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ABSTRACT: The production performance of pigs has been significantly improved due to long-term artificial selection, and the specific variation characterizations (selection signatures) emerged from the selected genome regions. Different types of breeds are subjected to different selection intensities and had different selection signatures. Selective sweep analysis is one of major methods to detect the selection signatures. In this study, based on the 60K BeadChip genotyping data of both commercial Large White (n=45) and local Tongcheng pigs (n=45), genetic differentiation coefficient Fst was applied to detect the selection signatures. Using gPLINK software to set quality control standards, a total of 34 304 SNPs were selected for statistical analysis. Fst values between two breeds were estimated with Genepop package and the average Fst value was 0.3209. Setting Fst>0.7036 (1% of total number of Fst values) as selection threshold, 344 SNPs were obtained and SNP location annotation indicated that there were 79 candidate genes (Sus scrofa Build 9). Furthermore, network analysis was performed using Ingenuity Pathway Analysis and the preliminary results suggested that most genes were involved in growth, reproduction, and immune response, such as NCOA6, ERBB4, RUNX2, and APOB genes. The findings from this study will contribute to further identification of candidate genes and causal mutations implying for meat production and disease resistance in pig.
Hereditas (Beijing) 10/2012; 34(10):1271-81.
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ABSTRACT: In November 2009, scientists from the US, UK, and other countries announced the complete genome sequence draft of the domestic pig. With the release of improved versions of the pig genome assembly and the increase of correctly assembled sequenced fragments over the past two years, it is particularly urgent to have the pig genes annotated at whole-genome level. This article is aimed at introducing an excellent manual annotation tool, Otterlace software, developed by Sanger institute. We used CFL1 (Cofilin 1) gene as an example to expound the usage of the three main components of Otterlace, Zmap, Blixem, and Dotter tools, and developed a practical procedure for manual annotations. We have analyzed 243 immune-related genes, among which 180 genes have been completely or partially annotated, offering novel information to the porcine functional genomics.
Hereditas (Beijing) 10/2012; 34(10):1339-47.
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ABSTRACT: To improve the hatchability of introduced high-yield chickens in Tibet, and ameliorate the egg yield and reproduction traits
of the local Tibetan chickens, four mating combinations between the Recessive White and Tibetan chicken were employed to investigate
the effect of the mating combination and environmental factors on hatchability in this study. The results showed that the
fertility of the eggs with Tibetan chicken as female parent was significantly lower than that with Recessive White as female
parent (P < 0.05), while hatchability was the reverse (P < 0.05). The embryonic mortality of Recessive White was significantly higher by 7.95% than the Tibetan chickens, particularly
during the last stage of incubation. The hatchability of combination III, whose female parent was Tibetan chicken, was higher
by 20.44% than combination II, whose female parent was Recessive White. This provided a theoretical basis for a cross using
the Tibetan chicken as female parent. Binary logistic regression analysis results also showed that the mating combination
and environmental temperature were of importance to egg hatchability.
Frontiers of Agriculture in China 04/2012; 1(2):214-219.
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ABSTRACT: The nudix (nucleoside diphosphate linked moiety X)-type motif 6 (Nudt6) belongs to the cytosolic Nudix hydrolase family genes, and it has been identified as a fibroblast growth factor 2 (Fgf-2)'s anti-sense gene in humans and rats, and can regulate Fgf-2 stability by its 3' un-translated region (UTR) of mRNA. Here we cloned two completed mRNA of porcine NUDT6 variant transcripts and then analyzed the overlapping relationships of 3'UTR ends between NUDT6 and FGF-2 genes. The expression patterns of NUDT6 were detected in heart, liver, spleen, lung, kidney, muscle and fat tissues, suggesting a widespread mRNA expression of this gene in pigs. The real-time PCR results revealed the reverse expression patterns of NUDT6 and FGF-2 in Tongcheng and Yorkshire pig's tissues including heart, live, spleen, lung, kidney and fat tissues. A C/T single nucleotide polymorphism in NUDT6 was genotyped in two experimental populations, and the association analyses revealed that it was significantly associated with intramuscular fat percentage (P < 0.01) and intramuscular lipid (P < 0.05) in experiment population 1, and it was significantly associated with percentage of leaf and caul fat (P < 0.05), percentage of leaf fat (P < 0.05), proportion of lean and bone of the ham (P < 0.05) in experimental population 2. The findings from this study could offer new evidences that NUDT6 maybe a candidate gene for fat deposition in pigs.
