Xianyong Lan

Northwest A & F University, Yang-ling-chen, Shaanxi, China

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Publications (89)154.49 Total impact

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    ABSTRACT: Eukaryotic translation elongation factor 1 delta (EEF1D) gene encodes guanine nucleotide exchange protein eEF1Bδ, which participates in the eukaryotic protein synthesis, and plays important roles in regulating cell cycling and milk production. This study firstly focused on detecting the isoforms of dairy goat EEF1D gene and their mRNA expression characterization. Herein, two novel isoforms, EEF1Da and EEF1Dc, were identified in dairy goat. The entire coding sequences of EEF1Da and EEF1Dc isoforms were 843 bp and 267 bp in length, respectively. Goat EEF1Da had complete conserved domains of elongation factor 1 (EF1) family, and the evolution of goat EEF1Da isoform was agreed with the evolution of species. Expression pattern analysis of different isoforms revealed relatively ubiquitous expression of EEF1D and EEF1Da. While EEF1Dc only expressed in heart, lung, kidney, adipose and muscle. Combining with the analysis results of cloning, qRT-PCR and bioinformatics, EEF1Da is the major alternative splicing form of EEF1D gene. Interestingly, qRT-PCR result showed that the highest expression of EEF1D was in adipose, which is the major component of mammary. This result was consistent with the early research that EEF1D expressed highly in the mammary, which indicated that EEF1D played a potential key role in regulating adipose development and milk production. All these findings would provide a foundation for the further research of EEF1D gene and development of dairy goat industry.
    No preview · Article · Jan 2016 · Gene
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    ABSTRACT: Background: Identification of genetic variants, including SNPs (Single Nucleotide Polymorphisms), CNVs (Copy Number Variations) and alternative splicing, within functional genes has received increasing attention in animal science research. HGF (Hepatocyte Growth Factor) is a very important growth factor that works as a mitogen or a morphogen during tissue growth, development and regeneration. However, to date, the functions of genetic variants within the bovine HGF gene, particularly their effects on mRNA expression, have not been determined well. Results: The present study aimed to perform association analysis between genetic variants and mRNA expression for the bovine HGF gene in Qinchuan cattle using various strategies, including PCR-RFLP (Restriction Fragment Length Polymorphism), qPCR (Quantitative Real-time quantitative PCR), TA cloning, DNA sequencing and bioinformatics analysis. A total of five SNPs were identified and only SV1 locus significantly affected HGF mRNA expression in fetal skeletal muscle (P < 0.05). Heterozygous genotype individuals showed significantly higher HGF expression (P < 0.05), which was significantly greater in the "CTCCAGGGTT" combined genotype than that in the "CCCCGGGGTT" combined genotype (P < 0.05). In addition, two alternative splicing variations, HGF-W and HGF-M, were identified, which resulted from alternative 3' splice sites of exon 5, and HGF-W showed higher mRNA levels than HGF-M in all tissues. Conclusion: In summary, genetic variations within the HGF gene affected mRNA expression. These findings provide new insight into the molecular characteristics and functions of bovine HGF.
    Preview · Article · Dec 2015 · Journal of Animal Science and Biotechnology
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    ABSTRACT: Current evidences show that copy number variations (CNVs) are linked to complex phenotypic traits. Leptin receptor (LEPR) gene plays a critical role in energy homeostasis and fat development and re-sequencing of the cattle genome revealed the CNV region (herein referred to as "I3 DNA") within the LEPR intron 3. In the present study, we qualified copy numbers of I3 DNA within LEPR gene in four cattle breeds (Qinchuan, Nanyang, Jinnan and Xianan) by quantitative PCR, and explored their impacts on LEPR gene expression and phenotypic traits in Qinchuan and Nanyang cattle. The results showed that more individuals in Nanyang are with loss of the I3 DNA copy number than that in the others. Additionally, I3 DNA CNVs exhibited a significant negative correlation with LEPR gene expression (P < 0.05). Association analysis showed that gain/normal copy number types performed better traits of body weight, body height and body length than the loss type in Nanyang. To the best of our knowledge, this is the first evidence of the association between LEPR CNVs and cattle traits, and this may help deep understanding of the function of CNVs which may be promising markers for beef cattle breeding and genetics. © 2015 Japanese Society of Animal Science.
