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1
Hayes, Ryan J., Carlos H. Galeano, Yaguang Luo, Rudie Antonise e Ivan Simko. "Inheritance of Decay of Fresh-cut Lettuce in a Recombinant Inbred Line Population from ‘Salinas 88’ × ‘La Brillante’". Journal of the American Society for Horticultural Science 139, n. 4 (luglio 2014): 388–98. http://dx.doi.org/10.21273/jashs.139.4.388.
Abstract (sommario):
Fresh-cut lettuce (Lactuca sativa) packaged as salad mixes are increasingly popular to consumers but are highly perishable. Cultivars bred with extended shelf life could increase overall production efficiency by reducing the frequency of product replacement in the marketplace. Understanding the inheritance of shelf life is needed to develop efficient breeding strategies for this trait. A population of 95 recombinant inbred lines (RILs) from slow-decaying ‘Salinas 88’ × rapidly decaying ‘La Brillante’ was grown in four field experiments. Cut lettuce was evaluated for decay in modified atmosphere (MA) packages flushed with N2 or air (control). Correlations between field experiments ranged from 0.47 to 0.84 (P < 0.01). Three quantitative trait loci (QTL) for decay of cut lettuce were detected on linkage groups (LGs) 1, 4, and 9 with ‘Salinas 88’ alleles associated with slower decay. The QTL on LG 4 (qSL4) was a major determinant of decay explaining 40% to 74% of the total phenotypic variance of the trait. The greatest effect of this QTL was observed between 29 and 50 days after harvest. QTL × environment interactions contributed less than 14% to the total variation. RILs with the ‘Salinas 88’ allele of qSL4 had slower decay when packaged in air compared with N2, whereas no difference between air and N2 packaging was detected with the ‘La Brillante’ allele. A subset of RILs with either the ‘Salinas 88’ or ‘La Brillante’ allele of qSL4 was grown in two field experiments and evaluated for decay of whole heads. Genetic variation among RILs for whole-head decay was found but could not be attributed to qSL4. Decay of cut lettuce in ‘Salinas 88’ × ‘La Brillante’ is a highly heritable trait conditioned by a few QTL and phenotypic selection is likely to be effective. However, shelf life evaluations are time-consuming, destructive, and require large amounts of field-grown lettuce. Therefore, qSL4 is a good QTL to develop molecular markers for marker-assisted selection. The mechanism of decay controlled by qSL4 is unknown but appears to be specific to cut lettuce and may have allele specific interactions with packaging atmospheric compositions.
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Schwander, Tanja, Bernard J. Crespi, Regine Gries e Gerhard Gries. "Neutral and selection-driven decay of sexual traits in asexual stick insects". Proceedings of the Royal Society B: Biological Sciences 280, n. 1764 (7 agosto 2013): 20130823. http://dx.doi.org/10.1098/rspb.2013.0823.
Abstract (sommario):
Environmental shifts and lifestyle changes may result in formerly adaptive traits becoming non-functional or maladaptive. The subsequent decay of such traits highlights the importance of natural selection for adaptations, yet its causes have rarely been investigated. To study the fate of formerly adaptive traits after lifestyle changes, we evaluated sexual traits in five independently derived asexual lineages, including traits that are specific to males and therefore not exposed to selection. At least four of the asexual lineages retained the capacity to produce males that display normal courtship behaviours and are able to fertilize eggs of females from related sexual species. The maintenance of male traits may stem from pleiotropy, or from these traits only regressing via drift, which may require millions of years to generate phenotypic effects. By contrast, we found parallel decay of sexual traits in females. Asexual females produced altered airborne and contact signals, had modified sperm storage organs, and lost the ability to fertilize their eggs, impeding reversals to sexual reproduction. Female sexual traits were decayed even in recently derived asexuals, suggesting that trait changes following the evolution of asexuality, when they occur, proceed rapidly and are driven by selective processes rather than drift.
3
Fois, Mattia, Andrea Bellucci, Marta Malinowska, Morten Greve, Anja Karine Ruud e Torben Asp. "Genome-Wide Association Mapping of Crown and Brown Rust Resistance in Perennial Ryegrass". Genes 13, n. 1 (22 dicembre 2021): 20. http://dx.doi.org/10.3390/genes13010020.
Abstract (sommario):
A population of 239 perennial ryegrass (Lolium perenne L.) genotypes was analyzed to identify marker-trait associations for crown rust (Puccinia coronata f. sp. lolii) and brown rust (Puccinia graminis f. sp. loliina) resistance. Phenotypic data from field trials showed a low correlation (r = 0.17) between the two traits. Genotypes were resequenced, and a total of 14,538,978 SNPs were used to analyze population structure, linkage disequilibrium (LD), and for genome-wide association study. The SNP heritability (h2SNP) was 0.4 and 0.8 for crown and brown rust resistance, respectively. The high-density SNP dataset allowed us to estimate LD decay with the highest possible precision to date for perennial ryegrass. Results showed a low LD extension with a rapid decay of r2 value below 0.2 after 520 bp on average. Additionally, QTL regions for both traits were detected, as well as candidate genes by applying Genome Complex Trait Analysis and Multi-marker Analysis of GenoMic Annotation. Moreover, two significant genes, LpPc6 and LpPl6, were identified for crown and brown rust resistance, respectively, when SNPs were aggregated to the gene level. The two candidate genes encode proteins with phosphatase activity, which putatively can be induced by the host to perceive, amplify and transfer signals to downstream components, thus activating a plant defense response.
4
Fernández-Trujillo, Juan Pablo, Javier Obando, Juan Antonio Martínez, Antonio Luis Alarcón, Iban Eduardo, Pere Arús e Antonio José Monforte. "Mapping Fruit Susceptibility to Postharvest Physiological Disorders and Decay Using a Collection of Near-isogenic Lines of Melon". Journal of the American Society for Horticultural Science 132, n. 5 (settembre 2007): 739–48. http://dx.doi.org/10.21273/jashs.132.5.739.
Abstract (sommario):
Melon (Cucumis melo L.) is a perishable fruit that requires refrigeration to extend its shelf life. Postharvest behavior differs substantially among melon varieties due to genetic differences. In this work, we use a collection of near-isogenic lines (NILs) derived from a cross between the Spanish cultivar Piel de Sapo (PS) and an exotic Korean accession ‘Shongwan Charmi’ [SC (PI161375)], each of them with a single introgressed region from SC into the PS background, to detect and map quantitative trait loci (QTLs) involved in postharvest life traits, such as total losses, water-soaking, necrosis of the placental tissue, chilling injury (CI), decay, fruit over-ripening, flesh browning, hollow flesh disorder, and flavor loss during storage. Fruit were examined at harvest and after 35 days at 8 °C. Three QTLs induced desirable quality traits: flv4.1 reduced the loss of fruit flavor after refrigeration, tl8.1 reduced total losses, and fus8.4 reduced the susceptibility to fusarium rot (Fusarium Link). Another 11 QTLs produced a detrimental effect on other quality traits. The NIL population was useful for dissecting complex, difficult-to-measure pre- and postharvest disorder traits of different degrees of development and for investigating flavor loss during storage. Further studies with the QTLs described herein will shed light on the genetic control of melon shelf life and help breeders who are interested in this fruit quality trait.
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Puentes Rodriguez, Y., A. Zubizarreta Gerendiain, A. Pappinen, H. Peltola e P. Pulkkinen. "Differences in wood decay by Heterobasidion parviporum in cloned Norway spruce (Picea abies)". Canadian Journal of Forest Research 39, n. 1 (gennaio 2009): 26–35. http://dx.doi.org/10.1139/x08-159.
Abstract (sommario):
In forest breeding, growth has been used as the main selection trait in Norway spruce (Picea abies L. Karst.), whereas wood properties or resistance to pathogens have been taken as secondary traits. We aimed to investigate, in laboratory conditions, the rate of wood decay caused by Heterobasidion parviporum (Fr.) Niemelä & Korhonen (strains 5 and 7) in 20 Norway spruce clones. We also studied if, on average, growth, wood density, and fibre properties differed in the most and least decayed clones as well as from pith to bark. After 6 months of incubation, strain 7 effected significantly higher wood decay than strain 5 (mean 16.9% and 1.7%, respectively). The difference between the five most decayed and five least decayed clones by strain 7 was also statistically significant (P < 0.05). Moreover, regardless of clone or strain, the wood decay was highest near the pith and lowest near the bark, which is the opposite for wood density and fibre length and width. However, neither wood density nor fibre properties explained, statistically, the differences in average wood decay and decay from pith to bark. On the other hand, we could identify clones that simultaneously provided high wood quantity and relatively high wood density and low decay rate.
6
Kampfraath, Andries Augustus, Tjeerd Pieter Dudink, Ken Kraaijeveld, Jacintha Ellers e Zaira Valentina Zizzari. "Male Sexual Trait Decay in Two Asexual Springtail Populations Follows Neutral Mutation Accumulation Theory". Evolutionary Biology 47, n. 4 (20 agosto 2020): 285–92. http://dx.doi.org/10.1007/s11692-020-09511-z.
Abstract (sommario):
Abstract The transition to asexual reproduction is frequent and widespread across the tree of life and constitutes a major life history change. Without sexual reproduction, selection on sexually selected traits is expected to be weaker or absent, allowing the decay and ultimately loss of sexual traits. In this study, we applied an experimental approach to investigate the decay of reproductive traits under asexuality in two asexual populations of the springtail Folsomia candida. Specifically, we compared several key male sexual traits of a sexual population and two distinct parthenogenetic lines. To allow direct comparisons between sexual and asexual individuals we first determined a suite of life history characteristics in the sexual F. candida population, which performs an indirect transfer of sperm packages (spermatophores).To investigate the decay of male sexual traits under asexuality we measured the size of spermatophores, quantified the amount of sperm DNA material, and tested spermatophore attractiveness to females in all three populations. The amount of sperm DNA material in the sperm droplets and the attractiveness of spermatophores were lower in the asexual lines compared to the sexual population. However, the two asexual lines differed in the extent of decay of these traits. Our results are consistent with predictions from neutral mutation accumulation theory, and thus suggest this to be the main evolutionary process underlying the decay of male traits in F. candida.
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Strauss, S. H., R. Lande e G. Namkoong. "Limitations of molecular-marker-aided selection in forest tree breeding". Canadian Journal of Forest Research 22, n. 7 (1 luglio 1992): 1050–61. http://dx.doi.org/10.1139/x92-140.
