Revolutions in agriculture chart a course for targeted breeding of old and new crops

Science ◽  
2019 ◽  
Vol 366 (6466) ◽  
pp. eaax0025 ◽  
Author(s):  
Yuval Eshed ◽  
Zachary B. Lippman
Keyword(s):  
Genetic Variation ◽  
Large Scale ◽  
Plant Architecture ◽  
Farming Practices ◽  
Underutilized Crops ◽  
Human Diet ◽  
Breeding Programs ◽  
Plant Parts ◽  
New Crops ◽  
Core Components

The dominance of the major crops that feed humans and their livestock arose from agricultural revolutions that increased productivity and adapted plants to large-scale farming practices. Two hormone systems that universally control flowering and plant architecture, florigen and gibberellin, were the source of multiple revolutions that modified reproductive transitions and proportional growth among plant parts. Although step changes based on serendipitous mutations in these hormone systems laid the foundation, genetic and agronomic tuning were required for broad agricultural benefits. We propose that generating targeted genetic variation in core components of both systems would elicit a wider range of phenotypic variation. Incorporating this enhanced diversity into breeding programs of conventional and underutilized crops could help to meet the future needs of the human diet and promote sustainable agriculture.

scholarly journals Ethnomedical uses, chemical constituents, and evidence-based pharmacological properties of Chenopodium ambrosioides L.: extensive overview

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Félicien Mushagalusa Kasali ◽  
Jonans Tusiimire ◽  
Justin Ntokamunda Kadima ◽  
Amon Ganafa Agaba
Keyword(s):  
Large Scale ◽  
Chemical Constituents ◽  
Main Body ◽  
Pharmacological Properties ◽  
Chenopodium Ambrosioides ◽  
Traditional Medicines ◽  
Plant Parts ◽  
Chemical Studies ◽  
Ethnomedicinal Uses ◽  
Significant Health

Abstract Background The Chenopodium genus is a plant family widely spread worldwide that includes various plant species reputed to possess several medicinal virtues in folk medicines. Chenopodium ambrosioides L. is among the most used plants in traditional medicines worldwide. This review aimed to highlight ethnomedicinal uses, phytochemical status, and pharmacological properties of C. ambrosioides L. Main body of the abstract The analysis of relevant data highlights various ethnomedicinal uses against human and veterinary diseases in forty countries. Most indications consisted of gastrointestinal tract dysfunctioning troubles and worms parasitemia. Around 330 chemical compounds have been identified in different plant parts, especially in its essential oil fractions (59.84%). However, only a few compounds—mainly monoterpenes and glycosides—have been isolated and characterized. Experimental pharmacological studies validated a large scale of significant health benefits. It appeared that many monoterpenes are antioxidant, insecticidal, trypanocidal, analgesic, antifungal, anti-inflammatory, anti-arthritic, acaricidal, amoebicidal, anthelmintic, anticancer, antibacterial, antidiabetic, antidiarrheal, antifertility, antifungal, anti-leishmanial, antimalarial, antipyretic, antisickling, antischistosomal, antiulcer, anxiolytic, immunomodulatory, molluscicidal, and vasorelaxant agents. Short conclusion Thus, the Chenopodium ambrosioides species necessitates further chemical studies to isolate and characterize new bioactive secondary metabolites and pharmacological investigations to precise the mechanisms of action before clinical trials.

scholarly journals Genetic variation in recombination rate in the pig

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Martin Johnsson ◽  
Andrew Whalen ◽  
Roger Ros-Freixedes ◽  
Gregor Gorjanc ◽  
Ching-Yi Chen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Recombination Rate ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Genetic Material ◽  
A Genome ◽  
Pig Genome ◽  
Genetic Length ◽  
Trait Locus ◽  
Genomic Regions

Abstract Background Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assessed the genetic variation in recombination rate along the genome and between individuals in the pig using multilocus iterative peeling on 150,000 individuals across nine genotyped pedigrees. We used these data to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig. Results Our results confirmed known features of the recombination landscape of the pig genome, including differences in genetic length of chromosomes and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, there were differences in average autosome-wide recombination rate between lines. The heritability of autosome-wide recombination rate was low but not zero (on average 0.07 for females and 0.05 for males). We found six genomic regions that are associated with recombination rate, among which five harbour known candidate genes involved in recombination: RNF212, SHOC1, SYCP2, MSH4 and HFM1. Conclusions Our results on the variation in recombination rate in the pig genome agree with those reported for other vertebrates, with a low but nonzero heritability, and the identification of a major quantitative trait locus for recombination rate that is homologous to that detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes.