    Full-text · Article · Nov 2015 · Animal Science Journal
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    ABSTRACT: The activity of SIRT1 is regulated by many chemical compounds, such as nicotinamide and resveratrol. Here, we probed the specific functions of nicotinamide and resveratrol on bovine adipocyte proliferation and differentiation and showed that inhibition of SIRT1 by nicotinamide increased the number of preadipocytes and expression of adipocyte markers. Resveratrol-induced SIRT1 activation significantly repressed proliferation of preadipocyte, and lessened the expression levels of adipogenic gene. By using an shRNA approach, nicotinamide and resveratrol were further shown to modulate bovine adipogenesis through a SIRT1-dependent mechanism because there were no fat changes responding to drug treatment in SIRT1 knockdown adipocytes. Taken together, the data in this work not only enhanced the theory that resveratrol has pronounced anti-obesity effects in adipose tissue but also indicated that nicotinamide has a positive impact on bovine adipogenesis, and orally administered nicotinamide may be a potential means to promote bovine adipogenesis.
    No preview · Article · Oct 2015 · Journal of Functional Foods
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    ABSTRACT: Transmembrane protein 95 (TMEM95) is closely related to male reproductive performance in cattle, but does not affect semen quality. Alternative splicing plays an important role in regulating biological function as well as in generating proteomic and functional diversity in metazoan organisms. Thus, the aim of this study was to clone and identify transcripts of the TMEM95 gene in cattle using RT-PCR, characterize them via bioinformatics analysis, and detect their expression patterns using qRT-PCR. Two transcripts of TMEM95 were identified in cattle, including TMEM95-SV1 and TMEM95-SV2. Bioinformatics predicted that TMEM95-SV1 has a leucine-rich repeat C-terminal domain and a Pfam: IZUMO. These regions are closely related to protein interactions and the acrosome reaction, respectively. Interestingly, the two transcripts were exclusively expressed in the testes and brain in male fetus cattle, and TMEM95-SV1 was expressed in the brain at significantly higher levels than in the testis (P<0.05, 4.06-fold) and TMEM95-SV2 in the brain (P<0.05, 4.95-fold). These findings enrich the understanding of the TMEM95 gene function and benefit for enhancing male reproduction in cattle industry.
    No preview · Article · Sep 2015 · Gene
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    ABSTRACT: As a critical regulator of nuclear factors affecting adipogenesis, deleted in breast cancer 1 (DBC1) leads to the hyperacetylation of p53, a target of the NAD+-dependent histone deacetylase Sirtuin 1, and activation of the apoptotic pathway. To date, the transcript variants of DBC1 and their functions have never been reported in dairy goats. Herein, we identified two novel transcripts of dairy goat DBC1, namely, DBC1 and DBC1a. DBC1 was 42 base pairs longer than DBC1a, and the splice site of the 42- nucleotide deletion complied with the classic “GT-AG” rule. The goat DBC1a in this study had a high degree of homology with other predicted goat DBC1 variants as well as the only known bovine DBC1 variant, DBC1-X4. DBC1 and DBC1a were widely expressed in different tissues and highly expressed in the pancreas, spleen, lung, liver, kidney, and mammary gland. Moreover, DBC1 has a significantly higher expression than DBC1a in the pancreas, kidney, liver, heart, muscle, brain, and testis. Interestingly, in mammary gland, DBC1 and DBC1a demonstrated similar mRNA expression levels, implying that DBC1a variant plays an important role in milk production. This is the first report on the alternative splicing of goat DBC1 and its mRNA expression profile, which will provide a foundation for further study the function of DBC1 in dairy goat industry.