Abstract (sommario):
The advances to date with quantitative trait locus identification in agronomic crops, which have mostly been with studies of inter- and intra-specific hybrids, are of little relevance to assessing the potential for marker-aided selection in nonhybrid forest tree populations. Although molecular markers provide great opportunities for dissection of quantitative traits in experimental populations, we expect that their near-term usefulness in most operational tree breeding programs will be limited. In addition to cost, this limitation results from quantitative trait locus–marker associations being limited to specific genetic backgrounds as a result of linkage equilibrium, interactions of quantitative trait locus effects with genetic backgrounds, genotype by environment interaction, and changes of quantitative trait locus allele frequencies among generations. Marker-aided selection within individually mapped full-sib families can substantially aid phenotypic selection, but only where large restrictions of genetic base are tolerated, trait heritabilities are low, markers are able to explain much of the additive variance, selection intensities within families are high compared with that among families, and very large numbers of progeny are examined. Broad use of marker-aided selection in the longer term will require substantial technical advances in a number of areas, including means for precise quantitative trait locus identification; reduction of large-scale mapping and genotyping costs; and changes in breeding and propagation systems. Consideration of trait characteristics suggests that marker-aided selection will be most efficient in direct selection with high-value, low-heritability traits such as height and diameter growth. These traits, however, often show genotype by environment interaction and unfavorable genetic correlations with other desirable traits, and are likely to be controlled by a large number of minor genes rather than relatively few major ones. Traits with the most potential for marker-aided selection in nonhybrid tree populations will therefore be strongly inherited ones for which phenotypic assay is difficult; examples might include wood quality, resistance to biotrophic pathogens, and resistance to air pollutants. Because of the large disequilibrium generated during hybridization and the great phenotypic variance that segregates in F2 and backcross generations, interspecific hybrid programs lend themselves much more readily to marker-aideed selection. Segregation distortion and related meiotic aberrations, however, may substantially hamper precise estimation of quantitative trait locus locations and phenotypic effects. Nonadditive quantitative trait locus effects will likely be greater in hybrid populations than in intraspecific populations. Rapid decay of disequilibrium due to recombination, and allele frequency shifts due to selective breeding and natural selection during early generations after hybridization, are likely to cause instability for quantitative trait locus - marker associations and quantitative trait locus phenotypic effects. Finally, interspecific hybridization of highly heterozygous individuals from species in linkage equilibrium will impede marker-aided selection.
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Poulin, Robert, Boris R. Krasnov, David Mouillot e David W. Thieltges. "The comparative ecology and biogeography of parasites". Philosophical Transactions of the Royal Society B: Biological Sciences 366, n. 1576 (27 agosto 2011): 2379–90. http://dx.doi.org/10.1098/rstb.2011.0048.
Abstract (sommario):
Comparative ecology uses interspecific relationships among traits, while accounting for the phylogenetic non-independence of species, to uncover general evolutionary processes. Applied to biogeographic questions, it can be a powerful tool to explain the spatial distribution of organisms. Here, we review how comparative methods can elucidate biogeographic patterns and processes, using analyses of distributional data on parasites (fleas and helminths) as case studies. Methods exist to detect phylogenetic signals, i.e. the degree of phylogenetic dependence of a given character, and either to control for these signals in statistical analyses of interspecific data, or to measure their contribution to variance. Parasite–host interactions present a special case, as a given trait may be a parasite trait, a host trait or a property of the coevolved association rather than of one participant only. For some analyses, it is therefore necessary to correct simultaneously for both parasite phylogeny and host phylogeny, or to evaluate which has the greatest influence on trait expression. Using comparative approaches, we show that two fundamental properties of parasites, their niche breadth, i.e. host specificity, and the nature of their life cycle, can explain interspecific and latitudinal variation in the sizes of their geographical ranges, or rates of distance decay in the similarity of parasite communities. These findings illustrate the ways in which phylogenetically based comparative methods can contribute to biogeographic research.
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Stork, Sydney, Joseph Jalinsky e Maurine Neiman. "Evidence for stronger discrimination between conspecific and heterospecific mating partners in sexual vs. asexual female freshwater snails". PeerJ 10 (24 novembre 2022): e14470. http://dx.doi.org/10.7717/peerj.14470.
Abstract (sommario):
Once-useful traits that no longer contribute to fitness tend to decay over time. Here, we address whether the expression of mating-related traits that increase the fitness of sexually reproducing individuals but are likely less useful or even costly to asexual counterparts seems to exhibit decay in the latter. Potamopyrgus antipodarum is a New Zealand freshwater snail characterized by repeated transitions from sexual to asexual reproduction. The frequent coexistence of sexual and asexual lineages makes P. antipodarum an excellent model for the study of mating-related trait loss. Under the presumption (inherent in the Biological Species Concept) that failure to discriminate between conspecific and heterospecific mating partners represents a poor mate choice, we used a mating choice assay including sexual and asexual P. antipodarum females and conspecific (presumed better choice) vs. heterospecific (presumed worse choice) males to evaluate the loss of behavioral traits related to sexual reproduction. We found that sexual females engaged in mating behaviors with conspecific mating partners more frequently and for a greater duration than with heterospecific mating partners. By contrast, asexual females mated at similar frequency and duration as sexual females, but did not mate more often or for longer duration with conspecific vs. heterospecific males. While further confirmation will require inclusion of a more diverse array of sexual and asexual lineages, these results are consistent with a scenario where selection acting to maintain effective mate discrimination in asexual P. antipodarum is weak or ineffective relative to sexual females and, thus, where asexual reproduction is associated with the evolutionary decay of mating-related traits in this system.
10
Souza, Tancredo, Edjane Oliveira de Lucena, Leonaldo Alves de Andrade, Lucas Jónatan Rodrigues da Silva, Gislaine dos Santos Nascimento e Helena Freitas. "Litter Deposition and Nutrient Cycling of Invaded Environments by Cryptostegia madagascariensis at Tropical Cambisols from Northeastern Brazil". International Journal of Plant Biology 14, n. 1 (20 febbraio 2023): 254–65. http://dx.doi.org/10.3390/ijpb14010021.
Abstract (sommario):
Cryptostegia madagascariensis is an invasive plant species that covers 11% of the Brazilian northeastern territory, but its role on the litter trait in tropical ecosystems remains unclear. Here, we analyzed and compared the litter deposition, litter nutrient content, soil organic matter, and the litter decay rate from invaded and non-invaded environments by C. madagascariensis at a tropical Cambisol. The PCA analysis revealed that litter deposition, litter quality, and soil organic matter were correlated with the invaded environment. We grew plant species in greenhouse conditions to obtain a standard litter material to use in our litter bags in field conditions. We found that litter decay rate was higher in the invaded environment than in the non-invaded one. Our results suggest that C. madagascariensis changes litter traits in tropical ecosystems that in turn create negative plant–soil feedback to the native species by creating a physical barrier on soil surface and to promote its own rhizosphere.
11
Treiber, Erin L., Laise S. Moreira e Matthew D. Clark. "Postharvest Potential of Cold-hardy Table Grapes". HortScience 57, n. 10 (ottobre 2022): 1242–48. http://dx.doi.org/10.21273/hortsci16642-22.
Abstract (sommario):
The University of Minnesota Grape Breeding Program has developed cold-hardy wine grape cultivars that have facilitated the establishment of an economically important grape industry for the Midwest region. In recent years, the program has renewed efforts to breed cold-hardy table grapes. Table grapes might require postharvest storage if they are to be transported or stored for any period of time. Rachis dehydration, berry splitting, and decay can affect the postharvest quality of table grapes. In this study, we evaluated these postharvest traits in six released cultivars and nine advanced selections in the breeding program. For two growing seasons, we used industry standard packaging to assess postharvest traits (rachis dehydration, berry splitting, decay, and overall acceptability) at 2, 4, and 6 weeks of cold storage at 2.2 °C. The growing season had a significant effect on postharvest traits; therefore, the two were examined separately. There were significant differences in postharvest storage times for all traits, except berry splitting in 2020. Mean rachis dehydration reached unacceptable values (>3) after 4 weeks of postharvest storage in 2019 and after 6 weeks in 2020. All other trait means remained acceptable for many cultivars even after 6 weeks of postharvest storage. Advanced selections performed at and above the level of released cultivars, suggesting that selections will perform well in cold-hardy regions. The data collected regarding fruit quality and postharvest storage for two seasons will help to inform and improve breeding of cold-hardy grape cultivars.
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Hoshino, Masakazu, Tatsufumi Okino e Kazuhiro Kogame. "Parthenogenetic female populations in the brown algaScytosiphon lomentaria(Scytosiphonaceae, Ectocarpales): decay of a sexual trait and acquisition of asexual traits". Journal of Phycology 55, n. 1 (6 dicembre 2018): 204–13. http://dx.doi.org/10.1111/jpy.12812.
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Shet, Ratnakar M., T. Shantappa, Ashok ., Shivanand Hongal, Raghavendra Gunnaiah e R. C. Jagadeesha. "Evaluation of postharvest shelf life of south Indian culinary melon (Cucumis melo var. acidulus) accessions". Journal of Applied Horticulture 24, n. 01 (17 agosto 2022): 84–88. http://dx.doi.org/10.37855/jah.2022.v24i01.16.
Abstract (sommario):
Culinary melon (Cucumis melo var. acidulus) also known as Mangalore melon is reported with extended shelf life of more than six months. A study was conducted to assess the variability in the fruit traits with shelf life for selected 52 accessions of culinary melon at room temperature. Fruits were hanged in the air tied with smooth plastic fiber and psuedostem banana fiber, hanged to the roof of a laboratory and observations were recorded on fruit weight loss, change in the color of rind and fruit decay. Significant variation in shelf life and rind color change was observed among the accessions during storage period. The correlation analysis revealed that shelf life had significant positive high association with weight loss during storage (0.602) followed by fruit weight (0.544), flesh thickness (0.401), fruit length (0.359), days to harvest (0.346), peduncle length (0.332) and fruit width (0.322). Twenty-six accessions exhibited shelf life of more than 150 days. Green rind fruits were less vulnerable for discoloration and decay. Among the accessions MS30, MS28, MS79, MS74, MS78, MS39, MS74 and MS6 were identified as promising accessions for shelf life with marginal weight loss, rind color change and fruit traits. Understanding of physiological and biochemical changes in fruits during storage period and identifying candidate genes for shelf life will help exploit this trait to improve the muskmelon.
