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Find video protocols related to scientific articles indexed in Pubmed.
Two novel polymorphisms of bovine SIRT2 gene are associated with higher body weight in Nanyang cattle.
Mol. Biol. Rep.
PUBLISHED: 11-08-2014
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Identification of polymorphisms associated with economic traits is important for successful marker-assisted selection in cattle breeding. The family of mammalian sirtuin regulates many biological functions, such as life span extension and energy metabolism. SIRT2, a most abundant sirtuin in adipocytes, acts as a crucial regulator of adipogenic differentiation and plays a key role in controlling adipose tissue function and mass. Here we investigated single nucleotide polymorphisms (SNPs) of bovine SIRT2 in 1226 cattle from five breeds and further evaluated the effects of identified SNPs on economically important traits of Nanyang cattle. Our results revealed four novel SNPs in bovine SIRT2, one was located in intronic region and the other three were synonymous mutations. Linkage disequilibrium and haplotype analyses based on the identified SNPs showed obvious difference between crossbred breed and the other four beef breeds. Association analyses demonstrated that SNPs g.17333C > T and g.17578A > G have a significantly effect on 18-months-old body weight of Nanyang population. Animals with combined genotype TTGG at the above two loci exhibited especially higher body weight. Our data for the first time demonstrated that polymorphisms in bovine SIRT2 are associated with economic traits of Nanyang cattle, which will be helpful for future cattle selection practices.
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Detection of copy number variations and their effects in Chinese bulls.
BMC Genomics
PUBLISHED: 06-10-2014
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Copy number variations (CNVs) are a main source of genomic structural variations underlying animal evolution and production traits. Here, with one pure-blooded Angus bull as reference, we describe a genome-wide analysis of CNVs based on comparative genomic hybridization arrays in 29 Chinese domesticated bulls and examined their effects on gene expression and cattle growth traits.
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Identification of bovine NPC1 gene cSNPs and their effects on body size traits of Qinchuan cattle.
Gene
PUBLISHED: 02-24-2014
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NPC1 gene is an important gene closely related to the Niemann-Pick type C (NPC). Mutations in the NPC1 gene tend to cause Niemann-Pick type C, a lysosomal storage disorder. Previous studies have shown that NPC1 protein plays an important role in subcellular lipid transport, homeostasis, platelet function and formation, which are basic metabolic activities in the process of development. In this study, to explore the association between the NPC1 gene variation and body size traits in Qinchuan cattle, we detected four novel coding single nucleotide polymorphisms (cSNPs) in the bovine NPC1 gene, including one missense mutation (SNP1) and three synonymous mutations (SNP2, SNP3 and SNP4). Population genetic analyses of 518 individuals and association correlations between cSNPs and bovine body size traits were conducted in this research. A missense mutation at SNP1 locus was found to be significantly related to the heart girth, hip width and body weight (P<0.01 or P<0.05, 3.5-year-old). Two synonymous mutations at SNP2 and SNP3 loci also showed significant effects on hip width (P<0.05, 3.5-year-old). One synonymous mutation at SNP4 locus showed significant effect on body weight (P<0.05, 2.0-year-old). Combined haplotypes H2H6 and H6H6 showed significant effects on body size traits such as heart girth, hip width, and body weight (3.5-year-old, P<0.01 or P<0.05). This study provides evidence that the NPC1 gene might be involved in the regulation of bovine growth and body development, and may be considered as a candidate gene for marker assisted selection (MAS) in beef cattle breeding industry.
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SNP and haplotype analysis of paired box 3 (PAX3) gene provide evidence for association with growth traits in Chinese cattle.
Mol. Biol. Rep.
PUBLISHED: 02-14-2014
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Paired box 3 (PAX3) belongs to the PAX superfamily of transcription factors and plays essential roles in the embryogenesis and postnatal formation of limb musculature through affecting the survival of muscle progenitor cells. By genetic mapping, PAX3 gene is assigned in the interval of quantitative trait loci for body weight on bovine BTA2. The objectives of this study were to detect polymorphisms of PAX3 gene in 1,241 cattle from five breeds and to investigate their effects on growth traits. Initially, three novel single nucleotide polymorphisms (SNPs) were identified by DNA pool sequencing and aCRS-RFLP methods (AC_000159: g.T-580G, g.A4617C and g.79018Ins/del G), which were located at 5'-UTR, exon 4 and intron 6, respectively. A total of eight haplotypes were constructed and the frequency of the three main haplotypes H1 (TAG), H2 (GCG) and H3 (GAG) accounted for over 81.7 % of the total individuals. Statistical analysis revealed that the three SNPs were associated with body height and body length of Nanyang and Chinese Caoyuan cattle at the age of 6 and/or 12 months old (P < 0.05), and consistently significant effects were also found in the haplotype combination analysis on these traits (P < 0.05). This study presented a complete scan of variations within bovine PAX3 gene, which could provide evidence for improving the economic traits of cattle by using these variations as potentially genetic markers in early marker-assisted selection programs.
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When and how did Bos indicus introgress into Mongolian cattle?
Gene
PUBLISHED: 01-11-2014
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The Mongolian cattle are one of the most widespread breeds with strictly Bos taurus morphological features in northern China. In our current study, we presented a diversity of mitochondrial DNA (mtDNA) D-loop region and Y chromosome SNP markers in 25 male and 8 female samples of Mongolian cattle from the Xinjiang Uygur autonomous region in Western China, and detected 21 B. taurus and four Bos indicus (zebu) mtDNA haplotypes. Among four B. indicus mtDNA haplotypes, two haplotypes belonged to I1 haplogroup and the remaining two haplotypes belonged to I2 haplogroup. In contrast, all 25 male Mongolian cattle samples revealed B. taurus Y chromosome haplotype and no B. indicus haplotypes were found. Historical and archeological records indicate that B. taurus was introduced to Xinjiang during the second millennium BC and B. indicus appeared in this region by the second century AD. The two types of cattle coexisted for many centuries in Xinjiang, as depicted in clay and wooden figurines unearthed in the Astana cemetery in Turfan (3rd-8th century AD). Multiple lines of evidence suggest that the earliest B. indicus introgression in the Mongolian cattle may have occurred during the 2nd-7th centuries AD through the Silk Road around the Xinjiang region. This conclusion differs from the previous hypothesis that zebu introgression to Mongolian cattle happened during the Mongol Empire era in the 13th century.
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Comparative transcriptome analysis reveals significant differences in MicroRNA expression and their target genes between adipose and muscular tissues in cattle.
PLoS ONE
PUBLISHED: 01-01-2014
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The posttranscriptional gene regulation mediated by microRNAs (miRNAs) plays an important role in various species. However, to date limited miRNAs have been reported between fat and muscle tissues in beef cattle. In this paper, 412 known and 22 novel miRNAs in backfat as well as 334 known and 10 novel miRNAs in longissimus thoracis were identified in the Chinese Qinchuan beef cattle. Bta-miR-199a-3p, -154c, -320a and -432 were expressed at higher levels in backfat tissue, while bta-miR-1, -133a, -206, and -378 were also significantly enriched in muscle tissue. Functional analysis revealed that fat-enriched miRNAs targeted PRKAA1/2, PPARA and PPARG genes to modulate lipid and fatty acid metabolism, and muscle-enriched miRNAs targeted CSRP3 gene to present function involved in skeletal and muscular system development. The results obtained may help in the design of new selection strategies to improve beef quality.
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Characterization of transcriptional complexity during adipose tissue development in bovines of different ages and sexes.
PLoS ONE
PUBLISHED: 01-01-2014
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Adipose tissue has long been recognized to play an extremely important role in development. In bovines, it not only serves a fundamental function but also plays a key role in the quality of beef and, consequently, has drawn much public attention. Age and sex are two key factors that affect the development of adipose tissue, and there has not yet been a global study detailing the effects of these two factors on expressional differences of adipose tissues.
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Identification and profiling of microRNAs and their target genes from developing caprine skeletal Muscle.