    No preview · Article · Aug 2015 · Small Ruminant Research
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    ABSTRACT: In contrast to high genetic diversity of mitochondrial DNA (mtDNA), equine Y chromosome shows extremely low variability, implying limited patrilines in the domesticated horse. In this study, we applied direct sequencing and restriction fragment length polymorphism (RFLP) methods to investigate the polymorphisms of 33 Y chromosome specific loci in 304 Chinese indigenous horses from 13 breeds. Consequently, two Y-single nucleotide polymorphisms (SNPs) (Y-45701/997 and Y-50869) and one Y-indel (Y-45288) were identified. Of those, the Y-50869 (T>A) revealed the highest variation frequency (24.67%), whereas it was only 3.29% and 1.97% in Y-45288 (T/-) and Y-45701/997 (G>T) locus, respectively. These three mutations accounted for 27.96% of the total samples and identified five Y-SNP haplotypes, demonstrating genetic diversity of Y chromosome in Chinese horses. In addition, all the five Y-SNP haplotypes were shared by different breeds. Among 13 horse breeds analyzed, Balikun horse displayed the highest nucleotide diversity (π = 5.6×10(-4)) and haplotype diversity (h = 0.527), while Ningqiang horse showed the lowest nucleotide diversity (π = 0.00000) and haplotype diversity (h = 0.000). The results also revealed that Chinese horses had a different polymorphic pattern of Y chromosome from European and American horses. In conclusion, Chinese horses revealed genetic diversity of Y chromosome, however more efforts should be made to better understand the domestication and paternal origin of Chinese indigenous horses.
    Full-text · Article · Aug 2015 · Asian Australasian Journal of Animal Sciences
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    ABSTRACT: The AT motif-binding factor (ATBF1) not only interacts with protein inhibitor of activated signal transducer and activator of transcription 3 (STAT3) (PIAS3) to suppress STAT3 signaling regulating embryo early development and cell differentiation, but is required for early activation of the pituitary specific transcription factor 1 (Pit1) gene (also known as POU1F1) critically affecting mammalian growth and development. The goal of this study was to detect novel nucleotide variations and haplotypes structure of the ATBF1 gene, as well as to test their associations with growth-related traits in goats. Herein, a total of seven novel single nucleotide polymorphisms (SNPs) (SNP 1-7) within this gene were found in two well-known Chinese native goat breeds. Haplotypes structure analysis demonstrated that there were four haplotypes in Hainan black goat while seventeen haplotypes in Xinong Saanen dairy goat, and both breeds only shared one haplotype (hap1). Association testing revealed that the SNP2, SNP5, SNP6, and SNP7 loci were also found to significantly associate with growth-related traits in goats, respectively. Moreover, one diplotype in Xinong Saanen dairy goats significantly linked to growth related traits. These preliminary findings not only would extend the spectrum of genetic variations of the goat ATBF1 gene, but also would contribute to implementing marker-assisted selection in genetics and breeding in goats.
    Preview · Article · Jun 2015 · Asian Australasian Journal of Animal Sciences
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    Full-text · Article · Jun 2015 · Animal Genetics
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    ABSTRACT: The aim of this study was to identify DNA methylation pattern of estrogen receptor alpha (ERα) gene promoter region and to evaluate its association with milk production performance of Xinong Saanen dairy goats. The results showed that there was no significant difference in DNA methylation percentage (MP) in mammary glands samples collected during dry period and milking period. Interestingly, the methylation of ERα gene was breed-specific, and the high milk yielding breed of Xinong Saanen dairy goats appeared to be linked with hypomethylation of the gene (P<0.001) when compared with other dairy breeds. Methylation share rate (MSR) of Xinong Saanen dairy goats ranged from 0 to 0.105. Furthermore, the DNA MP in whole blood samples was significantly higher than that in mammary gland (P<0.001), suggesting that the methylation of this gene was tissue-specific. For the average milk density (AMD), the DNA methylation level of ERα gene in junior AMD group (JP) was significantly lower than that in senior AMD group (SP) (P<0.05). The MP of CpG-12 and CpG-15 dinucleotide loci of SP group were significantly higher than those of JP group (P<0.05 and P<0.05), respectively. Therefore, the two specific CpG-dinucleotide loci can be considered as epigenetic markers, which may contribute in improving milk production performance through epigenetic marker-assisted selection (eMAS) in dairy goats. © 2015, Pakistan Agricultural Scientists Forum. All right reserved.
