a vital role in regulating the growth and development of the body, for example the pleomorphic adenoma gene (PLAG). However, there is no study of CNV in PLAG1 gene. We qualified copy numbers within PLAG1 gene in 8 cattle breeds (Qinchuan, Qaidamu, Jinjiang, Guangfeng, Ji'an, Jiaxian, Pinan and Xianan cattle) by quantitative PCR, and explored their impacts on CNV of PLAG1 gene and phenotypic traits in Xianan cattle. We defined Deletion into CN = 0, Normal into CN = 1 and Duplication into CN = 2. The results showed that the individual with type of CN = 1 has a significant better effect on heart girth in JA cattle population (p < 0.01); the individual with type of CN = 1 and CN = 0 has a better effect on Rump length in JX cattle population (p < 0.05); the individual with type of CN = 0 has a better effect on cannon bone circumference in XN cattle population (p < 0.05). Association analysis showed that in JA cattle, the number of CN = 2 is great in JA cattle population, and the performance of CN = 2 in heart girth is better than CN = 1; in JX cattle, the rump length of CN = 2 is less than individual with CN = 0 and CN = 1; in XN cattle, individuals with CN = 0 have a better performance on cannon bone circumference than others. The results can provide a theoretical basis for molecular breeding of Chinese cattle, molecular mark-assist selection (MAS) of growth traits of Chinese cattle, and rapidly establish a Chinese cattle population with excellent genetic resources. Simple summaryWith the living standards rising, people's demand for beef is getting higher and higher, and there is a great significance to improve the growth performance of cattle. We measured body size data and detected copy number type of different cattle breeds (Xianan cattle, Ji'an cattle and Jiaxian cattle), and analyzed the correlation between the two object. We found that copy number variation of PLAG1 gene significantly affected some growth traits of XN cattle, JA cattle, and JX cattle. This may provide the basic material for molecular marker-assisted selection breeding of Chinese cattle breeds.

Effect of copy number variation of PLA2G2A gene to growth traits in Chinese cattle.

SIMPLE SUMMARY: As a member of genetic polymorphism, copy number variation has been a commonly used method in the world for investigating effect of genetic polymorphism on gene expression. Effect of genetic polymorphism made on livestock development has been more and more important in beef cattle molecular breeding. The characteristics of Chinese cattle are excellent meat quality, tolerant to rough feeding, good environmental adaptability and so on. But there are some obvious weaknesses still exist in the process of cattle growth and development, such as weak hindquarters and growth slowly. To improve the growth performance and market competitiveness of Chinese cattle, a lot of studies have been made about finding and investigating effective molecular marker. In this study, Q-PCR and data association analysis were used for PLA2G2A gene copy number variation detection and related effect analysis in Chinese cattle. Results showed that PLA2G2A gene has a significant effect on two breeds of Chinese cattle on growth traits, which could be a basic materials and effective information of cattle molecular markers breeding. PLA2G2A, member of secreted phospholipases A2 (sPLA2) in superfamily of phospholipase A2, could catalyze the process of glycerophospholipids hydrolysis from position of sn-2 acyl with the release of free fatty acids and lysophospholipids. Researches about PLA2G2A gene are mostly focus on disease, including tumors and diabetes, the number of study occurred on animal breeding is weak. In this study, blood samples were collected from five breeds of Chinese cattle (Qingchuan cattle, Xianan cattle, Yunling cattle, Pinan cattle and Guyuan cattle) for PLA2G2A gene CNV type detection. SPSS 20.0 software and method of ANOVA were used to analyzed the association between types of CNV and growth traits. Results reveal that the distribution of different copy number types in different cattle breeds is different. In QC, XN and GY cattle, the frequencies of Deletion and Duplication are about 40%; in YL cattle, the frequency of Deletion type exceeds 60%; in PN cattle, the frequency of Duplication is closed to 80%. Association analysis indicate that CNV of PLA2G2A gene showed a positive effect in cattle growth: in QC cattle, Chest depth with Normal type copy number possess a increased trend (P < 0.05); individuals with Deletion type copy number have better performance on Height at sacrum, Heart girth and Body height in GY cattle (P < 0.05). The functional role and molecular mechanism of PLA2G2A gene in animal growth and development are still unclear, and it is necessary for processing a further research. This research aims to provide basic materials for molecular breeding of Chinese cattle.

