Population structure of Moniliophthora perniciosa in the main cacao producing departments of Colombia

The witches’ broom (Moniliophthora perniciosa) is considered as one of the main threats for cacao production and, consequently, for chocolate production worldwide.. In this work, the genetic diversity and population structure of M. perniciosa were analyzed for 59 isolates collected in five departments of Colombia and using 10 microsatellite markers. Analyses revealed 35 multilocus genotypes (MLGs) and clonal populations structure according to linkage disequilibrium analysis. One of the objectives of this study was to determine whether populations were differentiated by geographic origin or T. cacao host genotype. Analysis of molecular variance, Discriminant Analysis of Principal Components (DAPC) and Bruvo genetic distance suggested that the genetic structure was driven by geographic origin and not by T. cacao genotype. The results of this study were consistent with previous findings obtained in other cocoa producing countries. Important insights were discussed regarding the dispersal patterns of the pathogen in Colombia and the genetic change of its populations due to different environmental conditions.

Association Analysis of MBL1 Gene SNPs, Genotype and Haplotypes with Clinical Mastitis in Murrah Buffaloes

Mannose-binding lectins (MBL1) gene a most important constituent of immune response system of an organism, the primary role of this gene in the classical and lectin-activation pathways is to provide protection against various dieases or bacterial pathogens. In this study, eight novel SNPs identified in the promoter region of MBL1 gene were 154C>T, 235G>A, 252A>T, 265C>A, 268T>C, 282G>A, 431G>A and 551C>G, when compared to reference sequence of Bubalus bubalis (NCBI accession number KC415281). Genomic DNA isolated from 200 lactating Murrah buffaloes was amplified for the targeted sequence of MBL1. PCR products were custom sequenced, edited and used for further analysis. The results indicated that only 551C>G polymorphism locus met Hardy–Weinberg equilibrium (c2 (2df) = 4.4: P=0.11). Pair linkage disequilibrium analysis and haplotype construction of MBL1 gene were performed using SHEsis software. Pair linkage disequilibrium analysis revealed moderate to strong linkage disequilibrium between the eight SNPs loci A total of 17 haplotypes were generated from eight SNPs in promoter region of MBL1 gene. Association between eight SNPs of MBL1 gene in Murrah buffalo has been analyzed and relative risks of the alleles for clinical mastitis were estimated with an odds ratio. Allelic association analysis showed that T allele of 154C>T, A allele of 235G>A, A allele of 252A>T, A allele of 265C>A , T allele of 268T>C, A allele of 282G>A , A allele of 431G>A and G allele of 551C>G had significant association with increased risk of clinical mastitis (P< 0.01). Haplotype analysis showed that Hap15 (CAAATAAG) and Hap16 (TAAATAAG) i.e. the haplotypes containing all 8 “at-risk” alleles, were significantly associated with clinical mastitis (P< 0.01). Hap6 (CGAATAAC) and Hap8 (CGTCCGGC) were significantly associated with a lower risk of clinical mastitis in Murrah buffaloes (P< 0.01).On the other hand, the Hap6 (CGAATAAC) and Hap8 (CGTCCGGC) which are unrepresented in affected group and without “at-risk” alleles were significantly associated with a lower risk for clinical mastitis (P<0.01).These findings indicated a MBL1 gene polymorphism could be used as genetic marker for mastitis resistance in Murrah buffaloes.

LDkit: a parallel computing toolkit for linkage disequilibrium analysis

Background Linkage disequilibrium (LD) analysis is broadly utilized in genetics to understand the evolutionary and demographic history and helps geneticists identify genes associated with interested inherited traits, such as diseases. There are some tools for linkage disequilibrium analysis either in a local or online way; however, there has been no such tool supporting both graphical user interface (GUI) and parallel computing. Results We developed a GUI software called LDkit for LD analysis, which supports parallel computing. The LDkit supports both variant call format (VCF) and PLINK ‘ped + map’ format. At the same time, users could also just analyze a subset of individuals from the whole population. The LDkit reads the data by block and then paralleled the computation process by monitoring the usage of processes. Assessment on the Human 1000 genome data showed that when paralleled with 32 threads, the running time was reduced to less than 6 minutes from ~77 minutes using the chromosome 22 dataset with 1,103,547 SNPs and 2504 individuals. Conclusions The software LDkit can be effectively used to calculate and plot LD decay, LD block, and linkage disequilibrium analysis between a site and a given region. Most importantly, both graphical user interface (GUI) and stand-alone packages are available for users’ convenience. LDkit was written in JAVA language under cross-platform support.

Worldwide recombination in emergent white-nose syndrome pathogen Pseudogymnoascus destructans

Pseudogymnoascus destructans (Pd), the emergent fungus causing bat “White-Nose Syndrome”, responsible for ∼6 million mortalities in the United States (US), is thought to expand clonally in North America and Europe. Presence of distinct mating-types in Europe led to numerous research attempts searching for population sexuality worldwide. This study not only presents the first evidence of genetic recombination in Pd but also detects recombination in Pd genotype data generated by previous studies in Europe and North America, through clone-corrected linkage disequilibrium analysis. Portuguese and other European populations are apparently reproducing through sex between two mating-types. Seeming parasexual recombination in the invasive single mating-type US population rings alarms for the North American bat populations and deserves urgent attention. This study emphasizes on clone-correction in linkage disequilibrium analysis.One Sentence SummaryClone-correction yielded signs of elusive recombination in the global “clonal” populations of white-nose syndrome pathogen.