Biology subjects

Munoz, P.

Publications and source records attributed to Munoz, P..

23 records · Page 2Linked to original sources

bioRxiv2020

Haplotype Reconstruction in Connected Tetraploid F1 Populations

In diploid species, many multi-parental populations have been developed to increase genetic diversity and quantitative trait loci (QTL) mapping resolution. In these populations, haplotype reconstruction has been used as a standard practice to increase QTL detection power in comparison with the marker-based association analysis. To realize similar benefits in tetraploid species (and eventually higher ploidy levels), a statistical framework for haplotype reconstruction has been developed and implemented in the software PolyOrigin for connected tetraploid F1 populations with shared parents. Haplotype reconstruction proceeds in two steps: first, parental genotypes are phased based on multi-locus linkage analysis; second, genotype probabilities for the parental alleles are inferred in the progeny. PolyOrigin can utilize genetic marker data from single nucleotide polymorphism (SNP) arrays or from sequence-based genotyping; in the latter case, bi-allelic read counts can be used (and are preferred) as input data to minimize the influence of genotype call errors at low depth. To account for errors in the input map, PolyOrigin includes functionality for filtering markers, inferring inter-marker distances, and refining local marker ordering. Simulation studies were used to investigate the effect of several variables on the accuracy of haplotype reconstruction, including the mating design, the number of parents, population size, and sequencing depth. PolyOrigin was further evaluated using an autotetraploid potato dataset with a 3x3 half-diallel mating design. In conclusion, PolyOrigin opens up exciting new possibilities for haplotype analysis in tetraploid breeding populations.

bioinformatics↗

bioRxiv2020

Allelic Variation of MYB10 is the Major Force Controlling Natural Variation of Skin and Flesh Color in Strawberry (Fragaria spp.) fruit

Anthocyanins are the principal color-producing compounds synthesized in developing fruits of strawberry (Fragaria spp.). Substantial natural variation in color have been observed in fruits of diploid and octoploid accessions, resulting from distinct accumulation and distribution of anthocyanins in fruits. Anthocyanin biosynthesis is controlled by a clade of R2R3 MYB transcription factors, among which MYB10 has been shown as the main activator in strawberry fruit. Here, we show that MYB10 mutations cause most of the anthocyanin variation observed in diploid woodland strawberry (F. vesca) and octoploid cultivated strawberry (F. xananassa). Using a mapping-by-sequencing approach, we identified a gypsy-transposon insertion in MYB10 that truncates the protein and knocks out anthocyanin biosynthesis in a white-fruited F. vesca ecotype. Two additional loss-of-function MYB10 mutations were identified among geographically diverse white-fruited F. vesca ecotypes. Genetic and transcriptomic analyses in octoploid Fragaria spp. revealed that FaMYB10-2, one of three MYB10 homoeologs identified, residing in the F. iinumae-derived subgenome, regulates the biosynthesis of anthocyanins in developing fruit. Furthermore, independent mutations in MYB10-2 are the underlying cause of natural variation in fruit skin and flesh color in octoploid strawberry. We identified a CACTA-like transposon (FaEnSpm-2) insertion in the MYB10-2 promoter of red-fleshed accessions that was associated with enhanced expression and anthocyanin accumulation. Our findings suggest that putative cis regulatory elements provided by FaEnSpm-2 are required for high and ectopic MYB10-2 expression and induction of anthocyanin biosynthesis in fruit flesh. We developed MYB10-2 (sub-genome) specific DNA markers for marker-assisted selection that accurately predicted anthocyanin phenotypes in octoploid segregating populations.

plant biology↗

bioRxiv2020

Discrimination among Cryptococcus deneoformans, C. neoformans and interspecies hybrids using MALDI-TOF Mass Spectrometry

BackgroundDifferentiation of the species within the Cryptococcus neoformans complex (C. deneoformans, C. neoformans and C. neoformans interspecies hybrids -C. deneoformans x C. neoformans-) is important to define the epidemiology of the infection. ObjectivesIn this study we attempted the discrimination of three C. neoformans species using MALDI-TOF MS coupled with an in-house library. MethodsAll Cryptococcus spp. isolates were identified by AFLP markers. An in-house database was constructed 26 well characterized C. deneoformans, C. neoformans and interspecies hybrids. Forty-four Cryptococcus spp. isolates were blindly identified using MALDI-TOF MS (Bruker Daltonics) and the expanded library. Their protein spectra were also submitted to hierarchical clustering and the resulting species were verified via Partial Least Squares Differential Analysis (PLS-DA) and Support-Vector Machine (SVM). ResultsMALDI-TOF MS coupled with the in-house library allowed 100% correct identification of C. deneoformans and C. neoformans but misidentified the interspecies hybrids. The same level of discrimination among C. deneoformans and C. neoformans was achieved applying SVM. The application of the PLS-DA and SVM algorithms in a two-step analysis allowed 96.95% and 96.55% correct discrimination of C. neoformans from the interspecies hybrids, respectively. Besides, PCA analysis prior to SVM provided 98.45% correct discrimination of the 3 species analysed in a one-step analysis. ConclusionsOur results indicate that MALDI-TOF MS could be a rapid and reliable tool for the correct discrimination of C. deneoformans and C. neoformans. The correct identification of the interspecies hybrids could only be achieved by hierarchical clustering with other protein spectra from the same species.

microbiology↗

bioRxiv2018

Olfactory sensory neurons mediate ultra-rapid antiviral immune responses in teleosts in a TrkA-dependent manner

The nervous system is known to regulate host immune responses. However, the ability of neurons to detect danger and initiate immune responses at barrier tissues is unclear. Vertebrate olfactory sensory neurons (OSNs) are located in direct contact with the external environment and therefore directly exposed to pathogens. Here, we report that nasal delivery of rhadboviruses induced apoptosis in crypt OSNs in rainbow trout olfactory organ (OO) via the interaction of the OSN TrkA receptor with viral glycoprotein. This signal resulted in pro-inflammatory responses in the OO and dampened inflammation in the olfactory bulb (OB). CD8+ cells infiltrated the OO within minutes of nasal viral delivery and this response was abrogated when TrkA was blocked. Infiltrating CD8+ cells originated from the microvasculature surrounding the OB and not the periphery. Ablation of crypt neurons in zebrafish resulted in increased susceptibility to rhabdoviral challenge. Our results, therefore, indicate a novel function for OSNs as a first layer of pathogen detection in vertebrates.

immunology↗

bioRxiv2018

Temporal Dynamics of the Origin and Domestication of Sweet Potato and Implications for Dispersal to Polynesia

In a study focussed on the origin of Ipomoea batatas (L.) Lam. (the sweet potato) and its close relatives [1], the authors claimed that a specimen of sweet potato collected by Banks and Solander in 1769 in Polynesia was distinct and along with some other varieties had levels of genetic variation of more than 100,000 years. This timeframe, along with several other lines of evidence, was interpreted, by the authors, as questioning human-mediated transport of the sweet potato to Polynesia within the last 1,000 years. This aspect of the paper received widespread media coverage as well as a number of critical remarks, and correspondence. The criticism questioned whether claims in the paper were justified. Here, three authors from the paper take the opportunity to fully explain the reasoning for calling into question the need to invoke human mediated transport of the sweet potato to Polynesia.

plant biology↗