scholarly journals Detection of breeding signatures in wheat using a linkage disequilibrium-corrected mapping approach

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Said Dadshani ◽  
Boby Mathew ◽  
Agim Ballvora ◽  
Annaliese S. Mason ◽  
Jens Léon
Keyword(s):  
Linkage Disequilibrium ◽  
Agronomic Traits ◽  
Population Analysis ◽  
Stress Factors ◽  
Frequency Change ◽  
Aegilops Ventricosa ◽  
Genetic Studies ◽  
Outlier Loci ◽  
Genome Assemblies ◽  
Over Time

AbstractMarker assisted breeding, facilitated by reference genome assemblies, can help to produce cultivars adapted to changing environmental conditions. However, anomalous linkage disequilibrium (LD), where single markers show high LD with markers on other chromosomes but low LD with adjacent markers, is a serious impediment for genetic studies. We used a LD-correction approach to overcome these drawbacks, correcting the physical position of markers derived from 15 and 135 K arrays in a diversity panel of bread wheat representing 50 years of breeding history. We detected putative mismapping of 11.7% markers and improved the physical alignment of 5.4% markers. Population analysis indicated reduced genetic diversity over time as a result of breeding efforts. By analysis of outlier loci and allele frequency change over time we traced back the 2NS/2AS translocation of Aegilops ventricosa to one cultivar, “Cardos” (registered in 1998) which was the first among the panel to contain this translocation. A “selective sweep” for this important translocation region on chromosome 2AS was found, putatively linked to plant response to biotic stress factors. Our approach helps in overcoming the drawbacks of incorrectly anchored markers on the wheat reference assembly and facilitates detection of selective sweeps for important agronomic traits.

scholarly journals Clinical and psychosocial stress factors are associated with decline in physical activity over time in children with juvenile idiopathic arthritis

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Liane D. Heale ◽  
Kristin M. Houghton ◽  
Elham Rezaei ◽  
Adam D. G. Baxter-Jones ◽  
Susan M. Tupper ◽  
...  
Keyword(s):  
Physical Activity ◽  
Juvenile Idiopathic Arthritis ◽  
Disease Activity ◽  
Psychosocial Stress ◽  
Juvenile Arthritis ◽  
Stress Factors ◽  
Healthy Children ◽  
Newly Diagnosed ◽  
Z Score ◽  
Over Time

Abstract Background Physical activity (PA) patterns in children with juvenile idiopathic arthritis (JIA) over time are not well described. The aim of this study was to describe associations of physical activity (PA) with disease activity, function, pain, and psychosocial stress in the 2 years following diagnosis in an inception cohort of children with juvenile idiopathic arthritis (JIA). Methods In 82 children with newly diagnosed JIA, PA levels, prospectively determined at enrollment, 12 and 24 months using the Physical Activity Questionnaire for Children (PAQ-C) and Adolescents (PAQ-A) raw scores, were evaluated in relation to disease activity as reflected by arthritis activity (Juvenile Arthritis Disease Activity Score (JADAS-71)), function, pain, and psychosocial stresses using a linear mixed model approach. Results in the JIA cohort were compared to normative Pediatric Bone Mineral Accrual Study data derived from healthy children using z-scores. Results At enrollment, PA z-score levels of study participants were lower than those in the normative population (median z-score − 0.356; p = 0.005). At enrollment, PA raw scores were negatively associated with the psychosocial domain of the Juvenile Arthritis Quality of Life Questionnaire (r = − 0.251; p = 0.023). There was a significant decline in PAQ-C/A raw scores from baseline (median and IQR: 2.6, 1.4–3.1) to 24 months (median and IQR: 2.1, 1.4–2.7; p = 0.003). The linear mixed-effect model showed that PAQ-C/A raw scores in children with JIA decreased as age, disease duration, and ESR increased. The PAQ-C/A raw scores of the participants was also negatively influenced by an increase in disease activity as measured by the JADAS-71 (p <  0.001). Conclusion Canadian children with newly diagnosed JIA have lower PA levels than healthy children. The decline in PA levels over time was associated with disease activity and higher disease-specific psychosocial stress.

scholarly journals Spatiotemporal Changes in Plasmodium vivax msp142 Haplotypes in Southern Mexico: From the Control to the Pre-Elimination Phase

2022 ◽  
Vol 10 (1) ◽  
pp. 186
Author(s):  
Alejandro Flores-Alanis ◽  
Lilia González-Cerón ◽  
Frida Santillán-Valenzuela ◽  
Cecilia Ximenez ◽  
Marco A. Sandoval-Bautista ◽  
...  
Keyword(s):  
Plasmodium Vivax ◽  
Haplotype Diversity ◽  
Haplotype Network ◽  
Southern Mexico ◽  
Single Nucleotide ◽  
Genetic Studies ◽  
Elimination Phase ◽  
Infected Blood ◽  
Malaria Species ◽  
Over Time