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Li, Delin, Qiang Liu e Patrick S. Schnable. "TWAS results are complementary to and less affected by linkage disequilibrium than GWAS". Plant Physiology 186, n. 4 (6 aprile 2021): 1800–1811. http://dx.doi.org/10.1093/plphys/kiab161.
Abstract (sommario):
Abstract A genome-wide association study (GWAS) is used to identify genetic markers associated with phenotypic variation. In contrast, a transcriptome-wide association study (TWAS) detects associations between gene expression levels and phenotypic variation. It has previously been shown that in the cross-pollinated species, maize (Zea mays), GWAS, and TWAS identify complementary sets of trait-associated genes, many of which exhibit characteristics of true positives. Here, we extend this conclusion to the self-pollinated species, Arabidopsis thaliana and soybean (Glycine max). Linkage disequilibrium (LD) can result in the identification, via GWAS, of false-positive associations. In all three analyzed plant species, most trait-associated genes identified via TWAS are well separated physically from other candidate genes. Hence, TWAS is less affected by LD than is GWAS, demonstrating that TWAS is particularly well suited for association studies in genomes with slow rates of LD decay, such as soybean. TWAS is reasonably robust to the plant organs/tissues used to determine expression levels. In summary, this study confirms that TWAS is a promising approach for accurate gene-level association mapping in plants that is complementary to GWAS, and established that TWAS can exhibit substantial advantages relative to GWAS in species with slow rates of LD decay.
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Lustenhouwer, Nicky, Daniel S. Maynard, Mark A. Bradford, Daniel L. Lindner, Brad Oberle, Amy E. Zanne e Thomas W. Crowther. "A trait-based understanding of wood decomposition by fungi". Proceedings of the National Academy of Sciences 117, n. 21 (13 maggio 2020): 11551–58. http://dx.doi.org/10.1073/pnas.1909166117.
Abstract (sommario):
As the primary decomposers of organic material in terrestrial ecosystems, fungi are critical agents of the global carbon cycle. Yet our ability to link fungal community composition to ecosystem functioning is constrained by a limited understanding of the factors accounting for different wood decomposition rates among fungi. Here we examine which traits best explain fungal decomposition ability by combining detailed trait-based assays on 34 saprotrophic fungi from across North America in the laboratory with a 5-y field study comprising 1,582 fungi isolated from 74 decomposing logs. Fungal growth rate (hyphal extension rate) was the strongest single predictor of fungal-mediated wood decomposition rate under laboratory conditions, and accounted for up to 27% of the in situ variation in decomposition in the field. At the individual level, decomposition rate was negatively correlated with moisture niche width (an indicator of drought stress tolerance) and with the production of nutrient-mineralizing extracellular enzymes. Together, these results suggest that decomposition rates strongly align with a dominance-tolerance life-history trade-off that was previously identified in these isolates, forming a spectrum from slow-growing, stress-tolerant fungi that are poor decomposers to fast-growing, highly competitive fungi with fast decomposition rates. Our study illustrates how an understanding of fungal trait variation could improve our predictive ability of the early and midstages of wood decay, to which our findings are most applicable. By mapping our results onto the biogeographic distribution of the dominance-tolerance trade-off across North America, we approximate broad-scale patterns in intrinsic fungal-mediated wood decomposition rates.
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Oberle, Brad, Marissa R. Lee, Jonathan A. Myers, Oyomoare L. Osazuwa‐Peters, Marko J. Spasojevic, Maranda L. Walton, Darcy F. Young e Amy E. Zanne. "Accurate forest projections require long‐term wood decay experiments because plant trait effects change through time". Global Change Biology 26, n. 2 (15 novembre 2019): 864–75. http://dx.doi.org/10.1111/gcb.14873.
17
Zhang, Mian, Man-Man Fu, Cheng-Wei Qiu, Fangbin Cao, Zhong-Hua Chen, Guoping Zhang e Feibo Wu. "Response of Tibetan Wild Barley Genotypes to Drought Stress and Identification of Quantitative Trait Loci by Genome-Wide Association Analysis". International Journal of Molecular Sciences 20, n. 3 (12 febbraio 2019): 791. http://dx.doi.org/10.3390/ijms20030791.
Abstract (sommario):
Tibetan wild barley has been identified to show large genetic variation and stress tolerance. A genome-wide association (GWA) analysis was performed to detect quantitative trait loci (QTLs) for drought tolerance using 777 Diversity Array Technology (DArT) markers and morphological and physiological traits of 166 Tibetan wild barley accessions in both hydroponic and pot experiments. Large genotypic variation for these traits was found; and population structure and kinship analysis identified three subpopulations among these barley genotypes. The average LD (linkage disequilibrium) decay distance was 5.16 cM, with the minimum on 6H (0.03 cM) and the maximum on 4H (23.48 cM). A total of 91 DArT markers were identified to be associated with drought tolerance-related traits, with 33, 26, 16, 1, 3, and 12 associations for morphological traits, H+K+-ATPase activity, antioxidant enzyme activities, malondialdehyde (MDA) content, soluble protein content, and potassium concentration, respectively. Furthermore, 7 and 24 putative candidate genes were identified based on the reference Meta-QTL map and by searching the Barleymap. The present study implicated that Tibetan annual wild barley from Qinghai–Tibet Plateau is rich in genetic variation for drought stress. The QTLs detected by genome-wide association analysis could be used in marker-assisting breeding for drought-tolerant barley genotypes and provide useful information for discovery and functional analysis of key genes in the future.
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Hidalgo, Jorge, Daniela Lourenco, Shogo Tsuruta, Yutaka Masuda, Vivian Breen, Rachel Hawken, Matias Bermann e Ignacy Misztal. "44 Accuracy of Genomic Predictions over Time in Broilers". Journal of Animal Science 99, Supplement_3 (8 ottobre 2021): 28. http://dx.doi.org/10.1093/jas/skab235.047.
Abstract (sommario):
Abstract The objectives of this research were to investigate trends for accuracy of genomic predictions over time in a broiler population accumulating data, and to test if data from distant generations are useful in maintaining the accuracy of genomic predictions in selection candidates. The data contained 820k phenotypes for a growth trait (GROW), 200k for two feed efficiency traits (FE1 and FE2), and 42k for a dissection trait (DT). The pedigree included 1.2M animals across 7 years, over 100k from the last 4 years were genotyped. Accuracy was calculated by the linear regression method. Before genotypes became available for training populations, accuracy was nearly stable despite the accumulation of phenotypes and pedigrees. When the first year of genomic data was included in the training population, accuracy increased 56, 77, 39, and 111% for GROW, FE1, FE2, and DT, respectively. With genomic information, the accuracies increased every year except the last one, when they declined for GROW and FE2. The decay of accuracy over time was evaluated in progeny, grand-progeny, and great-grand-progeny of training populations. Without genotypes, the average decline in accuracy across traits was 41% from progeny to grand-progeny, and 19% from grand-progeny to great-grand-progeny. Whit genotypes, the average decline across traits was 14% from progeny to grand-progeny, and 2% from grand-progeny to great-grand-progeny. The accuracies in the last 3 generations were the same when the training population included 5 or 2 years of data, and a marginal decrease was observed when the training population included only 1 year of data. Training sets including genomic information provided an increased accuracy and persistence of genomic predictions compared to training sets without genomic data. The two most recent years of data were enough to maintain the accuracy of predictions in selection candidates.
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Ficco, Donatella B. M., Romina Beleggia, Ivano Pecorella, Valentina Giovanniello, Alfonso S. Frenda e Pasquale De Vita. "Relationship between Seed Morphological Traits and Ash and Mineral Distribution along the Kernel Using Debranning in Durum Wheats from Different Geographic Sites". Foods 9, n. 11 (23 ottobre 2020): 1523. http://dx.doi.org/10.3390/foods9111523.
Abstract (sommario):
Debranning was applied to durum wheat to the study the relationship between kernel shape and size, and ash and mineral distribution having implications for semolina yield. To this aim four durum wheat genotypes carried out over three environments were selected to determine the morphological and yield traits as well as the distribution along the kernel of the ash, macro- (Na, K, P, Ca, and Mg), and micro-elements (Mn, Fe, Cu, Zn, and Mo). A descendent ash gradient within the kernel reflects the decreases in the minerals that occurred during debranning. Perciasacchi with high seed weight (TKW) and greater thickness followed by Cappelli showed a more uniform distribution of ash content along the kernels. High r Pearson coefficient (p < 0.01) showed an inverse relationship between thickness and ash decay. Since thickness was strongly affected by the genotype, it could represent a useful trait for breeding programs to predict the milling quality.
20
Dawson, Chris. "How Persistent Is Generalised Trust?" Sociology 53, n. 3 (27 luglio 2017): 590–99. http://dx.doi.org/10.1177/0038038517718991.
Abstract (sommario):
There are at least two competing views on the foundations of generalised trust: experiential and cultural. The experiential perspective emphasises that trust is fragile and remains open to environmental influences throughout life, whilst the cultural perspective asserts that trust is a stable trait established early in pre-adult life through intergenerational transmission mechanisms. Utilising an innovative methodology applied to a major UK longitudinal survey, this article tests these alternative accounts by analysing the persistence of generalised trust throughout the life-course. In support of the cultural perspective, trust is found to be a relatively stable, persistent human trait. Whilst generalised trust is open to change, these changes are however temporary with an overriding tendency for individuals to revert back to their initial, long-term level. Greater emphasis should be placed on the establishment of initial, pre-adult trust, as changes induced by post-childhood environmental forces are likely to be prone to rapid decay.
21
LI, C. Q., N. J. AI, Y. J. ZHU, Y. Q. WANG, X. D. CHEN, F. LI, Q. Y. HU e Q. L. WANG. "Association mapping and favourable allele exploration for plant architecture traits in upland cotton (Gossypium hirsutum L.) accessions". Journal of Agricultural Science 154, n. 4 (22 maggio 2015): 567–83. http://dx.doi.org/10.1017/s0021859615000428.
