scholarly journals The barley pan-genome reveals the hidden legacy of mutation breeding

Nature ◽  
2020 ◽  
Vol 588 (7837) ◽  
pp. 284-289 ◽  
Author(s):  
Murukarthick Jayakodi ◽  
Sudharsan Padmarasu ◽  
Georg Haberer ◽  
Venkata Suresh Bonthala ◽  
Heidrun Gundlach ◽  
...  
Keyword(s):  
Crop Improvement ◽  
Mutation Breeding ◽  
Climatic Conditions ◽  
Crop Species ◽  
Genomic Structural Variation ◽  
Pan Genome ◽  
Wide Range ◽  
Full Complement ◽  
High Quality Sequence ◽  
Barley Germplasm

AbstractGenetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the ‘pan-genome’1). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Hordeum vulgare L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions2. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley—comprising landraces, cultivars and a wild barley—that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.

scholarly journals CONTRIBUTION OF INDUCED MUTATION IN CROPS TO GLOBAL FOOD SECURITY

2021 ◽  
Vol 12 (3) ◽  
pp. 10
Author(s):  
Fatma Sarsu
Keyword(s):  
Food Security ◽  
Crop Improvement ◽  
Mutation Breeding ◽  
Climatic Conditions ◽  
Mutation Induction ◽  
Crop Species ◽  
Genetic Changes ◽  
Global Food Security ◽  
Pests And Diseases ◽  
Global Food

Mutation breeding for crop improvement is a technique used for over 70 years. It is a fast way to increase the rate of spontaneous genetic variation in plants contributing to global food security.  The genetic variability, created through mutagenesis i.e. physical or chemical, is an important breeding material for developing improved varieties and many studies in the field of functional genomics. The randomly generated heritable genetic changes are expressed in the mutant plants, which are selected for new and useful traits, such as high yielding, disease resistance, tolerance to abiotic stresses and improved nutritional quality. The technique helps to improve the tolerance of crop species to adverse climatic conditions, such as extremes of temperatures, drought, occurrence of pests and diseases. Through support provided by the Joint FAO/IAEA Division, significant agronomic and economic impact has been generated in many countries. The FAO/IAEA Mutant Variety Database (MVD) (http://mvd.iaea.org) demonstrates the significance of mutation induction as an efficient tool in crop improvement. The extensive use of induced mutant germplasms in crop improvement programmes resulted in releasing of more than 3,332 mutant varieties from around 228 crop species (20 July 2020).

scholarly journals MUTATION BREEDING FOR CROP IMPROVEMENT: A REVIEW

2021 ◽  
Vol 2 (1) ◽  
pp. 31-35
Author(s):  
Rishav Pandit ◽  
Bishnu Bhusal ◽  
Rashmi Regmi ◽  
Pritika Neupane ◽  
Kushal Bhattarai ◽  
...  
Keyword(s):  
Crop Improvement ◽  
Mutation Breeding ◽  
Grain Legume ◽  
Rapid Phase ◽  
Induced Mutation ◽  
Chemical Mutagens ◽  
Oil Seed ◽  
Crop Varieties ◽  
Cereal Grain ◽  
Wide Range

Despite the fact that the world is at the rapid phase of agricultural modernization, but we are still concerned about food security. To meet the demand of exponential increase in population there is requirement of 70% more food by 2050. To overcome this situation we have to improve our existing crop varieties and make them genetically diverse, adaptive to climate change, input use efficient, high yielding, enhanced nutritional attributes, and better adaptable to a wide range of agro-ecosystems and should not deteriorate existing environment. Among the various methods of breeding to improve crop varieties mutation breeding (induced mutation) plays a crucial role for the development of genetic variation among themselves. Over past five decade mutation breeding is getting more popular and till now 3,362 mutant plant varieties from 240 different plant species in more than 75 countries are released. Different types of physical, chemical and combined mutagens have been used by various breeder to induce genetic variability in various crops. 2635 varieties are developed by physical mutagens, 398 varieties are developed by chemical mutagens and 37 varieties are developed by combination of physical and chemical mutagens. Continent wise, 82 varieties are developed by Africa, 2049 by Asia, 10 by Australia and Pacific, 959 by Europe, 53 by Latin America, and 209 by North America. Similarly, 1602 major cereals, 501 major legumes and 86 major oil seed mutant crop varieties are developed by mutation breeding/induced mutation. Mutation breeding improve several qualitative and quantitative characters of crop plant and is successfully applied in several cereal, grain legume, oil seed, vegetable, fruits, medicinal plant, ornamental plants and fodder crops. With the advancement of various plant breeding, genetics, and biotechnological tools mutation breeding contribute toward the increase in global food and agriculture production which ultimately overcome global hunger and improve the nutritional status of the globe.

