Chicken single nucleotide polymorphism identification and selection for genetic mapping

In Silico Mining and Characterization of High-Quality SNP/Indels in Some Agro-Economically Important Species Belonging to the Family Euphorbiaceae

(1) Background: To assess the genetic makeup among the agro-economically important members of Euphorbiaceae, the present study was conducted to identify and characterize high-quality single-nucleotide polymorphism (SNP) markers and their comparative distribution in exonic and intronic regions from the publicly available expressed sequence tags (ESTs). (2) Methods: Quality sequences obtained after pre-processing by an EG assembler were assembled into contigs using the CAP3 program at 95% identity; the mining of SNP was performed by QualitySNP; GENSCAN (standalone) was used for detecting the distribution of SNPs in the exonic and intronic regions. (3) Results: A total of 25,432 potential SNPs (pSNP) and 14,351 high-quality SNPs (qSNP), including 2276 indels, were detected from 260,479 EST sequences. The ratio of quality SNP to potential SNP ranged from 0.22 to 0.75. A higher frequency of transitions and transversions was observed more in the exonic than the intronic region, while indels were present more in the intronic region. C↔T (transition) was the most dominant nucleotide substitution, while in transversion, A↔T was the dominant nucleotide substitution, and in indel, A/- was dominant. (4) Conclusions: Detected SNP markers may be useful for linkage mapping; marker-assisted breeding; studying genetic diversity; mapping important phenotypic traits, such as adaptation or oil production; or disease resistance by targeting and screening mutations in important genes.

Development of reference transcriptomes for the major field insect pests of cowpea: a toolbox for insect pest management approaches in west Africa

Cowpea is a widely cultivated and major nutritional source of protein for many people that live in West Africa. Annual yields and longevity of grain storage is greatly reduced by feeding damage caused by a complex of insect pests that include the pod sucking bugs, Anoplocnemis curvipes Fabricius (Hemiptera: Coreidae) and Clavigralla tomentosicollis Stål (Hemiptera: Coreidae); as well as phloem-feeding cowpea aphids, Aphis craccivora Koch (Hemiptera: Aphididae) and flower thrips, Megalurothrips sjostedti Trybom (Thysanoptera: Thripidae). Efforts to control these pests remain a challenge and there is a need to understand the structure and movement of these pest populations in order to facilitate the development of integrated pest management strategies (IPM). Molecular tools have the potential to help facilitate a better understanding of pest populations. Towards this goal, we used 454 pyrosequencing technology to generate 319,126, 176,262, 320,722 and 227,882 raw reads from A. curvipes, A. craccivora, C. tomentosicollis and M. sjostedti, respectively. The reads were de novo assembled into 11,687, 7,647, 10,652 and 7,348 transcripts for A. curvipes, A. craccivora, C. tomentosicollis and M. sjostedti, respectively. Functional annotation of the resulting transcripts identified genes putatively involved in insecticide resistance, pathogen defense and immunity. Additionally, sequences that matched the primary aphid endosymbiont, Buchnera aphidicola, were identified among A. craccivora transcripts. Furthermore, 742, 97, 607 and 180 single nucleotide polymorphisms (SNPs) were respectively predicted among A. curvipes, A. craccivora, C. tomentosicollis and M. sjostedti transcripts, and will likely be valuable tools for future molecular genetic marker development. These results demonstrate that Roche 454-based transcriptome sequencing could be useful for the development of genomic resources for cowpea pest insects in West Africa.

A novel SNP of the PNRC1 gene and its association with reproductive traits in Tsaiya ducks