Abstract (sommario):
SUMMARYAssociation mapping based on linkage disequilibrium (LD) is a promising tool to identify genes responsible for quantitative variations underlying complex traits. The present paper presents an association mapping panel consisting of 172 upland cotton (Gossypium hirsutum L.) accessions. The panel was phenotyped for five cotton plant architecture traits across multiple environments and genotyped using 386 simple sequence repeat (SSR) markers. Of these markers, 101 polymorphic SSR markers were used in the final analysis. There were abundant phenotypic variations within this germplasm panel and a total of 267 alleles ranging from two to seven per locus were identified in all collections. The threshold of LD decay was set to r2 = 0·1 and 0·2, and the genome-wide LD extended up to about 13–14 and 6–7 cM, respectively, providing the potential for association mapping of agronomically important traits in upland cotton. A total of 66 marker–trait associations were detected based on a mixed linear model, of which 35 were found in more than one environment. The favourable alleles from 35 marker loci can be used in marker-assisted selection of target traits. Both the synergistic alleles and the negative alleles for some traits, especially plant height and fruit branch angle, can be utilized in plant architecture breeding programmes according to specific breeding objectives.
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Gao, Yuanyuan, Zhaohui Liu, Justin D. Faris, Jonathan Richards, Robert S. Brueggeman, Xuehui Li, Richard P. Oliver, Bruce A. McDonald e Timothy L. Friesen. "Validation of Genome-Wide Association Studies as a Tool to Identify Virulence Factors in Parastagonospora nodorum". Phytopathology® 106, n. 10 (ottobre 2016): 1177–85. http://dx.doi.org/10.1094/phyto-02-16-0113-fi.
Abstract (sommario):
Parastagonospora nodorum is a necrotrophic fungal pathogen causing Septoria nodorum blotch on wheat. We have identified nine necrotrophic effector–host dominant sensitivity gene interactions, and we have cloned three of the necrotrophic effector genes, including SnToxA, SnTox1, and SnTox3. Because sexual populations of P. nodorum are difficult to develop under lab conditions, genome-wide association study (GWAS) is the best population genomic approach to identify genomic regions associated with traits using natural populations. In this article, we used a global collection of 191 P. nodorum isolates from which we identified 2,983 single-nucleotide polymorphism (SNP) markers and gene markers for SnToxA and SnTox3 to evaluate the power of GWAS on two popular wheat breeding lines that were sensitive to SnToxA and SnTox3. Strong marker trait associations (MTA) with P. nodorum virulence that mapped to SnTox3 and SnToxA were first identified using the marker set described above. A novel locus in the P. nodorum genome associated with virulence was also identified as a result of this analysis. To evaluate whether a sufficient level of marker saturation was available, we designed a set of primers every 1 kb in the genomic regions containing SnToxA and SnTox3. Polymerase chain reaction amplification was performed across the 191 isolates and the presence/absence polymorphism was scored and used as the genotype. The marker proximity necessary to identify MTA flanking SnToxA and SnTox3 ranged from 4 to 5 and 1 to 7 kb, respectively. Similar analysis was performed on the novel locus. Using a 45% missing data threshold, two more SNP were identified spanning a 4.6-kb genomic region at the novel locus. These results showed that the rate of linkage disequilibrium (LD) decay in P. nodorum and, likely, other fungi is high compared with plants and animals. The fast LD decay in P. nodorum is an advantage only if sufficient marker density is attained. Based on our results with the SnToxA and SnTox3 regions, markers are needed every 9 or 8 kb, respectively, or in every gene, to guarantee that genes associated with a quantitative trait such as virulence are not missed.
23
Carlson, Maryn O., Daniel P. Rice, Jeremy J. Berg e Matthias Steinrücken. "Polygenic score accuracy in ancient samples: Quantifying the effects of allelic turnover". PLOS Genetics 18, n. 5 (6 maggio 2022): e1010170. http://dx.doi.org/10.1371/journal.pgen.1010170.
Abstract (sommario):
Polygenic scores link the genotypes of ancient individuals to their phenotypes, which are often unobservable, offering a tantalizing opportunity to reconstruct complex trait evolution. In practice, however, interpretation of ancient polygenic scores is subject to numerous assumptions. For one, the genome-wide association (GWA) studies from which polygenic scores are derived, can only estimate effect sizes for loci segregating in contemporary populations. Therefore, a GWA study may not correctly identify all loci relevant to trait variation in the ancient population. In addition, the frequencies of trait-associated loci may have changed in the intervening years. Here, we devise a theoretical framework to quantify the effect of this allelic turnover on the statistical properties of polygenic scores as functions of population genetic dynamics, trait architecture, power to detect significant loci, and the age of the ancient sample. We model the allele frequencies of loci underlying trait variation using the Wright-Fisher diffusion, and employ the spectral representation of its transition density to find analytical expressions for several error metrics, including the expected sample correlation between the polygenic scores of ancient individuals and their true phenotypes, referred to as polygenic score accuracy. Our theory also applies to a two-population scenario and demonstrates that allelic turnover alone may explain a substantial percentage of the reduced accuracy observed in cross-population predictions, akin to those performed in human genetics. Finally, we use simulations to explore the effects of recent directional selection, a bias-inducing process, on the statistics of interest. We find that even in the presence of bias, weak selection induces minimal deviations from our neutral expectations for the decay of polygenic score accuracy. By quantifying the limitations of polygenic scores in an explicit evolutionary context, our work lays the foundation for the development of more sophisticated statistical procedures to analyze both temporally and geographically resolved polygenic scores.
24
Hollifield, Mary Kate, Daniela Lourenco, Jeremy Howard, Yijian Huang e Ignacy Misztal. "25 Determining stability of genomic predictivity in future generations in commercial pig populations". Journal of Animal Science 98, Supplement_4 (3 novembre 2020): 21. http://dx.doi.org/10.1093/jas/skaa278.039.
Abstract (sommario):
Abstract Genomic predictivity is expected to decay over time as predictions are evaluated to more distant generations. More data increases predictive ability; however, data from distant ancestors may not add a significant amount of value compared to the data from closely related individuals. The objective of this study was to evaluate the decay in genomic predictivity over time and to compare the magnitude of decay when including ancestral data versus data from 2 and 3 most recent generations for body weight at off-test (BW). The data set included 211,812 phenotypic records. The pedigree included 406,983 animals from 2001 to 2020, of which 55,118 were genotyped. A single-trait model was used with all ancestral data and sliding subsets of two- and three-generation intervals. Single-step GBLUP was used to calculate GEBVs. Predictive abilities were calculated by the correlation between GEBVs and adjusted phenotypes. Validation populations consisted of single generations succeeding the training population and continued for all generations available. Predictive ability was slightly higher, with all ancestral data in the training population compared to three- and two-generation intervals. The decay of predictivity was similar when comparing the three training population subsets. The average predictivity for the validation population immediately following the training population was 0.40 for 2016, 0.39 for 2017, 0.35 for 2018, and 0.29 for 2019. Predictive ability reached a maximum in the year 2017 (0.45) for the ancestral training population, 2017 (0.43) for the 3-year training population, and 2016 (0.38) for the 2-year training population. The average decay of predictive ability from the first year after the training population to the second year was -0.08. Realized predictivity is affected by selection pressure. The drop in predictive ability suggests declining heritability. With more data and with consistent selection pressure, predictive abilities should increase.
25
Pai, Athma A., Carolyn E. Cain, Orna Mizrahi-Man, Sherryl De Leon, Noah Lewellen, Jean-Baptiste Veyrieras, Jacob F. Degner et al. "The Contribution of RNA Decay Quantitative Trait Loci to Inter-Individual Variation in Steady-State Gene Expression Levels". PLoS Genetics 8, n. 10 (11 ottobre 2012): e1003000. http://dx.doi.org/10.1371/journal.pgen.1003000.
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Srungarapu, Rajasekhar, Mahesh Damodhar Mahendrakar, Lal Ahamed Mohammad, Uttam Chand, Venkata Ramana Jagarlamudi, Kiran Prakash Kondamudi, Himabindu Kudapa e Srinivasan Samineni. "Genome-Wide Association Analysis Reveals Trait-Linked Markers for Grain Nutrient and Agronomic Traits in Diverse Set of Chickpea Germplasm". Cells 11, n. 15 (8 agosto 2022): 2457. http://dx.doi.org/10.3390/cells11152457.
Abstract (sommario):
Chickpea is an inexpensive source of protein, minerals, and vitamins to the poor people living in arid and semi-arid regions of Southern Asia and Sub-Saharan Africa. New chickpea cultivars with enhanced levels of protein, Fe and Zn content are a medium-term strategy for supplying essential nutrients for human health and reducing malnutrition. In the current study, a chickpea reference set of 280 accessions, including landraces, breeding lines, and advanced cultivars, was evaluated for grain protein, Fe, Zn content and agronomic traits over two seasons. Using a mid-density 5k SNP array, 4603 highly informative SNPs distributed across the chickpea genome were used for GWAS analysis. Population structure analysis revealed three subpopulations (K = 3). Linkage disequilibrium (LD) was extensive, and LD decay was relatively low. A total of 20 and 46 marker-trait associations (MTAs) were identified for grain nutrient and agronomic traits, respectively, using FarmCPU and BLINK models. Of which seven SNPs for grain protein, twelve for Fe, and one for Zn content were distributed on chromosomes 1, 4, 6, and 7. The marker S4_4477846 on chr4 was found to be co-associated with grain protein over seasons. The markers S1_11613376 and S1_2772537 co-associated with grain Fe content under NSII and pooled seasons and S7_9379786 marker under NSI and pooled seasons. The markers S4_31996956 co-associated with grain Fe and days to maturity. SNP annotation of associated markers were found to be related to gene functions of metal ion binding, transporters, protein kinases, transcription factors, and many more functions involved in plant metabolism along with Fe and protein homeostasis. The identified significant MTAs has potential use in marker-assisted selection for developing nutrient-rich chickpea cultivars after validation in the breeding populations.
27
Wagoner, Wendy, J. Stamp, H. Matthews, J. Kellogg e R. Bestwick. "473 PB 367 AGROBACTERIUM- MEDIATED TRANSFORMATION OF CAULIFLOWER FOR CONTROL OF FLOWER SENESCENCE". HortScience 29, n. 5 (maggio 1994): 499a—499. http://dx.doi.org/10.21273/hortsci.29.5.499a.
