scholarly journals Evidence for the Accumulation of Nonsynonymous Mutations and Favorable Pleiotropic Alleles During Wheat Breeding

2020 ◽  
Vol 10 (11) ◽  
pp. 4001-4011
Author(s):  
Elie Raherison ◽  
Mohammad Mahdi Majidi ◽  
Roos Goessen ◽  
Nia Hughes ◽  
Richard Cuthbert ◽  
...  
Keyword(s):  
Green Revolution ◽  
Purifying Selection ◽  
Wheat Breeding ◽  
Nucleotide Polymorphisms ◽  
Negative Effects ◽  
Careful Evaluation ◽  
Modern Cultivar ◽  
Large Numbers ◽  
Conserved Genes ◽  
Segregating Population

Plant breeding leads to the genetic improvement of target traits by selecting a small number of genotypes from among typically large numbers of candidate genotypes after careful evaluation. In this study, we first investigated how mutations at conserved nucleotide sites normally viewed as deleterious, such as nonsynonymous sites, accumulated in a wheat, Triticum aestivum, breeding lineage. By comparing a 150 year old ancestral and modern cultivar, we found recent nucleotide polymorphisms altered amino acids and occurred within conserved genes at frequencies expected in the absence of purifying selection. Mutations that are deleterious in other contexts likely had very small or no effects on target traits within the breeding lineage. Second, we investigated if breeders selected alleles with favorable effects on some traits and unfavorable effects on others and used different alleles to compensate for the latter. An analysis of a segregating population derived from the ancestral and modern parents provided one example of this phenomenon. The recent cultivar contains the Rht-B1b green revolution semi-dwarfing allele and compensatory alleles that reduce its negative effects. However, improvements in traits other than plant height were due to pleiotropic loci with favorable effects on traits and to favorable loci with no detectable pleiotropic effects. Wheat breeding appears to tolerate mutations at conserved nucleotide sites and to only select for alleles with both favorable and unfavorable effects on traits in exceptional situations.

scholarly journals Politics is making us sick: The negative impact of political engagement on public health during the Trump administration

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0262022
Author(s):  
Kevin B. Smith
Keyword(s):  
Presidential Election ◽  
Negative Impact ◽  
Political Engagement ◽  
The Political ◽  
Negative Effects ◽  
Large Numbers ◽  
Political Left ◽  
Nationally Representative ◽  
Significant Health ◽  
Trump Administration

Objectives To quantify the effect of politics on the physical, psychological, and social health of American adults during the four-year span of the Trump administration. Methods A previously validated politics and health scale was used to compare health markers in nationally representative surveys administered to separate samples in March 2017 (N = 800) and October 2020 (N = 700). Participants in the 2020 survey were re-sampled approximately two weeks after the 2020 election and health markers were compared to their pre-election baselines. Results Large numbers of Americans reported politics takes a significant toll on a range of health markers—everything from stress, loss of sleep, or suicidal thoughts to an inability to stop thinking about politics and making intemperate social media posts. The proportion of Americans reporting these effects stayed stable or slightly increased between the spring of 2017 and the fall of 2020 prior to the presidential election. Deterioration in measures of physical health became detectably worse in the wake of the 2020 election. Those who were young, politically interested, politically engaged, or on the political left were more likely to report negative effects. Conclusions Politics is a pervasive and largely unavoidable source of chronic stress that exacted significant health costs for large numbers of American adults between 2017 and 2020. The 2020 election did little to alleviate those effects and quite likely exacerbated them.

scholarly journals Challenges of digitalization and artificial intelligence for modern economies, societies and management

2020 ◽  
Vol 28 (3) ◽  
pp. 556-567
Author(s):  
Rolf Clauberg
Keyword(s):  
Artificial Intelligence ◽  
New Technologies ◽  
Technical Information ◽  
Developed Countries ◽  
Negative Effects ◽  
Physical Systems ◽  
Large Numbers ◽  
Official Policy ◽  
The Usa ◽  
New Jobs

