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Horticulturae ◽  
2022 ◽  
Vol 8 (1) ◽  
pp. 66
Author(s):  
Hui Zhang ◽  
Xiaochao Ma ◽  
Xitong Liu ◽  
Shifan Zhang ◽  
Fei Li ◽  
...  

European fodder turnips (Brassica rapa ssp. rapifera) were identified as sources of clubroot resistance (CR) and have been widely used in Brassica resistance breeding. An F2 population derived from a cross between a resistant turnip and a susceptible Chinese cabbage was used to determine the inheritance and locating the resistance Quantitative Trait Loci (QTLs). The parents showed to be very resistant/susceptible to the field isolates (pathotype 4) of clubroot from Henan in China. After inoculation, 27 very resistant or susceptible individuals were selected to construct bulks, respectively. Next-generation-sequencing-based Bulk Segregant Analysis Sequencing (BSA-Seq) was used and located resistance QTL on chromosome A03 (3.3–7.5 Mb) and A08 (0.01–6.5 Mb), named Bcr1 and Bcr2, respectively. Furthermore, an F3 population including 180 families derived from F2 individuals was phenotyped and used to verify and narrow candidate regions. Ten and seven Kompetitive Allele-Specific PCR (KASP) markers narrowed the target regions to 4.3–4.78 Mb (A03) and 0.02–0.79 Mb (A08), respectively. The phenotypic variation explained (PVE) of the two QTLs were 33.3% and 13.3% respectively. The two candidate regions contained 99 and 109 genes. In the A03 candidate region, there were three candidate R genes, namely Bra006630, Bra006631 and Bra006632. In the A08 candidate region, there were two candidate R genes, namely Bra030815 and Bra030846.


2022 ◽  
Author(s):  
Mariah McIntosh ◽  
Jorge Gonzalez-Campos ◽  
Patrick Demaree ◽  
Omayra Toro-Salamanca ◽  
Roberto Ipinza ◽  
...  

As global commitments to restoration are underway, science is needed to support capacity to achieve meaningful gains for ecosystems and human communities. In Chile, identification and generation of appropriate plant material is a barrier to achieving major restoration goals under the Paris Climate Agreement. Understanding genetic differentiation among plant populations is needed to maximize restoration success. For Araucaria araucana, a highly threatened iconic South American tree, this information is greatly needed to guide restoration and conservation efforts because this species occurs across a strong climate gradient. We grew seedlings from 12 populations of A. araucana across its range in Chile in a common garden to assess regional (coastal versus Andes mountain ranges) and population variation in key plant traits and relate this variation to environmental variables. We demonstrate that A. araucana is differentiated within regions and populations across its range in Chile by a suite of traits, particularly branch number and length (showing plant architectural differences) and needle width (showing leaf investment differences). We show that this variation is at least partly explained by climate and soil variables, with the most variation explained by differences between regions in temperature annual range. Thus, we recommend that restoration efforts focus on conserving genetic variation among and within regions and their populations and preventing the translocations of genotypes between coastal and Andes populations.


2021 ◽  
Vol 21 (4) ◽  
pp. 293-298
Author(s):  
Sapna Mandoli ◽  
Deepak Sharma ◽  
Hem Chandra Joshi

Research Purpose. The study aimed to develop a discriminant model for cricketers on the basis of physiological & anthropometric variables. Material and Methods. The study included sixty female seniors BCCI board players representing five different states with mean age 23.4 ± 2.03, mean height 152.1 ± 3.44, and mean weight 52.4 ± 4.21. A multivariate technique was used to predict the cricket performance by classifying the players into batsmen and pace bowlers on the basis of selected physiological & anthropometrical variables. Results. All the assumptions were positively full-filled (Shapiro-Wilk test p > 0.05 and F = 8.121, p = 0.264 for Box’sM test) for applying discriminant analysis to develop the model. A total of eleven performance variables were initially selected for the study and after applying the stepwise statistical technique of discriminant analysis, the model selected certain variables, namely Muscle Mass (1.311), Fat (-0.182) & Shoulder Diameter (0.292) and showed its effectiveness as the Eigenvalue for the fit model was 0.848. Conclusion. A discriminant function F1 = -29.531 + (1.311 × Muscle Mass) + (-0.182 × Fat) + (0.292 × Shoulder Diameter) was developed. The percentage of total variation explained by the model was 71.9%. A total of 93.2% of the observations were correctly classified using the proposed discriminant model.


2021 ◽  
Author(s):  
Naíla Barbosa da Costa ◽  
Marie-Pier Hébert ◽  
Vincent Fugère ◽  
Yves Terrat ◽  
Gregor Fussmann ◽  
...  

