Quantitative mapping
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Identifying the genetic factors impacting the adaptation of crops to environmental conditions is of key interest for conservation and selection purposes. It can be achieved using population genomics, and evolutionary or quantitative genetics. Here we present a sorghum multireference back-cross nested association mapping population composed of 3,901 lines produced by crossing 24 diverse parents to 3 elite parents from West and Central Africa-back-cross nested association mapping. The population was phenotyped in environments characterized by differences in photoperiod, rainfall pattern, temperature levels, and soil fertility. To integrate the multiparental and multi-environmental dimension of our data we proposed a new approach for quantitative trait loci (QTL) detection and parental effect estimation. We extended our model to estimate QTL effect sensitivity to environmental covariates, which facilitated the integration of envirotyping data. Our models allowed spatial projections of the QTL effects in agro-ecologies of interest. We utilized this strategy to analyze the genetic architecture of flowering time and plant height, which represents key adaptation mechanisms in environments like West Africa. Our results allowed a better characterization of well-known genomic regions influencing flowering time concerning their response to photoperiod with Ma6 and Ma1 being photoperiod-sensitive and the region of possible candidate gene Elf3 being photoperiod-insensitive. We also accessed a better understanding of plant height genetic determinism with the combined effects of phenology-dependent (Ma6) and independent (qHT7.1 and Dw3) genomic regions. Therefore, we argue that the West and Central Africa-back-cross nested association mapping and the presented analytical approach constitute unique resources to better understand adaptation in sorghum with direct application to develop climate-smart varieties.
Association mapping of the central part of porcine chromosome 2 harboring QTLs for carcass and meat quality traits was performed with 17 gene-tagged SNPs located between 44.0 and 77.5 Mb on a physical map (Sscrofa10.2) in Italian Large White pigs. For the analyzed animals records of estimated breeding values for average daily gain, back fat thickness, lean cuts, ham weight, feed conversion ratio, pH1, pHu, CIE L*, CIE a*, CIE b* and drip loss were available. A significant QTL for fat deposition (adjusted P=0.0081) and pH1 (adjusted P=0.0972) to MYOD1 at position 44.4 Mb and a QTL for growth and meatiness (adjusted P=0.0238-0.0601) to UBL5 at position 68.9 Mb were mapped. These results from association mapping are much more accurate than those from linkage mapping and facilitate further search for position candidate genes and causative mutations needed for application of markers through marker assisted selection.
- MeSH
- chov MeSH
- fenotyp MeSH
- jednonukleotidový polymorfismus MeSH
- koncentrace vodíkových iontů MeSH
- kvalita jídla * MeSH
- lokus kvantitativního znaku * MeSH
- mapování chromozomů metody MeSH
- maso analýza MeSH
- MyoD Protein genetika MeSH
- prasata genetika MeSH
- tělesná hmotnost MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The porcine orthologues of human chromosome HSA9q22.31 genes osteoglycin (OGN) and asporin (ASPN) were mapped to porcine chromosome SSC3 using linkage analysis and a somatic cell hybrid panel. This mapping was refined to SSC3q11 using fluorescence in situ hybridization. These results confirm the existence of a small conserved synteny group between SSC3 and HSA9. Polymorphisms were revealed in both genes, including a pentanucleotide microsatellite (SCZ003) in OGN and two single nucleotide polymorphisms (AM181682.1:g.780G>T and AM181682.1:g.825T>C) in ASPN. The two genes were included in a set of markers for quantitative trait loci (QTL) mapping on SSC3 in the Hohenheim Meishan x Piétrain F2 family. Major QTL for growth and carcass traits were centred in the ASPN-SW902 region.
- MeSH
- financování organizované MeSH
- glykoproteiny genetika MeSH
- jednonukleotidový polymorfismus MeSH
- křížení genetické MeSH
- lidé MeSH
- lokus kvantitativního znaku MeSH
- mapování chromozomů MeSH
- mezibuněčné signální peptidy a proteiny MeSH
- mikrosatelitní repetice MeSH
- prasata genetika růst a vývoj MeSH
- proteoglykany genetika MeSH
- syntenie MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- srovnávací studie MeSH
Parkinson's disease (PD) is a common neurodegenerative disease, and apart from a few rare genetic causes, its pathogenesis remains largely unclear. Recent scientific interest has been captured by the involvement of iron biochemistry and the disruption of iron homeostasis, particularly within the brain regions specifically affected in PD. The advent of Quantitative Susceptibility Mapping (QSM) has enabled non-invasive quantification of brain iron in vivo by MRI, which has contributed to the understanding of iron-associated pathogenesis and has the potential for the development of iron-based biomarkers in PD. This review elucidates the biochemical underpinnings of brain iron accumulation, details advancements in iron-sensitive MRI technologies, and discusses the role of QSM as a biomarker of iron deposition in PD. Despite considerable progress, several challenges impede its clinical application after a decade of QSM studies. The initiation of multi-site research is warranted for developing robust, interpretable, and disease-specific biomarkers for monitoring PD disease progression.