Molecular Biology Reports 07/2011; 39(4):4119-26. · 2.93 Impact Factor
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ABSTRACT: The Wingless-type MMTV integration site (Wnt) family encodes secreted glycoproteins that are ligands for the frizzled family of seven-transmembrane receptors and the low density lipoprotein receptor-related protein family of co-receptors. The WNT10B gene inhibits differentiation of preadipocytes in vitro and impairs adipose development in vivo. In the present study, a 1,615-bp cDNA sequence of the porcine WNT10B gene was obtained by RT-PCR. The porcine WNT10B gene was assigned to 5p11-p15 by using the somatic cell hybrid panel (SCHP) and the radiation hybrid (IMpRH) panel. One SNP in the 3'-untranslated region (3'-UTR) was found and association analysis suggested that the SNP was associated with backfat thickness. Semi-quantitative RT-PCR showed that the porcine WNT10B gene was expressed in all tissues examined in 35d and adult pigs and the mRNA expression of WNT10B in fat tissue of Tongcheng pigs was dramatically higher than that in Large White pigs.
Molecular Biology Reports 06/2011; 38(5):3095-9. · 2.93 Impact Factor
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ABSTRACT: The recent completion of the swine genome sequencing project and development of a high density porcine SNP array has made genome-wide association (GWA) studies feasible in pigs.
Using Illumina's PorcineSNP60 BeadChip, we performed a pilot GWA study in 820 commercial female pigs phenotyped for backfat, loin muscle area, body conformation in addition to feet and leg (FL) structural soundness traits. A total of 51,385 SNPs were jointly fitted using Bayesian techniques as random effects in a mixture model that assumed a known large proportion (99.5%) of SNPs had zero effect. SNP annotations were implemented through the Sus scrofa Build 9 available from pig Ensembl. We discovered a number of candidate chromosomal regions, and some of them corresponded to QTL regions previously reported. We not only have identified some well-known candidate genes for the traits of interest, such as MC4R (for backfat) and IGF2 (for loin muscle area), but also obtained novel promising genes, including CHCHD3 (for backfat), BMP2 (for loin muscle area, body size and several FL structure traits), and some HOXA family genes (for overall leg action). The candidate regions responsible for body conformation and FL structure soundness did not overlap greatly which implied that these traits were controlled by different genes. Functional clustering analyses classified the genes into categories related to bone and cartilage development, muscle growth and development or the insulin pathway suggesting the traits are regulated by common pathways or gene networks that exert roles at different spatial and temporal stages.
This study is one of the earliest GWA reports on important quantitative traits in pigs, and the findings will contribute to the further biological function analysis of the identified candidate genes and potential utilization of them in marker assisted selection.