Agrochemicals often contaminate freshwater bodies, affecting microbial communities that underlie aquatic food webs. For example, Roundup, a widely-used glyphosate-based herbicide (GBH), has the potential to indirectly select for antibiotic resistant bacteria. Such cross-selection could occur, for example, if the same genes (e.g. encoding efflux pumps) confer resistance to both glyphosate and antibiotics. To test for cross-resistance in natural aquatic bacterial communities, we added Roundup to 1,000-L mesocosms filled with water from a pristine lake. Over 57 days, we tracked changes in bacterial communities with shotgun metagenomic sequencing, and annotated metagenome-assembled genomes (MAGs) for the presence of known antibiotic resistance genes (ARGs), plasmids, and resistance mutations in the enzyme targeted by glyphosate (enolpyruvyl-shikimate-3-phosphate synthase; EPSPS). We found that high doses of GBH significantly increased ARG frequency and selected for multidrug efflux pumps in particular. The relative abundance of MAGs after a high dose of GBH was predictable based on the number of ARGs encoded in their genomes (17% of variation explained) and, to a lesser extent, by resistance mutations in EPSPS (2% of variation explained). Together, these results indicate that GBHs have the potential to cross-select for antibiotic resistance in natural freshwater bacteria.


Agronomy ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 2519
Author(s):  
Shuhao Yu ◽  
Silvano Assanga ◽  
Joseph Awika ◽  
Amir Ibrahim ◽  
Jackie Rudd ◽  
...  

To meet the demands of different wheat-based food products, traits related to end-use quality become indispensable components in wheat improvement. Thus, markers associated with these traits are valuable for the timely evaluation of protein content, kernel physical characteristics, and rheological properties. Hereunder, we report the mapping results of quantitative trait loci (QTLs) linked to end-use quality traits. We used a dense genetic map with 5199 SNPs from a 90K array based on a recombinant inbred line (RIL) population derived from ‘CO960293-2′/’TAM 111′. The population was evaluated for flour protein concentration, kernel characteristics, dough rheological properties, and grain mineral concentrations. An inclusive composite interval mapping model for individual and across-environment QTL analyses revealed 22 consistent QTLs identified in two or more environments. Chromosomes 1A, 1B, and 1D had clustered QTLs associated with rheological parameters. Glu-D1 loci from CO960293-2 and either low-molecular-weight glutenin subunits or gliadin loci on 1A, 1B, and 1D influenced dough mixing properties substantially, with up to 34.2% of the total phenotypic variation explained (PVE). A total of five QTLs associated with grain Cd, Co, and Mo concentrations were identified on 3B, 5A, and 7B, explaining up to 11.6% of PVE. The results provide important genetic resources towards understanding the genetic bases of end-use quality traits. Information about the novel and consistent QTLs provided solid foundations for further characterization and marker designing to assist selections for end-use quality improvements.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Meghan J. Chenoweth ◽  
Lisa Sanderson Cox ◽  
Nikki L. Nollen ◽  
Jasjit S. Ahluwalia ◽  
Neal L. Benowitz ◽  
...  

AbstractNicotine is inactivated by the polymorphic CYP2A6 enzyme to cotinine and then to 3′hydroxycotinine. The Nicotine Metabolite Ratio (NMR; 3′hydroxycotinine/cotinine) is a heritable nicotine metabolism biomarker, varies with sex and ancestry, and influences smoking cessation and disease risk. We conducted sex-stratified genome-wide association studies of the NMR in European American (EA) and African American (AA) smokers (NCT01314001, NCT00666978). In EA females (n = 389) and males (n = 541), one significant (P < 5e−8) chromosome 19 locus was found (top variant: rs56113850, CYP2A6 (intronic), for C vs. T: females: beta = 0.67, P = 7.5e−22, 21.8% variation explained; males: beta = 0.75, P = 1.2e−37, 26.1% variation explained). In AA females (n = 503) and males (n = 352), the top variant was found on chromosome 19 but differed by sex (females: rs11878604, CYP2A6 (~ 16 kb 3′), for C vs. T: beta = − 0.71, P = 6.6e−26, 16.2% variation explained; males: rs3865454, CYP2A6 (~ 7 kb 3′), for G vs. T: beta = 0.64, P = 1.9e−19, 18.9% variation explained). In AA females, a significant region was found on chromosome 12 (top variant: rs12425845: P = 5.0e−9, TMEM132C (~ 1 Mb 5′), 6.1% variation explained) which was not significant in AA males. In AA males, significant regions were found on chromosomes 6 (top variant: rs9379805: P = 4.8e−9, SLC17A2 (~ 8 kb 5′), 8.0% variation explained) and 16 (top variant: rs77368288: P = 3.5e−8, ZNF469 (~ 92 kb 5′), 7.1% variation explained) which were not significant in AA females. Further investigation of these associations outside of chromosome 19 is required, as they did not replicate. Understanding how sex and ancestry influence nicotine metabolism genetics may improve personalized approaches for smoking cessation and risk prediction for tobacco-related diseases.


2021 ◽  
Author(s):  
Attila Lengyel ◽  
Sándor Barabás ◽  
Boglárka Berki ◽  
Anikó Csecserits ◽  
Adrienn Gyalus ◽  
...  

