Mapping microsatellite markers identified in porcine EST sequences

Reduced representation approach for identification of genome-wide SNPs and their annotation for economically important traits in Indian Tharparkar cattle

The present study was carried out in Tharparkar cattle for identification of genome-wide SNPs and microsatellites, and then annotate the identified high-quality SNPs to milk production, fertility, carcass, adaptability and immune response of economically important traits. A total of 146,011 SNPs were identified with respect to Bos taurus reference genome which are indicus specific, out of which 10,519 SNPs were found to be novel. Similarly, a total of 87,047 SNPs were identified with respect to Bos indicus reference genome. After final annotation of SNPs identified with respect to Bos indicus reference genome, 2871 SNPs were found to be associated in 383 candidate genes having to do with milk production, fertility, carcass, immune response and adaptability traits. Following that, 2571 microsatellites were identified. The information mined from the data might be of importance for the future breed improvement programs, conservation efforts and for enhancing the SNPs density of the existing bovine SNP chips.

Characterization of porcine simple sequence repeat variation on a population scale with genome resequencing data

Simple sequence repeats (SSRs) are used as polymorphic molecular markers in many species. They contribute very important functional variations in a range of complex traits; however, little is known about the variation of most SSRs in pig populations. Here, using genome resequencing data, we identified ~0.63 million polymorphic SSR loci from more than 100 individuals. Through intensive analysis of this dataset, we found that the SSR motif composition, motif length, total length of alleles and distribution of alleles all contribute to SSR variability. Furthermore, we found that CG-containing SSRs displayed significantly lower polymorphism and higher cross-species conservation. With a rigorous filter procedure, we provided a catalogue of 16,527 high-quality polymorphic SSRs, which displayed reliable results for the analysis of phylogenetic relationships and provided valuable summary statistics for 30 individuals equally selected from eight local Chinese pig breeds, six commercial lean pig breeds and Chinese wild boars. In addition, from the high-quality polymorphic SSR catalogue, we identified four loci with potential loss-of-function alleles. Overall, these analyses provide a valuable catalogue of polymorphic SSRs to the existing pig genetic variation database, and we believe this catalogue could be used for future genome-wide genetic analysis.

Transcriptome analysis of leaf tissue from Bermudagrass (Cynodon dactylon) using a normalised cDNA library

A normalised cDNA library was constructed from Bermudagrass to gain insight into the transcriptome of Cynodon dactylon L. A total of 15 588 high-quality expressed sequence tags (ESTs) from the cDNA library were subjected to The Institute for Genomic Research Gene Indices clustering tools to produce a unigene set. A total of 9414 unigenes were obtained from the high-quality ESTs and only 39.6% of the high-quality ESTs were redundant, indicating that the normalisation procedure was effective. A large-scale comparative genomic analysis of the unigenes was carried out using publicly available tools, such as BLAST, InterProScan and Gene Ontology. The unigenes were also subjected to a search for EST-derived simple sequence repeats (EST-SSRs) and conserved-intron scanning primers (CISPs), which are useful as DNA markers. Although the candidate EST-SSRs and CISPs found in the present study need to be empirically tested, they are expected to be useful as DNA markers for many purposes, including comparative genomic studies of grass species, by virtue of their significant similarities to EST sequences from other grasses. Thus, knowledge of Cynodon ESTs will empower turfgrass research by providing homologues for genes that are thought to confer important functions in other plants.

Simple sequence repeats in zebra finch (Taeniopygia guttata) expressed sequence tags: a new resource for evolutionary genetic studies of passerines

Background

Passerines (perching birds) are widely studied across many biological disciplines including ecology, population biology, neurobiology, behavioural ecology and evolutionary biology. However, understanding the molecular basis of relevant traits is hampered by the paucity of passerine genomics tools. Efforts to address this problem are underway, and the zebra finch (Taeniopygia guttata) will be the first passerine to have its genome sequenced. Here we describe a bioinformatic analysis of zebra finch expressed sequence tag (EST) Genbank entries.

Results

A total of 48,862 ESTs were downloaded from GenBank and assembled into contigs, representing an estimated 17,404 unique sequences. The unique sequence set contained 638 simple sequence repeats (SSRs) or microsatellites of length ≥20 bp and purity ≥90% and 144 simple sequence repeats of length ≥30 bp. A chromosomal location for the majority of SSRs was predicted by BLASTing against assembly 2.1 of the chicken genome sequence. The relative exonic location (5' untranslated region, coding region or 3' untranslated region) was predicted for 218 of the SSRs, by BLAST search against the ENSEMBL chicken peptide database. Ten loci were examined for polymorphism in two zebra finch populations and two populations of a distantly related passerine, the house sparrow Passer domesticus. Linkage was confirmed for four loci that were predicted to reside on the passerine homologue of chicken chromosome 7.