Copy number variation of bovine DYNC1I2 gene is associated with body conformation traits in chinese beef cattle.

Previous, studies have shown that the dynein transporter compound has a role in diseases such as intellectual disability and cerebral malformations. However, the study of CNV in DYNC1I2 gene has not been reported. Q-PCR and data association analysis were used for DYNC1I2 gene copy in this study. In this study, blood samples were collected from five breeds of Chinese cattle (Qingchuan cattle, Xianan cattle, Yunling cattle, Pinan cattle and Guyuan cattle) for DYNC1I2 gene CNV type detection. SPSS 20.0 software and method of ANOVA were used to analyzed the association between types of CNV and growth traits. Results reveal that the distribution of different copy number types in different cattle breeds is different. Association analysis indicate that CNV of DYNC1I2 gene showed a positive effect in cattle growth: in XN cattle, individuals with deletion types showed better performance on height at hip cross (P < 0.05); individuals with duplication types have better performance on body length (P < 0.05) in PN cattle; individuals with deletion types was significantly correlated with chest width and Hucklebone width (P < 0.05) in QC cattle; individuals with duplication types in Yunling cattle were better than the normal types, and there was a significant correlation between copy number variant and chest depth (P < 0.05). The results showed that CNV markers closely related to cattle production traits were detected at DNA level, which could be used as an important candidate molecular marker for marker-assisted selection of growth traits in Chinese cattle, and provided a new research basis for genetics and breeding of Chinese beef cattle.

CircRILPL1 promotes muscle proliferation and differentiation via binding miR-145 to activate IGF1R/PI3K/AKT pathway.

Many novel non-coding RNAs, such as microRNAs (miRNAs) and circular RNAs (circRNAs), are involved in various physiological and pathological processes. The PI3K/AKT signaling pathway is important for its role in regulating skeletal muscle development. In this study, molecular and biochemical assays were used to confirm the role of miRNA-145 (miR-145) in myoblast proliferation and apoptosis. Based on sequencing data and bioinformatics analysis, we identified a new circRILPL1, which acts as a sponge for miR-145. The interactions between circRILPL1 and miR-145 were examined by bioinformatics, a luciferase assay, and RNA immunoprecipitation. Mechanistically, knockdown or exogenous expression of circRILPL1 in the primary myoblasts was performed to prove the functional significance of circRILPL1. We investigated the inhibitory effect of miR-145 on myoblast proliferation by targeting IGF1R to regulate the PI3K/AKT signaling pathway. A novel circRILPL1 was identified that could sponge miR-145 and is related to AKT activation. In addition, circRILPL1 was positively correlated with muscle proliferation and differentiation in vitro and could inhibit cell apoptosis. The newly identified circRILPL1 functions as a miR-145 sponge to regulate the IGF1R gene and rescue the inhibitory effect of miR-145 on the PI3K/AKT signaling pathway, thereby promoting myoblast growth.

Circular RNA circMYL1 Inhibit Proliferation and Promote Differentiation of Myoblasts by Sponging miR-2400.

Circular RNAs (circRNAs) are a class of endogenous non-coding RNAs (ncRNAs) involved in regulating skeletal muscle development by sponging miRNAs. In this study, we found that the circMYL1 expression was down-regulated during myoblast proliferation, while gradually up-regulated in myoblast differentiation. The potential role of circMYL1 was identified in the proliferation of bovine myoblast through mRNA and protein expression of proliferation marker genes (PCNA, CyclinD1, and CDK2), cell counting kit-8 assay, flow cytometry analysis, and 5-ethynyl 2'-deoxyuridine (EdU) assay. Analysis of the expression of differentiation marker genes (MyoD, MyoG, and MYH2) and immunofluorescence of Myosin heavy chain (MyHC) was used to assess cell differentiation. The proliferation analysis revealed that circMYL1 inhibited the proliferation of bovine primary myoblast. Furthermore, the differentiation analysis demonstrated that circMYL1 promoted the differentiation of bovine primary myoblast. The luciferase screening and RNA immunoprecipitation (RIP) assays found that circMYL1 could have interaction with miR-2400. Additionally, we demonstrated that miR-2400 promoted proliferation and inhibited differentiation of bovine primary myoblast, while circMYL1 may eliminate the effects of miR-2400, as showed by rescue experiments. Together, our results revealed that a novel circular RNA of circMYL1 could inhibit proliferation and promote differentiation of myoblast by sponging miR-2400.