scholarly journals Post-Dropping Behavior of Potato Aphids (Macrosiphum euphorbiae)

2021 ◽  
Vol 34 (4) ◽  
pp. 223-239
Author(s):  
Rosalind K. Humphreys ◽  
Graeme D. Ruxton ◽  
Alison J. Karley
Keyword(s):  
Recovery Rate ◽  
Tactile Stimulus ◽  
Plant Architecture ◽  
Tonic Immobility ◽  
Macrosiphum Euphorbiae ◽  
Chrysoperla Carnea ◽  
Antipredator Defense ◽  
Plant Parts ◽  
Potato Aphids ◽  
Lower Plant

AbstractDropping behavior is an effective antipredator defense utilized by many insects including aphids, which drop from plants to lower plant parts or underlying substrates to avoid attack from predatory invertebrates. While research commonly focusses on triggers of dropping, less attention is given to what happens to prey individuals following escape drops. In this study, the duration of tonic immobility, recovery rates, and cases of “instant recovery” (re-clinging to lower plant parts) exhibited by potato aphids (Macrosiphum euphorbiae) that dropped from potted seedlings in response to introduced ladybird (Adalia bipunctata) adults, lacewing (Chrysoperla carnea) larvae, and a standardized tactile stimulus were investigated in relation to a range of environmental factors. Air temperature had a negative correlation with the duration of post-dropping tonic immobility; as temperature increased, time spent motionless decreased. Aphids also showed a pattern of increased recovery rate at higher temperatures. Aphids may be selected to move off the substrate quicker to avoid risks of overheating/desiccation at higher temperatures; and/or higher body temperature facilitates locomotion. Stimulus type also influenced recovery rate back to the original seedling, with aphids generally recovering after the standardized stimulus quicker than after dropping triggered by a real predator. Considering cases of instant recovery onto lower-reaches of the host seedling, seedling height influenced the likelihood of re-clinging, with aphids that managed to instantly recover dropping from, on average, taller seedlings than aphids that dropped to the substrate. Plant architecture could mitigate the costs of dropping for aphids, but further studies quantifying understory foliage cover are needed.

scholarly journals VARIABILIDADE GENÉTICA UTILIZANDO DESCRITORES MORFOLÓGICOS PARA ACESSOS DE Capsicum spp. PARA FINS ORNAMENTAIS

Nativa ◽  
2019 ◽  
Vol 7 (6) ◽  
pp. 675
Author(s):  
Petterson Baptista da Luz ◽  
Alessandro Aparecido Brito dos Santos ◽  
Valdete Campos Ambrosio
Keyword(s):  
Genetic Variability ◽  
Ornamental Plants ◽  
Growth Potential ◽  
Breeding Programs ◽  
Canonical Correlations ◽  
Plant Parts ◽  
Potted Plants ◽  
Capsicum Spp ◽  
Biometric Templates

O mercado de pimentas para fins ornamentais é um setor recém explorado, mas com grande potencial de crescimento no ramo de floricultura e paisagismo. As pimenteiras que possuem folhagem variegada, porte baixo, frutos com coloração variada em seus diferentes estádios de maturação, contrastando com as folhagens, já são utilizadas como plantas ornamentais, cultivadas e comercializadas em vasos. O presente trabalho teve como objetivo avaliar a variabilidade genética visando o potencial ornamental de acessos de Capsicum spp. através de modelos biométricos. Foram utilizados 55 acessos de Capsicum spp, e a caracterização morfoagronômica dos acessos foi realizada avaliando diferentes partes da planta. O terceiro par de correlações canônicas, com correlação de 0,51, associa plantas com área do dossel compacto-densa, com menor comprimento e largura de dossel e de pequeno porte, associado com folhagens estreitas e de pecíolo grande. Esta associação é vantajosa para ornamentação. Ficou evidenciada a presença de variabilidade genética na população, o que é bastante favorável ao melhoramento na medida em que a heterogeneidade genética possibilita a obtenção de ganhos por meio de seleção.Palavras-chave: pimenta; modelos biométricos; correlações canônicas; análise de trilha. GENETIC VARIABILITY FOCUSED ON ORNAMENTAL POTENTIAL OF A Capsicum spp. ACCESSION ABSTRACT: Pepper market for ornamental purposes is recently exploited; however, it has a great growth potential in floriculture and landscaping. Pepper with variegated foliage, small size, and varied fruit coloration at different ripening stages contrasting with leaves have already been used as ornamental plants cultivated and purchased as potted plants. This study aimed to evaluate genetic variability of Capsicum spp. focusing on its ornamental potential by means of biometric templates. Fifty-five Capsicum spp. accessions were used and a morpho-agronomic characterization of the accessions were performed by evaluating different plant parts. The third canonical correlations are 0.51 and it associates compact-dense, small, shorter length and width canopy plants with narrow foliage and large petiole, which is advantageous for ornamentation. Genetic variation was evidenced in the population being very favorable for plant breeding programs once genetic heterogeneity enables obtaining gains through selections.Keywords: pepper; biometric templates; canonic correlations; trail analysis.

