Dataset Information

Characterization of Duck (Anas platyrhynchos) Short Tandem Repeat Variation by Population-Scale Genome Resequencing.

ABSTRACT: Short tandem repeats (STRs) are usually associated with genetic diseases and gene regulatory functions, and are also important genetic markers for analysis of evolutionary, genetic diversity and forensic. However, for the majority of STRs in the duck genome, their population genetic properties and functional impacts remain poorly defined. Recent advent of next generation sequencing (NGS) has offered an opportunity for profiling large numbers of polymorphic STRs. Here, we reported a population-scale analysis of STR variation using genome resequencing in mallard and Pekin duck. Our analysis provided the first genome-wide duck STR reference including 198,022 STR loci with motif size of 2-6 base pairs. We observed a relatively uneven distribution of STRs in different genomic regions, which indicates that the occurrence of STRs in duck genome is not random, but undergoes a directional selection pressure. Using genome resequencing data of 23 mallard and 26 Pekin ducks, we successfully identified 89,891 polymorphic STR loci. Intensive analysis of this dataset suggested that shorter repeat motif, longer reference tract length, higher purity, and residing outside of a coding region are all associated with an increase in STR variability. STR genotypes were utilized for population genetic analysis, and the results showed that population structure and divergence patterns among population groups can be efficiently captured. In addition, comparison between Pekin duck and mallard identified 3,122 STRs with extremely divergent allele frequency, which overlapped with a set of genes related to nervous system, energy metabolism and behavior. The evolutionary analysis revealed that the genes containing divergent STRs may play important roles in phenotypic changes during duck domestication. The variation analysis of STRs in population scale provides valuable resource for future study of genetic diversity and genome evolution in duck.

SUBMITTER: Fan W

PROVIDER: S-EPMC6218588 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Publications

Characterization of Duck (<i>Anas platyrhynchos</i>) Short Tandem Repeat Variation by Population-Scale Genome Resequencing.

Fan Wenlei W Xu Lingyang L Cheng Hong H Li Ming M Liu Hehe H Jiang Yong Y Guo Yuming Y Zhou Zhengkui Z Hou Shuisheng S

Frontiers in genetics 20181030

Short tandem repeats (STRs) are usually associated with genetic diseases and gene regulatory functions, and are also important genetic markers for analysis of evolutionary, genetic diversity and forensic. However, for the majority of STRs in the duck genome, their population genetic properties and functional impacts remain poorly defined. Recent advent of next generation sequencing (NGS) has offered an opportunity for profiling large numbers of polymorphic STRs. Here, we reported a population-sc ...[more]

PMID: 30425731

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Project description:Background: Skeletal muscle growth and development is highly orchestrated in gene expressions. Understanding the location-specific and breed-specific genes and pathways are agriculturally important on meat products and meat quality. In the present study, RNA-Seq was performed to elucidate the difference of muscle deposition between locations and breeds for functional genomics studies. To achieve those goals, skeletal muscle samples were collected for pectoral muscle (PM) and leg muscle (LM) of two genetically different duck breeds, Heiwu duck (H) and Peking duck (P), at embryonic 15 days. Functional genomics studies were performed in two experiments: Experiment 1 directly compared location-specific genes between PM and LM, while Experiment 2 compared the two breeds (H and P) at the same development stage (embryonic 15 days). Results: Almost 13 million clean reads was generated using Illumina technology on each library, and more than 70% reads mapped to Anas platyrhynchos breed Peking duck genome. We identified 246, 258, 20 and 54 differentially expressed genes (DEGs) (log2.fold-change >0.5, and P-value <0.05) for H-PM vs H-LM, P-PM vs P-LM, H-LM vs P-LM and H-PM vs P-PM library, separately. A total of 168 genes were differentially expressed by over locations in experiment 1, while only 8 genes were differentially expressed by over breeds in experiment 2. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathways (KEGG) were used to functionally annotate DGEs. In experiment 1, DEGs mainly involved in Focal adhesion, PI3K-Akt signaling pathway and ECM-receptor interaction pathways (corrected P-value<0.05). In experiment 2, DEGs only associated with ribosome signal pathway (corrected P-value<0.05). In addition, quantitative real-time PCR was employed to confirm 15 differentially expressed genes detected by RNA-Seq. Conclusions: Comparative transcript analysis of leg muscle and pectoral muscle of two duck breeds not only improves our understanding of those location-specific and breed-specific genes and pathways, but also provides some candidate molecular targets for increase muscle products and meat quality by genetic control. Conclusions: Our study represents the first detailed analysis of duck breed muscle transcriptomes generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

Dataset Information

Characterization of Duck (Anas platyrhynchos) Short Tandem Repeat Variation by Population-Scale Genome Resequencing.

Publications

Characterization of Duck (<i>Anas platyrhynchos</i>) Short Tandem Repeat Variation by Population-Scale Genome Resequencing.

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