PLoS ONE 01/2011; 6(2):e14726. · 4.09 Impact Factor
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ABSTRACT: JHDM1A, a member of the JHDM (JmjC-domain-containing histone demethylase) family, plays an central role in gene silencing, cell cycle, cell growth and cancer development through histone H3K36 demethylation modification. Here reported the cloning, expression, chromosomal location and association analysis with growth traits of porcine JHDM1A gene. Sequence analysis showed that the porcine JHDM1A gene encodes 1,162 amino acids and contains JmjC, F-box, and CXXC zinc-finger domains, which coding sequence and deduced protein shares 91 and 99% similarity with human JHDM1A, respectively. Spatio-Temporal expression analysis indicated that the mRNA expression of porcine JHDM1A had significantly higher levels in the middle (65 days) and later (90 days) period's embryo skeletal muscle than that of 33 days, and showed a ubiquitously expression but with the highest abundance in kidney, lung and liver of an adult pig. Radiation hybrid mapping and the following linkage mapping data indicate that JHDM1A maps to 2p17 region of pig chromosome 2 (SSC2). Allele frequency differences were detected in different pig breeds and an association study was performed with a SNP within 3'UTR. The results showed that there is a tendency for allele frequencies to differ between the fast growth breeds (Yorkshire) and slow growth pig breeds (Qingping pigs, Yushan Black pigs, Erhualian pigs and Dahuabai pigs). The association analysis using a Berkshire × Yorkshire F(2) population indicated that the C224G polymorphism had a highly significant association with average daily gain on test (P < 0.01), a trend association with average back fat thickness (P < 0.07), and significant associations (P < 0.01) on percent of average drip loss, Fiber Type II Ratio, muscle shear force and average lactate content in μmol/g. This study provides the first evidence that JHDM1A is differentially expressed in porcine embryonic skeletal muscle and associated with meat growth and quality traits.
Molecular Biology Reports 12/2010; 38(7):4697-704. · 2.93 Impact Factor
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ABSTRACT: The gradually discovered sarcomeric proteins play important roles for structural integrity and signal transduction of sarcomere during myofibril genesis. TCAP (also described as telethonin, T-cap), one of the sarcomeric protein genes, is regulated developmentally. In this study, we reported the molecular characteristics of porcine TCAP gene. A 979 bp TCAP cDNA nucleotide sequence was obtained in pig and the deduced amino acid sequence had 92 and 91% identity to those of human and mouse homologous genes, respectively. One SNP was discovered and the allele frequency analysis showed that G allele frequency was low among 221 unrelated pigs from seven breeds. The tissue distribution patterns revealed that TCAP mRNA was expressed abundantly in skeletal and heart muscle tissue. Real-time quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) results displayed TCAP mRNA was up-regulated in both Tongcheng and Landrace pigs during prenatal skeletal muscle development stages. This study suggested that TCAP gene might be a prospective candidate gene affecting muscle mass and meat quality traits in the pig, and also implicated the possible significance of TCAP on sarcomere assembly.
Molecular Biology Reports 07/2009; 37(3):1641-7. · 2.93 Impact Factor
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ABSTRACT: CRP3 is the muscle-specific form of the cysteine and glycine-rich protein family and plays an important role in myofiber differentiation. Here we isolated and characterized its coding gene CSRP3 from porcine muscle. Phylogenic analyses demonstrated that CSRP3 diverged first and is distinguished from two other members, CSRP1 and CSRP2. CSRP3 mRNA was up-regulated during the development of porcine embryonic skeletal muscle, indicating its potential importance in muscle growth. Genetic variant analyses detected multiple variations in an approximately 400 bp region covering exon 4 and its downstream intron, and two haplotypes were identified by sequencing. One of synonymous substitutions C1924T was used for linkage and association analyses. It was revealed that the substitution of C1924T had significant associations with firmness (P < 0.01), Lab Loin pH, Off Flavor Score and Water Holding Capacity (P < 0.05), and a suggestive effect (P < 0.1) on Flavor Score and Average Glycolytic Potential in a Berkshire x Yorkshire F2 population. The association analyses results agreed with the gene's localization to a QTL region for meat quality traits on porcine chromosome 2p14-17 demonstrated by both linkage mapping and RH mapping. These results provide fundamental evidence for CSRP3 as a functional candidate gene affecting pig meat quality.
Molecular Biology Reports 07/2009; 37(1):451-9. · 2.93 Impact Factor
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ABSTRACT: Abstract
Background
Identification and culling of replacement gilts with poor skeletal conformation and feet and leg (FL) unsoundness is an approach used to reduce sow culling and mortality rates in breeding stock. Few candidate genes related to soundness traits have been identified in the pig.
Methods
In this study, 2066 commercial females were scored for 17 traits describing body conformation and FL structure, and were used for association analyses. Genotyping of 121 SNPs derived from 95 genes was implemented using Sequenom's MassARRAY system.
