The association of follicle stimulating hormone receptor (FSHR) gene polymorphism of on egg productivity in hybrid chicken (Gallus gallus gallus, Linnaeus 1758)

Kurnia RR, Lesmana I, Ernanto AR, Perdamaian ABI, Trijoko, Daryono BS. 2021. The association of follicle stimulating hormone receptor (FSHR) gene polymorphism of on egg productivity in hybrid chicken (Gallus gallus gallus, Linnaeus 1758). Biodiversitas 22: 1221-1226. Pelung chicken genetics Improvement by selective breeding to Layer Lohmann Brown was successfully developed F1 which yielded 140 eggs for 300 days of production. BC1 chicken derived from ♀ Layer and ♂ F1 (♀ Layer vs ♂ Pelung chicken). Polymorphism on cFSHR gene promoter was potential genetic marker candidate to assist the selection. This research aims to study the BC1 chicken egg-related traits performance for 16 weeks and study the correlation of cFSHR polymorphism to egg productivity. FSHR gene promoter was showed using sanger sequencing. Chicken were grouped based on their haplotype. Chicken were maintained in battery cage for observation of egg production. The results show that there is a difference of BC1 chicken DOC weight from different egg weight. The six SNP polymorphisms exist on cFSHR gene promoter fragments on 10, 51, 59, 121, 233, 331 nucleotides and conducted 7 haplotype group. The highest egg production in BC1 chicken on TTGCYA and lowest egg production on TTGYYG haplotype. Based on the correlation test there was a positive correlation at p> 0.05 between BC1 chicken TTGCYA haplotype with egg production and positive correlation at p <0.05 between BC1 TAGTTA haplotype with egg length.

69 Automated TRB locus haplotype analysis by long-amplicon TCRB chain sequencing for potential immune-related adverse events biomarker research

BackgroundIdentifying potential predictive biomarkers for immune related adverse events (irAEs) following checkpoint blockade inhibition (CPI) remains an outstanding goal of immune-oncology translational research. Polymorphism with the T cell receptor variable gene (TRBV) has been proposed as a potential risk factor for irAEs owing to a potential link between TRBV polymorphism and chronic autoimmune disease. Efforts to interrogate the potential biomarker utility of TRBV polymorphism have been hampered by the repetitive nature of the TRB locus. Our research has demonstrated a method for inferring TRB locus haplotypes from long-amplicon TCRB chain sequencing data, which we used to identify major haplotype groups in from nucleic acid. Here we present our research for a potential automated method for haplotype group assignment from TCRB chain sequencing data.MethodsRearranged TCRB chains from 10 blood samples were amplified and sequenced from 25ng peripheral blood total RNA via the Oncomine™ TCRB-LR assay using the Genexus™ Integrated Sequencer. 12 samples were run per chip with 4 samples run in each lane. TCRB clonotyping and repertoire feature analysis was performed using Genexus™ analysis software. Automated haplotype group assignment was performed by generation and comparison of TRBV allele profiles to those presented previously.1 For context, TCR evenness, convergence, and haplotype group assignment were compared to values obtained following analysis of the same samples via the GeneStudio™ S5 platform and Ion Reporter™ 5.12 software.ResultsTCR Evenness and convergence values were highly correlated across replicates run on the Genexus™ Integrated Sequencer (Spearman correlation >0.95 and >0.70, respectively). Evenness at equivalent clone count and convergence at equivalent sequencing depth were not significantly different across platforms (Spearman correlation >0.88). Haplotype group assignments demonstrated 100% agreement across replicates on both platforms.ConclusionsOur research has demonstrated a potential automated and reproducible method for TRB haplotype group assignment via the Oncomine™ TCR-Beta LR Assay, GX run on the Genexus™ Integrated Sequencer. Future studies will be needed to evaluate the potential biomarker utility of TRB haplotyping for the prediction of irAEs.For research use only not for diagnostic procedures.ReferenceLooney T, Duose D, Lowman G, Linch E, Hajjar J, Topacio-Hall D, Xu M, Zheng J, Alshawa A, Tapia C, Stephen B, Wang L, Meric-Bernstam F, Miller L, Glavin A, Lin L, Gong J, Conroy J, Morrison C, Hyland F, Naing A. Haplotype Analysis of the T-Cell Receptor Beta (TCRB) Locus by Long-amplicon TCRB Repertoire Sequencing. J Immunother Precis Oncol 2019;2:137–143.