    No preview · Article · Jun 2015 · Journal of Animal and Plant Sciences
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    ABSTRACT: The signal transducer and activator of transcription 3 (STAT3) has been shown to play key roles in cell development and apoptosis. In this study, we reported three novel single nucleotide polymorphisms (SNPs) within the STAT3 gene: AC_000176:g.45204 C > T (SNP1), g.62058 A > G (SNP2), and g.62230 C > T (SNP3) in the second, tenth, and eleventh introns, among two Chinese native goat breeds. By using the forced polymerase chain reaction-restriction fragment length polymorphism technique, the SNPs were genotyped and we determined the minor allelic frequencies of Xinong Saanen dairy (XNSN) goats and Hainan black (HN) goats. Haplotype frequencies and linkage disequilibrium (LD) coefficients demonstrated that the CAC and CGT haplotypes had the highest frequencies, and the SNP2 and SNP3 loci had strong LD values in these breeds. Statistical analyses indicated a positive association between either a single SNP locus or and combined genotypes of two- or three-loci associations with some growth traits (P < 0.05 or P < 0.01). Next, we found the different genotypes were significantly associated with mRNA expression levels of the STAT3 gene. Together, we show that the expression of STAT3 is associated with goat growth traits, which will be beneficial for animal breeding in the future.
    No preview · Article · May 2015 · Small Ruminant Research
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    ABSTRACT: The nuclear factor I/X (NFIX) is a member of NFI family and contributes to muscle and brain development. Numerous genes coding for alternative splicing isoforms play potential but different roles in biological process. To date, transcript variants of NFIX gene and their expression profiles have never been elucidated in dairy goat. Herein, we identified and verified the expression of two novel transcripts (NFIXa and NFIXb) of NFIX gene in dairy goat. Compared with the normal transcript (NFIX), the NFIXa variant lacked the first and ninth exons, while the NFIXb variant lacked the first, seventh and ninth exons; The NFIXa variant was 69 nt longer than the normal transcript in the 5' end site of the seventh exon, while the NFIXb variant was 66 nt longer in the 5' end site of the seventh exon. Quantitative real-time PCR results showed that the expression levels of the three variants were significantly different. The normal NFIX variant was abundantly expressed in the lungs, the NFIXa variant was highly expressed in the pancreas, and the NFIXb variant was abundantly expressed in both the lung and the pancreas. Additionally, the NFIXa variant showed a significantly higher expression level than those of the normal NFIX and the alternative NFIXb variants in the liver, spleen, adipose, intestine and the testis (P<0.01 or P<0.05), respectively. Expression of the NFIXa variant in the brain was significantly higher than that of the NFIXb variant (P<0.01). These findings suggest that the NFIXa isoform is the most abundant isoform in certain tissues of the dairy goat. This study represents the first report on alternative splicing variants of the goat NFIX gene and their expression profiles. It should help elucidate the function of NFIX gene in dairy goat. Copyright © 2015. Published by Elsevier B.V.
