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Articles by Jian-Lin Han
Total Records ( 4 ) for Jian-Lin Han
  Juan Yin , Sheng-Cheng Zeng , Yu-Zhu Luo and Jian-Lin Han
  To understand DNA sequence structural variation and its relationship with allelic distribution pattern obtained from genotyping data of microsatellite markers, Polymerase Chain Reaction (PCR) products of major alleles at two supposedly simple di-nucleotide chicken microsatellite loci of MCW0330 and LEI0094 were directly sequenced. The new sequences were compared with published data retrieved from the GenBank and Ensembl databases. The results showed that repeat unit at LEI0094 locus was a simple di-nucleotide of (AC)n for most alleles while the remaining alleles had their (AC) n irregularly interrupted by one or two (GA) nucleotides. On the other hand, MCW0330 locus carried a very complicated compound microsatellite consisted of three big structural blocks as its repeat units. These units consisted of CACAGACACA, CAGACACA and CTCAGACA. A few SNPs detected in upstream flanking sequences and specific combinations of basic structural units in repeat sequences of MCW0330 and LEI0094 loci contributed to define not only alleles different in both fragment sizes and sequence structures but also to alleles of the same fragment sizes but different in sequence structures that may lead to different peak patterns observed during genotyping exercise. Such ‘cryptic’ alleles of the same sizes but different in sequences can lead to an underestimated value in diversity and an ascertainment bias in interpreting microsatellite data. Therefore, an intensive characterization of DNA sequences in major microsatellite alleles derived from different genetic backgrounds is warranted to understand the evolutionary mechanism of different microsatellite DNA markers.
  Mei-Qing Wei , Sheng-Cheng Zeng , Yan-Ming Wei and Jian-Lin Han
  To verify the quality of genotyping data and understand the property of microsatellite markers to elucidate chicken genetic diversity, the DNA sequence variations of major alleles at two chicken microsatellites of MCW0216 and LEI0234 were assessed through direct sequencing of the PCR products of 26 selected chicken blood samples. The results of MCW0216 locus were interesting and useful because they showed very complicated DNA sequence structures within both flanking and repeat regions which validated alleles that were different from each other by single nucleotides. The three SNPs present within both primer regions for genotyping the MCW0216 locus called for an action to re-design new genotyping primers to avoid allelic drop-out during genotyping exercises. The LEI0234 locus was a complex of either perfect or compound tetra-nucleotide microsatellite carrying small-sized alleles with 7 to 18 perfect CTTT repeat units while all big alleles longer than 275 bp consisted of more than 20 basic CTTT repeats being interrupted by a few CCTT motifs as a stabilizing effecter contributing to the expansion of microsatellite length and allelic polymorphism. The presence of many cryptic alleles that were identical in fragment sizes but different in either flanking sequences or repeat unit compositions at both loci further warranted an intensive DNA sequence characterization of major alleles for a correct interpretation of microsatellite data.
  Zhen-Yang Wu , Sheng-Cheng Zeng , Yu-Zhu Luo and Jian-Lin Han
  Domestic duck production plays a very important role in producing meat, eggs and down. To support the conservation of closely related species of wild Mallard as well as Muscovy ducks and to understand the origin, domestication process, genetic diversity as well as differentiation of domestic ducks, the partial D-loop sequence of mitochondrial DNA has been employed as the most popular molecular marker. In this study, a total of four pairs of primers located in different D-loop portions were used to amplify and sequence the partial D-loop fragment from definite domestic Mallard and Muscovy ducks together with domestic duck samples of unknown species of origin. Intensive sequencing profiles identified a homoplasmic D-loop in domestic Muscovy ducks but ‘heteroplasmic’ mtDNA D-loop fragments in domestic Mallard ducks. The results supported the presence of Numts in blood samples of domestic Mallard duck. This phenomenon has not been recognized or reported before and it can certainly confound the application of D-loop sequence as a molecular marker to genetic study of domestic Mallard duck. Further investigation on tissue specificity of the Numts and establishment of specific primers to generate the true D-loop sequences are warranted for an accurate genetic characterization and species identification of domestic ducks.
  Dan-Ping Zhang , Hui-Jing Zhao , Yu-Zhu Luo and Jian-Lin Han
  Chicken interleukin 2 (chIL-2), a primary cytokine excreted mainly by activated T cells, can significantly enhance immunity. The chIL-2 has been proven to play an important role not only in the host’s response to coccidiosis and salmonella among parasite and bacterial diseases but also in the host’s enhanced immune responses to vaccines. To examine the genetic polymorphisms and their potential impact on the structure and function of the chIL-2, we first reviewed the history of identification of chIL-2 mRNA and genomic DNA sequences and analyzed the distribution of nucleotide variation in both coding and intronic sequences that were deposited in the GenBank database. Then a short DNA fragment of 374 bp to 386 bp within chIL-2 intron 2, in which a number of discontinuous insertions/deletions (in/dels) were involved in defining major sequence variations and structures, was targeted for re-sequencing in this study. A total of 15 novel haplotypes were identified in 66 indigenous and commercial chickens sampled from six countries. Three major haplogroups were characterized by two big in/dels of eight and 11 nucleotides, of which one group seemed to have experienced a recent and rapid expansion associated with domestication. Complete chIL-2 genomic DNA sequences comprised of these haplotypes are expected to match the major structural lineages and groups within the coding and intronic sequences and to contribute to a deeper understanding of the evolution and function of chIL-2 gene.
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