Abstract (sommario):
Ethylene is a known causal factor in the decay and senescence of fruits and vegetables. The aim of the present study was to incorporate a gene for control of ethylene biosynthesis in order to prevent or delay the senescence of the cauliflower curds. We first developed a reproducible transformation system using marker genes for beta glucuronidase (GUS) and antibiotic resistance. Brassica oleraceae L. var. botrytis was transformed by inoculating hypocotyl explants with the Agrobacterium tumefaciens strains C58 or EHA101 containing plasmids pAG5110, pAG5420, or pAG5520. The plasmid pAG5110 contains the genes for neomycin phosphotransferase II (NPTII) and GUS. The plasmids pAG5420 and pAG5520 contain a functional gene for S-adenosylmethionine hydrolase (SAMase) under an ethylene or wound inducible promoter, respectively. Hypocotyl explants were screened on regeneration medium with kanamycin for selection of transformants. Shoot regeneration occured within 4-6 weeks and morphologically normal plants developed within 3-4 months. The transgenic nature of the plants was confirmed by histochemical GUS assay, an ELISA based NPTII assay and Southern blot analysis. Transgenic plants outplanted in the greenhouse are being evaluated and selfed to study expression and inheritance pattern of the introduced trait.
28
Błaszczyk, Jan, e Krzysztof Gasparski. "INFLUENCE OF 1-METHYLOCYCLOPROPENE (1-MCP) ON THE QUALITY AND STORABILITY OF ‘RED JONAPRINCE’ APPLES STORED IN DIFFERENT CONDITIONS". Acta Scientiarum Polonorum Hortorum Cultus 18, n. 6 (22 dicembre 2019): 7–15. http://dx.doi.org/10.24326/asphc.2019.6.1.
Abstract (sommario):
The research was carried out on apples of the cultivar ‘Red Jonaprince’ in two storage seasons of 2015/2016 and 2016/2017. Both 1-MCP-treated and untreated apples were stored for 120 and 150 days at 2°C and 90–92% relative humidity in a regular cold store (NA) and in two atmospheric controlled storages, i.e. 2% CO2 and 2% O2 (CA) and 2% CO2 and 1.2% O2 (ULO). Apples were evaluated directly after the storage and after 7 days of simulated shelf-life. It was shown that storage conditions had significant impact on the value of apple quality traits. The effectiveness of the post-harvest 1-MCP treatment of apples manifested in different manner depending on the tested trait and storage conditions. 1-MCP delayed the softening of apples, but only those stored in CA and ULO. It effectively limited the decrease in titratable acidity, especially of apples from NA and ULO. A positive effect of 1-MCP in NA conditions on the soluble solids content was observed, as well as a reduction in the natural loss of weight and the percentage of fruits with the symptoms of fungal decay.
29
Partanen, Jouni, Anni M. Harju, Martti Venäläinen e Katri Kärkkäinen. "Highly heritable heartwood properties of Scots pine: possibilities for selective seed harvest in seed orchards". Canadian Journal of Forest Research 41, n. 10 (ottobre 2011): 1993–2000. http://dx.doi.org/10.1139/x11-116.
Abstract (sommario):
The stilbenes pinosylvin (PS) and its monomethyl ether (PSM) provide natural decay resistance to Scots pine ( Pinus sylvestris L.) heartwood timber. For growing trees, the inducible stilbene production serves as a defence against biotic and abiotic stresses. To improve the potential of reforestation material to produce stilbenes, we assessed the possibilities of selective harvesting from seed orchards. Half-sib progenies growing in a field trial and their grafted mothers in seed orchards were surveyed for several chemical and dimensional heartwood characteristics. The correlations between the clonal means of grafted mothers and the family means of their progenies were high for concentration of PS (r = 0.83, p = 0.000) and PSM (r = 0.60, p = 0.010) and for heartwood density (r = 0.72, p = 0.001). For these traits, the narrow-sense heritabilities (h2) estimated from the progeny trial and the broad-sense heritabilities (H2) in seed orchards were high as well. For the concentration of PS, both h2 (0.67) and H2 (0.81) showed the highest values of any trait. The selective collection of Scots pine seed from seed orchards is a promising way to obtain seedlings that possess genetic potential for active defence and to produce high-quality heartwood as mature trees.
30
Campa, Ana, Elena Pérez-Vega, Aida Pascual e Juan José Ferreira. "Genetic Analysis and Molecular Mapping of Quantitative Trait Loci in Common Bean Against Pythium ultimum". Phytopathology® 100, n. 12 (dicembre 2010): 1315–20. http://dx.doi.org/10.1094/phyto-06-10-0161.
Abstract (sommario):
Pythium ultimum is a soil pathogen that can cause seed decay and damage to roots in common bean. In this study, the response of a set of 40 common bean genotypes to P. ultimum and inheritance of the resistance in the 92 F7 recombinant inbred lines (RIL) developed from a cross between Xana and Cornell 49242 was investigated by using emergence rate and seedling vigor. Emergence of the 40 genotypes showed a significant association between white seed coat and response to this pathogen. Among these, 11 common bean genotypes, all with colored seeds, exhibited a high percentage of emergence and seedling vigor not significantly different (P > 0.05) to noninoculated plants. Response of the RIL population revealed both qualitative and quantitative modes of inheritance. A major gene (Py-1) controlling the emergence rate was mapped in the region of the gene P, a basic color gene involved in control of seed coat color, located on LG 7. Using the RIL subpopulation with colored seeds, a significant quantitative trait loci (QTL) associated with the emergence rate (ER3XC) and another with seedling vigor (SV6XC) were identified on the LG 3 and 6, respectively. QTL SV6XC was mapped in the region of the gene V, another gene involved the genetic control of color. QTLs associated with seed traits were mapped in the same relative position as regions involved in responses to P. ultimum suggesting the possible implication of avoidance mechanisms in the response to this pathogen.
31
Bharti, Sonu. "Identification and tagging of QTLs for arjunolic acid in Terminalia arjuna among Indian sub populations by association mapping and linkage disequilibrium". INTERNATIONAL JOURNAL OF PLANT SCIENCES 15, n. 2 (15 luglio 2020): 121–34. http://dx.doi.org/10.15740/has/ijps/15.2/121-134.
Abstract (sommario):
The content of cardiotonic arjunolic acid in Terminalia arjuna vary among the population. We studied the population structure and the association between the molecular markers and its active ingredient among 140 plants collected from various agroclimatic zones in India. Large variation was detected for the arjunolic acid in this study showing suitableness of the genotypes. The maximum arjunolic acid content was approximately 238 per cent higher than the lowest value for the genotypes and was found to be considerably correlated to bark thickness, bark fresh weight and bark dry weight. The population structure studies described the existence of nine subpopulations. As the distance increased between the associated markers, Linkage disequilibrium (LD) reduction and a considerable reduction in LD decay was ascertained. Eleven QTL regions associated with arjunolic acid were identified from a genome-wide marker-trait association study. Fine-scale resolution detected significant LD among 3.4 per cent RAPD paired loci and 8.7 per cent ISSR paired loci and 6.7 per cent RAPD paired loci and 13.3 per cent ISSR paired loci. Importantly LD decay found to start at a distance of >20bp from the loci on the genome of T. arjuna accessions. Finally, association mapping (AM) in arjun tightly linked to OPT09 which can be a possible substitute to QTL mapping methodology.
32
Jang, Seong-Gyu, So-Yeon Park, San Mar Lar, Hongjia Zhang, Ah-Rim Lee, Fang-Yuan Cao, Jeonghwan Seo, Tae-Ho Ham, Joohyun Lee e Soon-Wook Kwon. "Genome-Wide Association Study (GWAS) of Mesocotyl Length for Direct Seeding in Rice". Agronomy 11, n. 12 (13 dicembre 2021): 2527. http://dx.doi.org/10.3390/agronomy11122527.
Abstract (sommario):
Direct seeding is considered an efficient cultivation technology that reduces water use and labor costs. Mesocotyl length is one of the significant traits in cultivation; long mesocotyl is beneficial for the rate and uniformity of seedling emergence. In this study, we used a core collection of 137 rice accessions to identify quantitative trait loci (QTL) for mesocotyl elongation. A genome-wide association study (GWAS), combined with a principal component analysis (PCA) and a kinship matrix analysis, was conducted for the genotype analysis of 2 million, high-quality single nucleotide polymorphisms (SNPs). Through this GWAS analysis, 11 lead SNPs were confirmed to be associated with mesocotyl length, and a linkage disequilibrium (LD) decay analysis identified the 230 kb exploratory range for the detection of QTLs and candidate genes. Based on the gene expression database and haplotype analysis, five candidate genes (Os01g0269800, Os01g0731100, Os08g0136700, Os08g0137800, and Os08g0137900) were detected to be significantly associated with phenotypic variation. Five candidate gene expressions are reported to be associated with various plant hormone responses. Interestingly, two biotic stress response genes and two copper-containing redox proteins were detected as the candidate genes. The results of this study provide associated SNPs in candidate genes for mesocotyl length and strategies for developing direct seeding in breeding programs.
33
Obaid, Jamil M. A. S., Baleegh A. Alkadasi, Manea M. M. Alahmari, Ahmed A. Alzahrani, Thiyezen A. Aldhelai, Shaima A. H. Mohammed, Ebtesam M. M. Al-Gora’ee, Sadam A. Elayah e Mohammed M. Al Moaleem. "Periodontal Diseases and Salivary Secretion of ABH Blood Antigens in Yemeni Patients". Journal of Biomaterials and Tissue Engineering 13, n. 5 (1 maggio 2023): 706–13. http://dx.doi.org/10.1166/jbt.2023.3307.
Abstract (sommario):
This study explored the secretion trait as a risk factor for periodontal disease progression. 162 patients suffering from periodontal disease attended the Outpatient Dental Clinics at the Faculty of Dentistry, Ibb University, and 69 healthy volunteers were enrolled in this study. Clinical evaluation for periodontal disease was carried out according to international guidelines and expressed by pocket probing depth (PPD), bleeding on probing (BOP), and clinical attachment level (CAL) parameters. A blood sample was collected and tested for blood grouping test, and a saliva sample was analyzed for secretion using hemagglutination inhibition test. Secretor patients were 82% compared with 64% of healthy control. Mean score of BOB and PPD and the clinical magnitude of CAL parameters were increased within secretors. The development of periodontal diseases increased among secretors by 2.61 times more than non-secretors (OR = 2.61, CI, 1.382–4.914, p = 0.004). Significant periodontal complaints associated with secretion are Bleeding gums (OR = 1.95, CI, 1.011–3.759, p = 0.049), malaligned teeth (OR = 4.49 (CI, 1.842–10.958), p = 0.0001), gingival recession (OR = 2.48, CI, 1.322–4.648, p = 0.007), and teeth decay (OR = 1.86, CI, 1.006–3.438, p = 0.05). Secretion of ABH antigens is risk factor for progression of periodontal diseases. The odds of periodontal complaints, bleeding gums, malaligned teeth, gingival recession, and tooth decay prove the ABH secretion effect.
