Development of dense microsatellite markers in the entire SLA region and evaluation of their polymorphisms in porcine breeds

We developed 40 microsatellite markers in the entire swine leukocyte antigen (SLA) region, spanning over 2.35 Mb. The average span between markers was 59 kb, and the largest interval between markers was 127 kb. We also evaluated polymorphisms of length for the markers using 97 pigs derived from 12 breeds, including representative commercial breeds. All of the markers were successfully amplified in genomic DNA and shown to be polymorphic. These markers will provide an alternative method for determining the SLA haplotypes instead of direct typing of SLA genes per se. They will be valuable for transplantation studies and for association studies between immunological traits such as disease susceptibility and tumor rejection. Electronic supplementary material Supplementary material is available for this article at and accessible for authorised users.     

Genetic variability at the pig SLA complex in U.S. breeds of pigs1

Lymphocytes from 90 mature pigs and 548 growing pigs from 6.5 litters were screened with cytotoxic antibodies against swine lymphocyte antigens. Pigs included in the survey were from the Chester White, Duroc, Hampshire, Landrace and Yorkshire breeds. Significant differences between breeds were found in the frequency of the three haplotypes tested. Such differences may provide the genetic variability needed to determine associations between disease susceptibility and the pig's major histocompatibility gene complex.     

Microsatellite tagging of the stripe-rust resistance gene YrH52 derived from wild emmer wheat, Triticum dicoccoides, and suggestive negative crossover interference on chromosome 1B

 Stripe rust caused by Puccinia striifomis West. is one of the most devastating diseases relating to wheat production. Wild emmer wheat, Triticum dicoccoides, the tetraploid progenitor of cultivated wheat, has proven to be a valuable source of novel stripe-rust resistance genes for wheat breeding. For example, T. dicoccoides accessions from Mt. Hermon, Israel, are uniformly and highly resistant to stripe-rust. The main objective of the present study is to map a stripe-rust resistance gene, derived from the unique Mt. Hermon population of wild emmer, using microsatellite markers. An F₂ mapping population was established by crossing stripe-rust resistant T. dicoccoides accession H52 from Mt. Hermon with the Triticum durum cultivar Langdon. The stripe-rust resistance derived from accession H52 was found to be controlled by a single dominant gene which was temporarily designated as YrH52. Out of 120 microsatellite markers tested, 109 (91%) showed polymorphism between the parental lines. Among 79 segregating microsatellite loci generated from 56 microsatellite primer pairs, nine were linked to YrH52 with recombination frequencies of 0.02–0.35, and LOD scores of 3.56–54.22. A genetic map of chromosome 1B, consisting of ten microsatellite loci and the stripe-rust resistance gene YrH52, was constructed with a total map length of 101.5 cM. YrH52 is also closely linked to RFLP marker Nor1 with a map distance of 1.4 cM and a LOD value of 29.62. Apparent negative crossover interference was observed in chromosome 1B, especially in the region spanning the centromere. Negative crossover interference may be a common characteristic of gene-rich regions or gene clusters in specific chromosomes. Received: 30 October 1998 / Accepted: 2 November 1998     

Characterization of bovine MHC DRB3 diversity in Latin American Creole cattle breeds

In cattle, bovine leukocyte antigens (BoLAs) have been extensively used as markers for diseases and immunological traits. However, none of the highly adapted Latin American Creole breeds have been characterized for BoLA gene polymorphism by high resolution typing methods. In this work, we sequenced exon 2 of the BoLA class II DRB3 gene from 179 cattle (113 Bolivian Yacumeño cattle and 66 Colombian Hartón del Valle cattle breeds) using a polymerase chain reaction sequence-based typing (PCR-SBT) method. We identified 36 previously reported alleles and three novel alleles. Thirty-five (32 reported and three new) and 24 alleles (22 reported and two new) were detected in Yacumeño and Hartón del Valle breeds, respectively. Interestingly, Latin American Creole cattle showed a high degree of gene diversity despite their small population sizes, and 10 alleles including three new alleles were found only in these two Creole breeds. We next compared the degree of genetic variability at the population and sequence levels and the genetic distance in the two breeds with those previously reported in five other breeds: Holstein, Japanese Shorthorn, Japanese Black, Jersey, and Hanwoo. Both Creole breeds presented gene diversity higher than 0.90, a nucleotide diversity higher than 0.07, and mean number of pairwise differences higher than 19, indicating that Creole cattle had similar genetic diversity at BoLA-DRB3 to the other breeds. A neutrality test showed that the high degree of genetic variability may be maintained by balancing selection. The F_ST index and the exact G test showed significant differences across all cattle populations (F_ST = 0.0478; p < 0.001). Results from the principal components analysis and the phylogenetic tree showed that Yacumeño and Hartón del Valle breeds were closely related to each other. Collectively, our results suggest that the high level of genetic diversity could be explained by the multiple origins of the Creole germplasm (European, African and Indicus), and this diversity might be maintained by balancing selection.     