For 20 years, Plasmodium vivax has been the only prevalent malaria species in Mexico, and cases have declined significantly and continuously. Spatiotemporal genetic studies can be helpful for understanding parasite dynamics and developing strategies to weaken malaria transmission, thus facilitating the elimination of the parasite. The aim of the current contribution was to analyze P. vivax-infected blood samples from patients in southern Mexico during the control (1993–2007) and pre-elimination phases (2008–2011). Nucleotide and haplotype changes in the pvmsp142 fragment were evaluated over time. The majority of multiple genotype infections occurred in the 1990s, when the 198 single nucleotide sequences exhibited 57 segregating sites, 64 mutations, and 17 haplotypes. Nucleotide and genetic diversity parameters showed subtle fluctuations from across time, in contrast to the reduced haplotype diversity and the increase in the R2 index and Tajima’s D value from 2008 to 2011. The haplotype network consisted of four haplogroups, the geographical distribution of which varied slightly over time. Haplogroup-specific B-cell epitopes were predicted. Since only high-frequency and divergent haplotypes persisted, there was a contraction of the parasite population. Given that 84% of haplotypes were exclusive to Mesoamerica, P. vivax flow is likely circumscribed to this region, representing important information for parasite surveillance.

Stress Reduction in Child-Abusing Families: Global and Specific Measures

1994 ◽  
Vol 75 (1) ◽  
pp. 287-304 ◽  
Author(s):  
Keith Barton ◽  
Christopher Scott Baglio ◽  
Marc T. Braverman
Keyword(s):  
At Risk ◽  
Stress Reduction ◽  
Home Treatment ◽  
Stress Factors ◽  
Home Therapy ◽  
Total Stress ◽  
Therapy Program ◽  
The Individual ◽  
Over Time ◽  
County Services

This study compared in-home treatment to traditional county services for their ability to reduce stress in child-abusing families. 47 families who were at risk for having at least one child removed from the home for child abuse were referred to Families First for an intensive 6-wk., in-home therapy program. A comparison group of 29 families who were also at risk for having at least one child removed for abuse received traditional county services but no in-home therapy. Stress scores used were derived from a factor analysis of the Family Inventory of Life Events and Changes (FILE) that had identified 10 stress factors. The stress data were analyzed by a series of 2 × 2 analyses of variance, group and time being the independent variables and the stress factors the dependent variables. Total stress was significantly reduced over time for both groups, and several specific stress factors were also significantly reduced over time. In secondary analyses, 2 × 3 (group by time) analyses identified interactions for total stress and three of the individual stress factors. In-home treatment was effective in reducing stress, but traditional services were also effective. Some possible explanations were discussed. A major finding was that, by including analyses using the specific stress factors (rather than just the Total Stress score), a much richer understanding of the role stress plays in abusive families is provided. It was concluded that, although global stress may be reduced by different methods, some specific types of stress are more likely to be reduced than others.

scholarly journals Physiological and Molecular Characterization of Crop Resistance to Abiotic Stresses

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1308
Author(s):  
Monica Boscaiu ◽  
Ana Fita
Keyword(s):  
Abiotic Stress ◽  
Stress Tolerance ◽  
Crop Yields ◽  
Agronomic Traits ◽  
Abiotic Stress Tolerance ◽  
Genetic Material ◽  
Morphological Characteristics ◽  
Stress Factors ◽  
Special Issue ◽  
Heat And Cold Stress

Abiotic stress represents a main constraint for agriculture, affecting plant growth and productivity. Drought and soil salinity, especially, are major causes of reduction of crop yields and food production worldwide. It is not unexpected, therefore, that the study of plant responses to abiotic stress and stress tolerance mechanisms is one of the most active research fields in plant biology. This Special Issue compiles 22 research papers and 4 reviews covering different aspects of these responses and mechanisms, addressing environmental stress factors such as drought, salinity, flooding, heat and cold stress, deficiency or toxicity of compounds in the soil (e.g., macro and micronutrients), and combination of different stresses. The approaches used are also diverse, including, among others, the analysis of agronomic traits based on morphological characteristics, physiological and biochemical studies, and transcriptomics or transgenics. Despite its complexity, we believe that this Special Issue provides a useful overview of the topic, including basic information on the mechanisms of abiotic stress tolerance as well as practical aspects such as the alleviation of the deleterious effects of stress by different means, or the use of local landraces as a source of genetic material adapted to combined stresses. This knowledge should help to develop the agriculture of the (near) future, sustainable and better adapted to the conditions ahead, in a scenario of global warming and environmental pollution.