scholarly journals A global barley panel revealing genomic signatures of breeding in modern cultivars

2020 ◽  
Author(s):  
Camilla Beate Hill ◽  
Tefera Tolera Angessa ◽  
Xiao-Qi Zhang ◽  
Kefei Chen ◽  
Gaofeng Zhou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Genetic Erosion ◽  
Germplasm Collection ◽  
Geographic Region ◽  
Climatic Conditions ◽  
Crop Species ◽  
Diverse Range ◽  
The Impact

AbstractThe future of plant cultivar improvement lies in the evaluation of genetic resources from currently available germplasm. Recent efforts in plant breeding have been aimed at developing new and improved varieties from poorly adapted crops to suit local environments. However, the impact of these breeding efforts is poorly understood. Here, we assess the contributions of both historical and recent breeding efforts to local adaptation and crop improvement in a global barley panel by analysing the distribution of genetic variants with respect to geographic region or historical breeding category. By tracing the impact breeding had on the genetic diversity of barley released in Australia, where the history of barley production is relatively young, we identify 69 candidate regions within 922 genes that were under selection pressure. We also show that modern Australian barley varieties exhibit 12% higher genetic diversity than historical cultivars. Finally, field-trialling and phenotyping for agriculturally relevant traits across a diverse range of Australian environments suggests that genomic regions under strong breeding selection and their candidate genes are closely associated with key agronomic traits. In conclusion, our combined dataset and germplasm collection provide a rich source of genetic diversity that can be applied to understanding and improving environmental adaptation and enhanced yields.Author summaryToday’s gene pool of crop genetic diversity has been shaped during domestication and more recently by breeding. Genetic diversity is vital for crop species to be able to adapt to changing environments. There is concern that recent breeding efforts have eroded the genetic diversity of many domesticated crops including barley. The present study assembled a global panel of barley genotypes with a focus on historical and modern Australian varieties.Genome-wide data was used to detect genes that are thought to have been under selection during crop breeding in Australian barley. The results demonstrate that despite being more extensively bred, modern Australian barley varieties exhibit higher genetic diversity than historical cultivars, countering the common perception that intensive breeding leads to genetic erosion of adaptive diversity in modern cultivars. In addition, some loci (particularly those related to phenology) were subject to selection during the introduction of other barley varieties to Australia – these genes might continue to be important targets in breeding efforts in the face of changing climatic conditions.

scholarly journals Transcription Factors Associated with Abiotic and Biotic Stress Tolerance and Their Potential for Crops Improvement

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 771 ◽  
Author(s):  
Baillo ◽  
Kimotho ◽  
Zhang ◽  
Xu
Keyword(s):  
Transcription Factors ◽  
Stress Tolerance ◽  
Stress Responses ◽  
Biotic Stress ◽  
Crop Improvement ◽  
Abiotic And Biotic Stress ◽  
Crop Species ◽  
Biotic Stresses ◽  
Wide Range ◽  
Tf Gene

In field conditions, crops are adversely affected by a wide range of abiotic stresses including drought, cold, salt, and heat, as well as biotic stresses including pests and pathogens. These stresses can have a marked effect on crop yield. The present and future effects of climate change necessitate the improvement of crop stress tolerance. Plants have evolved sophisticated stress response strategies, and genes that encode transcription factors (TFs) that are master regulators of stress-responsive genes are excellent candidates for crop improvement. Related examples in recent studies include TF gene modulation and overexpression approaches in crop species to enhance stress tolerance. However, much remains to be discovered about the diverse plant TFs. Of the >80 TF families, only a few, such as NAC, MYB, WRKY, bZIP, and ERF/DREB, with vital roles in abiotic and biotic stress responses have been intensively studied. Moreover, although significant progress has been made in deciphering the roles of TFs in important cereal crops, fewer TF genes have been elucidated in sorghum. As a model drought-tolerant crop, sorghum research warrants further focus. This review summarizes recent progress on major TF families associated with abiotic and biotic stress tolerance and their potential for crop improvement, particularly in sorghum. Other TF families and non-coding RNAs that regulate gene expression are discussed briefly. Despite the emphasis on sorghum, numerous examples from wheat, rice, maize, and barley are included. Collectively, the aim of this review is to illustrate the potential application of TF genes for stress tolerance improvement and the engineering of resistant crops, with an emphasis on sorghum.

scholarly journals Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in thePseudomonas syringaespecies complex