Results
Based on the association results from single trait and principal components using mixed linear model analyses and false discovery rate testing, it was observed that APOE, BMP8, CALCR, COL1A2, COL9A1, DKFZ, FBN1 and VDBP were very highly significantly (P < 0.001) associated with body conformation traits. The genes ALOX5, BMP8 , CALCR, OPG , OXTR and WNT16 were very highly significantly (P < 0.001) associated with FL structures, and APOE, CALCR, COL1A2, GNRHR, IHH , MTHFR and WNT16 were highly significantly (P < 0.01) associated with overall leg action. Strong linkage disequilibrium between CALCR and COL1A2 on SSC9 was detected, and haplotype -ACGACC- was highly significantly (P < 0.01) associated with overall leg action and several important FL soundness traits.
Conclusion
The present findings provide a comprehensive list of candidate genes for further use in fine mapping and biological functional analyses.
Genetics Selection Evolution. 01/2009;
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ABSTRACT: To investigate candidate genes involved in human type 2 diabetes (T2D) for obesity-related phenotypes in pigs. Statistical association analyses of genes with fat deposition were realized in a pig reference family constructed by two breeds, Berkshire and Yorkshire. Extensive sequencing was then attempted to discover the causative polymorphism. Genes implied in human T2D development, TCF7L2, WFS1, FTO, SLC30A8, and GCKR, were mapped on Sus scrofa chromosomes 14, 8, 6, 4, and 3, respectively. Only TCF7L2 was significantly associated with five fat traits in pigs. Further investigation demonstrated that one haplotype (HapB), but not the HapA (homologous to the region for human T2D susceptibility where single-nucleotide polymorphism (SNP) rs7903146 is located), is significantly associated with the fat-related traits. In HapB, two SNPs in TCF7L2 exon 8 and intron 10 are significantly associated with five fat traits, and may be in linkage disequilibrium with the causative variant with additive effects on all four backfat traits, and the total lipid percentage. Pigs of genotype TT for the SNP in exon 8 have only one transcript isoform (the one without exon 4), and lower backfat depth. Candidate gene analyses could provide novel ideas about how these genes function in T2D susceptibility in human, and support that the pig can be a suitable model for human obesity and T2D research. Further replication of this research in other pig populations should be considered, so that the possibility of utilizing these genetic markers in pig breeding or in animal model research can be explored.
Obesity 01/2009; 17(2):323-9. · 4.28 Impact Factor
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ABSTRACT: The association of the FTO gene with obesity has been implicated in various human populations. The FTO gene is also most likely involved in the regulation of energy balance and feed intake. Here, the FTO gene was studied as a candidate gene for fatness and growth rate traits in pigs. The amino acid sequence of the FTO gene showed high conservation among human, pig, and other important domestic animals. Twelve variants including ten SNPs and two indels were detected, and then five SNPs within different genomic regions were genotyped in the ISU Berkshire x Yorkshire pig resource family. The linkage disequilibrium analyses revealed that most of these FTO variants were not in strong LD with each other. The SNPs c.46-139A > T within intron 1 and a synonymous mutation c.594C > G (Ala198Ala) within exon 3 had significant (P < 0.01) associations with average daily gain on test and total lipid percentage in muscle, respectively. Five major haplotypes were identified and the subsequent association analyses suggested that haplotype 2 (-CTTGG-) was the most favorable for increased growth rate, while haplotype 1 (-CTACG-) was unfavorably associated with intramuscular fatness traits.