This study aims at identifying the challenges of digitalization and artificial intelligence for modern economies, societies and business administration. The implementation of digitalization schemes as Industry 4.0 are presently official policy of many developed countries. The goal is optimization of production processes and supply chains. Artificial intelligence is also affecting many fields. Both technologies are expected to substantially change working conditions for many people. It is important to identify the kind and impact of these changes and possible means to minimize negative effects. For this purpose, this study uses previous results about the disappearance of manufacturing jobs in the USA and their impact on different groups of society together with technical information about the new technologies to deduce expected changes caused by digitalization and artificial intelligence. Results are that both technologies will destroy large numbers of jobs and complete job classes while at the same time creating new jobs very different from the ones destroyed. Extensive permanent education and re-education of employees will be necessary to minimize negative effects, probably even changes to a more broad-based education to improve the potential of job changes into completely new fields. In addition, the technical information about digitalization in cyber-physical systems points to dangers that will require solutions on the international level.

scholarly journals Conserved noncoding elements influence the transposable element landscape in Drosophila

2018 ◽  
Author(s):  
Manee M. Manee ◽  
John Jackson ◽  
Casey M. Bergman
Keyword(s):  
Transposable Element ◽  
Significant Proportion ◽  
Purifying Selection ◽  
Noncoding Dna ◽  
Frequency Spectra ◽  
Noncoding Regions ◽  
Selective Constraints ◽  
Large Numbers ◽  
Random Expectation ◽  
Conserved Noncoding Elements

AbstractHighly conserved noncoding elements (CNEs) comprise a significant proportion of the genomes of multicellular eukaryotes. The function of most CNEs remains elusive, but growing evidence indicates they are under some form of purifying selection. Noncoding regions in many species also harbor large numbers of transposable element (TE) insertions, which are typically lineage specific and depleted in exons because of their deleterious effects on gene function or expression. However, it is currently unknown whether the landscape of TE insertions in noncoding regions is random or influenced by purifying selection on CNEs. Here we combine comparative and population genomic data in Drosophila melanogaster to show that abundance of TE insertions in intronic and intergenic CNEs is reduced relative to random expectation, supporting the idea that selective constraints on CNEs eliminate a proportion of TE insertions in noncoding regions. However, we find no difference in the allele frequency spectra for polymorphic TE insertions in CNEs versus those in unconstrained spacer regions, suggesting that the distribution of fitness effects acting on observable TE insertions is similar across different functional compartments in noncoding DNA. Our results provide evidence that selective constraints on CNEs contribute to shaping the landscape of TE insertion in eukaryotic genomes, and provide further evidence supporting the conclusion that CNEs are indeed functionally constrained and not simply mutational cold spots.

Science and the Green Revolution 1945-1975

1998 ◽  
Author(s):  
John H. Perkins
Keyword(s):  
World War Ii ◽  
Soil Fertility ◽  
Plant Breeding ◽  
Fungal Pathogens ◽  
Plant Disease ◽  
Green Revolution ◽  
Wheat Breeding ◽  
Wheat Varieties ◽  
Number Of Factors ◽  
Major Factors

In the years after the end of World War II, farmers, agricultural scientists, and policy makers in many countries all knew, or learned, that higher yields of wheat were what they wanted, and they were successful in achieving them. Their specific motivations were different, but their objectives were not. Not only were the objectives clear, but a central method by which the higher yields were to be achieved was plant breeding. Plant breeding itself was an applied science that had to be nested within organizations that supported it and its allies in the agricultural, biological, and engineering sciences. By 1950 wheat breeders believed that the number of factors governing yield was small, which meant that the research avenues likely to be fruitful were also few in number. The amount of water available and the responsiveness to soil fertility, especially nitrogen, were in most cases the key ingredients for higher yields. For wheat, the ability of the plant to resist invasion by fungal pathogens was almost as important as water and soil fertility. Water and fertility were needed in every crop year, but damage from fungal pathogens varied with weather. Thus plant disease was not necessarily a destructive factor every year. Control of water, soil fertility, and plant disease was therefore at the center of research programs in wheat breeding. A wheat breeder would find success if his or her program produced new varieties that gave higher yields within the context of water, soil fertility, and plant disease existing in the area. Ancillary questions also existed and in some cases matched the major factors in importance. Weed control was always a problem, so high-yielding wheat had to have some capacity to resist competition from weeds. Similarly, in some areas and some years, insects could cause damage. Wheat varieties therefore had to be able to withstand them somehow. Other factors of importance to wheat breeders were habit of growth and the color and quality of the grain. Winter wheats were useful in climates that had winters mild enough to allow planting in the fall and thus higher yields the next summer.