PLoS ONE
PUBLISHED: 01-01-2014
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Goat is an important agricultural animal for meat production. Functional studies have demonstrated that microRNAs (miRNAs) regulate gene expression at the post-transcriptional level and play an important role in various biological processes. Although studies on miRNAs expression profiles have been performed in various animals, relatively limited information about goat muscle miRNAs has been reported. To investigate the miRNAs involved in regulating different periods of skeletal muscle development, we herein performed a comprehensive research for expression profiles of caprine miRNAs during two developmental stages of skeletal muscles: fetal stage and six month-old stage. As a result, 15,627,457 and 15,593,721 clean reads were obtained from the fetal goat library (FC) and the six month old goat library (SMC), respectively. 464 known miRNAs and 83 novel miRNA candidates were identified. Furthermore, by comparing the miRNA profile, 336 differentially expressed miRNAs were identified and then the potential targets of the differentially expressed miRNAs were predicted. To understand the regulatory network of miRNAs during muscle development, the mRNA expression profiles for the two development stages were characterized and 7322 differentially expressed genes (DEGs) were identified. Then the potential targets of miRNAs were compared to the DEGs, the intersection of the two gene sets were screened out and called differentially expressed targets (DE-targets), which were involved in 231 pathways. Ten of the 231 pathways that have smallest P-value were shown as network figures. Based on the analysis of pathways and networks, we found that miR-424-5p and miR-29a might have important regulatory effect on muscle development, which needed to be further studied. This study provided the first global view of the miRNAs in caprine muscle tissues. Our results help elucidation of complex regulatory networks between miRNAs and mRNAs and for the study of muscle development.
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Discovery of novel and differentially expressed microRNAs between fetal and adult backfat in cattle.
PLoS ONE
PUBLISHED: 01-01-2014
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The posttranscriptional gene regulation mediated by microRNAs (miRNAs) plays an important role in various species. Recently, a large number of miRNAs and their expression patterns have been identified. However, to date, limited miRNAs have been reported to modulate adipogenesis and lipid deposition in beef cattle. Total RNAs from Chinese Qinchuan bovine backfat at fetal and adult stages were used to construct small RNA libraries for Illumina next-generation sequencing. A total of 13,915,411 clean reads were obtained from a fetal library and 14,244,946 clean reads from an adult library. In total, 475 known and 36 novel miRNA candidates from backfat were identified. The nucleotide bias, base editing, and family of the known miRNAs were also analyzed. Based on stem-loop qPCR, 15 specific miRNAs were detected, and the results showed that bta-miRNAn25 and miRNAn26 were highly expressed in backfat tissue, suggesting these small RNAs play a role in the development and maintenance of bovine subcutaneous fat tissue. Putative targets for miRNAn25 and miRNAn26 were predicted, and the 61 most significant target transcripts were related to lipid and fatty acid metabolism. Of interest, the canonical pathway and gene networks analyses revealed that PPAR?/RXR? activation and LXR/RXR activation were important components of the gene interaction hierarchy results. In the present study, we explored the backfat miRNAome differences between cattle of different developmental stages, expanding the expression repertoire of bovine miRNAs that could contribute to further studies on the fat development of cattle. Predication of target genes analysis of miRNA25 and miRNA26 also showed potential gene networks that affect lipid and fatty acid metabolism. These results may help in the design of new intervention strategies to improve beef quality.
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An Asp7Gly substitution in PPARG is associated with decreased transcriptional activation activity.
PLoS ONE
PUBLISHED: 01-01-2014
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As the master regulator of adipogenesis, peroxisome proliferator-activated receptor gamma (PPARG) is required for the accumulation of adipose tissue and hence contributes to obesity. A previous study showed that the substitution of +20A>G in PPARG changed the 7(th) amino acid from Asp to Gly, creating a mutant referred to as PPARG Asp7Gly. In this study, association analysis indicated that PPARG Asp7Gly was associated with lower body height, body weight and heart girth in cattle (P<0.05). Overexpression of PPARG in NIH3T3-L1 cells showed that the Asp7Gly substitution may cause a decrease in its adipogenic ability and the mRNA levels of CIDEC (cell death-inducing DFFA-like effector c) and aP2, which are all transcriptionally activated by PPARG during adipocyte differentiation. A dual-luciferase reporter assay was used to analyze the promoter activity of CIDEC. The results confirmed that the mutant PPARG exhibited weaker transcriptional activation activity than the wild type (P<0.05). These findings likely explain the associations between the Asp7Gly substitution and the body measurements. Additionally, the Asp7Gly mutation may be used in molecular marker assisted selection (MAS) of cattle breeding in the future.
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The novel coding region SNPs of PPARGC1A gene and their associations with growth traits in Chinese native cattle.
Mol. Biol. Rep.
PUBLISHED: 10-26-2013
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The peroxisome proliferator-activated receptor gamma coactivator-1 alpha protein, encoded by the PPARGC1A gene, is a metabolic switch, which transcriptionally activates a complex pathway of mitochondrial biogenesis, lipid and glucose metabolism. Three SNPs (exon 3 c.396G>A, intron 9 c.1892 + 19C>T and exon 10 c.1971C>T) were found and identified in three Chinese native cattle breeds by PCR-SSCP, PCR-RFLP and DNA sequencing methods. All three populations had a low genetic diversity at SNP396 locus (PIC <0.25) while possessed a moderate genetic diversity at SNP1892 locus (0.25 < PIC < 0.5). Association study indicated that the synonymous mutation c.396G>A significantly associated with body weight and average daily gain in Nanyang cattle at the adult age (P < 0.05). Our investigation will not only extend the spectrum of genetic variation of bovine PPARGC1A gene, but also provide useful information for the marker assisted selection in beef cattle breeding program.
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Association analysis of bovine Foxa2 gene single sequence variant and haplotype combinations with growth traits in Chinese cattle.
Gene
PUBLISHED: 10-03-2013
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Forkhead box A2 (Foxa2) has been recognized as one of the most potent transcriptional activators that is implicated in the control of feeding behavior and energy homeostasis. However, similar researches about the effects of genetic variations of Foxa2 gene on growth traits are lacking. Therefore, this study detected Foxa2 gene polymorphisms by DNA pool sequencing, PCR-RFLP and PCR-ACRS methods in 822 individuals from three Chinese cattle breeds. The results showed that four sequence variants (SVs) were screened, including two mutations (SV1, g. 7005 C>T and SV2, g. 7044 C>G) in intron 4, one mutation (SV3, g. 8449 A>G) in exon 5 and one mutation (SV4, g. 8537 T>C) in the 3UTR. Notably, association analysis of the single mutations with growth traits in total individuals (at 24months) revealed that significant statistical difference was found in four SVs, and SV4 locus was highly significantly associated with growth traits throughout all three breeds (P<0.05 or P<0.01). Meanwhile, haplotype combination CCCCAGTC also indicated remarkably associated to better chest girth and body weight in Jiaxian Red cattle (P<0.05). We herein described a comprehensive study on the variability of bovine Foxa2 gene that was predictive of molecular markers in cattle breeding for the first time.
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Associations of MYH3 gene copy number variations with transcriptional expression and growth traits in Chinese cattle.
Gene
PUBLISHED: 09-14-2013
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Copy number variations (CNVs) have been recently recognized as another important genetic variability complementary to single nucleotide polymorphisms (SNPs). Compelling evidence has indicated that CNVs are responsible for phenotypic traits by changing the copy numbers of functional genes. Myosin heavy chain 3 (MYH3) gene is a critical regulatory factor in skeletal muscle development, and has been detected in the CNVs region by comparative genomic hybridization (CGH) array. This study was conducted to validate and detect the distribution of MYH3 copy numbers (relative to Angus cattle) in four Chinese cattle breeds (NY, QC, LX, and CY), and further to investigate the associations of the copy number changes with its transcriptional expression and cattle growth traits. Substantial genetic differences of MYH3 copy numbers were identified between NY and the other three breeds (P<0.01). The copy numbers of MYH3 gene presented the positive correlations with the transcript level of MYH3 gene in both fetal and adult skeletal muscles (P<0.05). Statistical analysis revealed that CNVs of MYH3 gene were significantly associated with growth traits of NY cattle, and the individuals with copy number gain showed better phenotypes than the loss and/or median groups (P<0.05). This study firstly attempted to establish the correlations between CNVs of candidate genes and growth traits, and our results suggested that the CNVs of MYH3 gene may be utilized as the potential markers for economic traits in selection breeding programs of Chinese cattle.
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Cell death-inducing DFFA-like effector c (CIDEC/Fsp27) gene: molecular cloning, sequence characterization, tissue distribution and polymorphisms in Chinese cattles.
Mol. Biol. Rep.