    No preview · Article · May 2015 · Gene
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    ABSTRACT: Hirschsprung's disease (HSCR) is a congenital disease in neonates characterized by the absence of the enteric ganglia in a variable length of the distal colon. This disease results from multiple genetic interactions that modulate the ability of enteric neural crest cells to populate developing gut. We previously reported that three rat strains with different backgrounds (susceptible AGH-Ednrbsl/sl, resistant F344-Ednrbsl/sl, and LEH-Ednrbsl/sl) but the same null mutation of Ednrb show varying severity degrees of aganglionosis. This finding suggests that strain-specific genetic factors affect the severity of HSCR. Consistent with this finding, a quantitative trait locus (QTL) for the severity of HSCR on chromosome (Chr) 2 was identified using an F2 intercross between AGH and F344 strains. In the present study, we performed QTL analysis using an F2 intercross between the susceptible AGH and resistant LEH strains to identify the modifier/resistant loci for HSCR in Ednrb-deficient rats. A significant locus affecting the severity of HSCR was also detected within the Chr 2 region. These findings strongly suggest that a modifier gene of aganglionosis exists on Chr 2. In addition, two potentially causative SNPs (or mutations) were detected upstream of a known HSCR susceptibility gene, Gdnf. These SNPs were possibly responsible for the varied length of gut affected by aganglionosis.
    Full-text · Article · Mar 2015 · PLoS ONE
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    ABSTRACT: Acyl-CoA dehydrogenase, very long chain (ACADVL), encoding ACADVL protein, targets the inner mitochondrial membrane where it catalyzes the first step of the mitochondrial fatty acid beta-oxidation pathway and plays an important role in body metabolism and oxidation of long chain fatty acid releasing energy. Tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) is an easy-to-operate, rapid, inexpensive, and exact method for SNP genotyping. Herein, T-ARMS-PCR was carried out to detect a critical missense mutation (AC_000176:g.2885C>A; Pro236Thr) within the ACADVL gene in 644 individuals from two cattle breeds. In order to evaluate the accuracy of the T-ARMS-PCR at this locus, the genotype of the sampled individuals was also identified by PCR-RFLP. The concordance between these two methods was 98.76%. Statistical analysis showed that the bovine ACADVL gene had a significant effect on chest width (P<0.05), chest depth (P<0.05), and hip width (P<0.05) in the Qinchuan breed. The cattle with AA genotype had superior growth traits compared to cattle with AC and/or CC genotypes. The "A" allele had positive effects on growth traits. Therefore, T-ARMS-PCR can replace PCR-RFLP for rapid genotyping of this mutation, which could be used as a DNA marker for selecting individuals with superior growth traits in the Qinchuan breed. These findings contribute to breeding and genetics in beef cattle industry. Copyright © 2015. Published by Elsevier B.V.
    Full-text · Article · Jan 2015 · Gene
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    ABSTRACT: 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.
    No preview · Article · Nov 2014 · Molecular Biology Reports
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    ABSTRACT: Signal transducer and activator of transcription 5A (STAT5A), previously known as mammary gland factor (MGF), belongs to the prolactin/JAK2/STAT5 pathway, and plays an important role in growth and development, milking, and lipid accumulation in mammals. The aim of this study was to identify novel genetic variants of the goat STAT5A gene, as well as to test the possible effects of these variants on body measurement traits in the Xinong Saanen dairy goat (XNSN, milking breed) and the Hainan black goat (HNBG, meat breed) that thrive in Northwest China and Southeast China, respectively, which concurrently need improvement in terms of growth. Three novel single nucleotide polymorphisms (SNPs) (IVS1 + 254C > T, SNP1; Tyr90Tyr, SNP2; and IVS3 + 303T > C, SNP3) within the goat STAT5A gene were identified in intron 1, exon 2, and intron 3, respectively, as well as a documented SNP (Pro268Pro, SNP4) was also detected in exon 7. These SNPs were genotyped using the amplification created restriction site-polymerase chain reaction-restriction fragment length polymorphism (aCRS-PCR-RFLP) and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methods; their minor allelic frequencies varied from 0.079 (SNP4) to 0.372 (SNP2) in the HNBG breed as well as from zero (SNP1) to 0.362 (SNP4) in the XNSN breed, respectively. The PIC values of these loci varied from zero to 0.358. Haplotype analysis uncovered only 8 haplotypes; the major haplotypes were Hap1 (CCCC), Hap2 (CCTC), and Hap4 (CTTC). During linkage disequilibrium analysis, only SNP1 and SNP3 loci showed strong linkage (r2 = 0.999) in the HNBG breed. Statistical analyses indicated that only the known variant (SNP4, Pro268Pro) was significantly associated with body measurement traits in the two breeds when analyzed separately or in combination (P < 0.05 or P < 0.01), implying that this SNP significantly affected goat body measurement traits. Therefore, the STAT5A gene is a candidate gene affecting goat body measurement traits and could contribute to goat breeding improvement programs through marker-assisted selection (MAS).