scholarly journals Durum Wheat Breeding in the Mediterranean Region: Current Status and Future Prospects

Agronomy ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 432 ◽  
Author(s):  
Ioannis N. Xynias ◽  
Ioannis Mylonas ◽  
Evangelos G. Korpetis ◽  
Elissavet Ninou ◽  
Aphrodite Tsaballa ◽  
...  
Keyword(s):  
Durum Wheat ◽  
Mediterranean Region ◽  
Seed Quality ◽  
Green Revolution ◽  
Historical Review ◽  
Wheat Breeding ◽  
Molecular Techniques ◽  
Current Status ◽  
Before And After ◽  
The Mediterranean

This brief historical review focuses on durum wheat domestication and breeding in the Mediterranean region. Important milestones in durum wheat breeding programs across the countries of the Mediterranean basin before and after the Green Revolution are discussed. Additionally, the main achievements of the classical breeding methodology are presented using a comparison of old and new cultivars. Furthermore, current breeding goals and challenges are analyzed. An overview of classical breeding methods in combination with current molecular techniques and tools for cultivar development is presented. Important issues of seed quality are outlined, focusing on protein and characteristics that affect human health and are connected with the consumption of wheat end-products.

scholarly journals Multiplex, fluorescent, solid-phase minisequencing for efficient screening of DNA sequence variation

1996 ◽  
Vol 42 (9) ◽  
pp. 1391-1397 ◽  
Author(s):  
T Pastinen ◽  
J Partanen ◽  
A C Syvänen
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Solid Phase ◽  
Point Mutations ◽  
Nucleotide Polymorphisms ◽  
Dna Templates ◽  
Single Nucleotide ◽  
Large Numbers ◽  
Dna Sequence Variation ◽  
Hla Dqa1 ◽  
Efficient Screening

Abstract We developed a multiplex, solid-phase minisequencing method to detect multiple single-nucleotide polymorphisms in an undivided sample. The amplified DNA templates are first captured on a manifold. Then, with multiple minisequencing primers of various sizes, single-nucleotide extension reactions are carried out simultaneously with fluorescently labeled dideoxynucleotides. The size of the extended product, determined by using a DNA sequencing instrument, defines the site of the polymorphisms, and the incorporated nucleotide gives the identity of the nucleotide at each site. HLA-DQA1 typing was used as a model system to evaluate the method. The DR2 subgroup of the HLA-DRB1 gene was typed along with the DQA1 gene to demonstrate the feasibility of the method in analyzing multiple genes at multiple sites simultaneously. The method is generally applicable for screening any single-nucleotide polymorphisms or point mutations, and its manifold format allows practical handling of large numbers of samples.

Competition in Plant Communities

Ecology ◽  
2012 ◽  
Author(s):  
Paul A. Keddy ◽  
James Cahill
Keyword(s):  
Experimental Design ◽  
Plant Communities ◽  
Managed Forests ◽  
Negative Effects ◽  
Large Numbers ◽  
Multiple Species ◽  
Choice Of Species ◽  
Intensity Of Competition ◽  
Plant Coexistence ◽  
Growth And Reproduction