Conclusion

We show that SSRs are abundant within zebra finch ESTs, and that their genomic location can be predicted from sequence similarity with the assembled chicken genome sequence. We demonstrate that a useful proportion of zebra finch EST-SSRs are likely to be polymorphic, and that they can be used to build a linkage map. Finally, we show that many zebra finch EST-SSRs are likely to be useful in evolutionary genetic studies of other passerines.

The molecular ecologist's guide to expressed sequence tags

Genomics and bioinformatics have great potential to help address numerous topics in ecology and evolution. Expressed sequence tags (ESTs) can bridge genomics and molecular ecology because they can provide a means of accessing the gene space of almost any organism. We review how ESTs have been used in molecular ecology research in the last several years by providing sequence data for the design of molecular markers, genome-wide studies of gene expression and selection, the identification of candidate genes underlying adaptation, and the basis for studies of gene family and genome evolution. Given the tremendous recent advances in inexpensive sequencing technologies, we predict that molecular ecologists will increasingly be developing and using EST collections in the years to come. With this in mind, we close our review by discussing aspects of EST resource development of particular relevance for molecular ecologists.

A genome-wide distribution of 8-oxoguanine correlates with the preferred regions for recombination and single nucleotide polymorphism in the human genome

8-Oxoguanine (8-oxoG), a major spontaneous form of oxidative DNA damage, is considered to be a natural cause of genomic diversity in organisms because of its mutagenic potential. The steady-state level of 8-oxoG in the nuclear genome of a human cell has been estimated to be several residues per 10(6) guanines. In the present study, to clarify the genome-wide distribution of 8-oxoG in the steady state, we performed fluorescence in situ detection of 8-oxoG on human metaphase chromosomes using a monoclonal antibody. Multiple dot-like signals were observed on each metaphase chromosome. We then mapped the position of the signal at megabase resolution referring to the cytogenetically identified chromosomal band, and demonstrated that 8-oxoG is unevenly distributed in the normal human genome and that the distribution pattern is conserved among different individuals. Moreover, we found that regions with a high frequency of recombination and single nucleotide polymorphisms (SNPs) are preferentially located within chromosomal regions with a high density of 8-oxoG. Our findings suggest that 8-oxoG is one of the main causes of frequent recombinations and SNPs in the human genome, which largely contribute to the genomic diversity in human beings.

Isolation and enrichment of abundant microsatellites from a channel catfish (Ictalurus punctatus) brain cDNA library

Efforts to construct a genetic linkage map of channel catfish have involved identification of random genomic microsatellite markers, as well as anchored Type I loci (expressed genes) from channel catfish. To identify Type I markers we constructed a directional cDNA library from brain tissue to obtain expressed catfish sequences that could be used for single nucleotide polymorphism (SNP) marker development. These cDNA sequences surprisingly contained a high proportion of microsatellites (about 14%) in noncoding regions of expressed sequence tags (ESTs), many of which were not associated with known sequences. To further identify cDNAs with microsatellites and reduce the number of sequencing reactions needed for marker development, we enriched this library for repeat sequences and sequenced clones from both directions. A total of 1644 clones from seven repeat-enriched captures (CA, GT, CT, GA, MTT, TAG, and TAC) were sequenced from both ends, and 795 nonredundant clones were assembled. Thirty-seven percent of the clones contained microsatellites in the trimmed sequence. After assembly in the TIGR Catfish Gene Index (CfGI), 154 contigs matched known vertebrate genes and 92 contigs contained microsatellites. When BLAST-matched orthologues were available for similarity alignments, 28% of these contigs contained repeats in the 5'-UTR, 72% contained repeats in the 3'-UTR, and 8% contained repeats at both ends. Using biotinylated repeat oligonucleotides coupled with streptavidin-coated magnetic beads, and rapid; single-pass hybridization, we were able to enrich our plasmid library greater than two-fold for repeat sequences and increase the ability to link these ESTs with known sequences greater than six-fold.

Development of EST-SSR markers by data mining in three species of shrimp: Litopenaeus vannamei, Litopenaeus stylirostris, and Trachypenaeus birdy

We report on the data mining of publicly available Litopenaeus vannamei expressed sequence tags (ESTs) to generate simple sequence repeat (SSRs) markers and on their transferability between related Penaeid shrimp species. Repeat motifs were found in 3.8% of the evaluated ESTs at a frequency of one repeat every 7.8 kb of sequence data. A total of 206 primer pairs were designed, and 112 loci were amplified with the highest success in L. vannamei. A high percentage (69%) of EST-SSRs were transferable within the genus Litopenaeus. More than half of the amplified products were polymorphic in a small testing panel of L. vannamei. Evaluation of those primers in a larger testing panel showed that 72% of the markers fit Hardy-Weinberg equilibrium, which shows their utility for population genetic analysis. Additionally, a set of 26 of the EST-SSRs were evaluated for Mendelian segregation. A high percentage of monomorphic markers (46%) proved to be polymorphic by singles-stranded conformational polymorphism analysis. Because of the high number of ESTs available in public databases, a data mining approach similar to the one outlined here might yield high numbers of SSR markers in many animal taxa.

Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss)

BACKGROUND

Comparative genomics, through the integration of genetic maps from species of interest with whole genome sequences of other species, will facilitate the identification of genes affecting phenotypes of interest. The development of microsatellite markers from expressed sequence tags will serve to increase marker densities on current salmonid genetic maps and initiate in silico comparative maps with species whose genomes have been fully sequenced.

RESULTS

Eighty-nine polymorphic microsatellite markers were generated for rainbow trout of which at least 74 amplify in other salmonids. Fifty-five have been associated with functional annotation and 30 were mapped on existing genetic maps. Homologous sequences were identified for 20 of the EST containing microsatellites to identify comparative assignments within the tetraodon, mouse, and/or human genomes.

CONCLUSION

The addition of microsatellite markers constructed from expressed sequence tag data will facilitate the development of high-density genetic maps for rainbow trout and comparative maps with other salmonids and better studied species.

Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley

Background

Earlier comparative maps between the genomes of rice (Oryza sativa L.), barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.) were linkage maps based on cDNA-RFLP markers. The low number of polymorphic RFLP markers has limited the development of dense genetic maps in wheat and the number of available anchor points in comparative maps. Higher density comparative maps using PCR-based anchor markers are necessary to better estimate the conservation of colinearity among cereal genomes. The purposes of this study were to characterize the proportion of transcribed DNA sequences containing simple sequence repeats (SSR or microsatellites) by length and motif for wheat, barley and rice and to determine in-silico rice genome locations for primer sets developed for wheat and barley Expressed Sequence Tags.

Results

The proportions of SSR types (di-, tri-, tetra-, and penta-nucleotide repeats) and motifs varied with the length of the SSRs within and among the three species, with trinucleotide SSRs being the most frequent. Distributions of genomic microsatellites (gSSRs), EST-derived microsatellites (EST-SSRs), and transcribed regions in the contiguous sequence of rice chromosome 1 were highly correlated. More than 13,000 primer pairs were developed for use by the cereal research community as potential markers in wheat, barley and rice.

Conclusion

Trinucleotide SSRs were the most common type in each of the species; however, the relative proportions of SSR types and motifs differed among rice, wheat, and barley. Genomic microsatellites were found to be primarily located in gene-rich regions of the rice genome. Microsatellite markers derived from the use of non-redundant EST-SSRs are an economic and efficient alternative to RFLP for comparative mapping in cereals.

Survey of a cDNA library from the turkey (Meleagris gallopavo)

Genome characterization and analysis is an imperative step in identifying and selectively breeding for improved traits of agriculturally important species. Expressed sequence tags (ESTs) represent a transcribed portion of the genome and are an effective way to identify genes within a species. Downstream applications of EST projects include DNA microarray construction and interspecies comparisons. In this study, 694 ESTs were sequenced and analyzed from a library derived from a 24-day-old turkey embryo. The 437 unique sequences identified were divided into 76 assembled contigs and 361 singletons. The majority of significant comparative matches occurred between the turkey sequences and sequences reported from the chicken. Whole genome sequence from the chicken was used to identify potential exon–intron boundaries for selected turkey clones and intron-amplifying primers were developed for sequence analysis and single nucleotide polymorphism (SNP) discovery. Identified SNPs were genotyped for linkage analysis on two turkey reference populations. This study significantly increases the number of EST sequences available for the turkey.Key words: turkey, cDNA, expressed sequence tag, single nucleotide polymorphism.

Inverted Gcg/CGC trinucleotide microsatellites in the 5'-region of Mus IDS mRNA: recurrent induction of aberrant reverse transcripts

An investigation was initiated to explore previously published results indicating that approximately 80 bp of the 5'-end of the iduronate sulfatase (IDS) cDNA sequence (Accession No L07291) are 100% homologous with the 3'-UTR of isoform I of the sodium hydrogen exchanger (Acc. No. U51112). 5'-RACE carried out on IDS mRNA demonstrated the apparent homology to be a cloning artifact. A sequence comparison of the IDS 5'-RACE product with a mouse BAC clone covering the region, and with various IDS ESTs, suggested that the region is highly susceptible to cloning artifacts, a common one of which is template switching by reverse transcriptase. The nucleotide sequence flanking the translation start site is unusual in containing two inverted repeats composed of the complementary trinucleotide microsatellites, (GCG)9 and (CGC)6. These likely form a highly stable stem of 20-21 nt, through which reverse transcription is compromised. Such a stem could be involved in the regulation of IDS expression by directly affecting translation, message turnover, or serving as a substrate for siRNA production. Though such mRNA features are relatively rare, they may be more abundant but overlooked due to difficulties in their reverse transcription.