PUBLISHED: 09-14-2013
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Cell death-inducing DFFA-like effector c (CIDEC) protein, also known as fat specific protein 27 (Fsp27), is localized to lipid droplets. CIDEC protein is required for unilocular lipid droplet formation and optimal energy storage in addition to controlling lipid metabolism in adipocytes and hepatocytes. Research found that Ad-36 could induce lipid droplets in the cultured skeletal muscle cells and this process may be mediated by promoting CIDEC expression. The content of intermuscular fat is an important index for evaluation of beef quality, so the CIDEC gene appeared to be a candidate gene for regulation of intermuscular fat, however similar research for the bovine CIDEC gene is lacking. This paper examined the tissue expression profile of CIDEC gene in cattle using real-time RT-PCR to suggest that bovine CIDEC is highly expressed in adipose tissue. In addition, the Bovine CIDEC gene was cloned and inserted into the eukaryotic expression vector pET-28a(+), whereupon recombinant bovine CIDEC protein was induced and identified by Western-blot. A phylogenetic analysis showed that the animo acid sequence of bovine CIDEC was closer to mammalian CIDEC than rasorial CIDEC. We found ten single nucleotide polymorphisms sites (SNPs) in bovine CIDEC gene, of which SNP 2, 3, 4, 6 and 9, and SNP 8 and 10 were in complete linkage disequilibrium, respectively. SNP 1, 2 and 10 were used in further haplotype studies. Eight different haplotypes were identified in 973 cattle, of which haplotype 8 predominated with frequencies ranging from 42.90 to 54.30 %. This research provides a basis for future functional studies of CIDEC in cattle.
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Haplotype combination of polymorphisms in the ADIPOQ gene promoter is associated with growth traits in Qinchuan cattle.
Genome
PUBLISHED: 08-15-2013
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Adiponectin modulates lipid and glucose metabolism in adipose tissues and is also related to bone metabolism. Polymorphisms in the ADIPOQ gene likely have an impact on growth traits in cattle. In this study, we examined the relationship between ADIPOQ polymorphisms and body measurement parameters in Chinese beef cattle. First, we sequenced ADIPOQ and 1.2 kb of DNA upstream of its promoter, and we found 14 polymorphisms. With the luciferase reporter assay, we showed that the two polymorphisms SNP PR_-135 A>G and PR_-68 G>C, which are located in the core region of promoter, influence promoter activity of ADIPOQ. Second, we identified three haplotypes involved in these two polymorphic sites: A (A-135/C-68), B (A-135/G-68), and C (G-135/G-68). Haplotypes B and C are major haplotypes in five Chinese populations of cattle (Qinchuan, Nanyang, Jiaxian, Hazakh, and Chinese Holstein). We studied the effects of these three haplotypes on body measurements, gene expression, and promoter activity, and we found that the genotypes are associated with body measurement parameters in Qinchuan cattle. Individuals with genotype BC (AG/GG) had significantly higher body height and heart girth than others, and this result may be interpreted by the following two observations. The promoter activity with haplotype B (A/G) is significantly higher than those with A (A/C) and C (G/G) in driving reporter gene transcription; the ADIPOQ mRNA level in cattle with genotype BC (AG/GG) is relatively lower than that in cattle with genotype BB (AA/GG).
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Genetic variants and effects on milk traits of the caprine paired-like homeodomain transcription factor 2 (PITX2) gene in dairy goats.
Gene
PUBLISHED: 07-23-2013
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The paired-like homeodomain transcription factor 2 (PITX2) gene plays a critical role in cell proliferation, differentiation, hematopoiesis and organogenesis. This gene regulates several genes expressions in the Wnt/beta-catenin and POU1F1 pathways, thereby probably affecting milk performance. The goal of this study was to characterize the genetic variants of the PITX2 gene and test their associations with milk traits in dairy goats. Herein, four novel single nucleotide polymorphisms (SNPs), AC_000163:g.18117T>C, g.18161C>G, g.18322C>A and g.18353T>C, within the caprine PITX2 gene, were found in two famous Chinese dairy goat breeds. These SNPs mapping at Cys28Arg, Pro42Pro, IVS1+79C>A and IVS1+110T>C, were genotyped by the MvaI, SmaI, MspI and RsaI aCRS-RFLP or PCR-RFLP methods, respectively. Accordingly, two main haplotypes (CGCT and CGCC) were identified among the specimens. Association testing revealed that the SmaI and RsaI polymorphisms were significantly associated with the milk fat content, milk lactose content and milk density (P<0.05 or P<0.01) in the Guanzhong (GZ) dairy goats, respectively. At the same time, the RsaI locus was also found to significantly link to the second lactation milk yield, milk fat content, milk lactose content, milk density and milk total solid content (P<0.05 or P<0.01) in the Xinong Saanen (XNSN) dairy goats, respectively. These results indicated that the caprine PITX2 gene had the significant effects on milk traits. Hence, the RsaI and SmaI loci could be regarded as two DNA markers for selecting superior milk performance in dairy goats. These preliminary findings not only would extend the spectrum of genetic variation of the goat PITX2 gene, but also would contribute to implementing marker-assisted selection (MAS) in breeding and genetics in dairy goats.
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Novel polymorphisms of the APOA2 gene and its promoter region affect body traits in cattle.
Gene
PUBLISHED: 07-12-2013
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Apolipoprotein A-II (APOA2) is one of the major constituents of high-density lipoprotein and plays a critical role in lipid metabolism and obesity. However, similar research for the bovine APOA2 gene is lacking. In this study, polymorphisms of the bovine APOA2 gene and its promoter region were detected in 1021 cows from four breeds by sequencing and PCR-RFLP methods. Totally, we detected six novel mutations which included one mutation in the promoter region, two mutations in the exons and three mutations in the introns. There were four polymorphisms within APOA2 gene were analyzed. The allele A, T, T and G frequencies of the four loci were predominant in the four breeds when in separate or combinations analysis which suggested cows with those alleles to be more adapted to the steppe environment. The association analysis indicated three SVs in Nangyang cows, two SVs in Qinchun cows and the 9 haplotypes in Nangyang cows were significantly associated with body traits (P<0.05 or P<0.01). The results of this study suggested the bovine APOA2 gene may be a strong candidate gene for body traits in the cattle breeding program.
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Copy number variations of MICAL-L2 shaping gene expression contribute to different phenotypes of cattle.
Mamm. Genome
PUBLISHED: 07-06-2013
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Copy number variations (CNVs) recently have been recognized as an important source of genetic variability. Compelling evidence has indicated that CNVs are responsible for phenotypic traits by altering the copy numbers of functional genes. The molecule interacting with CasL-like protein 2 (MICAL-L2) gene plays a critical role in muscle fiber development and has been identified in the CNV region by comparative genomic hybridization array. In the present study, we detected the different distributions of MICAL-L2 gene copy numbers in four Chinese cattle breeds (QC, NY, LX, and CY) and investigated the functional effects of MICAL-L2 CNVs on the genes expression level and the phenotypic traits in QC and NY cattle. The results showed that the copy number loss (relative to Angus cattle) was more frequent in CY than in the other breeds. The MICAL-L2 gene copy number presented a moderate negative correlation with the transcriptional expression in fetal skeletal muscles (P < 0.05). Statistical analysis revealed that the MICAL-L2 CNVs were significantly associated with body weight, body height, and body length of NY cattle in the early stages (6 and 12 months old), and the copy number loss showed better traits than the gain and/or median groups (P < 0.05). No significance was found at the late stages in QC (24 months old) and NY cattle (18 and 24 months old). These observations provided further insight into the associations between cattle CNVs and economic traits, suggesting that the CNVs may be considered promising markers for the molecular breeding of Chinese beef cattle.
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SIRT1 gene polymorphisms are associated with growth traits in Nanyang cattle.
Mol. Cell. Probes
PUBLISHED: 05-07-2013
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Growth is under complex genetic control and uncovering the molecular mechanisms how the genes and polymorphisms affect economic growth traits, are important for successful marker-assisted selection and more efficient management strategies in commercial cattle populations. SIRT1 is a NAD(+)-dependent deacetylase that belongs to the class III histone deacetylases. It plays an important role in numerous fundamental cellular processes including gene silencing, DNA repair, and metabolic regulation. In addition, SIRT1 acts as an inhibitor of adipogenesis and has been associated with body weight regulation. The objective of the present study was to identify single nucleotide polymorphisms (SNPs) of bovine SIRT1 using 1255 animals representing the five main Chinese breeds and to determine if these SNPs are associated with economically important traits in Nanyang cattle. The approach consisted of resequencing SIRT1 using a panel of DNA from unrelated animals of five different breeds and the process revealed five novel SNPs. SNPs g.17324T>C and g.17491G>A exhibited a high degree of linkage disequilibrium in all tested breeds. Seven major haplotypes accounting for 91.2% of the alleles were observed and the haplotype GCCGA was the most common haplotype in NY, QC, LX and JX breeds. An association analysis was performed between the five SNPs and six performance traits. SNP g.-274C>G was demonstrated to have a strong effect on 24-months-old body weight and g.17379A>G polymorphism was related to 6 and 12-months-old body weight in NY population, although these effects did not remained significant after the Bonferroni correction. Our results provide evidence that polymorphisms in SIRT1 are associated with growth efficiency traits, and may be used for marker-assisted selection and management in feedlot cattle.
