[Show abstract][Hide abstract] 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.
Asian Australasian Journal of Animal Sciences 08/2015; 28(8). DOI:10.5713/ajas.14.0784 · 0.56 Impact Factor
[Show abstract][Hide abstract] 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.
Small Ruminant Research 05/2015; DOI:10.1016/j.smallrumres.2015.05.014 · 1.10 Impact Factor
[Show abstract][Hide abstract] 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.
PLoS ONE 03/2015; 10(3):e0122068. DOI:10.1371/journal.pone.0122068 · 3.23 Impact Factor
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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).
Small Ruminant Research 10/2014; 121(2-3). DOI:10.1016/j.smallrumres.2014.09.002 · 1.10 Impact Factor
[Show abstract][Hide abstract] 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.
PLoS ONE 07/2014; 9(7):e102142. DOI:10.1371/journal.pone.0102142 · 3.23 Impact Factor
[Show abstract][Hide abstract] 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.
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.
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.
PLoS ONE 07/2014; 9(7):e101261. DOI:10.1371/journal.pone.0101261 · 3.23 Impact Factor
[Show abstract][Hide abstract] 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.
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.
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.
[Show abstract][Hide abstract] 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.
PLoS ONE 05/2014; 9(5):e96857. DOI:10.1371/journal.pone.0096857 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The aim of this study was to detect splicing variants of the bovine NFIX gene and determine their expression regulations. Through bioinformatics analysis, we predicted five isoforms of the bovine NFIX transcript product and validated their existence using cDNA pool and sequencing methods. The five isoforms had a common 5′-terminal sequence and various 3′-terminal sequences. Nuclear factor I family genes can activate or repress transcription by a highly variable C-terminal region. Thus, the five isoform products from a single gene may function differently. Quantitative PCR results showed that NFIX had highest expression in brain; medial expression in lung and muscle; and lower expression in spleen, kidney, liver and heart of both embryo and adult cattle. However, the expression levels NFIX in adult tissues were significantly decreased, and the diversity of its alternative splicing events was lower. Each isoform was expressed differently in different tissues at the embryo and adult stages. One of the isoforms (Nfix2) was not detected in tissues of adult cattle. In brain, another of the isoforms (Nfix3) was not detected, whereas the other four isoforms were highly expressed. In the embryo, of the five isoforms, the profile of the one labeled Nfix4 was the most similar to that of total Nfix, and we proved that it was the major isoform. This study is the first that has detected five novel isoforms of the bovine NFIX transcript products and that has examined their profiles at spatial and temporal levels, which will provide essential information for better understanding the bovine NFIX gene.
[Show abstract][Hide abstract] ABSTRACT: Tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) offers fast detection and extreme simplicity at a negligible cost for SNP genotyping. SIRT2, the family member (sirtuins, SIRT1-7) with the greatest homology to the silent information regulator 2 (Sir2), is the most abundantly expressed sirtuins in adipocytes and has been implicated in promoting fatty acid oxidation (FAO) by deacetylating various substrates. In the current study, we have successfully genotyped a new identified bovine SIRT2 SNP g.4140A > G by T-ARMS-PCR method and validated the accuracy by PCR-RFLP assay using 1255 animals representing the five main Chinese breeds. The concordance between the two different methods was 98.8%. Individuals with discordant genotypes were retyped by direct DNA sequencing. 40% of the discrepancies could be attributed to incomplete digestion in the PCR-RFLP assay. 60% of discordant genotypes resulted from allele failure in the T-ARMS-PCR assay. Chi-square test shows that the frequencies of SNP g.4140A > G are in Hardy-Weinberg equilibrium in all the samples (P > 0.05), which suggested that the five populations are almost a dynamic equilibrium even in artificial selection. Association analysis showed that the g.4140A > G polymorphism is significantly related to 24 months-old body weight in Nanyang cattle. Our results provide direct evidence that T-ARMS-PCR is a rapid, reliable, and cost-effective method for SNP genotyping and g.4140A > G polymorphism in bovine SIRT2 is associated with growth efficiency traits. These findings may be used for marker-assisted selection and management in feedlot cattle.
[Show abstract][Hide abstract] ABSTRACT: 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.
[Show abstract][Hide abstract] ABSTRACT: 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 PPARα/RXRα 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.
PLoS ONE 02/2014; 9(2):e90244. DOI:10.1371/journal.pone.0090244 · 3.23 Impact Factor