Proline-rich nuclear receptor coactivator (PNRC)1 is a member of a new family of nuclear receptor coactivators capable of potentiating the transcriptional activity of nuclear receptors. The objective was to investigate the relationship between PNRC1 genotypes of single nucleotide polymorphism (SNP) and reproductive traits in ducks. Brown Tsaiya ducks (N = 305) from two lines, a control line with no selection and the selected line, were used. Polymerase chain reaction-single strand polymorphism and DNA sequencing were done to screen polymorphisms of the PNRC1 gene. A novel SNP (G98T) in 3'-untranslated region of the PNRC1 gene was identified and resulted in two genotypes, GG and GT. The frequencies of genotype GG and allele G were higher in both lines investigated. Regarding egg weight at first egg (EWFE), based on SNP trait association analysis, ducks with the GG genotype had a 4.48 g per egg greater egg weight at first egg when compared with ducks of the GT genotype in the control line (P < 0.05). In addition, this SNP was associated with the hatchability rate (HR) in the selected line; ducks with the GT genotype had a 6.70% higher hatchability rate than those with the GG genotype (P < 0.05). Therefore, we inferred that the PNRC1 gene could be a candidate locus or linked to a major gene that influenced egg weight-related and hatchability traits in Tsaiya ducks. Further investigations on additional duck populations with larger sample sizes are needed to confirm these results.

Novel genetic markers of the carbonic anhydrase II gene associated with egg production and reproduction traits in Tsaiya ducks

In our previous cDNA microarray study, we found that the carbonic anhydrase II (CA2) gene is one of the differentially expressed transcripts in the duck isthmus epithelium during egg formation period. The aim of this study was to identify the single-nucleotide polymorphisms (SNPs) in the CA2 gene of Tsaiya ducks. The relationship of SNP genotype with egg production and reproduction traits was also investigated. A total of 317 ducks from two lines, a control line with no selection and a selected line, were employed for testing. Three SNPs (C37T, A62G and A65G) in the 3'-untranslated region of the CA2 gene were found. SNP-trait association analysis showed that SNP C37T and A62G were associated with duck egg weight besides fertility. The ducks with the CT and AG genotypes had a 1.46 and 1.62 g/egg lower egg weight as compared with ducks with the CC and AA genotypes, respectively (p < 0.05). But the ducks with CT and AG genotypes had 5.20% and 4.22% higher fertility than those with CC and AA genotypes, respectively (p < 0.05). Diplotype constructed on these three SNPs was associated with duck fertility, and the diplotype H1H4 was dominant for duck fertility. These findings might provide the basis for balanced selection and may be used in marker-assisted selection to improve egg weight and fertility simultaneously in the Tsaiya ducks.

Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna

BACKGROUND

Daphnia (Crustacea: Cladocera) plays a central role in standing aquatic ecosystems, has a well known ecology and is widely used in population studies and environmental risk assessments. Daphnia magna is, especially in Europe, intensively used to study stress responses of natural populations to pollutants, climate change, and antagonistic interactions with predators and parasites, which have all been demonstrated to induce micro-evolutionary and adaptive responses. Although its ecology and evolutionary biology is intensively studied, little is known on the functional genomics underpinning of phenotypic responses to environmental stressors. The aim of the present study was to find genes expressed in presence of environmental stressors, and target such genes for single nucleotide polymorphic (SNP) marker development.

RESULTS

We developed three expressed sequence tag (EST) libraries using clonal lineages of D. magna exposed to ecological stressors, namely fish predation, parasite infection and pesticide exposure. We used these newly developed ESTs and other Daphnia ESTs retrieved from NCBI GeneBank to mine for SNP markers targeting synonymous as well as non synonymous genetic variation. We validate the developed SNPs in six natural populations of D. magna distributed at regional scale.

CONCLUSIONS

A large proportion (47%) of the produced ESTs are Daphnia lineage specific genes, which are potentially involved in responses to environmental stress rather than to general cellular functions and metabolic activities, or reflect the arthropod's aquatic lifestyle. The characterization of genes expressed under stress and the validation of their SNPs for population genetic study is important for identifying ecologically responsive genes in D. magna.

Quality assessment parameters for EST-derived SNPs from catfish

Background

SNPs are abundant, codominantly inherited, and sequence-tagged markers. They are highly adaptable to large-scale automated genotyping, and therefore, are most suitable for association studies and applicable to comparative genome analysis. However, discovery of SNPs requires genome sequencing efforts through whole genome sequencing or deep sequencing of reduced representation libraries. Such genome resources are not yet available for many species including catfish. A large resource of ESTs is to become available in catfish allowing identification of large number of SNPs, but reliability of EST-derived SNPs are relatively low because of sequencing errors. This project was designed to answer some of the questions relevant to quality assessment of EST-derived SNPs.