34
Healey, John F., Ernest Parker e John (Pete) S. Lollar. "Comparative Decay Rates of Human, Rhesus Macaque, Cynomolgus, and Porcine Activated Factor VIII." Blood 114, n. 22 (20 novembre 2009): 3164. http://dx.doi.org/10.1182/blood.v114.22.3164.3164.
Abstract (sommario):
Abstract Abstract 3164 Poster Board III-104 The proteolytic conversation by thrombin of factor VIII (fVIII) to fVIIIa produces a A1/A2/A3-C1-C2 heterotrimer that spontaneously dissociates into inactive A1/A3-C1-C2 and A2 species. Human mutations that increase the rate of A2 subunit dissociation produce hemophilia A, indicating that A2 subunit dissociation is physiologically relevant and is an important regulatory feature of the blood coagulation mechanism. The A2 subunit dissociation rate from human fVIIIa is significantly faster than the corresponding dissociation rates from porcine or murine fVIIIa. The fast decay rate of human fVIIIa raises the question whether the f8 gene is under positive selection for this trait. To determine whether fast A2 dissociation occurs elsewhere in the primate lineage, we cloned cDNAs encoding B-domain deleted (BDD) fVIII from rhesus macaque and cynomolgus monkey liver. The deduced BDD amino acid sequences of rhesus and cynomolgus fVIII were 97.9 % and 98% identical to human fVIII, respectively, and were 99.9% identical to each other. The expression of rhesus and cynomolgus fVIII from baby hamster kidney-derived cells was similar to human fVIII and ten-fold lower than porcine fVIII. BDD human, rhesus, cynomolgus, and porcine fVIII molecules were purified to homogeneity by tandem ion-exchange chromatography. Concentrations of the purified constructs were calculated using a molar extinction coefficient at 280 nm based on their predicted tyrosine, tryptophan and cysteine compositions. Human, rhesus, and cynomolgus fVIII displayed similar specific coagulant activities by one-stage coagulation assay (6800, 4500, and 5200 units per mg, respectively). The kinetics of decay of human, rhesus, cynomolgus and porcine fVIIIa were measured following rapid activation of 1 nM fVIII by thrombin using a chromogenic substrate assay of purified intrinsic fXase complex under conditions in which fVIIIa was limiting. Decay curves were fit using nonlinear least-squares regression to a first-order model (Fig. 1). Decay rate constants for rhesus and cynomolgus fVIIIa were similar (0.31 and 0.27 min-1, respectively) and were slightly, but significantly lower than human fVIIIa (0.40 min-1). In contrast, the decay rate constant for porcine fVIIIa, 0.17 min-1, was 2.3-fold lower than human fVIIIa, consistent with previous observations. These results suggest that fast A2 subunit dissociation rates evolved before evolution of the primate lineage. Disclosures No relevant conflicts of interest to declare.
35
van Vliet, Simon, e Michael Doebeli. "The role of multilevel selection in host microbiome evolution". Proceedings of the National Academy of Sciences 116, n. 41 (23 settembre 2019): 20591–97. http://dx.doi.org/10.1073/pnas.1909790116.
Abstract (sommario):
Animals are associated with a microbiome that can affect their reproductive success. It is, therefore, important to understand how a host and its microbiome coevolve. According to the hologenome concept, hosts and their microbiome form an integrated evolutionary entity, a holobiont, on which selection can potentially act directly. However, this view is controversial, and there is an active debate on whether the association between hosts and their microbiomes is strong enough to allow for selection at the holobiont level. Much of this debate is based on verbal arguments, but a quantitative framework is needed to investigate the conditions under which selection can act at the holobiont level. Here, we use multilevel selection theory to develop such a framework. We found that selection at the holobiont level can in principle favor a trait that is costly to the microbes but that provides a benefit to the host. However, such scenarios require rather stringent conditions. The degree to which microbiome composition is heritable decays with time, and selection can only act at the holobiont level when this decay is slow enough, which occurs when vertical transmission is stronger than horizontal transmission. Moreover, the host generation time has to be short enough compared with the timescale of the evolutionary dynamics at the microbe level. Our framework thus allows us to quantitatively predict for what kind of systems selection could act at the holobiont level.
36
Gardarin, Antoine, Carolyne Dürr, Maria R. Mannino, Hugues Busset e Nathalie Colbach. "Seed mortality in the soil is related to seed coat thickness". Seed Science Research 20, n. 4 (22 settembre 2010): 243–56. http://dx.doi.org/10.1017/s0960258510000255.
Abstract (sommario):
AbstractModels that quantify the effects of cropping systems on weed dynamics are useful tools for testing innovative cropping systems. In these models, seed mortality in the soil is a key parameter to account for the cumulated effect of cropping systems over time via the soil seed-bank. Since seed mortality is difficult to measure, our objective was to develop a method to estimate it from easily accessible information. Seeds of 13 weed species were buried 30 cm deep in fields and were recovered regularly for 2 years to measure their viability. Seed mass, dimensions, shape, and protein and lipid contents as well as coat thickness were measured. To estimate seed mortality of species not included in the study, we searched for relationships between mortality rates and seed traits. Seed viability mainly decreased during the second year of burial, with mortality rates ranging from 0.01 to 0.63 seeds·seeds− 1·year− 1, depending on the species. Seed mortality decreased with increasing seed coat thickness. No correlation was found with other measured traits or with seed persistence data in the literature. These results were confirmed when the effects of phylogenetic relatedness with phylogenetically independent contrasts were included. The thickness of the seed coat, which varied between 17 and 231 μm over the range of species studied, can protect the seed from external attacks in the soil and slow down seed decay. This trait can be easily measured via X-ray images and could be used to estimate the seed mortality rate for a wider range of species.
37
Fernández-Baca, Cristina P., Adam R. Rivers, Jude E. Maul, Woojae Kim, Ravin Poudel, Anna M. McClung, Daniel P. Roberts, Vangimalla R. Reddy e Jinyoung Y. Barnaby. "Rice Plant–Soil Microbiome Interactions Driven by Root and Shoot Biomass". Diversity 13, n. 3 (15 marzo 2021): 125. http://dx.doi.org/10.3390/d13030125.
Abstract (sommario):
Plant–soil microbe interactions are complex and affected by many factors including soil type, edaphic conditions, plant genotype and phenotype, and developmental stage. The rice rhizosphere microbial community composition of nine recombinant inbred lines (RILs) and their parents, Francis and Rondo, segregating for root and shoot biomass, was determined using metagenomic sequencing as a means to examine how biomass phenotype influences the rhizosphere community. Two plant developmental stages were studied, heading and physiological maturity, based on root and shoot biomass growth patterns across the selected genotypes. We used partial least squares (PLS) regression analysis to examine plant trait-driven microbial populations and identify microbial species, functions, and genes corresponding to root and shoot biomass as well as developmental stage patterns. Species identified correlated with increases in either root or shoot biomass were widely present in soil and included species involved in nitrogen cycling (Anaeromyxobacter spp.) and methane production (Methanocellaavoryzae), as well as known endophytes (Bradyrhizobium spp.). Additionally, PLS analysis allowed us to explore the relationship of developmental stage with species, microbial functions, and genes. Many of the community functions and genes observed during the heading stage were representative of cell growth (e.g., carbohydrate and nitrogen metabolism), while functions correlated with physiological maturity were indicative of cell decay. These results are consistent with the hypothesis that microbial communities exist whose metabolic and gene functions correspond to plant biomass traits.
38
Guerra, Fernando P., Alejandra Yáñez, Iván Matus e Alejandro del Pozo. "Genome-Wide Association of Stem Carbohydrate Accumulation and Remobilization during Grain Growth in Bread Wheat (Triticum aestivum L.) in Mediterranean Environments". Plants 10, n. 3 (12 marzo 2021): 539. http://dx.doi.org/10.3390/plants10030539.
Abstract (sommario):
Water deficit represents an important challenge for wheat production in many regions of the world. Accumulation and remobilization of water-soluble carbohydrates (WSCs) in stems are part of the physiological responses regulated by plants to cope with water stress and, in turn, determine grain yield (GY). The genetic mechanisms underlying the variation in WSC are only partially understood. In this study, we aimed to identify Single Nucleotide Polymorphism (SNP) markers that account for variation in a suite of WSC and GY, evaluated in 225 cultivars and advanced lines of spring wheat. These genotypes were established in two sites in the Mediterranean region of Central Chile, under water-limited and full irrigation conditions, and assessed in two growing seasons, namely anthesis and maturity growth periods. A genome-wide association study (GWAS) was performed by using 3243 SNP markers. Genetic variance accounted for 5 to 52% of phenotypic variation of the assessed traits. A rapid linkage disequilibrium decay was observed across chromosomes (r2 ≤ 0.2 at 2.52 kbp). Marker-trait association tests identified 96 SNPs related to stem weight (SW), WSCs, and GY, among other traits, at the different sites, growing seasons, and growth periods. The percentage of SNPs that were part of the gene-coding regions was 34%. Most of these genes are involved in the defensive response to drought and biotic stress. A complimentary analysis detected significant effects of different haplotypes on WSC and SW, in anthesis and maturity. Our results evidence both genetic and environmental influence on WSC dynamics in spring wheat. At the same time, they provide a series of markers suitable for supporting assisted selection approaches and functional characterization of genes.
39
Williams, Martin M., Brian J. Schutte e Yim F. So. "Maternal Corn Environment Influences Wild-Proso Millet (Panicum miliaceum) Seed Characteristics". Weed Science 60, n. 1 (marzo 2012): 69–74. http://dx.doi.org/10.1614/ws-d-11-00098.1.