Animal Biotechnology 01/2009; 20(2):58-70. · 0.93 Impact Factor
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ABSTRACT: The effects of breed, sex and birth parity on the traits of growth, carcass and meat quality were investigated in three different
breeds including Swedish Landrace, British Large White and an indigenous Chinese breed — Tongcheng pigs. The results indicated
that the Swedish Landrace and the British Large White had advantages over the Tongcheng pigs in growth rate, feed conversion
rate (FCR) and carcass traits, but had disadvantages in meat quality. In contrast to the British Large White, the Swedish
Landrace had higher average daily gain during the trial (ADG2) (877.04 g·day−1 vs. 813.95 g·day−1, P < 0.05), and marbling score (MS) (2.48 vs. 2.02, P < 0.01), larger eye muscle area (EMA) (41.80 cm2 vs. 35.14 cm, P < 0.01) and more efficient feed conversion rate (FCR) (3.06 vs. 3.29, P < 0.05), lower muscle shear force (MSF) (4.20 kgf (1 kgf = 9.80665 N) vs. 4.93 kgf, P < 0.05) and backfat thickness (BF) (all P < 0.01) including live backfat thickness (LBF), average backfat thickness at 3 points in the carcass (ABF), backfat thickness
between 6th and 7th ribs (6–7 th BF) and backfat thickness at 10th rib (10 th BF). There was a difference (P < 0.05) only inMS between castrated females (CF) and castrated males (CM). Birth parity affected ADG2 (P < 0.05), some carcass characteristics and meat quality, including CL1 (P < 0.001), CL2 (P < 0.05), BF (ABF, 6–7th BF and 10th BF, all P < 0.001), EMD (P, 0.001), EMA (P < 0.001), percentage of leaf and caul fat (PLC) (P < 0.05), proportion of lean and bone of the ham (PLBH) (P < 0.05), muscle drip loss percentage (DL) (P < 0.05) and intramuscular fat content (IMF) (P < 0.05). The breed-sex interaction only impacted the average daily gain from birth to marketing (ADG1) and DL (both P < 0.05). However, there was no significant effect of sex-parity interaction on all the traits tested.
Frontiers of Agriculture in China 08/2008; 2(3):331-337.
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ABSTRACT: Lectin, galactose-binding, soluble 1 (LGALS1) gene encodes galectin-1, an atypical secretory protein that plays an important role during myoblast proliferation and differentiation. In this study, the porcine LGALS1 gene was cloned and characterized from pig muscle. The predicted protein sequence shared a high identity with its mammalian counterparts. Reverse transcription-polymerase chain reaction revealed that porcine LGALS1 was expressed at 33 day post-coitus (dpc) and 65 dpc at a relatively high level, and then decreased to 90 dpc during fetal skeletal muscle development, suggesting that galectin-1 is a potent factor implicated in the formation of myofibers. LGALS1 was found widely expressed in all tissues and transient transfection indicated that galectin-1 locates both in cytoplasm and nucleus. Genomic sequences and analysis predicted a promoter region at approximately 1.279-1.529 kb, but dual-luciferase reporter assay indicated that it has little promoter activity.
Acta Biochimica et Biophysica Sinica 02/2008; 40(1):85-90. · 1.38 Impact Factor
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ABSTRACT: Genetic variability of 18 microsatellites in five Chinese goat breeds was characterized and then individual-breed assignments were implemented on the basis of microsatellite multi-genotypes. Although the low Gst value of 5.7% occurred among these breeds, the accumulated non-parental exclusion probabilities of 99.99% and the correct assignment percentage of 82% demonstrated that microsatellites were feasible for paternity testing and individual-breed assignments in caprine populations. All of loci showed high polymorphism except that MAF35 had only two alleles, and INRA0132 had potential null allele in these breeds. The non-parental exclusion probability per locus varied from 0.081 to 0.534 under case I for paternity testing and ranged from 0.161 to 0.699 under case II, respectively. Both of Excl 1 and Excl 2 were significantly correlated to the genetic diversity measures including genetic heterozygosity, polymorphism information content (PIC) and gene differential coefficients, and that suggested genetic polymorphism of marker provide enough information for microsatellite selection. In addition, the Bayesian method was proven to have superiority of the correct assignment percentage in comparison to gene frequency method and genetic distance methods, with the assumptions of locus-population Hardy–Weinberg Equilibrium and no linkage between loci. The correct assignment percentage were always higher in YC and Boer than other three goat breeds, implying assignment efficiency was positively relative to populations with greater uniformity and low population genetic variability. The correct assignment percentage rose with the increase of number of loci used, and it could reach 71.5% when nine microsatellites with the highest genetic polymorphism were combined together. © 2007 Published by Elsevier B.V. (K. Li).