scholarly journals Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies

Forests ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1185
Author(s):  
Helena Eklöf ◽  
Carolina Bernhardsson ◽  
Pär K. Ingvarsson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Picea Abies ◽  
Norway Spruce ◽  
Large Scale ◽  
Genotyping By Sequencing ◽  
Complexity Reduction ◽  
Exome Capture ◽  
Genome Wide ◽  
Targeted Capture

Conifer genomes are characterized by their large size and high abundance of repetitive material, making large-scale genotyping in conifers complicated and expensive. One of the consequences of this is that it has been difficult to generate data on genome-wide levels of genetic variation. To date, researchers have mainly employed various complexity reduction techniques to assess genetic variation across the genome in different conifer species. These methods tend to capture variation in a relatively small subset of a typical conifer genome and it is currently not clear how representative such results are. Here we take advantage of data generated in the first large-scale re-sequencing effort in Norway spruce and assess how well two commonly used complexity reduction methods, targeted capture probes and genotyping by sequencing perform in capturing genome-wide variation in Norway spruce. Our results suggest that both methods perform reasonably well for assessing genetic diversity and population structure in Norway spruce (Picea abies (L.) H. Karst.). Targeted capture probes were slightly more effective than GBS, likely due to them targeting known genomic regions whereas the GBS data contains a substantially greater fraction of repetitive regions, which sometimes can be problematic for assessing genetic diversity. In conclusion, both methods are useful for genotyping large numbers of samples and they greatly reduce the cost involved with genotyping a species with such a complex genome as Norway spruce.

scholarly journals Maximizing efficiency of genomic selection in CIMMYT’s tropical maize breeding program

2020 ◽  
Author(s):  
Sikiru Adeniyi Atanda ◽  
Michael Olsen ◽  
Juan Burgueño ◽  
Jose Crossa ◽  
Daniel Dzidzienyo ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Prediction Accuracy ◽  
Large Scale ◽  
Primary Objective ◽  
Breeding Program ◽  
Breeding Cycle ◽  
Training Set ◽  
Maize Breeding ◽  
Phenotypic Data ◽  
Breeding Programs

Abstract Key message Historical data from breeding programs can be efficiently used to improve genomic selection accuracy, especially when the training set is optimized to subset individuals most informative of the target testing set. Abstract The current strategy for large-scale implementation of genomic selection (GS) at the International Maize and Wheat Improvement Center (CIMMYT) global maize breeding program has been to train models using information from full-sibs in a “test-half-predict-half approach.” Although effective, this approach has limitations, as it requires large full-sib populations and limits the ability to shorten variety testing and breeding cycle times. The primary objective of this study was to identify optimal experimental and training set designs to maximize prediction accuracy of GS in CIMMYT’s maize breeding programs. Training set (TS) design strategies were evaluated to determine the most efficient use of phenotypic data collected on relatives for genomic prediction (GP) using datasets containing 849 (DS1) and 1389 (DS2) DH-lines evaluated as testcrosses in 2017 and 2018, respectively. Our results show there is merit in the use of multiple bi-parental populations as TS when selected using algorithms to maximize relatedness between the training and prediction sets. In a breeding program where relevant past breeding information is not readily available, the phenotyping expenditure can be spread across connected bi-parental populations by phenotyping only a small number of lines from each population. This significantly improves prediction accuracy compared to within-population prediction, especially when the TS for within full-sib prediction is small. Finally, we demonstrate that prediction accuracy in either sparse testing or “test-half-predict-half” can further be improved by optimizing which lines are planted for phenotyping and which lines are to be only genotyped for advancement based on GP.