2017 ◽  
Author(s):  
Marcus M. Dillon ◽  
Shalabh Thakur ◽  
Renan N.D. Almeida ◽  
David S. Guttman
Keyword(s):  
Pseudomonas Syringae ◽  
Species Complex ◽  
Bacterial Species ◽  
Orthologous Gene ◽  
Gene Families ◽  
Biological Species ◽  
Genetic Exchange ◽  
Crop Species ◽  
Pan Genome ◽  
Wide Range

ABSTRACTPseudomonas syringaeis a highly diverse bacterial species complex capable of causing a wide range of serious diseases on numerous agronomically important crop species. Here, we examine the evolutionary relationships of 391 agricultural and environmental strains from theP. syringaespecies complex using whole-genome sequencing and evolutionary genomic analyses. Our collection includes strains from 11 of the 13 previously described phylogroups isolated off of over 90 hosts. We describe the phylogenetic distribution of all orthologous gene families in theP. syringaepan-genome, reconstruct the phylogeny ofP. syringaeusing a core genome alignment and a hierarchical clustering analysis of pan-genome content, predict ecologically and evolutionary relevant loci, and establish the forces of molecular evolution operating on each gene family. We find that the common ancestor of the species complex likely carried a Rhizobium-like type III secretion system (TTSS) and later acquired the canonical TTSS. The phylogenetic analysis also showed that the species complex is subdivided into primary and secondary phylogroups based on genetic diversity and rates of genetic exchange. The primary phylogroups, which largely consist of agricultural isolates, are no more divergent than a number of other bacterial species, while the secondary phylogroups, which largely consists of environmental isolates, have levels of diversity more in line with multiple distinct species within a genus. An analysis of rates of recombination within and between phylogroups revealed a higher rate of recombination within primary phylogroups than between primary and secondary phylogroups. We also found that “ecologically significant” virulence-associated loci and “evolutionary significant” loci under positive selection are over-represented among loci that undergo inter-phylogroup genetic exchange. These results indicate that while inter-phylogroup recombination occurs relatively rarely in the species complex, it is an important force of genetic cohesion, particularly among the strains in the primary phylogroups. This level of genetic cohesion and the shared plant-associated niche argues for considering the primary phylogroups as a true biological species.

scholarly journals How the pan-genome is changing crop genomics and improvement

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Rafael Della Coletta ◽  
Yinjie Qiu ◽  
Shujun Ou ◽  
Matthew B. Hufford ◽  
Candice N. Hirsch
Keyword(s):  
Structural Variation ◽  
Crop Improvement ◽  
Sequencing Technology ◽  
Crop Species ◽  
Pan Genome ◽  
Content Variation ◽  
Genome Content ◽  
Computational Resources ◽  
Paradigm Shifting

AbstractCrop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. These advances have led to the development of new tools to facilitate crop improvement. The study of structural variation within species and the characterization of the pan-genome has revealed extensive genome content variation among individuals within a species that is paradigm shifting to crop genomics and improvement. Here, we review advances in crop genomics and how utilization of these tools is shifting in light of pan-genomes that are becoming available for many crop species.

scholarly journals Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
John T. Lovell ◽  
Nolan B. Bentley ◽  
Gaurab Bhattarai ◽  
Jerry W. Jenkins ◽  
Avinash Sreedasyam ◽  
...  
Keyword(s):  
Tree Breeding ◽  
Pathogen Resistance ◽  
Perennial Crop ◽  
Crop Species ◽  
Annotation Database ◽  
Pan Genome ◽  
Genome Integration ◽  
Transformative Potential ◽  
Genome Assemblies ◽  
Quantitative Genomics

AbstractGenome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence–absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts. To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the ‘Pawnee’ cultivar. Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. Further, by leveraging our pan-genome presence–absence and functional annotation database among genomes and within the two outbred haplotypes of the ‘Lakota’ genome, we identify candidate genes for pest and pathogen resistance. Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops.

scholarly journals Silicon Effects on the Root System of Diverse Crop Species Using Root Phenotyping Technology

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 885
Author(s):  
Pooja Tripathi ◽  
Sangita Subedi ◽  
Abdul Latif Khan ◽  
Yong-Suk Chung ◽  
Yoonha Kim
Keyword(s):  
Root System ◽  
Root Morphology ◽  
Morphological Traits ◽  
Crop Production ◽  
Spatial Configuration ◽  
Global Climate ◽  
Learning Technologies ◽  
Climate Change Scenarios ◽  
Crop Species ◽  
Wide Range