Systematic screening of sheep skin cDNA libraries for microsatellite sequences

65,000 sheep skin cDNA clones were gridded in high density on to nylon membranes and screened for (CA)n and (GA)n repeat containing clones. 296 dinucleotide repeat-containing clones were identified with approximately 85% non-redundancy. Clones were single-pass 5' sequenced and we compared the Expressed Sequence Tag (EST) sequences to the Swiss-Prot database to ascertain their identity and/or putative function. We then aligned the ESTs against the human genomic sequence to determine the locations of human orthologous sequences. Finally, we developed a subset of polymorphic microsatellite markers and positioned them on the ovine linkage map.

Fine mapping a quantitative trait locus affecting ovulation rate in swine on chromosome 8

Ovulation rate is an integral component of litter size in swine, but is difficult to directly select for in commercial swine production. Because a QTL has been detected for ovulation rate at the terminal end of chromosome 8p, genetic markers for this QTL would enable direct selection for ovulation rate in both males and females. Eleven genes from human chromosome 4p16-p15, as well as one physiological candidate gene, were genetically mapped in the pig. Large insert swine genomic libraries were screened, clones were isolated and then screened for microsatellite repeats, and informative microsatellite markers were developed for seven genes (GNRHR, IDUA, MAN2B2, MSX1, PDE6B, PPP2R2C, and RGS12). Three genes (LRPAP1, GPRK2L, and FLJ20425) were mapped using genotyping assays developed from single nucleotide polymorphisms. Two genes were assigned since they were present in clones that contained mapped markers (HGFAC and HMX1). The resulting linkage map of pig chromosome 8 contains markers associated with 14 genes in the first 27 cM. One inversion spanning at least 3 Mb in the human genome was detected; all other differences could be explained by resolution of mapping techniques used. Fourteen of the most informative microsatellite markers in the first 27 cM of the map were genotyped across the entire MARC swine resource population, increasing the number of markers typed from 2 to 14 and more than doubling the number ofgenotyped animals with ovulation rate data (295 to 600). Results from the revised data set for the QTL analysis, assuming breed specific QTL alleles, indicated that the most likely position of the QTL resided at 4.85 cM on the new linkage map (F1,592 = 20.5150, genome-wide probability less than 0.015). The updated estimate of the effect of an allele substitution was -1.65 ova for the Meishan allele. The F-ratio peak was closest to markers for MAN2B2 (4.80 cM) and was flanked on the other side by markers for PPP2R2C. Two positional candidate genes included in this study are MAN2B2 and RGS12. These results validate the presence of a QTL affecting ovulation rate on chromosome 8 and facilitate selection of positional candidate genes to be evaluated.

Comparative mapping of a region on chromosome 10 containing QTL for reproduction in swine

Several quantitative trait loci (QTL) for important reproductive traits (age of puberty, ovulation rate, nipple number and plasma FSH) have been identified on the long arm of porcine chromosome 10. Bi-directional chromosome painting has shown that this region is homologous to human chromosome 10p. Because few microsatellite or type I markers have been placed on SSC10, we wanted to increase the density of known ESTs mapped in this region of the porcine genome. Genes were chosen for their position on human chromosome 10, sequence availability from the TIGR pig gene indices, and their potential as a candidate gene. The PCR primers were designed to amplify across introns or 3'-UTR to maximize single nucleotide polymorphism (SNP) discovery. Parents of the mapping population (one sire and seven dams) were amplified and sequenced to find informative markers. The SNPs were genotyped using primer extension and mass spectrometry. These amplification products were also used to probe a BAC library (RPCI-44, Roswell Park Cancer Institute) for positive clones and screened for microsatellites. Six genes from human chromosome 10p (AKR1C2, PRKCQ, ITIH2, ATP5C1, PIP5K2A and GAD2) were mapped in the MARC swine mapping population. Gene order was conserved within these markers from centromere to telomere of porcine chromosome 10q, as compared with human chromosome 10p. Four of these genes (PIP5K2A, ITIH2, GAD2 and AKR1C2), which map under QTL, are potential candidate genes. Identification of porcine homologues near important QTL and development of a comparative map for this chromosome will allow further fine- mapping and positional cloning of candidate genes affecting reproductive traits.