Small Ruminant Research 01/2008; 75:154-161. · 1.29 Impact Factor
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ABSTRACT: Obese and lean pig breeds show obvious differences in muscle growth; however, the molecular mechanism underlying phenotype variation remains unknown. Prenatal muscle development programs postnatal performance. Here, we describe a genome-wide analysis of differences in prenatal skeletal muscle between Tongcheng (a typical indigenous Chinese breed) and Landrace (a leaner Western breed) pigs.
We generated transcriptome profiles of skeletal muscle from Tongcheng and Landrace pigs at 33, 65 and 90 days post coitus (dpc), using long serial analysis of gene expression (LongSAGE). We sequenced 317,115 LongSAGE tags and identified 1,400 and 1,201 differentially expressed transcripts during myogenesis in Tongcheng and Landrace pigs, respectively. From these, the Gene Ontology processes and expression patterns of these differentially expressed genes were constructed. Most of the genes showed different expression patterns in the two breeds. We also identified 532, 653 and 459 transcripts at 33, 65 and 90 dpc, respectively, that were differentially expressed between the two breeds. Growth factors, anti-apoptotic factors and genes involved in the regulation of protein synthesis were up-regulated in Landrace pigs. Finally, 12 differentially expressed genes were validated by quantitative PCR.
Our data show that gene expression phenotypes differ significantly between the two breeds. In particular, a slower muscle growth rate and more complicated molecular changes were found in Tongcheng pigs, while genes responsible for increased cellular growth and myoblast survival were up-regulated in Landrace pigs. Our analyses will assist in the identification of candidate genes for meat production traits and elucidation of the development of prenatal skeletal muscle in mammals.
Genome biology 02/2007; 8(6):R115. · 6.63 Impact Factor
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ABSTRACT: MicroRNAs (miRNAs) are recognized as one of the most important families of non-coding RNAs that serve as important sequence-specific post-transcriptional regulators of gene expression. Identification of miRNAs is an important requirement for understanding the mechanisms of post-transcriptional regulation. Hundreds of miRNAs have been identified by direct cloning and computational approaches in several species. However, there are still many miRNAs that remain to be identified due to lack of either sequence features or robust algorithms to efficiently identify them.
We have evaluated features valuable for pre-miRNA prediction, such as the local secondary structure differences of the stem region of miRNA and non-miRNA hairpins. We have also established correlations between different types of mutations and the secondary structures of pre-miRNAs. Utilizing these features and combining some improvements of the current pre-miRNA prediction methods, we implemented a computational learning method SVM (support vector machine) to build a high throughput and good performance computational pre-miRNA prediction tool called MiRFinder. The tool was designed for genome-wise, pair-wise sequences from two related species. The method built into the tool consisted of two major steps: 1) genome wide search for hairpin candidates and 2) exclusion of the non-robust structures based on analysis of 18 parameters by the SVM method. Results from applying the tool for chicken/human and D. melanogaster/D. pseudoobscura pair-wise genome alignments showed that the tool can be used for genome wide pre-miRNA predictions.
The MiRFinder can be a good alternative to current miRNA discovery software. This tool is available at http://www.bioinformatics.org/mirfinder/.
BMC Bioinformatics 02/2007; 8:341. · 2.75 Impact Factor
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ABSTRACT: Abstract
Background
MicroRNAs (miRNAs) are recognized as one of the most important families of non-coding RNAs that serve as important sequence-specific post-transcriptional regulators of gene expression. Identification of miRNAs is an important requirement for understanding the mechanisms of post-transcriptional regulation. Hundreds of miRNAs have been identified by direct cloning and computational approaches in several species. However, there are still many miRNAs that remain to be identified due to lack of either sequence features or robust algorithms to efficiently identify them.