The Study of Arc Teethed Automotive Synchronous Belt's Transmission Stability

2014 ◽  
Vol 915-916 ◽  
pp. 277-280
Author(s):  
Yao Chen Shi ◽  
Zhan Guo Li ◽  
Xiu Guang Yang
Keyword(s):  
Mathematical Model ◽  
Rotation Speed ◽  
Longitudinal Vibration ◽  
Dynamic Measurement ◽  
Frequency Change ◽  
Measurement Device ◽  
Transmission Process ◽  
Belt Transmission ◽  
The Mathematical Model ◽  
Over Time

The vibration of belt affected the transmission stability of automotive synchronous belt. The mathematical model of longitudinal vibration was established through analyzing the longitudinal vibration of automotive synchronous belt. Developed the vibration dynamic measurement device, aiming at RU style arc teethed synchronous belt transmission process, measured the variety of amplitude over time at the middle of the belt span obtained the rules of amplitude and frequency change along with the rotation speed. It is of certain importance to improving the transmission stability of arc teethed synchronous belt.

scholarly journals DYNAMICS OF THE LINKAGE DISEQUILIBRIUM FUNCTION UNDER MODELS OF GENE-FREQUENCY HITCHHIKING

Genetics ◽  
1981 ◽  
Vol 99 (2) ◽  
pp. 337-356
Author(s):  
Marjorie A Asmussen ◽  
Michael T Clegg
Keyword(s):  
Linkage Disequilibrium ◽  
Gene Frequency ◽  
Initial Conditions ◽  
Recombination Fraction ◽  
Qualitative Description ◽  
Selection Intensity ◽  
Gene Frequencies ◽  
Dependent Behavior ◽  
Wide Range ◽  
Over Time

ABSTRACT The dynamic behavior of the linkage disequilibrium (D) between a neutral and a selected locus is analyzed for a variety of deterministic selection models. The time-dependent behavior of D is governed by the gene frequency at the selected locus (p) and by the selection (s) and recombination (r) parameters. Thomson (1977) showed numerically that D may increase under certain initial conditions. We give exact conditions for D to increase in time, which require that the selection intensity exceed the recombination fraction (s &gt; r) and that p be near zero or one. We conclude from this result that gene frequency hitchhiking is most likely to be important when a new favorable mutant enters a population. We also show that, for what can be a wide range of gene frequencies, D will decay at a faster rate than the neutral rate. Consequently, the hitchhiking effect may quickly diminish as the selected gene becomes more common.—The method of analysis allows a complete qualitative description of the dynamics of D as a function of s and r. Two major findings concern the range of gene frequencies at the selected locus for which D either increases over time or decays at a faster rate than under neutrality. For all models considered, the region where D increases (i) first enlarges then shrinks as selection intensifies, and (ii) steadily shrinks as r increases. In contrast, the region of accelerated decay constantly enlarges as the selection intensity increases. This region will either shrink or enlarge as r increases, depending upon the form of selection in force.

scholarly journals An automated, high-throughput image analysis pipeline enables genetic studies of shoot and root morphology in carrot (Daucus carota L.)

2018 ◽  
Author(s):  
Sarah D. Turner ◽  
Shelby L. Ellison ◽  
Douglas A. Senalik ◽  
Philipp W. Simon ◽  
Edgar P. Spalding ◽  
...  
Keyword(s):  
Image Analysis ◽  
High Throughput ◽  
Root Morphology ◽  
Agronomic Traits ◽  
Automated Analysis ◽  
Root Characteristics ◽  
Analysis Pipeline ◽  
Genetic Studies ◽  
Daucus Carota L ◽  
Size And Shape

AbstractCarrot is a globally important crop, yet efficient and accurate methods for quantifying its most important agronomic traits are lacking. To address this problem, we developed an automated analysis platform that extracts components of size and shape for carrot shoots and roots, which are necessary to advance carrot breeding and genetics. This method reliably measured variation in shoot size and shape, leaf number, petiole length, and petiole width as evidenced by high correlations with hundreds of manual measurements. Similarly, root length and biomass were accurately measured from the images. This platform quantified shoot and root shapes in terms of principal components, which do not have traditional, manually-measurable equivalents. We applied the pipeline in a study of a six-parent diallel population and an F2 mapping population consisting of 316 individuals. We found high levels of repeatability within a growing environment, with low to moderate repeatability across environments. We also observed co-localization of quantitative trait loci for shoot and root characteristics on chromosomes 1, 2, and 7, suggesting these traits are controlled by genetic linkage and/or pleiotropy. By increasing the number of individuals and phenotypes that can be reliably quantified, the development of a high-throughput image analysis pipeline to measure carrot shoot and root morphology will expand the scope and scale of breeding and genetic studies.

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