Insight into m6A methylation from occurrence to functions.

RNA m6A methylation is a post-transcriptional modification that occurs at the nitrogen-6 position of adenine. This dynamically reversible modification is installed, removed and recognized by methyltransferases, demethylases and readers, respectively. This modification has been found in most eukaryotic mRNA, tRNA, rRNA and other non-coding RNA. Recent studies have revealed important regulatory functions of the m6A including effects on gene expression regulation, organism development and cancer development. In this review, we summarize the discovery and features of m6A, and briefly introduce the mammalian m6A writers, erasers and readers. Finally, we discuss progress in identifying additional functions of m6A and the outstanding questions about the regulatory effect of this widespread modification.

Identification of Genomic Characteristics and Selective Signals in a Du'an Goat Flock.

The Du'an goat is one of the most important farm animals in the Guangxi Autonomous Region of China, but the genetic basis underlying its adaptive traits has still not been investigated. Firstly, in this study, the genomes of 15 Du'an goats from a breeding farm were sequenced (mean depth: 9.50X) to analyze the patterns of genetic variation. A comparable diversity (17.3 million single nucleotide polymorphisms and 2.1 million indels) was observed to be associated with a lower runs of homozygosity-based inbreeding coefficient and smaller effective population size in comparison with other breeds. From selective sweep and gene set enrichment analyses, we revealed selective signals related to adaptive traits, including immune resistance (serpin cluster, INFGR1, TLR2, and immune-related pathways), body size (HMGA2, LCOR, ESR1, and cancer-related pathways) and heat tolerance (MTOR, ABCG2, PDE10A, and purine metabolism pathway). Our findings uncovered the unique diversity at the genomic level and will provide the opportunities for improvement of productivity in the Du'an goat.

Association analysis of KMT2D copy number variation as a positional candidate for growth traits.

Copy number variations (CNVs) are an important source of genetic variation, which can affect a wide range of economic traits by diverse mechanisms. KMT2D (Lysine methyltransferase 2D) is an important positional candidate for growth traits. Quantitative trait loci (QTLs) with large effects on economically important traits cover the KMT2D gene. The KMT2D gene overlays a CNV within its exons, hence it was chosen as a crucial candidate gene to study the association between CNV and growth traits. Further, KMT2D, a major mammalian histone H3K4 mono-methyltransferase, plays a critical role in regulating development, differentiation, metabolism, and tumor suppression. Therefore, we proposed the hypothesis that KMT2D CNV may have phenotypic effects on sheep growth traits. In our study, KMT2D CNVs in three Chinese sheep breeds were detected by quantitative polymerase chain reaction (qPCR), and the loss copy was found to be the dominant genotype. Association analysis between growth traits and KMT2D CNV was also performed, which revealed that individuals with the median copy showed better performance than those with the loss copy in all three breeds. This research suggested that KMT2D CNV can be used as a promising marker for sheep molecular breeding.

Genetic variant of SPARC gene and its association with growth traits in Chinese cattle.