Abstract (sommario):
Modification of the cropping environment to make weed seed more susceptible to fatal germination or decay processes is based, in part, on the premise that seed longevity is affected by the crop-influenced environment in which seed is produced, hereafter, called thematernal crop environment. The objective of this investigation was to determine the influence of maternal crop environment on wild-proso millet seed production, germinability, and seed coat tone (i.e., lightness), a trait previously associated with seed longevity in wild-proso millet. Maternal corn environments were established by growing wild-proso millet plants in four morphologically different sweet corn hybrids in four replicates over 2 yr. Wild-proso millet seed was collected at sweet corn harvest, enumerated, characterized for seed coat tone, and tested for germination. Principal component factor analysis reduced six sweet corn traits measured between silking and harvest into a single maternal corn environment factor that accounted for 84% of the variation among crop canopies. Functional relationships between maternal corn environment factor scores and wild-proso millet seed characteristics were clarified by fitting linear models. For each unit decrease in maternal environment factor score, wild-proso millet seed production increased 1,535 seed m−2, germination increased 2.2%, and seed coat tone was 1.8% lighter. These results show the size and germinability of wild-proso millet seed was highest in less-competitive maternal corn environments characterized by a short time to crop maturity and a small crop-canopy size.
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Posos-Parra, Omar, David Mota-Sanchez, Barry R. Pittendrigh, John C. Wise, Christina D. DiFonzo e Eric Patterson. "Characterization of the inheritance of field-evolved resistance to diamides in the fall armyworm (Spodoptera frugiperda) (Lepidoptera: Noctuidae) population from Puerto Rico". PLOS ONE 19, n. 2 (23 febbraio 2024): e0295928. http://dx.doi.org/10.1371/journal.pone.0295928.
Abstract (sommario):
The fall armyworm (Spodoptera frugiperda) is one of the most destructive pests of corn. New infestations have been reported in the East Hemisphere, reaching India, China, Malaysia, and Australia, causing severe destruction to corn and other crops. In Puerto Rico, practical resistance to different mode of action compounds has been reported in cornfields. In this study, we characterized the inheritance of resistance to chlorantraniliprole and flubendiamide and identified the possible cross-resistance to cyantraniliprole and cyclaniliprole. The Puerto Rican (PR) strain showed high levels of resistance to flubendiamide (RR50 = 2,762-fold) and chlorantraniliprole (RR50 = 96-fold). The inheritance of resistance showed an autosomal inheritance for chlorantraniliprole and an X-linked inheritance for flubendiamide. The trend of the dominance of resistance demonstrated an incompletely recessive trait for H1 (♂ SUS × ♀ PR) × and an incompletely dominant trait for H2 (♀ SUS × ♂ PR) × for flubendiamide and chlorantraniliprole. The PR strain showed no significant presence of detoxification enzymes (using synergists: PBO, DEF, DEM, and VER) to chlorantraniliprole; however, for flubendiamide the SR = 2.7 (DEM), SR = 3.2 (DEF) and SR = 7.6 (VER) indicated the role of esterases, glutathione S- transferases and ABC transporters in the metabolism of flubendiamide. The PR strain showed high and low cross-resistance to cyantraniliprole (74-fold) and cyclaniliprole (11-fold), respectively. Incomplete recessiveness might lead to the survival of heterozygous individuals when the decay of diamide residue occurs in plant tissues. These results highlight the importance of adopting diverse pest management strategies, including insecticide rotating to manage FAW populations in Puerto Rico and other continents.
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Taranto, Francesca, Nunzio D’Agostino, Marcello Catellani, Luca Laviano, Domenico Ronga, Justyna Milc, Barbara Prandi et al. "Characterization of Celiac Disease-Related Epitopes and Gluten Fractions, and Identification of Associated Loci in Durum Wheat". Agronomy 10, n. 9 (20 agosto 2020): 1231. http://dx.doi.org/10.3390/agronomy10091231.
Abstract (sommario):
While durum wheat is a major food source in Mediterranean countries, storage (i.e., gluten) proteins are however responsible for celiac disease (CD), a serious autoimmune disease that occurs in genetically predisposed subjects. Different gluten epitopes—defined as “immunogenic” (IP) and “toxic” (TP) peptides—are involved in the pathology and their content in wheat grain depends on environmental and genetic factors. Detection of IP and TP is not trivial, and no work has been conducted so far to identify the genomic regions associated with their accumulation in wheat. In the present study, a genome-wide association study was performed on a durum wheat collection to identify marker–trait associations (MTAs) between 5730 high quality SNPs and the accumulation of CD-related peptides and gluten protein composition measured in two consecutive cropping seasons (2015/2016 and 2016/2017). High-molecular-weight glutenin subunits (HMW-GS) were more stable between the two years, and differences in total gluten proteins were mainly due to low-molecular-weight glutenin subunits (LMW-GS) and accumulation of gliadins. In the first instance, association tests were conducted on yellow pigment content (YP), a highly inheritable trait with a well-known genetic basis, and several significant MTAs were found corresponding to loci already known for being related to YP. These findings showed that MTAs found for the rest of the measured traits were reliable. In total, 28 significant MTAs were found for gluten composition, while 14 were found to be associated with IP and TP. Noteworthy, neither significant (−log10p > 4.7) nor suggestive (−log10p > 3.3) MTAs for the accumulation of CD-triggering epitopes were found on Gli-A1/Glu-A3 and Gli-B1/Glu-B3 loci, thus suggesting regulatory rather than structural gene effect. A PBF transcription factor on chromosome 5B, known to be involved in the regulation of the expression of CD-related peptides, was identified among the positional candidate genes in the LD-decay range around significant SNPs. Results obtained in the present study provide useful insights and resources for the long-term objective of selecting low-toxic durum wheat varieties while maintaining satisfactory gluten quality.
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Li, Taotao, Meilin Jin, Huihua Wang, Wentao Zhang, Zehu Yuan e Caihong Wei. "Whole-Genome Scanning for Selection Signatures Reveals Candidate Genes Associated with Growth and Tail Length in Sheep". Animals 14, n. 5 (22 febbraio 2024): 687. http://dx.doi.org/10.3390/ani14050687.
Abstract (sommario):
Compared to Chinese indigenous sheep, Western sheep have rapid growth rate, larger physique, and higher meat yield. These excellent Western sheep were introduced into China for crossbreeding to expedite the enhancement of production performance and mutton quality in local breeds. Here, we investigated population genetic structure and genome-wide selection signatures among the Chinese indigenous sheep and the introduced sheep based on whole-genome resequencing data. The PCA, N-J tree and ADMIXTURE results showed significant genetic difference between Chinese indigenous sheep and introduced sheep. The nucleotide diversity (π) and linkage disequilibrium (LD) decay results indicated that the genomic diversity of introduced breeds were lower. Then, Fst & π ratio, XP-EHH, and de-correlated composite of multiple signals (DCMS) methods were used to detect the selection signals. The results showed that we identified important candidate genes related to growth rate and body size in the introduced breeds. Selected genes with stronger selection signatures are associated with growth rate (CRADD), embryonic development (BVES, LIN28B, and WNT11), body size (HMGA2, MSRB3, and PTCH1), muscle development and fat metabolism (MSTN, PDE3A, LGALS12, GGPS1, and SAR1B), wool color (ASIP), and hair development (KRT71, KRT74, and IRF2BP2). Thus, these genes have the potential to serve as candidate genes for enhancing the growth traits of Chinese indigenous sheep. We also identified tail-length trait-related candidate genes (HOXB13, LIN28A, PAX3, and VEGFA) in Chinese long-tailed breeds. Among these genes, HOXB13 is the main candidate gene for sheep tail length phenotype. LIN28A, PAX3, and VEGFA are related to embryonic development and angiogenesis, so these genes may be candidate genes for sheep tail type traits. This study will serve as a foundation for further genetic improvement of Chinese indigenous sheep and as a reference for studies related to growth and development of sheep.
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Zhang, Mingfeng, Soren Lykke-Andersen, Bin Zhu, Wenming Xiao, Jason W. Hoskins, Xijun Zhang, Lauren M. Rost et al. "Characterising cis-regulatory variation in the transcriptome of histologically normal and tumour-derived pancreatic tissues". Gut 67, n. 3 (20 giugno 2017): 521–33. http://dx.doi.org/10.1136/gutjnl-2016-313146.
Abstract (sommario):
ObjectiveTo elucidate the genetic architecture of gene expression in pancreatic tissues.DesignWe performed expression quantitative trait locus (eQTL) analysis in histologically normal pancreatic tissue samples (n=95) using RNA sequencing and the corresponding 1000 genomes imputed germline genotypes. Data from pancreatic tumour-derived tissue samples (n=115) from The Cancer Genome Atlas were included for comparison.ResultsWe identified 38 615 cis-eQTLs (in 484 genes) in histologically normal tissues and 39 713 cis-eQTL (in 237 genes) in tumour-derived tissues (false discovery rate <0.1), with the strongest effects seen near transcriptional start sites. Approximately 23% and 42% of genes with significant cis-eQTLs appeared to be specific for tumour-derived and normal-derived tissues, respectively. Significant enrichment of cis-eQTL variants was noted in non-coding regulatory regions, in particular for pancreatic tissues (1.53-fold to 3.12-fold, p≤0.0001), indicating tissue-specific functional relevance. A common pancreatic cancer risk locus on 9q34.2 (rs687289) was associated with ABO expression in histologically normal (p=5.8×10−8) and tumour-derived (p=8.3×10−5) tissues. The high linkage disequilibrium between this variant and the O blood group generating deletion variant in ABO (exon 6) suggested that nonsense-mediated decay (NMD) of the ‘O’ mRNA might explain this finding. However, knockdown of crucial NMD regulators did not influence decay of the ABO ‘O’ mRNA, indicating that a gene regulatory element influenced by pancreatic cancer risk alleles may underlie the eQTL.ConclusionsWe have identified cis-eQTLs representing potential functional regulatory variants in the pancreas and generated a rich data set for further studies on gene expression and its regulation in pancreatic tissues.
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Shi, Longqing, Meng Dong, Ling Lian, Junian Zhang, Yongsheng Zhu, Weilong Kong, Liangmiao Qiu et al. "Genome-Wide Association Study Reveals a New Quantitative Trait Locus in Rice Related to Resistance to Brown Planthopper Nilaparvata lugens (Stål)". Insects 12, n. 9 (17 settembre 2021): 836. http://dx.doi.org/10.3390/insects12090836.