    No preview · Article · Oct 2014 · Small Ruminant Research
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    ABSTRACT: 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.
    Full-text · Article · Jul 2014 · PLoS ONE
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    ABSTRACT: Background 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. Results In this study, total RNA from the back fat of fetal bovines, adult bulls, adult heifers and adult steers were used to construct libraries for Illumina next-generation sequencing. We detected the expression levels of 12,233 genes, with over 3,000 differently expressed genes when comparing fetal and adult patterns and an average of 1000 differently expressed genes when comparing adult patterns. Multiple Gene Ontology terms and pathways were found to be significantly enriched for these differentially expressed genes. Of the 12,233 detected genes, a total of 4,753 genes (38.85%) underwent alternative splicing events, and over 50% were specifically expressed in each library. Over 4,000 novel transcript units were discovered for one library, whereas only approximately 30% were considered to have coding ability, which supplied a large amount of information for the lncRNA study. Additionally, we detected 56,564 (fetal bovine), 65,154 (adult bull), 78,061 (adult heifer) and 86,965 (adult steer) putative single nucleotide polymorphisms located in coding regions of the four pooled libraries. Conclusion Here, we present, for the first time, a complete dataset involving the spatial and temporal transcriptome of bovine adipose tissue using RNA-seq. These data will facilitate the understanding of the effects of age and sex on the development of adipose tissue and supply essential information towards further studies on the genomes of beef cattle and other related mammals.
    Full-text · Article · Jul 2014 · PLoS ONE
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    ABSTRACT: Background 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. Results We identified 486 copy number variable regions (CNVRs), covering 2.45% of the bovine genome, in 24 taurine (Bos taurus), together with 161 ones in 2 yaks (Bos grunniens) and 163 ones in 3 buffaloes (Bubalus bubalis). Totally, we discovered 605 integrated CNVRs, with more “loss” events than both “gain” and “both” ones, and clearly clustered them into three cattle groups. Interestingly, we confirmed their uneven distributions across chromosomes, and the differences of mitochondrion DNA copy number (gain: taurine, loss: yak & buffalo). Furthermore, we confirmed approximately 41.8% (253/605) and 70.6% (427/605) CNVRs span cattle genes and quantitative trait loci (QTLs), respectively. Finally, we confirmed 6 CNVRs in 9 chosen ones by using quantitative PCR, and further demonstrated that CNVR22 had significantly negative effects on expression of PLA2G2D gene, and both CNVR22 and CNVR310 were associated with body measurements in Chinese cattle, suggesting their key effects on gene expression and cattle traits. Conclusions The results advanced our understanding of CNV as an important genomic structural variation in taurine, yak and buffalo. This study provides a highly valuable resource for Chinese cattle’s evolution and breeding researches. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-480) contains supplementary material, which is available to authorized users.
    Full-text · Article · Jun 2014 · BMC Genomics
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    ABSTRACT: 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.
    Full-text · Article · May 2014 · PLoS ONE

Publication Stats

453 Citations
154.49 Total Impact Points

Institutions

  • 2007-2014
    • Northwest A & F University
      • College of Animal Science and Technology
      Yang-ling-chen, Shaanxi, China
    • Jiangsu Normal University
      • Institute of Cellular and Molecular Biology
      Hsü-chuang, Shaanxi, China
  • 2010
    • Wake Forest University
      Winston-Salem, North Carolina, United States