Identification and phylogenetic analysis of 15 MHC class II DRB1 β1 expressed alleles in a ewe–lamb flock

iTRAQ-based quantitative analysis reveals proteomic changes in Chinese cabbage (Brassica rapa L.) in response to Plasmodiophora brassicae infection

Clubroot disease is one of the major diseases affecting Brassica crops, especially Chinese cabbage (Brassica rapa L. ssp. pekinensis), which is known to be highly susceptible to the disease. In this study, the obligate biotrophic protist Plasmodiophora brassicae Woronin was used to infect the roots of Chinese cabbage seedlings. The disease symptoms were noticeable at 28 and 35 days after inoculation (DAI) in the susceptible (CM) line. Using isobaric tags for relative and absolute quantitation (iTRAQ) analysis, a total of 5,003 proteins of differential abundance were identified in the resistant/susceptible lines, which could be quantitated by dipeptide or polypeptide segments. Gene ontology (GO) analysis indicated that the differentially expressed proteins (DEPs) between the susceptible (CM) and resistant (CCR) lines were associated with the glutathione transferase activity pathway, which could catalyze the combination of glutathione and other electrophilic compounds to protect plants from disease. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the DEPs may be significantly enriched cytokinin signaling or arginine biosynthesis pathways, both of which are responses to stimuli and are plant defense reactions. The cytokinins may facilitate cell division in the shoot, resulting in the hypertrophy and formation of galls and the presentation of typical clubroot symptoms. In this study, the proteomic results provide a new perspective for creating germplasm resistance to P. brassicae, as well as a genetic basis for breeding to improve Chinese cabbage.

The genetic architecture of the MHC class II region in British Texel sheep

Understanding the structure of the major histocompatibility complex, especially the number and frequency of alleles, loci and haplotypes, is crucial for efficient investigation of the way in which the MHC influences susceptibility to disease. Nematode infection is one of the most important diseases suffered by sheep, and the class II region has been repeatedly associated with differences in susceptibility and resistance to infection. Texel sheep are widely used in many different countries and are relatively resistant to infection. This study determined the number and frequency of MHC class II genes in a small flock of Texel sheep. There were 18 alleles at DRB1, 9 alleles at DQA1, 13 alleles at DQB1, 8 alleles at DQA2 and 16 alleles at DQB2. Several haplotypes had no detectable gene products at DQA1, DQB1 or DQB2, and these were defined as null alleles. Despite the large numbers of alleles, there were only 21 distinct haplotypes in the population. The relatively small number of observed haplotypes will simplify finding disease associations because common haplotypes provide more statistical power but complicate the discrimination of causative mutations from linked marker loci.

Organization and characteristics of the major histocompatibility complex class II region in the Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis)

Little is known about the major histocompatibility complex (MHC) in the genome of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) (YFP) or other cetaceans. In this study, a high-quality YFP bacterial artificial chromosome (BAC) library was constructed. We then determined the organization and characterization of YFP MHC class II region by screening the BAC library, followed by sequencing and assembly of positive BAC clones. The YFP MHC class II region consists of two segregated contigs (218,725 bp and 328,435 bp respectively) that include only eight expressed MHC class II genes, three pseudo MHC genes and twelve non-MHC genes. The YFP has fewer MHC class II genes than ruminants, showing locus reduction in DRB, DQA, DQB, and loss of DY. In addition, phylogenic and evolutionary analyses indicated that the DRB, DQA and DQB genes might have undergone birth-and-death evolution, whereas the DQB gene might have evolved under positive selection in cetaceans. These findings provide an essential foundation for future work, such as estimating MHC genetic variation in the YFP or other cetaceans. This work is the first report on the MHC class II region in cetaceans and offers valuable information for understanding the evolution of MHC genome in cetaceans.

A single nomenclature and associated database for alleles at the major histocompatibility complex class II DRB1 locus of sheep

The development of standardised nomenclatures with associated databases containing reference sequences for alleles at polymorphic loci within the major histocompatibility complex (MHC) has been facilitated by the development of the immuno polymorphism database (IPD). Recently, included within IPD-MHC is information on allelic diversity within sheep species (IPD-MHC-OLA). Here, we present the first report of progress in populating the sheep IPD-MHC database with alleles at the class II MHC DRB1 locus. The sequence of 63 Ovar-DRB1 alleles within 24 allelic families is now held within the database, each meeting the minimum requirement of a complete second exon. These sequences are derived from a combination of genomic and cDNA-based approaches and represent the most extensive collection of validated alleles at the sheep DRB1 locus yet described. Although these 63 alleles probably represent only a fraction of the DRB1 allelic diversity in sheep species worldwide, we encourage the research community to use the official allelic nomenclature and to contribute allelic sequences to the database via its web-based submission tool. In time, the IPD-MHC-OLA resource will underpin population-based MHC genotyping studies and help to simplify meta-analyses of multi-source data from wild and domestic sheep populations.

Genomic analysis of Ovis aries (Ovar) MHC class IIa loci

Determining the genomic organization of the Ovis aries (Ovar) major histocompatibility complex class IIa region is essential for future functional studies related to antigen presentation. In this study, a bacterial artificial chromosome (BAC) library of genomic DNA from peripheral blood leukocytes (PBL) of a Rambouillet ram was constructed, and BAC clone consisting of the major histocompatibility complex (MHC) class II DQB2, DQA2, DQB1, DQA1, and DRB1 loci was identified and completely sequenced. The BAC clone consists of 160,889 bp of finished sequence with the loci arranged in the following order: DQB2, DQA2, DQB1, DQA1, and DRB1 with 14.3, 25, 6.6, and 40.9 Kb spanning between the loci, respectively. All five of these loci were transcribed in the animal used to generate the MHC class II BAC clone. Repeat or retrotransposable elements along with MHC class II cis promoter elements consisting of S, X, and Y boxes were identified in the sequence. In addition, 16 non-coding conserved sequences amongst primates, carnivores, and ruminants were identified (p < 0.001). These conserved sequences include binding sites for transcription factors with known roles in immune cells, and they provide a basis for further functional investigation of the genes in this region. This is the first ruminant finished sequence of the DQB2-DRB1 region, and this sequence information will aid in whole genome and transcriptome analyses of MHC class II.