Spatial structure and genetic diversity of three tropical tree species with different habitat preferences within a natural forest

Analyses of the spatial distribution pattern, spatial genetic structure and genetic diversity were carried out using a 33-ha plot in a hill dipterocarp forest for three dipterocarps with different habitat preferences, i.e. Shorea curtisii on the ridges, Shorea leprosula in the valleys and Shorea macroptera both on the ridges and in the valleys. The significant spatial aggregation in small-diameter trees of all the three species was explained by limited seed dispersal. At the large-diameter trees, only S. macroptera showed random distribution and this might further prove that S. macroptera is habitat generalist, whilst S. curtisii and S. leprosula are habitat specific. The levels of genetic diversity estimated based on five microsatellite loci were high and comparable in all the three studied species. As the three studied species reproduced mainly through outcrossing, the observed high levels of genetic diversity might support the fact that the plant mating system can be used as guideline to infer the levels of genetic diversity, regardless of whether the species is habitat specific or habitat generalist. The lack of spatial genetic structure but significant aggregation in the small-diameter trees of all the three species might indicate limited seed dispersal but extensive pollen flow. Hence, if seed dispersal is restricted but pollen flow is extensive, significant spatial aggregation but no spatial genetic structure will be observed at the small-diameter trees, regardless of whether the species is habitat specific or habitat generalist. The inferred extensive pollen flow might indicate that energetic pollinators are involved in the pollination of Shorea species in the hill dipterocarp forests.     

Different coexpressions of arthritis-relevant genes between different body organs and different brain regions in the normal mouse population

Structural changes in different parts of the brain in rheumatoid arthritis (RA) patients have been reported. RA is not regarded as a brain disease. Body organs such as spleen and lung produce RA-relevant genes. We hypothesized that the structural changes in the brain are caused by changes of gene expression in body organs. Changes in different parts of the brain may be affected by altered gene expressions in different body organs. This study explored whether an association between gene expressions of an organ or a body part varies in different brain structures. By examining the association of the 10 most altered genes from a mouse model of spontaneous arthritis in a normal mouse population, we found two groups of gene expression patterns between five brain structures and spleen. The correlation patterns between the prefrontal cortex, nucleus accumbens, and spleen were similar, while the associations between the other three parts of the brain and spleen showed a different pattern. Among overall patterns of the associations between body organs and brain structures, spleen and lung had a similar pattern, and patterns for kidney and liver were similar. Analysis of the five additional known arthritis-relevant genes produced similar results. Analysis of 10 nonrelevant-arthritis genes did not result in a strong association of gene expression or clearly segregated patterns. Our data suggest that abnormal gene expressions in different diseased body organs may influence structural changes in different brain parts.     

Immunopeptidomic Analyses of Colorectal Cancers With and Without Microsatellite Instability

Colorectal cancer is the second leading cause of cancer death worldwide, and the incidence of this disease is expected to increase as global socioeconomic changes occur. Immune checkpoint inhibition therapy is effective in treating a minority of colorectal cancer tumors; however, microsatellite stable tumors do not respond well to this treatment. Emerging cancer immunotherapeutic strategies aim to activate a cytotoxic T cell response against tumor-specific antigens, presented exclusively at the cell surface of cancer cells. These antigens are rare and are most effectively identified with a mass spectrometry–based approach, which allows the direct sampling and sequencing of these peptides. Although the few tumor-specific antigens identified to date are derived from coding regions of the genome, recent findings indicate that a large proportion of tumor-specific antigens originate from allegedly noncoding regions. Here, we employed a novel proteogenomic approach to identify tumor antigens in a collection of colorectal cancer–derived cell lines and biopsy samples consisting of matched tumor and normal adjacent tissue. The generation of personalized cancer databases paired with mass spectrometry analyses permitted the identification of more than 30,000 unique MHC I–associated peptides. We identified 19 tumor-specific antigens in both microsatellite stable and unstable tumors, over two-thirds of which were derived from noncoding regions. Many of these peptides were derived from source genes known to be involved in colorectal cancer progression, suggesting that antigens from these genes could have therapeutic potential in a wide range of tumors. These findings could benefit the development of T cell–based vaccines, in which T cells are primed against these antigens to target and eradicate tumors. Such a vaccine could be used in tandem with existing immune checkpoint inhibition therapies, to bridge the gap in treatment efficacy across subtypes of colorectal cancer with varying prognoses. Data are available via ProteomeXchange with identifier PXD028309.