Competition is generally understood to refer to the negative effects on plant growth or fitness caused by the presence of neighbors, usually by reducing the availability of resources. Competition can be an important factor controlling plant communities, along with resources, disturbance, herbivory, and mutualisms. Since all plants require a few basic elements, the resource involved is generally light, water, nitrogen, or phosphorus, depending upon the species and the location. The effects of competition are widespread and easily observed in mixtures of crops and managed forests, which is why weeding and thinning are practiced. Competition is also widespread in native habitats, from deserts to wetlands, and is known to have important—indeed crucial—effects upon recruitment, growth, and reproduction. In the late 1800s, Darwin wrote extensively about the importance of competition in nature, particularly its role in driving natural selection. Thereafter, interest in the phenomenon grew. Many experiments with both crops and wild species were conducted. Models of competitive interactions were also constructed, with the number and size of the models increasing rapidly with the advent of computers in the 1970s. Because the word competition has a common usage in English, what it represents in biological systems is frequently assumed, rather than explicitly stated, leading to misunderstanding. Care must be taken in using or interpreting the word without specifying what kind of competition is being investigated, as different forms of competition can have different types of consequences. For example, competition may be looked at from the perspective of an individual, a population, or a species, it may be symmetric or asymmetric, and it can occur among single or multiple species simultaneously. Experimental design carries its own assumptions, which are often not stated in published articles. One of the most difficult tasks in exploring published studies is the need to sift through large numbers of experiments in which investigators have haphazardly selected (a pair of) species and grown them in mixture, without adequately justifying their choice of species or the experimental design. Another difficult task is distinguishing between models that, at least in principle, have measurable inputs or make measurable predictions (or both) and those that do not and cannot be tested. Overall, the very ease of growing plants in mixture, as well as the ease of making new models, may have made some people careless, with the result that basic questions are remaining unaddressed. Ongoing issues of importance include mechanisms of competition, types of competition, effects of competition on plant coexistence, and the intensity of competition under different sets of conditions.

scholarly journals Effect of gibberellin-sensitive Rht18 and gibberellin-insensitive Rht-D1b dwarfing genes on vegetative and reproductive growth in bread wheat

2020 ◽  
Author(s):  
Ting Tang ◽  
Tina Botwright Acuña ◽  
Wolfgang Spielmeyer ◽  
Richard A Richards
Keyword(s):  
Dry Matter ◽  
Green Revolution ◽  
Dominant Gene ◽  
Early Growth ◽  
Wheat Breeding ◽  
Dwarfing Genes ◽  
Coleoptile Length ◽  
Backcross Population ◽  
Wheat Improvement ◽  
Vegetative And Reproductive Growth

Abstract Gibberellin (GA)-insensitive dwarfing genes Rht-B1b and Rht-D1b that are responsible for the ‘Green Revolution’ have been remarkably successful in wheat improvement globally. However, these alleles result in shorter coleoptiles and reduced vigour, and hence poor establishment and growth in some environments. Rht18, on the other hand, is a GA-sensitive, dominant gene with potential to overcome some of the early growth limitations associated with Rht-B1b and Rht-D1b. We assessed progeny from both a biparental and a backcross population that contained tall, single dwarf, and double dwarf lines, to determine whether Rht18 differs from Rht-D1b and hence verify its value in wheat improvement. Progeny with Rht18 had an almost identical height to lines with Rht-D1b, and both were ~26% shorter than the tall lines, with the double dwarf 13% shorter again. However, coleoptile length of Rht18 was 42% longer than that of Rht-D1b. We detected no differences in time to terminal spikelet and anthesis, and few differences in stem or spike growth. Both dwarfing genes diverted more dry matter to the spike than tall lines from prior to heading. No differences were detected between Rht18 and Rht-D1b that could prevent the adoption of Rht18 in wheat breeding to overcome some of the limitations associated with the ‘Green Revolution’ genes.

scholarly journals Indirect predictions with a large number of genotyped animals using the algorithm for proven and young

2020 ◽  
Vol 98 (6) ◽  
Author(s):  
Andre L S Garcia ◽  
Yutaka Masuda ◽  
Shogo Tsuruta ◽  
Stephen Miller ◽  
Ignacy Misztal ◽  
...  
Keyword(s):  
Random Sample ◽  
Best Linear Unbiased Prediction ◽  
Single Step ◽  
Nucleotide Polymorphisms ◽  
Linear Unbiased Prediction ◽  
Single Nucleotide ◽  
Large Numbers ◽  
Minimum Number ◽  
Best Linear Unbiased ◽  
Estimated Breeding Values

