scholarly journals Functional Markers for Precision Plant Breeding

2020 ◽  
Vol 21 (13) ◽  
pp. 4792
Author(s):  
Romesh K. Salgotra ◽  
C. Neal Stewart
Keyword(s):  
Abiotic Stress ◽  
Plant Breeding ◽  
Stress Resistance ◽  
High Throughput Sequencing ◽  
Agronomic Traits ◽  
Direct Selection ◽  
Phenotypic Traits ◽  
Functional Markers ◽  
Grand Challenge ◽  
Biotic And Abiotic Stress

Advances in molecular biology including genomics, high-throughput sequencing, and genome editing enable increasingly faster and more precise cultivar development. Identifying genes and functional markers (FMs) that are highly associated with plant phenotypic variation is a grand challenge. Functional genomics approaches such as transcriptomics, targeting induced local lesions in genomes (TILLING), homologous recombinant (HR), association mapping, and allele mining are all strategies to identify FMs for breeding goals, such as agronomic traits and biotic and abiotic stress resistance. The advantage of FMs over other markers used in plant breeding is the close genomic association of an FM with a phenotype. Thereby, FMs may facilitate the direct selection of genes associated with phenotypic traits, which serves to increase selection efficiencies to develop varieties. Herein, we review the latest methods in FM development and how FMs are being used in precision breeding for agronomic and quality traits as well as in breeding for biotic and abiotic stress resistance using marker assisted selection (MAS) methods. In summary, this article describes the use of FMs in breeding for development of elite crop cultivars to enhance global food security goals.

scholarly journals Evolution and Application of Genome Editing Techniques for Achieving Food and Nutritional Security

2021 ◽  
Vol 22 (11) ◽  
pp. 5585
Author(s):  
Sajid Fiaz ◽  
Sunny Ahmar ◽  
Sajjad Saeed ◽  
Aamir Riaz ◽  
Freddy Mora-Poblete ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Food Security ◽  
Plant Breeding ◽  
Genome Editing ◽  
Crop Improvement ◽  
Hybrid Seed Production ◽  
Biotic And Abiotic Stress ◽  
Transcription Activator ◽  
Protein System ◽  
Breeding Techniques

A world with zero hunger is possible only through a sustainable increase in food production and distribution and the elimination of poverty. Scientific, logistical, and humanitarian approaches must be employed simultaneously to ensure food security, starting with farmers and breeders and extending to policy makers and governments. The current agricultural production system is facing the challenge of sustainably increasing grain quality and yield and enhancing resistance to biotic and abiotic stress under the intensifying pressure of climate change. Under present circumstances, conventional breeding techniques are not sufficient. Innovation in plant breeding is critical in managing agricultural challenges and achieving sustainable crop production. Novel plant breeding techniques, involving a series of developments from genome editing techniques to speed breeding and the integration of omics technology, offer relevant, versatile, cost-effective, and less time-consuming ways of achieving precision in plant breeding. Opportunities to edit agriculturally significant genes now exist as a result of new genome editing techniques. These range from random (physical and chemical mutagens) to non-random meganucleases (MegaN), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein system 9 (CRISPR/Cas9), the CRISPR system from Prevotella and Francisella1 (Cpf1), base editing (BE), and prime editing (PE). Genome editing techniques that promote crop improvement through hybrid seed production, induced apomixis, and resistance to biotic and abiotic stress are prioritized when selecting for genetic gain in a restricted timeframe. The novel CRISPR-associated protein system 9 variants, namely BE and PE, can generate transgene-free plants with more frequency and are therefore being used for knocking out of genes of interest. We provide a comprehensive review of the evolution of genome editing technologies, especially the application of the third-generation genome editing technologies to achieve various plant breeding objectives within the regulatory regimes adopted by various countries. Future development and the optimization of forward and reverse genetics to achieve food security are evaluated.

scholarly journals Characterization of Genetic Diversity in Accessions of Prunus salicina Lindl: Keeping Fruit Flesh Color Ideotype While Adapting to WaterStressed Environments

Agronomy ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 487 ◽  
Author(s):  
Acuña ◽  
Rivas ◽  
Brambilla ◽  
Cerrillo ◽  
Frusso ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Candidate Genes ◽  
Stress Resistance ◽  
Prunus Persica ◽  
Agronomic Traits ◽  
Phenotypic Traits ◽  
Flesh Color ◽  
Japanese Plum ◽  
Prunus Salicina