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mRNA expression pattern and association study with growth traits of bovine vaspin gene.
Mol. Biol. Rep.
PUBLISHED: 04-29-2013
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Visceral adipose tissue-derived serine protease inhibitor (vaspin) is an interesting novel adipocytokine with insulin-sensitizing effects. Some studies have suggested that vaspin could play an important role in the development of obesity and metabolic disorders. However, the tissue expression patterns in cattle and impact of vaspin gene variants on the growth traits has not been determined yet. Herein, we firstly investigated the tissue expression patterns of vaspin gene in new born and adult cattle. The results showed that vaspin was ubiquitously expressed in most tissues and strongly expressed in the heart, skeletal muscle and fat. Then, genetic variants within bovine vaspin gene were screened in 1235 individuals from five Chinese indigenous cattle breeds. Two novel mutations in coding region (NW_001494061: g.1124477 G>A and g.1118561 T>C) of bovine vaspin gene were identified using MspI PCR-RFLP and HhaI ACRS PCR-RFLP detection. Association analysis revealed both two mutations were significantly associated with bodyweight and chest girth at 24 months in cattle (P < 0.05). Therefore, the MspI and HhaI genetic variants of bovine vaspin gene were recommended as DNA markers related to growth traits through marker-assisted selection for genetics and breeding in cattle.
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Effect of genetic variations within the SH2B2 gene on the growth of Chinese cattle.
Gene
PUBLISHED: 04-12-2013
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As an adaptor protein, apart from potentiating Janus kinase 2 (JAK2) activation and promoting the insulin signaling pathway, Src homology 2 B 2 (SH2B2) indirectly takes part in the regulation of glucose uptake through the c-Cb1/CAP/TC10 pathway, which can in turn affect growth. In this study, we identified a 4bp indel mutation and three single nucleotide polymorphisms (SNPs) within the SH2B2 gene in 959 individuals from five Chinese cattle breeds by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and sequencing. Based on the four variations, 12 haplotypes were identified. Additionally, there was a tendency that in every population pair-wise linkages increased progressively from V1-V2 to V3-V4. By association analysis, positive effects of genotypes CC and CT (snp1220 locus), DI (4bp indel locus), and CC (snp21049 locus) on growth traits were obtained. Furthermore, when combined, individuals with the combination CCDITTCC showed the best performance at an early age. These results were suggestive of an association of snp1220, 4bp indel and snp12049 with growth performance in Nanyang cattle, indicating possibly the candidate role of the SH2B2 gene in marker assisted selection in a beef cattle breeding program.
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Molecular characterization, alternative splicing and expression analysis of bovine DBC1.
Gene
PUBLISHED: 03-24-2013
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Deleted in breast cancer 1 (DBC1, KIAA1967, p30 DBC) is a novel protein that has been recently shown to bind and regulate SIRT1. Loss of function of DBC1 increased SIRT1 deacetylase activity, which promotes "browning" of WAT by deacetylating peroxisome proliferator-activated receptor (PPAR?) on Lys268 and Lys293. In the present study, we have cloned and characterized the bovine DBC1 gene. Two transcript variants of bovine DBC1 were identified, designated DBC1-A and DBC1-B, respectively, which were both located in nucleus. Protein sequence analysis showed that DBC1-A was well conserved across species. Expression analysis of DBC1 in seven different tissues of calves and bulls by RT-PCR indicated that the two transcripts were ubiquitously expressed. However, the relatively level of DBC1-A was higher when compared to DBC1-B in all examined tissues. Surprisingly, the expression of DBC1-A was extraordinary high in calves adipose tissue, which implicated its potential key role in regulating calve adipocyte development. These findings provide new insight into our understanding of the biochemical characteristics and physiological role of bovine DBC1.
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Maternal Diet during Pregnancy Induces Gene Expression and DNA Methylation Changes in Fetal Tissues in Sheep.
Front Genet
PUBLISHED: 03-17-2013
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Studies in rats and mice have established that maternal nutrition induces epigenetic modifications, sometimes permanently, that alter gene expression in the fetus, which in turn leads to phenotypic changes. However, limited data is available on the influence of maternal diet on epigenetic modifications and gene expression in sheep. Therefore, the objectives of this study were to investigate the impact of different maternal dietary energy sources on the expression of imprinted genes in fetuses in sheep. Ewes were naturally bred to a single sire and from days 67?±?3 of gestation until necropsy (days 130?±?1), they were fed one of three diets of alfalfa haylage (HY; fiber), corn (CN; starch), or dried corn distillers grains (DG; fiber plus protein plus fat). A total of 26 fetuses were removed from the dams and longissimus dorsi, semitendinosus, perirenal adipose depot, and subcutaneous adipose depot tissues were collected for expression and DNA methylation analyses. Expression analysis of nine imprinted genes and three DNA methyltransferase (DNMTs) genes showed significant effects of the different maternal diets on the expression of these genes. The methylation levels of CpG islands of both IGF2R and H19 were higher in HY and DG than CN fetuses in both males and females. This result is consistent with the low amino acid content of the CN diet, a source of methyl group donors, compared to HY and DG diets. Thus, results of this study provide evidence of association between maternal nutrition during pregnancy and transcriptomic and epigenomic alterations of imprinted genes and DNMTs in the fetal tissues.
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SNPs of bovine HGF gene and their association with growth traits in Nanyang cattle.
Res. Vet. Sci.
PUBLISHED: 03-07-2013
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Hepatocyte growth factor (HGF) is one of the multifunctional cell factors that regulates cellular proliferation, motility and morphogenesis in mammalians. And its medical research has deep significance. In this paper, polymorphisms of HGF gene were investigated in 1433 health and irrelated Chinese cattle by PCR-RFLP and DNA sequencing approach. Ten novel Single nucleotide polymorphisms (SNPs) were identified, which included one missense mutation, g.72801G>A in the coding region, and the others in the intron. Association analysis between four of them, g.288T>C, g.72801G>A, g.77172G>T, and g.77408T>G, and growth traits in Nanyang, were performed. The results indicated that SNPs within bovine HGF gene were significantly associated with growth traits. Phylogenetic analysis showed that the genetic background of Caoyuan Red cattle was different from the others in the tested breeds. The findings will provide a background for application of bovine HGF gene in the selection program in Chinese cattle.
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A critical functional missense mutation (H173R) in the bovine PROP1 gene significantly affects growth traits in cattle.
Gene
PUBLISHED: 02-25-2013
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The PROP1 protein, encoded by the prophet of Pit-1 (PROP1) gene, exhibits both DNA-binding and transcriptional activation abilities. Its expression leads to the ontogenesis of growth hormone (GH), prolactin (PRL), thyroid-stimulating hormone (TSH), and pituitary hormone. The missense mutation H173R in PROP1 may result in deficiencies of GH, PRL, TSH, and Pit-1, thereby affecting growth traits. The objective of this study was to characterize the H173R mutation within the PROP1 gene and examine its associations with growth traits in cattle. Accordingly, the H173R mutation was genotyped in 1207 cows belonging to five Chinese native breeds. Three genotypes were identified among the specimens, with genotype AA being the major one. Consequently, the "G" allele was the minor allele. Association testing revealed that the H173R mutation was significantly associated with body weight, average daily weight gain and physical parameters in the analyzed breeds. Interestingly, the cows with genotype AG and/or AA had superior growth traits compared with those expressing the GG genotype, in all tested breeds. These findings revealed that the "A" allele had positive effects on growth traits, which was consistent with the increasing binding ability and enhanced activation capacity associated with the bovine isoform PROP1-173H, representing the "A" allele. Therefore, the H173R mutation can be considered as a DNA marker for selecting individuals with superior growth traits, thereby contributing to research on breeding and genetics in the beef industry.
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Integrating haplotypes and single genetic variability effects of the Pax7 gene on growth traits in two cattle breeds.