SPARC is a cysteine-rich acidic secreted protein. It is a non-collagen component of bone, which is widely distributed in humans and animals and plays an important role. SPARC has been found in a variety of human cancers (breast cancer, stomach cancer, ovarian cancer, etc.) and diabetes-related research. Especially the muscle and fat metabolism are closely related. In this study, we used a DNA pool to detect a new SNP site (g.12454T  >  C). A total of 616 samples of four breeds of Qinchuan cattle (QC, n = 176 ), Xianan cattle (XN, n = 160 ), Pinan cattle (PN, n = 136 ) and Jiaxian cattle (JX, n = 144 ) were analyzed and identified with ARMS-PCR. In addition, we correlated SNP with growth traits and showed significant correlation with growth traits such as rump length, hip width, and body length ( p < 0.05 ). Moreover, we tested the SPARC gene expression level in different tissues belonging to XN adult cattle ( n = 3 ) and found its high expression in muscle tissues (relative to the kidney). Further, we found the SNP is able to increase the SPARC expression level in skeletal muscle ( n = 12 ). According to statistical data, this SNP site may be applied to a molecular marker of an early marker-assisted selection for early growth of beef cattle.

Comparative Transcriptomics Analysis of Testicular miRNA from Cryptorchid and Normal Horses.

In the biological process of testicular spermatogenesis, the expression and interaction of many genes are regulated by microRNAs (miRNAs). However, comparisons of miRNA expression between descended testes (DTs) and undescended testes (UDTs) are rarely done in horses. In this study, we selected two UDTs (CKY2b and GU4b) from Chakouyi (CKY) and Guanzhong (GU) horses and eight DTs (GU1-3, CKY1, CKY3, CKY2a, GU4a, and GU5). Three groups were compared to evaluate expression patterns of testicular miRNA in stallion testes. Group 1 compared normal CKY horses and GU horses (CKY1 and CKY3 vs. GU1-3). Group 2 (CKY2a and GU4a (DTs) vs. CKY2b and GU4b (UDTs)) and group 3 (GU1-3, CKY1, CKY3 (DTs) vs. CKY2b and GU4b (UDTs)) compared the expression levels in unilateral retained testes to normal testes. The results show that 42 miRNAs (7 upregulated and 35 downregulated) had significantly different expression levels in both comparisons. The expression levels of eca-miR-545, eca-miR-9084, eca-miR-449a, eca-miR-9024, eca-miR-9121, eca-miR-8908e, eca-miR-136, eca-miR-329b, eca-miR-370, and eca-miR-181b were further confirmed by quantitative real-time PCR assay. The target genes of differentially expressed miRNAs in three comparisons were predicted, and the functions were annotated. The putative target genes of the 42 co-differentially expressed miRNAs were annotated to 15 functional terms, including metal ion binding, GTPase activator activity, zinc ion binding, intracellular, cytoplasm, and cancer pathways, and osteoclast differentiation. Our data indicate that the differentially expressed miRNAs in undescended testis suggests a potential role in male fertility and a relationship with cryptorchidism in horses. The discovery of miRNAs in stallion testes might contribute to a new direction in the search for biomarkers of stallion fertility.

The Distribution Characteristics of a 19-bp Indel of the PLAG1 Gene in Chinese Cattle.

Pleomorphic adenoma gene 1 (PLAG1) belongs to the PLAG family of zinc finger transcription factors. In cattle, a 19-bp insertion/deletion (indel) was identified in intron 1 of the PLAG1 gene (GenBank Accession No. AC_000171.1). Researches showed that the indel is polymorphic in Chinese cattle breeds such as Qinchuan cattle, Pinan cattle, Xianan cattle, and Jiaxian red cattle, and correlation analysis showed that the polymorphism is related to the height of these cattle breeds. Chinese cattle breeds show a difference in height related to geographical distribution. We investigated the distribution of the 19-bp indel polymorphism in 37 cattle breeds, including 1354 individuals. The results showed that there were three genotypes and two alleles (W, 366 bp; D, 347 bp). From northern cattle to southern cattle, the frequency of W allele gradually decreased, while the frequency of D allele showed an opposite trend, which was consistent with the distribution of cattle breeds of different height in China. Therefore, the polymorphism of this indel may be related to the regional distribution of cattle breeds in China. In addition, we chose Yunling cattle with a mixed genetic background to study the genetic effects of the 19-bp indel on body size traits. Statistical analysis showed that PLAG1 was significantly associated with the body height, cross height, and chest circumference of Yunling cattle (p < 0.05). This study provides new evidence that the 19-bp indel of the PLAG1 gene is a highly effective trait marker that can be used as a candidate molecular marker for cattle breeding.