The genetic diversity of 14 Japanese plum (Prunus salicina Lindl) landraces adapted to an ecosystem of alternating flooding and dry conditions was characterized using neutral simple sequence repeat (SSR) markers. Twelve SSRs located in six chromosomes of the Prunus persica reference genome resulted to be polymorphic, thus allowing identification of all the evaluated landraces. Differentiation between individuals was moderate to high (average shared allele distance (DAS) = 0.64), whereas the genetic diversity was high (average indices polymorphism information content (PIC) = 0.62, observed heterozygosity (Ho) = 0.51, unbiased expected heterozygosity (uHe) = 0.70). Clustering and genetic structure approaches grouped all individuals into two major groups that correlated with flesh color. This finding suggests that the intuitive breeding practices of growers tended to select plum trees according to specific phenotypic traits. These neutral markers were adequate for population genetic studies and cultivar identification. Furthermore, we assessed the SSR flanking genome regions (25 kb) in silico to search for candidate genes related to stress resistance or associated with other agronomic traits of interest. Interestingly, at least 26 of the 118 detected genes seem to be related to fruit quality, plant development, and stress resistance. This study suggests that the molecular characterization of specific landraces of Japanese plum that have been adapted to extreme agroecosystems is a useful approach to localize candidate genes which are potentially interesting for breeding.

scholarly journals Effects of Substrate-Binding Site Residues on the Biochemical Properties of a Tau Class Glutathione S-Transferase from Oryza sativa

Genes ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 25 ◽  
Author(s):  
Xue Yang ◽  
Jinchi Wei ◽  
Zhihai Wu ◽  
Jie Gao
Keyword(s):  
Amino Acids ◽  
Enzyme Activity ◽  
Abiotic Stress ◽  
Binding Site ◽  
Stress Responses ◽  
Stress Resistance ◽  
Substrate Binding ◽  
Biochemical Properties ◽  
Biotic And Abiotic Stress ◽  
Substrate Binding Site

Glutathione S-transferases (GSTs)—an especially plant-specific tau class of GSTs—are key enzymes involved in biotic and abiotic stress responses. To improve the stress resistance of crops via the genetic modification of GSTs, we predicted the amino acids present in the GSH binding site (G-site) and hydrophobic substrate-binding site (H-site) of OsGSTU17, a tau class GST in rice. We then examined the enzyme activity, substrate specificity, enzyme kinetics and thermodynamic stability of the mutant enzymes. Our results showed that the hydrogen bonds between Lys42, Val56, Glu68, and Ser69 of the G-site and glutathione were essential for enzyme activity and thermal stability. The hydrophobic side chains of amino acids of the H-site contributed to enzyme activity toward 4-nitrobenzyl chloride but had an inhibitory effect on enzyme activity toward 1-chloro-2,4-dinitrobenzene and cumene hydroperoxide. Different amino acids of the H-site had different effects on enzyme activity toward a different substrate, 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole. Moreover, Leu112 and Phe162 were found to inhibit the catalytic efficiency of OsGSTU17 to 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole, while Pro16, Leu112, and Trp165 contributed to structural stability. The results of this research enhance the understanding of the relationship between the structure and function of tau class GSTs to improve the abiotic stress resistance of crops.

scholarly journals Combined biotic and abiotic stress resistance in tomato

Euphytica ◽  
2015 ◽  
Vol 202 (2) ◽  
pp. 317-332 ◽  
Author(s):  
Christos Kissoudis ◽  
Rawnaq Chowdhury ◽  
Sjaak van Heusden ◽  
Clemens van de Wiel ◽  
Richard Finkers ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Resistance ◽  
Biotic And Abiotic Stress

scholarly journals Erratum to: Nicotiana tabacum Tsip1-interacting ferredoxin 1 affects biotic and abiotic stress resistance

2013 ◽  
Vol 35 (2) ◽  
pp. 176-176
Author(s):  
Sung Un Huh ◽  
In-Ju Lee ◽  
Byung-Kook Ham ◽  
Kyung-Hee Paek
Keyword(s):  
Abiotic Stress ◽  
Nicotiana Tabacum ◽  
Stress Resistance ◽  
Biotic And Abiotic Stress

scholarly journals Direct selection for phenotypic traits in carrot genotypes

2019 ◽  
Vol 37 (3) ◽  
pp. 354-358
Author(s):  
Agnaldo DF de Carvalho ◽  
Giovani O da Silva ◽  
Gabriel E Pereira
Keyword(s):  
Agronomic Traits ◽  
Block Design ◽  
Direct Selection ◽  
Phenotypic Traits ◽  
Crop Breeding ◽  
Breeding Programs ◽  
Randomized Block Design ◽  
Increase Productivity ◽  
Abstract Selection ◽  
Selection Of

ABSTRACT Selection of more productive carrot genotypes is fundamental for crop breeding programs aiming to increase productivity and reduce cost production. Thus, the aim of this work was to evaluate gains from direct selection and to measure its effects on other agronomic traits of interest in carrots. Thirty six carrot genotypes were evaluated in two experiments: the first, sown in the second half of November 2016 and the second one in the first week of March 2017. The experimental plots covered a useful area of 1.5 m2, in transversal rows and 0.10-m double spacing between single rows x 0.20-m between double rows in a randomized block design with 3 replicates. At 90 days, the incidence of leaf blight was evaluated using a note scale and 100 days after sowing, roots were harvested measuring the number and mass of total, commercial and non-commercial roots of each plot. The direct selection of commercial root mass allowed to estimate indirect and expressive gains for most evaluated traits, allowing to select seven genotypes (populations 758, 751, 737, 736, 735, 744 and 742) which can be released as cultivar or for the formation of a broader genetic-based population.