Genome
PUBLISHED: 01-14-2013
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The paired box 7 (Pax7) gene encoding for the transcription factor can regulate the conversion of stem cells into myogenic cells and participate in the development and regeneration of skeletal muscle. The aims of this study were to detect variations of the Pax7 gene by DNA pool sequencing and aCRS-RFLP methods in 1441 cattle from five breeds and to investigate their associations with growth traits in Nanyang and Chinese red steppe cattle. Altogether, three novel single nucleotide polymorphisms (SNPs) were identified in the last intron of the Pax7 gene: NC_007300: ss1 (g. G103688A), ss2 (g. T103735C), and ss3 (g. A103764T). Genotypes and the referring haplotype frequencies showed a high similarity trend among five breeds, and the G, T, and A allele frequencies of the three loci were always superior when separate or in combination. Association analysis of the single SNPs and haplotype combinations revealed that the T allele of ss2 and ss3 loci and the haplotype H(2)H(2) (GG-TT-TT) showed significant effects on growth traits such as body height, body mass, and chest girth in cattle at early stages (6 and 12 months old) (P < 0.05). The results showed that Pax7 gene variations and their corresponding genotypes may be considered as molecular markers for economic traits in cattle breeding.
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Haplotypes and effects on growth traits of bovine Wnt7a gene in Chinese Qinchuan cattle.
Gene
PUBLISHED: 01-10-2013
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Wnt7a is a member of the WNT gene family, which encodes secreted signaling proteins and responds to many biological processes. Specifically Wnt7a influences satellite stem cells and regulates the regenerative potential of the muscle. However, similar researches about the bovine Wnt7a gene are lacking. Therefore, in this study, polymorphisms of the bovine Wnt7a gene were detected in 488 individuals from Chinese Qinchuan cattle by DNA pooling, forced PCR-RFLP, and DNA sequencing methods. 3 novel SNPs were identified, two SNPs (g.T4926C and g.A21943G) were in the intron and the last one (g.C63777T) was in the exon. Five haplotypes involved in these three variant sites in the Wnt7a gene were identified and their effects on growth traits were analyzed. The results revealed that haplotype 1 had the highest haplotype frequencies and was highly significantly associated with body height (P<0.01), body weight (P<0.05), chest width (P<0.05) and height at hip cross (P<0.01) respectively.
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Identification and profiling of conserved and novel microRNAs from Chinese Qinchuan bovine longissimus thoracis.
BMC Genomics
PUBLISHED: 01-02-2013
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MicroRNAs (miRNAs) are a family of ~22 nucleotide small RNA molecules that regulate gene expression by fully or partially binding to their complementary sequences. Recently, a large number of miRNAs and their expression patterns have been identified in various species. However, to date no miRNAs have been reported to modulate muscle development in beef cattle.
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Exploring polymorphisms and associations of the bovine MOGAT3 gene with growth traits.
Genome
PUBLISHED: 12-20-2011
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Monoacylglycerol acyltransferase (MGAT3, also known as MOGAT3) catalyzes the synthesis of diacylglycerol (DAG) using 2-monoacylglycerol and fatty acyl coenzyme A. This enzymatic reaction is believed to be an essential and rate-limiting step for the absorption of dietary fat in the small intestine. However, similar research for the bovine MOGAT3 gene is lacking. Therefore, in this paper, polymorphisms of the bovine MOGAT3 gene were detected in 1145 individuals from five cattle breeds by DNA pooling, PCR-RFLP, and DNA sequencing methods. The results showed that 26 novel SNPs were identified, which included 16 mutations in the coding region and the others in the introns. Additionally, association analysis between two missense mutations, g.A229G and g.G1627A, and growth traits in Nanyang cattle up to 2 years of age and adult Qinchuan cattle was performed. The results indicated that polymorphisms were significantly associated with Nanyang cattle, but no convincing associations were observed for Qinchuan cattle for the studied traits.
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Exploring polymorphisms of the bovine RARRES2 gene and their associations with growth traits.
Mol. Biol. Rep.
PUBLISHED: 05-26-2011
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Retinoic acid receptor responder 2 gene (RARRES2) encodes a novel adipokine protein that plays a crucial role in regulating several biological processes, including immune responses, adipocyte differentiation, type 2 diabetes and metabolic syndrome. In this paper, polymorphisms of the bovine RARRES2 gene were detected in 1300 individuals from six breeds by DNA pooling, CRS-PCR-RFLP and DNA sequencing methods. The results showed that NC_007302:g.117035859A>G, 117035706G>A and 117034290A>G were in the coding region, which resulted in three synonymous mutations and only 117033779C>G was in the 3 UTR. Additionally, associations of the four novel SNPs with growth traits were analyzed in Nanyang cattle up to 2 years of age. In P1-PvuII locus, individuals with genotype BC had greater body height and hucklebone width than those with genotype AA, AC and AB at the age of 24 months. In P3-BamHI locus, individuals with genotype AG had higher hucklebone width than those with genotype GG at the age of 24 months. However, no statistically significant differences were observed in P5-SmaI locus. These results indicated that RARRES2 gene might be a potential candidate gene for marker-assisted selection (MAS).
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Polymorphisms of diacylglycerol acyltransferase 2 gene and their relationship with growth traits in goats.
Mol. Biol. Rep.
PUBLISHED: 05-21-2011
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Diacylglycerol acyltransferase (DGAT) plays a critical role in the synthesis of triacylglycerol. In this study, PCR-SSCP and DNA sequencing methods were employed to screen the genetic variations of DGAT-2 gene in 299 goats from three breeds (Boer goat, Chinese Xuhuai white goat and Chinese Haimen goat). Three fragments of DGAT-2 gene were investigated, only exon 3 of DGAT-2 gene showed polymorphism. The alignment between nucleotide sequences of NM_205793.2 in GenBank and the sequencing results of three PCR products with different patterns revealed that there was one mutation (A ? G) in exon 3 of DGAT-2 gene, which resulted in amino acid change (Lys ? Arg) and constructed two genotypes (AA, AB). The frequencies of allele A and genotype AA were dominant in all three breeds. And there was no significant difference for genotypic and allelic frequencies among the three breeds. The genotype distributions were in good agreement with Hardy-Weinberg equilibrium (P > 0.05) in each breed. Significant statistical differences were only found in withers heights (P < 0.05) in Xuhuai goat between genotypes. The results indicated that individuals with genotype AA were significantly higher than those of individuals with genotype AB in withers height (P < 0.05). No polymorphism was detected in the intron 3, exon 8 and 3 flanking region. So we suggested that DGAT-2 gene had the close relationship with growth traits in goats. And this mutation could be used as a perfect molecular marker for marker-assisted selection (MAS) in animal genetics and breeding.
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Polymorphism in a microsatellite of the acrp30 gene and its association with growth traits in goats.
Biochem. Genet.
PUBLISHED: 03-03-2011
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Acrp30 plays a critical role in the regulation of glucose and lipid homeostasis. In this study, polymorphism of the Acrp30 gene was detected by PCR-SSCP and DNA sequencing methods in 321 individuals from three goat breeds, and the association of Acrp30 gene polymorphism with growth traits in the three goat breeds was analyzed. A novel insert/deletion (GT)(5) microsatellite sequence was detected in the 5 flanking region of the gene. Three genotypes (AA, AB, and BB) were found in three breeds. There was moderate genetic diversity in the locus in the analyzed populations. Significant associations were observed between the genotypes of the locus and growth traits in the Boer goat population. The chest circumference of individuals with genotype BB was significantly greater than that of individuals with genotype AA.
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Analysis of genetic variability at codon 42 within caprine prion protein gene in relation to production traits in Chinese domestic breeds.
Mol. Biol. Rep.
PUBLISHED: 01-27-2011
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In this study, genetic variability at codon 42 within prion protein (PRNP) gene and its associations with production traits were investigated in 2002 goats from four Chinese domestic breeds. The frequencies of allele "A" ranged from 0.353 to 0.562 in analyzed goat breeds with Hardy-Weinberg equilibrium (P > 0.05) except Xinong Sannen (XNSN) dairy breed. The establishment of relationships between different genotypes and growth traits was performed in Inner Mongolia white Cashmere (IMWC) breed and revealed an association of the polymorphism with body weight at 7-year-old goats (P = 0.033). The individuals with genotype GG showed heavier body weight than those with genotype AA. Moreover, association analysis detected two significant associations between different genotypes and cashmere yield and fiber length in IMWC breed (P = 0.009, P = 0.048, respectively). In addition, three significant associations of different genotypes with density of milk (a.m. and p.m.), solids-not-fat of milk (P = 0.013, P = 0.009 and P = 0.002), respectively, were found in XNSN breed. Genotype GG had better milk quality than others. These findings suggested that the polymorphism of codon 42 within PRNP was a useful DNA marker for eliminating or selecting excellent individuals in relation to production traits in marker-assist selection breeding of goat.