Abstract (sommario):
The brown planthopper (BPH) is one of the main pests endangering rice yields. The development of rice varieties harboring resistance genes is the most economical and effective method of managing BPH. To identify new BPH resistance-related genes, a total of 123 rice varieties were assessed for resistance and durable resistance. Three varieties were immune, and nine were highly resistant to BPH. After whole-genome resequencing of all 123 varieties, 1,897,845 single nucleotide polymorphisms (SNPs) were identified. Linkage disequilibrium (LD) decay analysis showed that the average LD of the SNPs at 20 kb was 0.30 (r2) and attenuated to half value (~0.30) at a distance of about 233 kb. A genome-wide association study (GWAS) of durable resistance to BPH was conducted using the Fast-MLM model. One quantitative trait locus, identified on chromosome 2, included 13 candidate genes. Two candidate genes contained a leucine-rich repeat and CC-NBS-LRR or NB-ARC domains, which might confer resistance to pests or diseases. Interestingly, LOC_Os02g27540 was highly expressed and was induced by BPH; GWAS identified potential rice genes coding for durable resistance to BPH. This study helps to elucidate the mechanism of durable resistance to BPH in rice and provides essential genetic information for breeding and functional verification of resistant varieties.
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van Hooft, Pim, Wayne M. Getz, Barend J. Greyling, Bas Zwaan e Armanda D. S. Bastos. "A continent-wide high genetic load in African buffalo revealed by clines in the frequency of deleterious alleles, genetic hitchhiking and linkage disequilibrium". PLOS ONE 16, n. 12 (9 dicembre 2021): e0259685. http://dx.doi.org/10.1371/journal.pone.0259685.
Abstract (sommario):
A high genetic load can negatively affect population viability and increase susceptibility to diseases and other environmental stressors. Prior microsatellite studies of two African buffalo (Syncerus caffer) populations in South Africa indicated substantial genome-wide genetic load due to high-frequency occurrence of deleterious alleles. The occurrence of these alleles, which negatively affect male body condition and bovine tuberculosis resistance, throughout most of the buffalo’s range were evaluated in this study. Using available microsatellite data (2–17 microsatellite loci) for 1676 animals from 34 localities (from 25°S to 5°N), we uncovered continent-wide frequency clines of microsatellite alleles associated with the aforementioned male traits. Frequencies decreased over a south-to-north latitude range (average per-locus Pearson r = -0.22). The frequency clines coincided with a multilocus-heterozygosity cline (adjusted R2 = 0.84), showing up to a 16% decrease in southern Africa compared to East Africa. Furthermore, continent-wide linkage disequilibrium (LD) at five linked locus pairs was detected, characterized by a high fraction of positive interlocus associations (0.66, 95% CI: 0.53, 0.77) between male-deleterious-trait-associated alleles. Our findings suggest continent-wide and genome-wide selection of male-deleterious alleles driven by an earlier observed sex-chromosomal meiotic drive system, resulting in frequency clines, reduced heterozygosity due to hitchhiking effects and extensive LD due to male-deleterious alleles co-occurring in haplotypes. The selection pressures involved must be high to prevent destruction of allele-frequency clines and haplotypes by LD decay. Since most buffalo populations are stable, these results indicate that natural mammal populations, depending on their genetic background, can withstand a high genetic load.
46
De Grandis, Davide, Roberto Turolla, Roberto Taverna, Elisa Lucchetta, Toby S. Wood e Silvia Zane. "Three-dimensional Magnetothermal Simulations of Magnetar Outbursts". Astrophysical Journal 936, n. 2 (1 settembre 2022): 99. http://dx.doi.org/10.3847/1538-4357/ac8797.
Abstract (sommario):
Abstract The defining trait of magnetars, the most strongly magnetized neutron stars (NSs), is their transient activity in the X/γ-bands. In particular, many of them undergo phases of enhanced emission, the so-called outbursts, during which the luminosity rises by a factor ∼10–1000 in a few hours to then decay over months/years. Outbursts often exhibit a thermal spectrum, associated with the appearance of hotter regions on the surface of the star, which subsequently change in shape and cool down. Here we simulate the unfolding of a sudden, localized heat injection in the external crust of an NS with a 3D magnetothermal evolution code, finding that this can reproduce the main features of magnetar outbursts. A full 3D treatment allows us to study for the first time the inherently asymmetric hot spots that appear on the surface of the star as the result of the injection and to follow the evolution of their temperature and shape. We investigate the effects produced by different physical conditions in the heated region, highlighting in particular how the geometry of the magnetic field plays a key role in determining the properties of the event.
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Novakazi, Fluturë, Lene Krusell, Jens Jensen, Jihad Orabi, Ahmed Jahoor, Therése Bengtsson e on behalf of the PPP Barley Consortium. "You Had Me at “MAGIC”!: Four Barley MAGIC Populations Reveal Novel Resistance QTL for Powdery Mildew". Genes 11, n. 12 (18 dicembre 2020): 1512. http://dx.doi.org/10.3390/genes11121512.
Abstract (sommario):
Blumeria graminis f. sp. hordei (Bgh), the causal agent of barley powdery mildew (PM), is one of the most important barley leaf diseases and is prevalent in most barley growing regions. Infection decreases grain quality and yields on average by 30%. Multi-parent advanced generation inter-cross (MAGIC) populations combine the advantages of bi-parental and association panels and offer the opportunity to incorporate exotic alleles into adapted material. Here, four barley MAGIC populations consisting of six to eight founders were tested for PM resistance in field trials in Denmark. Principle component and STRUCTURE analysis showed the populations were unstructured and genome-wide linkage disequilibrium (LD) decay varied between 14 and 38 Mbp. Genome-wide association studies (GWAS) identified 11 regions associated with PM resistance located on chromosomes 1H, 2H, 3H, 4H, 5H and 7H, of which three regions are putatively novel resistance quantitative trait locus/loci (QTL). For all regions high-confidence candidate genes were identified that are predicted to be involved in pathogen defense. Haplotype analysis of the significant SNPs revealed new allele combinations not present in the founders and associated with high resistance levels.
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DE GREGORIO, ALBERTO G. "Neutron physics in the early 1930s". Historical Studies in the Physical and Biological Sciences 35, n. 2 (1 marzo 2005): 293–340. http://dx.doi.org/10.1525/hsps.2005.35.2.293.
Abstract (sommario):
ABSTRACT: Dawning neutron physics was more complex than one might expect. The chance that the neutron comprised a proton and an electron was diffusely taken into account after the discovery of the neutron. Moreover, uncertainties persisted about the composition of beryllium radiation until it was realized that the latter comprised both neutrons and γγ-rays. The interaction of neutrons with matter and nuclei was soon investigated. Both a spatial symmetry, a symmetry of charge, and a symmetry in the nuclear reactions soon emerged. The relation of negative ββ-decay to the neutron abundance in nuclei was moreover reviewed. Positive ββ-radioactivity induced by αα-particles was eventually announced, having been foreseen some weeks before. Accelerated deutons and protons shortly afterwards revealed to be efficient in inducing radioactivity. The physics institute in Rome got ready to start research on neutrons, but apparently it only planned to go through αα-induced radioactivity, at first. If so, it is then plausible that some new results achieved by foreign laboratories eventually bent Fermi to neutrons. Fermi's discovery of neutron-induced radioactivity is reviewed with regard to investigations then current, once more showing simplicity as a distinctive trait of Fermi's way of doing physics.
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Giron, Magdalena Y., e Jeffrey J. Morrell. "Fungi colonizing preservative-treated Douglas-fir poles after remedial treatment with fumigants". Canadian Journal of Microbiology 35, n. 2 (1 febbraio 1989): 283–88. http://dx.doi.org/10.1139/m89-042.
Abstract (sommario):
The microfungi present in transmission poles of preservative-treated Douglas-fir remedially treated with one of four fumigants were determined by removing increment cores 5 and 15 years later and culturing them on nutrient media. The microfungi isolated from the wood were then characterized according to their ability to cause a loss in wood weight, to tolerate conventional wood preservatives, and to tolerate wood fumigants. The wood treated with fumigants 5 years earlier was sparsely colonized, while that treated 15 years earlier was colonized more heavily. In general, many of the same species of microfungi occurred in treated and untreated poles. In both, fungal populations were dominated by Scytalidium and Trichoderma spp. None of the isolates caused losses in wood weight greater than 5%, but several exhibited tolerance to short fumigant exposures. The latter trait may help explain the presence of these fungi in wood still containing measurable levels of fumigant. The presence in fumigant-treated wood of fungi previously shown to be antagonistic toward wood decay fungi may help explain the ability of the four test fumigants to provide long-term protection.Key words: fungi, Scytalidium, Trichoderma, colonization, Douglas-fir.
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Olanrewaju, Rasaki Olawale, Sodiq Adejare Olanrewaju e Omodolapo Waliyat Isamot. "Hyper-parametric Generalized Autoregressive Scores (GASs): an application to the price of United States cooking gas". Statistics in Transition new series 24, n. 4 (8 settembre 2023): 93–107. http://dx.doi.org/10.59170/stattrans-2023-053.
Abstract (sommario):
This paper presents the framework of the Generalized Autoregressive Score (GAS) model with a variety of symmetric conditional densities of different time-varying hyperparameters. The distinctive trait and goal of the observation-driven GAS model is to use its score and information functions as the compeller of time-variation via hyper-parameters of conditional densities. 10 robust hyper-parametric conditional densities were used as random error drivers for the GAS model with an application to the price of the United States cooking gas in the period between 2005 and 2020. Out of the 10 robust hyper-parametric conditional noises for the GAS model, the Asymmetric Student–t with one tail decay parameter (AST1) outperformed other categories of its variants and other conditional densities subjected to the GAS model, achieving a minimum reduced-error performance of AIC=11943.277 and BIC=12014.525. The hyper-parametric model obtained a location score and scale score of - 1.2634 and 0.6636, respectively, while its location information and scale information was 0.2691 and 0.0362, respectively. Furthermore, the GAS model via AST1 proved more efficient than the core volatile conditional heteroscedasticity model of the Generalized Autoregressive Conditional Heteroscedasticity (GARCH) at GARCH (1,1) via a Gaussian distributed noise.