Ideotype breeding for improving yield in sorghum: recent advances and future perspectives.

2021 ◽  
pp. 498-516
Author(s):  
P. Sanjana Reddy
Keyword(s):  
Abiotic Stress ◽  
Plant Breeding ◽  
Stress Resistance ◽  
Cropping Systems ◽  
Climatic Conditions ◽  
Future Perspectives ◽  
Forage Sorghum ◽  
Production Constraints ◽  
Ideotype Breeding

Abstract This chapter focuses on ideotype breeding for improving the yield and related traits, abiotic stress resistance, and quality of grain and forage sorghum. Ideotype breeding involves defining and breeding for the target traits to reach the objectives and differs from classical plant breeding which focuses more on yield. Due to diversification of cropping systems and ever-changing climatic conditions, change in farmers' preferences and several production constraints, breeders need to focus on more traits simultaneously.

scholarly journals Harnessing Agronomics Through Genomics and Phenomics in Plant Breeding: A Review

2021 ◽  
Author(s):  
Zhiwu Zhang ◽  
Chunpeng Chen ◽  
Jessica Rutkoski ◽  
James Schnable ◽  
Seth Murray ◽  
...  
Keyword(s):  
Plant Breeding ◽  
Agronomic Traits ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Genetic Dissection ◽  
Biotic And Abiotic Stress ◽  
Bayesian Approaches ◽  
Genome Wide ◽  
Yield Quality ◽  
Best Linear Unbiased

Plant breeding primarily focuses on improving conventional agronomic traits, e.g. yield, quality, and resistance to biotic and abiotic stress; however, genetic improvement methods are being rapidly enhanced through genomics and phenomics. In the Genomics-Phenomics-Agronomics (GPA) paradigm, diverse research approaches have been conducted to bridge any two of these elements, and recently, all of them together. This review first highlights the progress to link i) genomics to agronomics; ii) genomics to phenomics; and iii) phenomics to agronomics. Secondly, the GPA domain is dissected into different layers, each addressing the three elements simultaneously. These dissected layers include genetic dissection through gene mapping using genome-wide association studies and genomic selection using Best Linear Unbiased Prediction, Bayesian approaches, and machine learning. The objective of the review is to help readers to grasp the core developments among the exponentially growing literature in each of these fields. Through this review, the connections among the three elements of the GPA paradigm are coherently integrated toward the prospect of sustainable development of agronomic traits through both genomics and phenomics.

scholarly journals Identification of Stress Associated microRNAs in Solanum lycopersicum by High-Throughput Sequencing

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 475 ◽  
Author(s):  
López-Galiano ◽  
Sentandreu ◽  
Martínez-Ramírez ◽  
Rausell ◽  
Real ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Solanum Lycopersicum ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Plant Defence ◽  
Stress Conditions ◽  
Differentially Expressed ◽  
Physiological Adaptation ◽  
Biotic And Abiotic Stress

Tomato (Solanum lycopersicum) is one of the most important crops around the world and also a model plant to study response to stress. High-throughput sequencing was used to analyse the microRNA (miRNA) profile of tomato plants undergoing five biotic and abiotic stress conditions (drought, heat, P. syringae infection, B. cinerea infection, and herbivore insect attack with Leptinotarsa decemlineata larvae) and one chemical treatment with a plant defence inducer, hexanoic acid. We identified 104 conserved miRNAs belonging to 37 families and we predicted 61 novel tomato miRNAs. Among those 165 miRNAs, 41 were stress-responsive. Reverse transcription quantitative PCR (RT-qPCR) was used to validate high-throughput expression analysis data, confirming the expression profiles of 10 out of 11 randomly selected miRNAs. Most of the differentially expressed miRNAs were stress-specific, except for sly-miR167c-3p upregulated in B. cinerea and P. syringae infection, sly-newmiR26-3p upregulated in drought and Hx treatment samples, and sly-newmiR33-3p, sly-newmiR6-3p and sly-newmiR8-3p differentially expressed both in biotic and abiotic stresses. From mature miRNAs sequences of the 41 stress-responsive miRNAs 279 targets were predicted. An inverse correlation between the expression profiles of 4 selected miRNAs (sly-miR171a, sly-miR172c, sly-newmiR22-3p and sly-miR167c-3p) and their target genes (Kinesin, PPR, GRAS40, ABC transporter, GDP and RLP1) was confirmed by RT-qPCR. Altogether, our analysis of miRNAs in different biotic and abiotic stress conditions highlight the interest to understand the functional role of miRNAs in tomato stress response as well as their putative targets which could help to elucidate plants molecular and physiological adaptation to stress.

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