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Polymorphism in GHRH gene and its association with growth traits in Chinese native cattle.
Res. Vet. Sci.
PUBLISHED: 01-13-2011
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Growth hormone-releasing hormone (GHRH) is secreted by the hypothalamus and stimulates growth hormone (GH) released from the pituitary. Mutations detected in GHRH gene showed associations with animal production traits. The purpose of this study was to investigate the association of the GHRH gene with growth traits in Chinese native cattle. PCR-SSCP and sequencing were used to detect mutations of the GHRH gene in this study. One novel mutation 4251nt (C>T) was found and the frequencies of C allele were 0.8778 and 0.8476 for Qinchuan and Nanyang cattle, respectively. Body weight with the CT genotype was significantly higher (P<0.05 or P<0.01) than those with CC genotype for different growth periods (6, 12, 18, and 24 months old) in Nanyang cattle. Our findings suggested that polymorphism in bovine GHRH might be one of the important genetic factors to influence body weight.
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Two novel coding SNPs of SREBP1c gene are associated with body weight and average daily gain in bovine.
Anim. Biotechnol.
PUBLISHED: 07-29-2010
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It is known that the SREBP1c gene is an important gene responsible for adipogenesis and regulation of the expression of genes controlling fatty acid biosynthesis. Its expression levels increase in parallel with obesity. Therefore, the present study focused on screening the genetic variation within bovine SREBP1c gene and analyzing its effect on growth traits in 1035 individuals belonging to four Chinese cattle breeds (QC, NY, JX, CH) using PCR-SSCP, DNA sequencing, and forced PCR-RFLP methods. The results revealed two novel mutations: NC_007317: g. 10781 C > A (457aa), 10914 G > A (502aa). Association analysis with growth traits in the Nangyang breed indicated that: The SNPs in the bovine SREBP1c gene had significant effects on body weight and average daily gain at birth, 6 and 12 months old (P < 0.05 or P < 0.01). Therefore, these results suggest that the SREBP1c gene is a strong candidate gene that affects growth traits in cattle.
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Association of IGF-I gene polymorphisms with milk yield and body size in Chinese dairy goats.
Genet. Mol. Biol.
PUBLISHED: 06-01-2010
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The association of IGF-I gene polymorphisms with certain traits in 708 individuals of two Chinese dairy-goat breeds (Guanzhong and Xinong Saanen) was investigated. Polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and DNA sequencing methods were employed in screening for genetic variation. Two novel mutations were detected in the 5-flanking region and in intron 4 of IGF-I gene, viz., g.1617 G > A and g.5752 G > C (accession D26119.2), respectively. The associations of the g.1617 G > A mutation with milk yield and the body size were not significant (p > 0.05). However, in the case of g.5752 G > C, Xinong Saanen dairy goats with the CG genotype presented longer bodies (p < 0.05). Chest circumference (p < 0.05) was larger in Guanzhong goats with the GG genotype. In Xinong Saanen dairy goats with the CC genotype, milk yields were significantly higher during the first and second lactations (p < 0.05). Hence, the g.5752 G > C mutation could facilitate association analysis and serve as a genetic marker for Chinese dairy-goat breeding and genetics.
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Novel single nucleotide polymorphisms of the caprine PC1 gene and association with growth traits.
Biochem. Genet.
PUBLISHED: 05-25-2010
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Proprotein convertase 1 (PC1) is an endopeptidase involved in proteolytic processing of peptide hormone precursors in granules of the regulated secretory pathway in endocrine cells. Mutations in the PC1 gene are thought to cause obesity, and multiple alternatively spliced transcript variants have been described for this gene. In this study, based on PCR-SSCP and DNA sequencing methods, polymorphisms of the PC1 gene were detected in 447 individuals from three breeds. Only the P1, P2, P3, P9, and P10 loci showed polymorphisms, and 12 SNPs in the PC1 gene were identified. Additionally, an association analysis between mutations in the 5-UTR and four growth traits indicated that the polymorphisms were significantly associated with caprine body height (P < 0.05) and chest circumference (P < 0.01).
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The polymorphisms of bovine VEGF gene and their associations with growth traits in Chinese cattle.
Mol. Biol. Rep.
PUBLISHED: 03-30-2010
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PCR-SSCP and DNA sequencing methods were employed to screen the genetic variation of VEGF gene in 671 individuals belonging to three Chinese indigenous cattle breeds including Nanyang, Jiaxian Red and Qinchuan. Three haplotypes (A, B and C), four observed genotypes (AA, AB, BB and AC) and three new SNPs (6765T>C ss130456744, 6860A>G ss130456745, 6893T>C ss130456746) were detected. The analysis suggested that one SNP (ss130456744) in the bovine VEGF gene had significant effects on birth weight, body weight and heart girth at 6 months old in the Nanyang breed (P < 0.05). The results showed that the SNP (ss130456744) in intron 2 of the VEGF gene is associated with early development and growth of Chinese cattle. These findings raise hope that this polymorphism can be a molecular breeding marker in breeding strategies through marker assisted selection (MAS) in Chinese domestic cattle.
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Effects of genetic variability of the dairy goat growth hormone releasing hormone receptor (GHRHR) gene on growth traits.
Mol. Biol. Rep.
PUBLISHED: 03-23-2010
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Growth hormone-releasing hormone receptor (GHRHR) plays a critical role in growth hormone (GH) synthesis, release and regulation of pituitary somatotroph expansion in vertebrates. The objective of this study was to investigate variations in goat GHRHR gene and their associations with growth traits in 668 dairy goats. The results showed four novel single nucleotide polymorphisms (SNPs): NC_007302:g.5203C>T, 7307C>G, 9583G>A and 9668A>C. In detail, the novel SNP C>T in the 5203rd nucleotide identified a missense mutation: CCC (Pro)>TCC (Phe) at position 116aa of the goat GHRHR (423aa). Besides, 9583G>A and 9668A>C polymorphism were in complete linkage disequilibrium. The genetic diversity analysis revealed that the Guanzhong dairy goat possessed intermediate genetic diversity in P3 and P7 loci, and the Xinong Sannen dairy goat belonged to poor genetic diversity in P4 locus. Significant associations between the genotypes of P3 locus and body length, body height and chest circumference was observed in Guanzhong goat (P<0.05). However, in Xinong saanen population, significant statistical difference was only found in body height and body length (P<0.05). In P4 and P7 loci, no significant associations were detected between any variant sites and body length, body height and chest circumference, as well as for the milk traits (P>0.05). These results strongly suggested that the goat GHRHR gene is a candidate gene that influences growth traits in dairy goat.
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Novel SNPs of butyrophilin (BTN1A1) and milk fat globule epidermal growth factor (EGF) 8 (MFG-E8) are associated with milk traits in dairy goat.
Mol. Biol. Rep.
PUBLISHED: 03-17-2010
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Butyrophilin (BTN1A1) and milk fat globule epidermal growth factor (EGF) 8 (MFG-E8) genes are both milk fat globule membrane proteins. BTN1A1 plays a key role in the secretion of milk lipid and production which has effects on performance traits, while the MFG-E8 is vital for the development of the mammary gland and phagocytic clearance of apoptotic cells. Therefore, BTN1A1 and MFG-E8 gene are candidate genes for quantitative traits in mammalian animals with respect to milk performance traits. The objective of this study is to investigate variations in goat BTN1A1 and MFG-E8 gene and analyze their associations with growth trait and milk performance. In this study, the goat BTN1A1 gene showed a novel single-nucleotide polymorphism (SNP): XM_001494179:g.8659C>T, resulting in a missense mutation: CTT (Leu)>TTT (Phe) at position 377 aa of the BTN1A1 (526 aa); the goat MFG-E8 gene showed four novel SNPs: NC_007319: g.843delA, 6417delC, 14892T>C and 14996A>C, only the 14892T>C result in a synonymous mutation. The associations between genotypes and production traits were analyzed. Significant statistical results implied that HinfI locus of BTN1A1 gene is associated with milk fat yield (P=0.004), total solid (P=0.002), solid-non fat (P=0.018) and first milk yield (P=0.030). The DA and EcoRV loci of MFG-E8 gene are associated with milk fat yield (DA locus: P=0.000; EcoRV locus: P=0.033) and total solid (DA locus: P=0.002; EcoRV locus: P=0.015) in the Xinong Saanen dairy goat.
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Analysis of the genetic variation of vascular endothelial growth factor gene in three Chinese indigenous cattle breeds.
Mol. Biol. Rep.