Roots play an essential function in the plant life cycle, as they utilize water and essential nutrients to promote growth and plant productivity. In particular, root morphology characteristics (such as length, diameter, hairs, and lateral growth) and the architecture of the root system (spatial configuration in soil, shape, and structure) are the key elements that ensure growth and a fine-tuned response to stressful conditions. Silicon (Si) is a ubiquitous element in soil, and it can affect a wide range of physiological processes occurring in the rhizosphere of various crop species. Studies have shown that Si significantly and positively enhances root morphological traits, including root length in rice, soybean, barley, sorghum, mustard, alfalfa, ginseng, and wheat. The analysis of these morphological traits using conventional methods is particularly challenging. Currently, image analysis methods based on advanced machine learning technologies allowed researchers to screen numerous samples at the same time considering multiple features, and to investigate root functions after the application of Si. These methods include root scanning, endoscopy, two-dimensional, and three-dimensional imaging, which can measure Si uptake, translocation and root morphological traits. Small variations in root morphology and architecture can reveal different positive impacts of Si on the root system of crops, with or without exposure to stressful environmental conditions. This review comprehensively illustrates the influences of Si on root morphology and root architecture in various crop species. Furthermore, it includes recommendations in regard to advanced methods and strategies to be employed to maintain sustainable plant growth rates and crop production in the currently predicted global climate change scenarios.

scholarly journals Environmental Drivers and Age Trends in Site Productivity for Oak in Southern Poland

Forests ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 209
Author(s):  
Luiza Tymińska-Czabańska ◽  
Jarosław Socha ◽  
Marek Maj ◽  
Dominika Cywicka ◽  
Xo Viet Hoang Duong
Keyword(s):  
Nitrogen Deposition ◽  
Management Practices ◽  
Additive Model ◽  
Climatic Conditions ◽  
Environmental Indicators ◽  
Environmental Drivers ◽  
Site Productivity ◽  
Site Factors ◽  
Wide Range ◽  
Si Model

Site productivity provides critical information for forest management practices and is a fundamental measure in forestry. It is determined using site index (SI) models, which are developed using two primary groups of methods, namely, phytocentric (plant-based) or geocentric (earth-based). Geocentric methods allow for direct site growth modelling, in which the SI is predicted using multiple environmental indicators. However, changes in non-static site factors—particularly nitrogen deposition and rising CO2 concentration—lead to an increase in site productivity, which may be visible as an age trend in the SI. In this study, we developed a geocentric SI model for oak. For the development of the SI model, we used data from 150 sample plots, representing a wide range of local topographic and site conditions. A generalized additive model was used to model site productivity. We found that the oak SI depended predominantly on physicochemical soil properties—mainly nitrogen, carbon, sand, and clay content. Additionally, the oak SI value was found to be slightly shaped by the topography, especially by altitude above sea level, and topographic position. We also detected a significant relationship between the SI and the age of oak stands, indicating the long-term increasing site productivity for oak, most likely caused by nitrogen deposition and changes in climatic conditions. The developed geocentric site productivity model for oak explained 77.2% of the SI variation.

scholarly journals Soil Nitrogen Dynamics in a Managed Temperate Grassland Under Changed Climatic Conditions

Water ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 931
Author(s):  
Mona Giraud ◽  
Jannis Groh ◽  
Horst H. Gerke ◽  
Nicolas Brüggemann ◽  
Harry Vereecken ◽  
...  
Keyword(s):  
Nitrogen Uptake ◽  
Inorganic Nitrogen ◽  
Nitrogen Concentration ◽  
Nitrogen Dynamics ◽  
Climatic Conditions ◽  
Undisturbed Soil ◽  
Nitrogen Emissions ◽  
Growing Period ◽  
Grassland Type ◽  
Wide Range

Grasslands are one of the most common biomes in the world with a wide range of ecosystem services. Nevertheless, quantitative data on the change in nitrogen dynamics in extensively managed temperate grasslands caused by a shift from energy- to water-limited climatic conditions have not yet been reported. In this study, we experimentally studied this shift by translocating undisturbed soil monoliths from an energy-limited site (Rollesbroich) to a water-limited site (Selhausen). The soil monoliths were contained in weighable lysimeters and monitored for their water and nitrogen balance in the period between 2012 and 2018. At the water-limited site (Selhausen), annual plant nitrogen uptake decreased due to water stress compared to the energy-limited site (Rollesbroich), while nitrogen uptake was higher at the beginning of the growing period. Possibly because of this lower plant uptake, the lysimeters at the water-limited site showed an increased inorganic nitrogen concentration in the soil solution, indicating a higher net mineralization rate. The N2O gas emissions and nitrogen leaching remained low at both sites. Our findings suggest that in the short term, fertilizer should consequently be applied early in the growing period to increase nitrogen uptake and decrease nitrogen losses. Moreover, a shift from energy-limited to water-limited conditions will have a limited effect on gaseous nitrogen emissions and nitrate concentrations in the groundwater in the grassland type of this study because higher nitrogen concentrations are (over-) compensated by lower leaching rates.

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