Abstract Reliable single-nucleotide polymorphisms (SNP) effects from genomic best linear unbiased prediction BLUP (GBLUP) and single-step GBLUP (ssGBLUP) are needed to calculate indirect predictions (IP) for young genotyped animals and animals not included in official evaluations. Obtaining reliable SNP effects and IP requires a minimum number of animals and when a large number of genotyped animals are available, the algorithm for proven and young (APY) may be needed. Thus, the objectives of this study were to evaluate IP with an increasingly larger number of genotyped animals and to determine the minimum number of animals needed to compute reliable SNP effects and IP. Genotypes and phenotypes for birth weight, weaning weight, and postweaning gain were provided by the American Angus Association. The number of animals with phenotypes was more than 3.8 million. Genotyped animals were assigned to three cumulative year-classes: born until 2013 (N = 114,937), born until 2014 (N = 183,847), and born until 2015 (N = 280,506). A three-trait model was fitted using the APY algorithm with 19,021 core animals under two scenarios: 1) core 2013 (random sample of animals born until 2013) used for all year-classes and 2) core 2014 (random sample of animals born until 2014) used for year-class 2014 and core 2015 (random sample of animals born until 2015) used for year-class 2015. GBLUP used phenotypes from genotyped animals only, whereas ssGBLUP used all available phenotypes. SNP effects were predicted using genomic estimated breeding values (GEBV) from either all genotyped animals or only core animals. The correlations between GEBV from GBLUP and IP obtained using SNP effects from core 2013 were ≥0.99 for animals born in 2013 but as low as 0.07 for animals born in 2014 and 2015. Conversely, the correlations between GEBV from ssGBLUP and IP were ≥0.99 for animals born in all years. IP predictive abilities computed with GEBV from ssGBLUP and SNP predictions based on only core animals were as high as those based on all genotyped animals. The correlations between GEBV and IP from ssGBLUP were ≥0.76, ≥0.90, and ≥0.98 when SNP effects were computed using 2k, 5k, and 15k core animals. Suitable IP based on GEBV from GBLUP can be obtained when SNP predictions are based on an appropriate number of core animals, but a considerable decline in IP accuracy can occur in subsequent years. Conversely, IP from ssGBLUP based on large numbers of phenotypes from non-genotyped animals have persistent accuracy over time.

Genetic gain in grain yield and drought tolerance of durum wheat breeding lines under rainfed conditions in Iran

2012 ◽  
Vol 60 (4) ◽  
pp. 417-432 ◽  
Author(s):  
R. Mohammadi
Keyword(s):  
Drought Tolerance ◽  
Grain Yield ◽  
Genetic Gain ◽  
Wheat Breeding ◽  
Tolerance Index ◽  
Yield Attributes ◽  
Modern Cultivar ◽  
Joint Project ◽  
Breeding Lines ◽  
Drought Tolerance Indices

The main objective of this study was to evaluate the genetic gain for grain yield, yield attributes and drought tolerance of 11 durum breeding lines and also to compare it with one modern cultivar and two durum and bread wheat landraces in contrasting environment groups in a period of four cropping seasons (2005–09) within the Iran/ICARDA joint project for moderately cold rainfed areas of Iran. The significant genotype × year interaction indicated that the average yield performance of genotypes across environments was not consistent over the years. Genetic gain (%) for grain yield was distinguishable between the stressed and non-stressed environments. A positive genetic gain (27.7 to 23.9%) was observed in the non-stressed environment and a negative genetic gain (−11.5 to −24.1%) in the stressed environment for the breeding lines, compared to the landraces, suggesting that the evaluation of breeding materials under non-stressed conditions should be continued. Unlike the modern cultivar, the landraces were low yielding, and less responsive to non-stressed environments for grain yield and yield attributes. The drought resistance indices, i.e. tolerance index (TOL) and stress susceptibility index (SSI), were better in landraces than breeding lines, while the drought tolerance indices, i.e. stress tolerance index (STI) and drought response index (DRI), were better in breeding lines. In contrast with landraces, the modern cultivar and the breeding lines showed significant changes for both grain yield and drought tolerance.

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