PUBLISHED: 02-07-2010
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PCR-SSCP and DNA sequencing methods were employed to screen the genetic variation of vascular endothelial growth factor (VEGF) gene in 675 individuals belonging to three Chinese indigenous cattle breeds including Qinchuan (QC), Jiaxian Red (JX) and Nanyang (NY) breed. Three new single nucleotide polymorphisms (SNPs) (g.6765T > C ss130456744, g.6860A > G ss130456745, g.6893T > C ss130456746) were found. One SNP (g.6765T > C) was detected in intron II of VEGF gene in all three breeds and the other two SNPs (g.6860A > G, g.6893T > C) were in exon III of VEGF gene only in NY breed. Among them, two synonymous mutations of exon III were identified: CCA (Pro) > CCG (Pro) at position 65th amino acid (aa) and TGT (Cys) > TGC (Cys) at position 76th aa of VEGF(190aa) in NY breed. Our study revealed that NY breed exhibited the most abundant genetic diversity in VEGF gene within the three cattle breeds. Furthermore, JX cattle breed was more similar to QC breed than to NY breed. Our genetic data in the present study supported the hypothesis that the distribution pattern of Chinese indigenous cattle breeds was closely related to the geographical and climatic background again.
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An economical single-sided antibody incubation method for Western blotting.
J. Virol. Methods
PUBLISHED: 01-24-2010
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A simple, single-sided antibody method for incubating primary and secondary antibodies in Western blotting was developed, which generates significant savings on the use of antibodies. Compared with the conventional immersion technique for antibody incubation, the present economical single-sided antibody incubation method resulted in a saving of 80% of antibody use. Besides, the present incubation method did not compromise the Western blot results and was not affected by the expression levels of target proteins.
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Novel SNPs in the caprine stearoyl-CoA desaturase (SCD) and decorin (DCN) genes that are associated with growth traits in Chinese goat breeds.
Mol. Biol. Rep.
PUBLISHED: 01-20-2010
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Stearoyl-CoA desaturase (SCD) is an iron-containing enzyme involving in the biosynthesis of monounsaturated fatty acids (MUFA) in mammary gland and adipose tissue, while decorin (DCN) consists of a protein core and a single dermatan or chondroitin sulfate glycosaminoglycan chain, contributing multifunctionally to matrix assembly, modulation of the activity of growth factors and cell migration and proliferation. However, few studies have focused on the genetic variability of them in goat. Herein, five Chinese goat breeds (1229 animals) were analyzed. Based on DNA pooling and PCR-RFLP, three nucleotide substitutions, one of which caused a amino acid substitution, were detected in SCD gene and three haploids (A, B, C) were constructed. According to SSCP analysis and DNA sequencing methods, a 2-bp deletion and two other SNPs were found existing in another analyzed gene DCN, and three haploids (X, Y, Z) were built. Associations between the genotypes and the growth traits (body length, body height, chest circumference, cannon circumference) were also analyzed. For SCD gene, genotype CC individuals had significant greater body height in Guanzhong and body length in both Guanzhong and Xinong saanen than genotype BC individuals (P < 0.05). For DCN gene, individuals with genotype XX was obviously higher than that with genotype XY (P < 0.05). These results indicated that genotype CC of SCD gene and genotype XX of DCN gene could be used for the breeding of new breeds of goat in China.
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A novel SNP of the Hesx1 gene in bovine and its associations with average daily gain.
Mol. Biol. Rep.
PUBLISHED: 10-02-2009
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As an essential repressor, the homeobox gene Hesx1/HESX1 is required within the anterior neural plate for normal forebrain development. Mutations within the Hesx1 gene have been associated with GH deficiency or combined pituitary hormone deficiency. We detected the polymorphism of Hesx1 gene by PCR-SSCP and DNA sequencing methods in 702 individuals from four Chinese cattle breeds. A novel single nucleotide polymorphism (SNP) (IVS1 + 382T > C) was detected. The frequencies of genotype TC in four breeds were 0.000-0.222. Polymorphism of the Hesx1 gene was shown to be associated with growth in the Nanyang breed. Individuals with genotype TC was significantly lower average daily gain than TT at 18 months (P < 0.05).
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The novel 5bp deletion polymorphism in the promoter region of bovine ACRP30 gene.
Mol. Biol. Rep.
PUBLISHED: 07-25-2009
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ACRP30 gene was located nearby the QTL affecting the marbling, ribeye muscle area and fat thickness on the BAT1 in Angus. In this study, a 5bp deletion mutation within the bovine ACRP30 gene was firstly detected and confirmed in 991 cattle by PCR-SSCP, DNA sequencing and direct PCR amplification. The deletion mutation was appeared in Qinchuan, Nanyang, Jiaxian and Hasake, but was not found in Jinnan, Chinese Holsteins and Angus. The association of the deletion polymorphism with growth traits (including birth weight, body weight, average daily gain and body sizes in different growth periods (6/12/18/24 month-old)) was analyzed in 224 Nanyang cattle. No signification association of the deletion polymorphism with growth traits were observed (P > 0.05). The deletion was located in the promoter region and it resulted in a new putative CCAAT/enhancer binding protein-beta response element (C/EBP-RE).
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A novel missense (A79V) mutation of goat PROP1 gene and its association with production traits.
Mol. Biol. Rep.
PUBLISHED: 07-10-2009
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As a paired class homeodomain transcription factor, mutations of PROP1 (Prophet of POU1F1) are responsible for deficiencies of GH, PRL, TSH, LH and FSH. Regarding mutations of GH, PRL, and POU1F1 genes significantly associating with different production traits, PROP1 gene is a novel important candidate gene for detecting genetic variation and association analysis in marked-assist selection (MAS) program. Therefore, the objective of this study is to detect goat PROP1 gene mutation and its association with production traits. Herein, a novel mutation (AF453512:g.1795C>T) within PROP1 gene is revealed by PCR-SSCP and DNA sequencing methods, and genotyped by Hin6I PCR-RFLP method in 1,344 individuals belonging to eight goat breeds. Only two genotypes (CC and CT) are revealed and the frequencies of allele C go from 0.9014 to 1.000 in analyzed populations. The genetic diversity analysis reveals that all PIC values are less than 0.1619, implying that the Hin6I locus within PROP1 gene possesses low genetic diversity in goat. Furthermore, nucleotide sequence analysis shows that AF453512:g.1795C>T results in a missense amino acid (A79V). But, association analysis demonstrates no significant differences between different genotypes and production traits (such as body weight, cashmere yield, fiber length and wool thickness) of Inner Mongolia White Cashmere goat (P > 0.05), as well as no significant relationship between different genotypes and average milk yield (P > 0.05). Although Hin6I polymorphism can not be used as a molecular marker for production traits in MAS, the present work presents preliminary novel missense mutation which extends the spectrum of genetic variations of goat PROP1 gene and may benefit for considering its association with other biophysical and biochemical indexes.
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[Cloning, prokaryotic expression of cattle Ghrelin gene and biological activity detection of the expressed protein].
Sheng Wu Gong Cheng Xue Bao
PUBLISHED: 05-16-2009
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The cDNA of cattle Ghrelin gene was amplified from abomasum fundic gland mRNA of Qinchuan Cattle by RT-PCR. PCR product was cloned into the T vector pGM-T to construct pGh-T1 for sequencing. Then the cDNA was subcloned into the prokaryotic expressing plasmid vector pET32a (+) and transformed into host Escherichia coli strain BL21 (DE3) for expression. The expression of pGh-32 mature Ghrelin protein was induced by IPTG and was identified by SDS-PAGE. The expression product was observed with soluble protein and inclusion body. Western blotting showed that the recombinant protein was recognized by his-antibody specifically. The protein was purified by Ni-NTA column and was used to inject rabbits to obtain polyclona antibody. ELISA result showed that the antibody titer was 1:12 800. The immunohistochemistry test between the hypothalamus arcuate nucleus and the antibody showed that fusion protein had biological activity. This will provide a basis for further study on the biological function of Ghrelin protein to growth and development and fat deposition of cattle.
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Effects of genetic variability of the caprine homeobox transcription factor HESX1 gene on performance traits.
Mol. Biol. Rep.