Phylogenetic diversity within the endemic brown trout Duero lineage: implications for conservation and management

Brown trout display great phenotypic and genetic variability. Use of mitochondrial DNA (mtDNA) variation has allowed the definition of seven different lineages in this species to date. One of them, the Duero (DU) lineage, was initially detected in the inner section of the Duero River in Spain, where it showed a parapatric distribution with the more widely distributed Atlantic (AT) lineage. Later mtDNA-RFLP (restriction fragment length polymorphism) studies detected the DU lineage in northern Spanish basins (Galicia). The aim of this work was to ascertain the origin and variability of these DU populations outside the Duero drainage. Using complete mtDNA control region sequencing, 11 novel DU haplotypes were identified. Several of them could be assigned to an endemic group in Galicia consistent with the long-time presence of the DU lineage outside the Duero River, and excluding a recent origin by human translocations. The DU haplotype group observed in north-western Iberian basins was estimated to diverge from that of the Duero River more than 100000 years ago. We therefore advocate for conservation strategies at regional and local scales rather than focussed in a single ESU as proposed in earlier works.

Risk of canine cranial cruciate ligament rupture is not associated with the major histocompatibility complex

SummaryObjectives: To investigate the association of the major histocompatability (MHC) class II allele haplotype frequencies with the diagnosis of cranial cruciate ligament (CCL) rupture in two breeds of dog.Methods: DNA samples from populations of Labrador Retrievers and Golden Retrievers with CCL rupture and general populations of the same breeds were characterised for three DLA class II loci (DRB1*, DQA1* and DQB1*) alleles using sequence-based typing or reference strand-mediated conformation analysis.Results: Although distinct differences in haplotype types, frequencies and homozygozity were observed between the two breeds, no disease specific association could be identified for the development of the CCL rupture within either population.Clinical significance: The risk for developing CCL rupture was not associated with DLA haplotype group(s) in Labrador Retrievers or Golden Retrievers, thus the hypothesis that there is an autoimmune basis to CCL rupture was not supported.

Endurance exercise training effects on body fatness, V̇o2max, HDL-C subfractions, and glucose tolerance are influenced by aPLINhaplotype in older Caucasians

Perilipins are lipid droplet-coating proteins that regulate intracellular lipolysis in adipocytes. A haplotype of two perilipin gene ( PLIN) single nucleotide polymorphisms, 13041A>G and 14995A>T, has been previously associated with obesity risk. Furthermore, the available data indicate that this association may be modified by sex. We hypothesized that this haplotype would associate with body fatness, aerobic fitness, and a number of cardiovascular (CV) risk factor phenotypes before and after a 6-mo endurance exercise training program in sedentary older Caucasians. The major haplotype group (13041A/14995A; n = 57) had significantly lower body mass index (BMI) and body fatness compared with noncarriers of the AA haplotype ( n = 44) before the training intervention. Training improved body composition in both groups, but fatness remained higher in noncarriers than AA carriers after training. This fat retention in noncarriers blunted their maximal oxygen uptake (V̇o2max) adaptation to training. Female noncarriers had substantially higher concentrations of several conventionally and NMR-measured HDL-C subfractions than male noncarriers before and after training, but only minimal differences were found between the sexes in the AA haplotype group. Haplotype group differences in baseline and after-training responses to an oral glucose tolerance test (OGTT) also differed by sex, as noncarrier men had the highest baseline area under the insulin curve (insulin AUC), but were the only group to significantly improve insulin AUC with training. The insulin sensitivity index and plasma glucose responses to the OGTT were more favorable in AA carriers than noncarriers before and after training. Overall, our findings suggest that PLIN variation explains some of the interindividual differences in the response of obesity and CV phenotypes to exercise training. Furthermore, these data contribute to the growing understanding of PLIN as a candidate gene for human obesity and the cardiometabolic consequences of excess adiposity.

Unusual pattern of single nucleotide polymorphism at the exuperantia2 locus of Drosophila pseudoobscura

We have investigated the pattern of DNA sequence variation at the exuperantia2 locus in Drosophila pseudoobscura. This adds to the increasing dataset of genetic variation in D. pseudoobscura, a useful model species for evolutionary genetic studies. The level of silent site nucleotide diversity and the divergence from an outgroup Drosophila miranda are comparable with those for other X-linked loci. One peculiar pattern at the exu2 locus of D. pseudoobscura is a complete linkage disequilibrium between two SNPs, one of which is a replacement site. As a result, there are two distinct haplotype groups in our dataset. Based upon the comparisons with the outgroup sequences from D. miranda and Drosophila persimilis, we show that the newly derived haplotype group has lower diversity than the ancestral haplotype group. The pattern of protein evolution at exu2 shows some deviation from the neutral model. Together, these and other characteristics of the exu2 locus suggest the action of selection on the pattern of SNP variation, consistent with a partial selective sweep associated with the newly derived haplotype.