Results
We have evaluated features valuable for pre-miRNA prediction, such as the local secondary structure differences of the stem region of miRNA and non-miRNA hairpins. We have also established correlations between different types of mutations and the secondary structures of pre-miRNAs. Utilizing these features and combining some improvements of the current pre-miRNA prediction methods, we implemented a computational learning method SVM (support vector machine) to build a high throughput and good performance computational pre-miRNA prediction tool called MiRFinder. The tool was designed for genome-wise, pair-wise sequences from two related species. The method built into the tool consisted of two major steps: 1) genome wide search for hairpin candidates and 2) exclusion of the non-robust structures based on analysis of 18 parameters by the SVM method. Results from applying the tool for chicken/human and D. melanogaster/D. pseudoobscura pair-wise genome alignments showed that the tool can be used for genome wide pre-miRNA predictions.
Conclusion
The MiRFinder can be a good alternative to current miRNA discovery software. This tool is available at http://www.bioinformatics.org/mirfinder/ .
BMC Bioinformatics. 01/2007;
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ABSTRACT: Phylogenetic relationships among and genetic variability within 13 Chinese indigenous goat breeds and Boer goat were analyzed using cytochrome b gene sequences. There were 44 variable sites found in a 642 bp sequence, and 46 Cyt b haplotypes were subsequently defined. The phylogeny analysis of haplotypes in combination with goat Cyt b sequences from GenBank shows that Chinese goats are obviously separated from wild goats and might come from Capra aegagrus. Further analysis indicated that indigenous Chinese goats might descend from at least two lineages; most of the individuals analyzed could be classified into lineage A as defined by Luikart, but five other goats were of uncertain lineage. The Tibet plateau is a possible place of origin for Chinese goats. The neighbor-joining tree based on pairwise differences among populations shows that most Tibetan goats, except the Middle Tibet type, cluster closely with North China goats, and then with South China goats. This result confirms that differences in genetic structure exist among goats in different geographic locations. Nucleotide diversity varied among populations. Tibet and North China goats had higher genetic diversity than South China goats. The fixation index (F (st)=87.72%) suggested that most of the total genetic variation was due to variation within populations. In addition, the results indicate that Cyt b gene sequence information alone might not be enough for phylogeny analysis among breeds within species, as shown by fewer polymorphic sites and lower bootstrap values on the neighbor-joining tree.
Biochemical Genetics 05/2006; 44(3-4):89-99. · 0.86 Impact Factor
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ABSTRACT: Genetic variation within exon 2 of chicken major histocompatibility complex B-LB // genes was investigated by PCR amplification, cloning and sequencing of a 374 bp fragment of the indigenous Tibetan chicken genomic DNA. Fifteen novel B-LB // alleles were found. Alignment and comparison of 18 allelic sequences from the individuals sampled revealed a total of 62 variable sites (total of 80 mutations) in exon 2, of which 41 were parsimony informative sites. The nucleotide diversity (pi) within the sequence of exon 2 was calculated to be 0.0718. Analysis of nucleotide variation confirmed a lower level of divergence (0.056 +/- 0.008) as estimated by average pairwise distance within the Tibetan chicken population than the five exotic breeds detected. The relative frequencies of synonymous and non-synonymous nucleotide substitutions within the region were 3.25 +/- 0.94% and 15.61 +/- 2.69% , respectively. These results indicated that the genetic variation within exon 2 seemed to have arisen largely by gene recombination and balancing selection. Alignment of the deduced amino acid sequences of beta1 domain coded by exon 2 revealed 11 synonymous mutations and 27 non-synonymous substitutions at the 38 separate sites. Fifty percent (12/24) of the proposed peptide-binding sites were variable within beta1 domain of chicken MHC B-LB // molecules, of which 11 were unique non-synonymous amino acid substitutions. These particular non-synonymous substitutions are considered to be associated with immunological specificity of MHC B-LB // molecule in Tibetan chicken, and they can provide a molecular biological basis for the study of disease resistance in chicken.
Acta Genetica Sinica 12/2005; 32(11):1136-46.