- MeSH
- biologické markery MeSH
- lidé MeSH
- magnetická rezonanční tomografie metody MeSH
- mapování mozku metody MeSH
- neurodegenerativní nemoci * MeSH
- neurozobrazování MeSH
- Parkinsonova nemoc * diagnostické zobrazování patologie MeSH
- progrese nemoci MeSH
- železo MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
Sledovali jsme interelektrodové a lokální koherence u 74 pacientů s ložiskovými lézemi mozku ověřenými CT nebo NMR. Norma interhemisferálních diferencí koherencí byla vytvořena na souboru 47 zdravých pacientu, specifita metody byla ověřena na souboru 46 pacientů. Nalezli jsme senzitivitu 36% při specifitě 98 %. Za cenný přinos této metody, která je součástí kvantitativního EEG, považujeme hodnocení veličiny vizuálním hodnocením neodhadnutelné. Tato metodika je pozitivní í v případě normálního EEG záznamu při vizuálním hodnocení.
The authors investigated the interelectrode and local coherence in 74 patients with focal brain lesions verified by CT or NMR. A standard of interhemispheric differences of coherence was estabUshed in a group of 47 healthy patients, the specificity of the method was tested in a group of 46 patients. The authors found a sensitivity of 36 %, the specificity being 98 %. In the authors opinion this method which is part of quantitative EEG, is valuable because it assesses values which cannot be assessed by visual evaluation. This method is positive even when on visual evaluation the EEG tracing is normal.
- MeSH
- elektroencefalografie metody MeSH
- lidé MeSH
- mapování mozku MeSH
- Check Tag
- lidé MeSH
- MeSH
- lokus kvantitativního znaku MeSH
- mapování chromozomů MeSH
- maso MeSH
- polymorfismus genetický MeSH
- Sus scrofa genetika MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: QTL cloning for the discovery of genes underlying polygenic traits has historically been cumbersome in long-lived perennial plants like Populus. Linkage disequilibrium-based association mapping has been proposed as a cloning tool, and recent advances in high-throughput genotyping and whole-genome resequencing enable marker saturation to levels sufficient for association mapping with no a priori candidate gene selection. Here, multiyear and multienvironment evaluation of cell wall phenotypes was conducted in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree and two partially overlapping populations of unrelated P. trichocarpa genotypes using pyrolysis molecular beam mass spectrometry, saccharification, and/ or traditional wet chemistry. QTL mapping was conducted using a high-density genetic map with 3,568 SNP markers. As a fine-mapping approach, chromosome-wide association mapping targeting a QTL hot-spot on linkage group XIV was performed in the two P. trichocarpa populations. Both populations were genotyped using the 34 K Populus Infinium SNP array and whole-genome resequencing of one of the populations facilitated marker-saturation of candidate intervals for gene identification. RESULTS: Five QTLs ranging in size from 0.6 to 1.8 Mb were mapped on linkage group XIV for lignin content, syringyl to guaiacyl (S/G) ratio, 5- and 6-carbon sugars using the mapping pedigree. Six candidate loci exhibiting significant associations with phenotypes were identified within QTL intervals. These associations were reproducible across multiple environments, two independent genotyping platforms, and different plant growth stages. cDNA sequencing for allelic variants of three of the six loci identified polymorphisms leading to variable length poly glutamine (PolyQ) stretch in a transcription factor annotated as an ANGUSTIFOLIA C-terminus Binding Protein (CtBP) and premature stop codons in a KANADI transcription factor as well as a protein kinase. Results from protoplast transient expression assays suggested that each of the polymorphisms conferred allelic differences in the activation of cellulose, hemicelluloses, and lignin pathway marker genes. CONCLUSION: This study illustrates the utility of complementary QTL and association mapping as tools for gene discovery with no a priori candidate gene selection. This proof of concept in a perennial organism opens up opportunities for discovery of novel genetic determinants of economically important but complex traits in plants.