AbstractA straightforward way to explore variation between communities is to calculate dissimilarity indices and relate them with environmental and spatial variables. Communities are most often represented by the (relative) abundances of taxa they comprise; however, more recently, the distribution of traits of organisms included in the communities has been shown more strongly related to ecosystem properties. In this study, we test whether taxon- or trait-based dissimilarity is correlated more tightly with environmental difference and geographical distance and how the abundance scale influences this correlation. Our study system is grassland vegetation in Hungary, where we sampled vegetation plots spanning a long productivity gradient from open dry grasslands to marshes in three sites. We considered three traits for vascular plants: canopy height, specific leaf area and seed mass. We obtained field estimates of normalized vegetation difference index (NDVI) as proxy of productivity (water availability) for each plot. We calculated between-community dissimilarities using a taxon-based and a trait-based index, using raw and square-root transformed abundances and presence/absence data. We fitted distance-based redundancy analysis models with NDVI difference and geographical distance on the dissimilarity matrices and evaluated them using variance partitioning. Then, using the pooled data, we calculated non-metric multidimensional scaling ordinations (NMDS) from all types of dissimilarity matrices and made pairwise comparisons using Procrustes analysis. Data analysis was done separately for the three sites.We found that taxonomical dissimilarity matches environmental and spatial variables better when presence/absence data is used instead of abundance. This pattern was mainly determined by the increasing variation explained by space at the presence/absence scale. In contrast to this trend, with trait-based dissimilarity, accounting for abundance increased explained variation significantly due to the higher explanatory power of NDVI. With abundance data, considering traits improved environmental matching to a great extent in comparison with taxonomical information. However, with presence/absence data, traits brought no advantage over taxon-based dissimilarity in any respect. Changing the abundance scale caused larger difference between ordinations in the case of trait-based dissimilarity than with taxonomical dissimilarity.We conclude that considering relevant traits improves environmental matching only if abundances are also accounted for.Supporting informationAdditional graphs supporting the results are presented as appendix.Open researchData used in this research are publicly available from Dryad ###link to be supplied upon acceptance###


2021 ◽  
Author(s):  
Mary-Francis LaPorte ◽  
Mishi Vachev ◽  
Matthew Fenn ◽  
Christine Diepenbrock

ABSTRACTMaize enriched in provitamin A carotenoids could be key in combatting vitamin A deficiency in human populations relying on maize as a food staple. Consumer studies indicate that orange maize may be regarded as novel and preferred. This study identifies genes of relevance for grain carotenoid concentrations and kernel color, through simultaneous dissection of these traits in 10 families of the U.S. maize nested association mapping population that have yellow to orange grain. Quantitative trait loci (QTL) were identified via joint-linkage analysis, with phenotypic variation explained for individual kernel color QTL ranging from 2.4 to 17.5%. These QTL were cross-analyzed with significant marker-trait associations in a genome-wide association study that utilized ∼27 million variants. Nine genes were identified: four encoding activities upstream of the core carotenoid pathway, one at the pathway branchpoint, three within the α- or β-pathway branches, and one encoding a carotenoid cleavage dioxygenase. Of these, three exhibited significant pleiotropy between kernel color and one or more carotenoid traits. Kernel color exhibited moderate positive correlations with β-branch and total carotenoids and negligible correlations with α-branch carotenoids. These findings can be leveraged to simultaneously achieve desirable kernel color phenotypes and increase concentrations of provitamin A and other priority carotenoids.


PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0251141
Author(s):  
Thibaud Quibel ◽  
Patrick Rozenberg ◽  
Camille Bouyer ◽  
Jean Bouyer

Introduction WHO has recommended using Robson’s Ten Group Classification System (TGCS) to monitor and analyze CD rates. Its failure to take some maternal and organizational factors into account, however, could limit the interpretation of CD rate comparisons, because it may contribute to variations in hospital CD rates. Objective To study the contribution of maternal socioeconomic and clinical characteristics and hospital organizational factors to the variation in CD rates when using Robson’s ten-group classification system for CD rate comparisons. Methods This prospective, observational, population-based study included all deliveries at a gestational age > 24 weeks at the 10 hospitals of the French MYPA perinatal network in the Paris area. CD rates were calculated for each TGCS group in each hospital. Interhospital variations in these rates were investigated with hierarchical logistic regression models to quantify the variation explained by differences in patient and hospital characteristics when the TGCS is considered. Variations in CD rates between hospitals were estimated with median odds ratios (MOR) to express interhospital variance on the standard odds ratio scale. The percentage of variation explained by TGCS and maternal and hospital characteristics was also calculated. Results The global CD rate was 24.0% (interhospital range: 17–32%). CD rates within each TGCS group differed significantly between hospitals (P<0.001). CD was significantly associated with maternal age (>40 years), severe preeclampsia, and two organizational factors: hospital status (private maternities) and the deliveries per staff member per 24 hours. The MOR in the empty model was 1.27 and did not change after taking the TGCS into account. Adding maternal characteristics and hospital organizational factors lowered the MOR to 1.14 and reduced the variation between hospital CD rates by 70%. Conclusion Maternal characteristics and hospital factors are needed to address variation in CD rates among the TGCS groups. Therefore, comparisons of these rates that do not consider these factors should be interpreted carefully.


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