Results

wo factors were found to be most significant for validation of EST-derived SNPs: the contig size (number of sequences in the contig) and the minor allele sequence frequency. The larger the contigs were, the greater the validation rate although the validation rate was reasonably high when the contigs contain four or more EST sequences with the minor allele sequence being represented at least twice in the contigs. Sequence quality surrounding the SNP under test is also crucially important. PCR extension appeared to be limited to a very short distance, prohibiting successful genotyping when an intron was present, a surprising finding.

Conclusion

Stringent quality assessment measures should be used when working with EST-derived SNPs. In particular, contigs containing four or more ESTs should be used and the minor allele sequence should be represented at least twice. Genotyping primers should be designed from a single exon, completely avoiding introns. Application of such quality assessment measures, along with large resources of ESTs, should provide effective means for SNP identification in species where genome sequence resources are lacking.

QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species

Background

Single nucleotide polymorphisms (SNPs) are important tools in studying complex genetic traits and genome evolution. Computational strategies for SNP discovery make use of the large number of sequences present in public databases (in most cases as expressed sequence tags (ESTs)) and are considered to be faster and more cost-effective than experimental procedures. A major challenge in computational SNP discovery is distinguishing allelic variation from sequence variation between paralogous sequences, in addition to recognizing sequencing errors. For the majority of the public EST sequences, trace or quality files are lacking which makes detection of reliable SNPs even more difficult because it has to rely on sequence comparisons only.

Results

We have developed a new algorithm to detect reliable SNPs and insertions/deletions (indels) in EST data, both with and without quality files. Implemented in a pipeline called QualitySNP, it uses three filters for the identification of reliable SNPs. Filter 1 screens for all potential SNPs and identifies variation between or within genotypes. Filter 2 is the core filter that uses a haplotype-based strategy to detect reliable SNPs. Clusters with potential paralogs as well as false SNPs caused by sequencing errors are identified. Filter 3 screens SNPs by calculating a confidence score, based upon sequence redundancy and quality. Non-synonymous SNPs are subsequently identified by detecting open reading frames of consensus sequences (contigs) with SNPs. The pipeline includes a data storage and retrieval system for haplotypes, SNPs and alignments. QualitySNP's versatility is demonstrated by the identification of SNPs in EST datasets from potato, chicken and humans.

Conclusion

QualitySNP is an efficient tool for SNP detection, storage and retrieval in diploid as well as polyploid species. It is available for running on Linux or UNIX systems. The program, test data, and user manual are available at and as Additional files.

Chicken functional genomics: an overview

Chickens have undergone intensive selection to produce highly productive strains with excellent growth rates and feed conversion ratios. There does not appear to be any reduction in the rate of strain improvement. The recently completed chicken genome sequencing project and adjunct projects cataloging single nucleotide polymorphisms demonstrate that there is still a high level of genetic variation present in modern breeds. The information provided by genome and transcriptome studies furnishes the chicken biologist with powerful tools for the functional analysis of gene networks. Gene microarrays have been constructed and used to investigate gene expression patterns associated with certain production traits and changes in expression induced by pathogen challenge. Such studies have the potential to identify important genes involved in biological processes influencing animal productivity and health. Fundamental regulatory mechanisms controlled by non-coding RNAs, such as microRNAs, can now be studied following the identification of many potential genes by homology with previously identified genes from other organisms. We demonstrate here that microarrays and northern blotting can be used to detect expression of microRNAs in chicken tissue. Other tools are being used for functional genomic analysis including the production of transgenic birds, still a difficult process, and the use of gene silencing. Gene silencing via RNA interference is having a large impact in many areas of functional genomics and we and others have shown that the mechanisms needed for its action are functional in chickens. The chicken genome sequence has revealed a large number of immune related genes that had not previously been identified in chickens. Functional analysis of these genes is likely to lead to applications aimed at improving chicken health and productivity.