Genome-Wide Association Study of Piscine Myocarditis Virus (PMCV) Resistance in Atlantic Salmon (Salmo salar)

2019 ◽  
Vol 110 (6) ◽  
pp. 720-726 ◽  
Author(s):  
Borghild Hillestad ◽  
Hooman K Moghadam
Keyword(s):  
Genetic Variation ◽  
Atlantic Salmon ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
Significant Quantitative Trait Locus ◽  
Viral Disease ◽  
Breeding Programs ◽  
Immunological Mechanisms ◽  
Trait Locus ◽  
Immune Related Genes

Abstract Cardiomyopathy syndrome is a severe, viral disease of Atlantic salmon that mostly affects farmed animals during their late production stage at sea. Caused by piscine myocarditis virus (PMCV), over the past few years outbreaks due to this disease have resulted in significant losses to the aquaculture industry. However, there is currently no vaccine that has proven effective against this virus. In this study, using a challenge model, we investigated the genetic variation for resistance to PMCV, by screening a large number of animals using a 55 K SNP array. In particular, we aimed to identify genetic markers that are tightly linked to higher disease resistance and can potentially be used in breeding programs. Using genomic information, we estimated a heritability of 0.51 ± 0.06, suggesting that resistance against this virus, to a great extent, is controlled by genetic factors. Through association analysis, we identified a significant quantitative trait locus (QTL) on chromosome 27, explaining approximately 57% of the total additive genetic variation. The region harboring this QTL contains various immune-related candidate genes, many of which have previously been shown to have a different expression profile between the naïve and infected animals. We also identified a suggestive association on chromosome 12, with the QTL linked markers located in 2 putatively immune-related genes. These results are of particular interest, as they can readily be implemented into breeding programs, can further assist in fine-mapping the causative mutations, and help in better understanding the biology of the disease and the immunological mechanisms underlying resistance against PMCV.

scholarly journals MoBPS - Modular Breeding Program Simulator

2020 ◽  
Vol 10 (6) ◽  
pp. 1915-1918 ◽  
Author(s):  
Torsten Pook ◽  
Martin Schlather ◽  
Henner Simianer
Keyword(s):  
Data Storage ◽  
Large Scale ◽  
R Package ◽  
Single Step ◽  
Computationally Efficient ◽  
Breeding Programs ◽  
Genetic Impact ◽  
Founder Populations ◽  
Genetic Contributions ◽  
Impact Simulations

The R-package MoBPS provides a computationally efficient and flexible framework to simulate complex breeding programs and compare their economic and genetic impact. Simulations are performed on the base of individuals. MoBPS utilizes a highly efficient implementation with bit-wise data storage and matrix multiplications from the associated R-package miraculix allowing to handle large scale populations. Individual haplotypes are not stored but instead automatically derived based on points of recombination and mutations. The modular structure of MoBPS allows to combine rather coarse simulations, as needed to generate founder populations, with a very detailed modeling of todays’ complex breeding programs, making use of all available biotechnologies. MoBPS provides pre-implemented functions for common breeding practices such as optimum genetic contributions and single-step GBLUP but also allows the user to replace certain steps with personalized and/or self-written solutions.

scholarly journals Morphological diversity and identification key for landraces of the Amerindian yam in central Amazon

2018 ◽  
Vol 53 (4) ◽  
pp. 405-418 ◽  
Author(s):  
Patrick Beyerlein ◽  
Henrique dos Santos Pereira
Keyword(s):  
Morphological Diversity ◽  
Identification Key ◽  
Ex Situ ◽  
Morphological Data ◽  
Morphological Descriptors ◽  
Breeding Programs ◽  
Central Amazon ◽  
Plant Parts ◽  
Optimal Set

Abstract: The objective of this work was to select an optimal set of morphological descriptors, in order to characterize the phenotipical diversity of Amerindian yam (Dioscorea trifida) landraces cultivated in the municipality of Caapiranga, in the central Amazon region of Brazil, and to develop a botanical identification key for them. A collection of 140 accessions and an experimental plot with a representative sample of 20 landraces were used to test 64 morphological descriptors for the aerial and subterranean plant parts. Forty-eight descriptors were selected, of which 13 were for tubers, 12 for stems, 14 for leaves, and 9 for inflorescences and seed. A cluster analysis based on the morphological data showed the formation of two landrace groups with greater similarity: white and purple pulp tubers. The results provide tools for in situ and ex situ conservation and for plant breeding programs, considering the importance of maintaining and recognizing the value of Ameridian yam as an important native genetic resource for food security in the region.

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