We generated the PEDE (Pig EST Data Explorer; http://pede.dna.affrc.go.jp/) database using sequences assembled from porcine 5' ESTs from oligo-capped full-length cDNA libraries. Thus far we have performed EST analysis of various organs (thymus, spleen, uterus, lung, liver, ovary and peripheral blood mononuclear cells) and assembled 68,076 high-quality sequences into 5546 contigs and 28,461 singlets. PEDE provides a search interface for getting results of homology searches and enables users to obtain information on sequence data and cDNA clones of interest. Single-nucleotide polymorphisms detected through comparison of the EST sequences are classified by origin (western and oriental breeds) and are searchable in the database. This database system can accelerate analyses of livestock traits and yields information that can lead to new applications in pigs as model systems for medical research.

We formerly released the porcine expressed sequence tag (EST) database Pig EST Data Explorer (PEDE; ), which comprised 68 076 high-quality ESTs obtained by using full-length-enriched cDNA libraries derived from seven tissues. We have added eight tissues and cell types to the EST analysis and have integrated 94 555 additional high-quality ESTs into the database. We also fully sequenced the inserts of 10 147 of the cDNA clones that had undergone EST analysis; the sequences and annotation of the cDNA clones were stored in the database. Further, we constructed an interface that can be used to perform various searches in the database. The PEDE database is the primary resource of expressed pig genes that are supported by full-length cDNA sequences. This resource not only enables us to pick cDNA clones of interest for a particular analysis, but it also confirms and thus contributes to the sequencing integrity of the pig genome, which is now being compiled by an international consortium (). PEDE has therefore evolved into what we now call ‘Pig Expression Data Explorer’.

Here, we report the variability in the KIT tyrosine kinase receptor and its ligand KITLG genes by determining single nucleotide polymorphisms (SNPs) in 384 individuals including 11 pig breeds, two synthetic‐line cross pigs, two cross breeds, and one Japanese wild boar. SNPs and indels within the coding sequence regions of KITLG and KIT and their 5′‐flanking regions were detected by aligning sequences from eight pigs, and subsequently the SNPs were genotyped using matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry (MALDI TOF‐MS). Principal component analysis using allele frequencies in the SNP locus showed a distant relationship between Asian and Euro‐American pig groups, except for Berkshire and Tokyo X breeds. These breeds were located within the mid‐portion of the distribution in the first principal component. The Hampshire breed was distant from the other pig groups on the axis of the second principal component. Haplotype frequencies that were deduced using non‐synonymous substitutions of the KIT gene revealed the uniqueness of Landrace, Large White, Middle White, and three‐way cross pigs (LWD) and of the Hampshire breed. On the other hand, the haplotypes of KITLG and KIT detected in the Berkshire breed were prevalent in Asian pig groups. This tendency is different from that observed in other Euro‐American pig breeds.

To investigate the genetic regulation of TL expression, 12 transgenic mouse strains on a C3H (TLnonexpressing) background have been derived: two Tg.Tlaa-3 strains with Tl-3 isolated from A-strain TL+ thymocytes, four Tg.T3b strains with T3V from a TL+ leukemia arising in a C57BL/6 (TL-) mouse, three Tg.Con.3 strains with an H-2Kb/T3b chimeric gene (construct 3, 5' flanking region and exon 1 of H-2K" and exons 2-6 of T3b), one Tg.Con.4 strain with a T3b/H-2Kb chimeric gene (construct 4, 5' flanking region and exon 1 of T3b and exons 2-8 of H-2Kb), and two Tg.H-2Kb strains with H-2Kb. Expression of the transgenes was determined by the presence of TL or H-2Kb products or transcripts. Both Tg.Tlaa-3 strains expressed high levels of TL antigen in thymus, indicating that (i) the 9.6-kilobase Tld-3 DNA fragment contains sufficient information for correct tissue-specific expression in thymocytes and (u) TL-thymocytes of C3H provide conditions for the transcriptional activation of Tld-3. In contrast, neither the four Tg.T3b strains nor the Tg.Con.4 strain expressed transgenes, indicating that (i) T3b lacks elements necessary for TL expression in normal thymocytes and (u) the corresponding endogenous TL genes of C3H mice also lack these elements. The pattern of TL expression in two of the three Tg.Con.3 strains was similar to that of H-2Kb expression, indicating that transcription of this H-2Kb/T3 chimeric gene was driven by the regulatory sequences of H-2K". The thymuses of mice derived from the Tg.Tlaa-3-1 strain were smaller than C3H thymuses, and the surface phenotype of Tg.Tlaa-3-1 thymocytes resembled thymocyte precursors (TL+ L3T4-Lyt-2-Thy-l+ H-2+). These mice developed a high incidence of lymphomas with the same thymocyte precursor phenotype. The study of TL transgenic strains should prove useful in defining the role of TL in normal and abnormal T-cell differentiation. TL (thymus leukemia) antigens are coded for by genes in the major histocompatibility complex (MHC) of the mouse (1). Although TL is similar in overall structure to other class I MHC antigens (H-2, Qa), TL expression is regulated in a highly distinctive fashion. In contrast to the broad distribution of H-2 antigens and the intermediate distribution of Qa antigens, TL expression is restricted to T cells during development in the thymus and is lost when T cells migrate to the periphery. Some mouse strains do not express TL antigens on thymocytes (TL-strains), but leukemias occurring in these mice can have a TL+ phenotype, indicating activation of normally silent TL genes.To examine the structural basis for the differential expression of TL, we and others have cloned and sequenced TL genes from various mouse strains (2-5). Further, we have constructed chimeric genes consisting of TL and H-2 sequences and analyzed the expression of these genes in transfected L cells (6). These studies showed that expressioncompetent TL genes exist in TL-as well as TL+ strains and that differential expression of TL and H-2 in L cells is due to regulatory sequence...

The recently published draft sequence of the human genome will provide a basic reference for the comparative mapping of genomes among mammals. In this study, we selected 214 genes with complete coding sequences on Homo sapiens chromosome 4 (HSA4) to search for orthologs and expressed sequence tag (EST) sequences in eight other mammalian species (cattle, pig, sheep, goat, horse, dog, cat, and rabbit). In particular, 46 of these genes were used as landmarks for comparative mapping of HSA4 and Sus scrofa chromosome 8 (SSC8); most of HSA4 is homologous to SSC8, which is of particular interest because of its association with genes affecting the reproductive performance of pigs. As a reference framework, the 46 genes were selected to represent different cytogenetic bands on HSA4. Polymerase chain reaction (PCR) products amplified from pig DNA were directly sequenced and their orthologous status was confirmed by a BLAST search. These 46 genes, plus 11 microsatellite markers for SSC8, were typed against DNA from a pig-mouse radiation hybrid (RH) panel with 110 lines. RHMAP analysis assigned these 57 markers to 3 linkage groups in the porcine genome, 52 to SSC8, 4 to SSC15, and 1 to SSC17. By comparing the order and orientation of orthologous landmark genes on the porcine RH maps with those on the human sequence map, HSA4 was recognized as being split into nine conserved segments with respect to the porcine genome, seven with SSC8, one with SSC15, and one with SSC17. With 41 orthologous gene loci mapped, this report provides the largest functional gene map of SSC8, with 30 of these loci representing new single-gene assignments to SSC8.