- MeSH
- alely MeSH
- buněčná stěna genetika MeSH
- celulosa metabolismus MeSH
- fenotyp MeSH
- genetická vazba MeSH
- genotyp MeSH
- jednonukleotidový polymorfismus MeSH
- lignin biosyntéza MeSH
- lod skóre MeSH
- lokus kvantitativního znaku MeSH
- mapování chromozomů MeSH
- Populus genetika MeSH
- rostlinné geny * MeSH
- rostlinné proteiny chemie genetika MeSH
- sekvence nukleotidů MeSH
- sekvenční seřazení MeSH
- transkripční faktory chemie genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
Leaf traits are often strongly correlated with yield, which poses a major challenge in rice breeding. In the present study, using a panel of Vietnamese rice landraces genotyped with 21,623 single-nucleotide polymorphism markers, a genome-wide association study (GWAS) was conducted for several leaf traits during the vegetative stage. Vietnamese landraces are often poorly represented in panels used for GWAS, even though they are adapted to contrasting agrosystems and can contain original, valuable genetic determinants. A panel of 180 rice varieties was grown in pots for four weeks with three replicates under nethouse conditions. Different leaf traits were measured on the second fully expanded leaf of the main tiller, which often plays a major role in determining the photosynthetic capacity of the plant. The leaf fresh weight, turgid weight and dry weight were measured; then, from these measurements, the relative tissue weight and leaf dry matter percentage were computed. The leaf dry matter percentage can be considered a proxy for the photosynthetic efficiency per unit leaf area, which contributes to yield. By a GWAS, thirteen QTLs associated with these leaf traits were identified. Eleven QTLs were identified for fresh weight, eleven for turgid weight, one for dry weight, one for relative tissue weight and one for leaf dry matter percentage. Eleven QTLs presented associations with several traits, suggesting that these traits share common genetic determinants, while one QTL was specific to leaf dry matter percentage and one QTL was specific to relative tissue weight. Interestingly, some of these QTLs colocalize with leaf- or yield-related QTLs previously identified using other material. Several genes within these QTLs with a known function in leaf development or physiology are reviewed.
- MeSH
- celogenomová asociační studie MeSH
- chromozomy rostlin genetika MeSH
- fenotyp MeSH
- genotyp MeSH
- jedlá semena genetika MeSH
- jednonukleotidový polymorfismus genetika MeSH
- listy rostlin genetika MeSH
- lokus kvantitativního znaku genetika MeSH
- mapování chromozomů metody MeSH
- rýže (rod) genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Vietnam MeSH
Quantitative maps of rotating frame relaxation (RFR) time constants are sensitive and useful magnetic resonance imaging tools with which to evaluate tissue integrity in vivo. However, to date, only moderate image resolutions of 1.6 x 1.6 x 3.6 mm3 have been used for whole-brain coverage RFR mapping in humans at 3 T. For more precise morphometrical examinations, higher spatial resolutions are desirable. Towards achieving the long-term goal of increasing the spatial resolution of RFR mapping without increasing scan times, we explore the use of the recently introduced Transform domain NOise Reduction with DIstribution Corrected principal component analysis (T-NORDIC) algorithm for thermal noise reduction. RFR acquisitions at 3 T were obtained from eight healthy participants (seven males and one female) aged 52 ± 20 years, including adiabatic T1ρ, T2ρ, and nonadiabatic Relaxation Along a Fictitious Field (RAFF) in the rotating frame of rank n = 4 (RAFF4) with both 1.6 x 1.6 x 3.6 mm3 and 1.25 x 1.25 x 2 mm3 image resolutions. We compared RFR values and their confidence intervals (CIs) obtained from fitting the denoised versus nondenoised images, at both voxel and regional levels separately for each resolution and RFR metric. The comparison of metrics obtained from denoised versus nondenoised images was performed with a two-sample paired t-test and statistical significance was set at p less than 0.05 after Bonferroni correction for multiple comparisons. The use of T-NORDIC on the RFR images prior to the fitting procedure decreases the uncertainty of parameter estimation (lower CIs) at both spatial resolutions. The effect was particularly prominent at high-spatial resolution for RAFF4. Moreover, T-NORDIC did not degrade map quality, and it had minimal impact on the RFR values. Denoising RFR images with T-NORDIC improves parameter estimation while preserving the image quality and accuracy of all RFR maps, ultimately enabling high-resolution RFR mapping in scan times that are suitable for clinical settings.
- MeSH
- algoritmy MeSH
- analýza hlavních komponent MeSH
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- magnetická rezonanční tomografie * metody MeSH
- mapování mozku MeSH
- mozek * diagnostické zobrazování MeSH
- poměr signál - šum * MeSH
- rotace MeSH
- senioři MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