PUBLISHED: 05-14-2009
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HESX1 plays a key role in the development of the forebrain and pituitary gland and produces potential effects on performance traits. The objective of this study was to detect and assess the associations of the possible polymorphisms of six loci within HESX1 gene with performance traits in Chinese 1,119 goats. Only one novel SNP (NM_001494116:g.307049A > G) locating on IVS1 + 348A > G was identified and detected by HaeIII forced-RFLP-PCR. The frequencies of allele "G" varied from 0.025 to 0.245 in analyzed populations with the Hardy-Weinberg equilibrium (P > 0.05). Genotypic and allelic frequencies were found to be significantly different in four breeds (chi(2) = 147.674, df = 6, P < 0.001; chi(2) = 157.250, df = 3, P < 0.001, respectively), implying that the distribution of genotypic and allelic frequencies of goat HESX1 gene was significantly associated with different goat utilities (cashmere, meat and dairy). Association analysis results revealed no significant effects of caprine HESX1 gene on body sizes in XNSN population (P > 0.05) and cashmere traits in IMWC population (P > 0.05). Significant statistical of HESX1 gene with body weight was found (*P < 0.05). The genotype AA showed significantly higher body weight than those of AG in 2-year-old age (*P < 0.05), while the AA genotype was senior to AG genotype in 4-year-old body weight trait (*P < 0.05). These suggestions indicated that the HESX1 gene has significant effect on goat body weight depending on ages, which is accordance with the function repressor of the HESX1.
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Associations of a HinfI PCR-RFLP of POU1F1 gene with growth traits in Qinchuan cattle.
Anim. Biotechnol.
PUBLISHED: 04-17-2009
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The objectives of the present study were to estimate the allele and genotype frequencies of the POU1F1/HinfI polymorphisms in beef cattle belonging to four different genetic groups and to determine the effects of these polymorphisms on growth traits in cattle. The 451-bp PCR products of POU1F1 gene digested with HinfI exhibited three genotypes and two alleles, which were at Hardy-Weinberg equilibrium (P > 0.05). Genotype BB was the predominant genotype and B the predominant allele in the studied populations. There was significant difference between Limousin x Qinchuan and Qinchuan in the distribution of genotypes (P < 0.0001). The association of the polymorphism of the POU1F1 gene with growth traits among Qinchuan, Limousin x Qinchuan, Angus x Qinchuan and Germany Yellow x Qinchuan crosses was analyzed. Body weight and wither height of individuals with genotypes AB were higher (P < 0.05)than that of individuals with genotype BB in the Germany Yellow x Qinchua cross, but were not in the other three populations (P > 0.05).
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Associations of polymorphism within the GHSR gene with growth traits in Nanyang cattle.
Mol. Biol. Rep.
PUBLISHED: 01-16-2009
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GH secretagogue receptor (ghrelin receptor, GHSR) is known to be involved in the control of GH release by mediating the strong stimulatory effect of the endogenous ligand, ghrelin, on GH secretion. Associations between the GHSR gene polymorphism and the growth traits were revealed in Nanyang cattle. The mutations at nt456(G > A) and nt667(C > T) were complete linkage and located in exon 1 of the coding region of the GHSR gene. Least squares analysis revealed a significant statistical effect (P < 0.05) of the GHSR gene different genotypes on body weight and average daily gain at 6 months of age in Nanyang cattle. Individuals with GHSR-MM genotype showed higher body weight and average daily gain than individuals with GHSR-MN genotype.
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Comparative transcriptome profiling of dairy goat microRNAs from dry period and peak lactation mammary gland tissues.
PLoS ONE
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MicroRNAs (miRNAs) are small noncoding RNA molecules that serve as important post-transcriptional gene expression regulators by targeting messenger RNAs for post-transcriptional endonucleolytic cleavage or translational inhibition. miRNAs play important roles in many biological processes. Extensive high-throughput sequencing studies of miRNAs have been performed in several animal models. However, little is known about the diversity of these regulatory RNAs in goat (Capra hircus), which is one of the most important agricultural animals and the oldest domesticated species raised worldwide. Goats have long been used for their milk, meat, hair (including cashmere), and skins throughout much of the world.
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SNP identification in FBXO32 gene and their associations with growth traits in cattle.
Gene
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The F-box protein 32 (FBXO32), also known as Atrogin-1, is one of the four subunits of the ubiquitin protein ligase complex. FBXO32 has been previously shown to be involved in regulation of initiation and development of muscle mass. In the present study, we investigated the polymorphism of FBXO32 gene in 1313 cattle from seven bovine breeds using DNA sequencing, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and PCR-based amplification-created restriction site (PCR-ACRS) methods. Four novel single nucleotide polymorphisms (SNPs) were identified within bovine FBXO32, and were deposited in the GenBank database. The association studies between these four SNPs and growth traits were performed in NanYang cattle. Notably, the SNPs ss411628932 and ss411628936 were shown to be significantly associated with body length of 24-month-old NanYang cattle. Based on the above four SNPs, 16 haplotypes were identified. The main haplotype was AATA, which occurred at a frequency of more than 40%. Additionally, phylogenetic analysis showed that geographical distance was essential to gene flow among seven cattle breeds. Indigenous bovine breeds displayed genetic difference in comparison to hybrid bovine breeds that have foreign origins. We herein describe for the first time a comprehensive study on the variability of bovine FBXO32 gene that is predictive of genetic potential for body length phenotype.
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Exploring polymorphisms and potential application roles of the bovine Nfix gene in breeding.
Genome
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The aim of this study was to detect mutations of the nuclear factor I/X (Nfix) gene and examine the association of its polymorphisms with growth traits in cattle. Six sequence variants (SVs) including five single-nucleotide mutations and an indel with multiple alleles were detected, among which four polymorphisms within the Nfix gene were identified in 1159 individuals of five cattle breeds by sequencing and forced PCR-RFLP methods. The results of haplotype analysis showed 14 haplotypes within the breeds. Three haplotypes were shared by the five cattle breeds. Hap1 (ACAI) was extremely predominant in all test populations, which suggested that individuals with Hap1 (ACAI) were more adapted to the steppe environment. Association analysis in Nanyang cattle showed that two SVs of the Nfix gene were significantly associated with growth traits at different ages. In addition, the locations of the SVs showed that the 3 terminal of the bovine Nfix gene was unstable. Combining this instability with its characteristic of multiple alternative splicing, we conjectured that some SVs might have a relationship with the formation of the splices through which growth traits are modulated. This study will provide useful information for the selection and detection of multiple forms of alternative splicing of the bovine Nfix gene.
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Haplotype combination of the bovine INSIG1 gene sequence variants and association with growth traits in Nanyang cattle.
Genome
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The insulin-induced gene 1 (INSIG1) gene encodes a protein that blocks proteolytic activation of sterol regulatory element binding proteins, which are transcription factors that activate genes that regulate cholesterol, fatty acid, and glucose metabolism. However, similar research for the bovine INSIG1 gene is lacking. Therefore, in this study, polymorphisms of the bovine INSIG1 gene were detected in 643 individuals from four cattle breeds by DNA pooling, forced PCR-RFLP, PCR-SSCP, and DNA sequencing methods. Only 10 novel SNPs were identified, which included four mutations in the coding region and the others in the introns. In Nanyang individuals, seven common haplotypes were identified based on four coding region SNPs. The haplotype GACT, with a frequency of 75.4%, was the most prevalent haplotypes and SNPs formed two linkage disequilibrium blocks with strong multi-allelic D (D = 1). Additionally, association analysis between mutations of the bovine INSIG1 gene and growth traits in Nanyang cattle at 6, 12, 18, and 24 months old was performed, and the results indicated that the polymorphisms were not significantly associated with body mass.
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Haplotype combinations of AdPLA gene polymorphisms associate with growth traits in Chinese cattle.
Mol. Biol. Rep.
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Ablation of AdPLA in mice could prevent obesity, which implicated AdPLA was a new candidate gene for growth traits. In this study, we screened the polymorphisms of AdPLA gene and revealed three novel SNPs (NC_007330.4:g.43638506 C>T, 43658457 T>C and 43661404 T>C) by DNA sequencing and forced PCR-RFLP methods in 1340 individuals from six breeds. A preliminary single SNP-traits association analysis demonstrated that CC genotype was significantly higher than TT genotype at two growth traits in P6-EcoRII locus (P < 0.05). Moreover, the P8-FbaI locus had a significant association with some growth traits, individuals with TT genotype were higher than CC genotype (P < 0.05). A further analysis confirmed that these two SNPs were in linkage disequilibrium, and haplotype H2, both advantage allelic in P6-EcoRII and P8-FbaI loci, was better than the others for bovine growth traits, which was consistent with single SNP-traits association results. Therefore, this study not only proved that these SNPs were in association with bovine growth traits, but also contributed to evaluate them as genetic markers in bovine genetics and breeding and had potential application in breeding programs.
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