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A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: closed (20 April 2023) | Viewed by 40517

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Dr. Roxana Yockteng

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AGROSAVIA (Corporación Colombiana de Investigación Agropecuaria), Tibaitatá 250047, Colombia
Interests: genetic diversity; plant genetics; genomics and transcriptomics; plant–pathogen interaction
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Dr. Andrés J. Cortés

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1. Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 vía Rionegro—Las Palmas, Rionegro 054048, Colombia
2. Facultad de Ciencias Agrarias, Departamento de Ciencias Forestales, Universidad Nacional de Colombia—Sede Medellín, Medellín 050034, Colombia
Interests: plant genomics; plant breeding; genetics of adaptation; population genomics
Special Issues, Collections and Topics in MDPI journals

Dr. María Ángeles Castillejo

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Guest Editor

Campus Rabanales, University of Cordoba, Cordoba, Spain
Interests: forest species; biotic and abiotic stresses; molecular markers; omics approaches; systems biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear colleagues,

The growing human population and climate change are imposing unprecedented challenges for the global food supply. To cope with these pressures, crop improvement demands enhancing agronomical important traits such as yield, resistance, and nutritional value by pivoting direct and indirect genetically-assisted approaches. The development of last-generation high-throughput screening technologies, known as omics, promises to speed up trait improvement in plants. Large-scale techniques such as genomics, transcriptomics, proteomics, metabolomics, and phenomics have already retrieved large volumes of data as never before that, merged through bioinformatics and machine-learning approaches, are helping us understand the mechanisms behind crop features. Omics datasets are not only being generated from tissues of a single genotype, but are also permeating macro-scale interactions to deepen our knowledge of crop behavior across the microbial, and environmental continua. However, despite these massive technological and computational developments, cohesive efforts to combine contrasting omic studies within common pathways and cellular networks of crop systems are in their infancy. Therefore, this Special Issue envisions offering updated views on multidimensional large-scale omics-based approaches. Specifically, we welcome studies that explore the uses of the omics paradigm, and their integration through trans-disciplinary bioinformatics, as tools to improve qualitative and quantitative traits in crop species.

Dr. Roxana Yockteng
Dr. Andrés J. Cortés
Dr. María Ángeles Castillejo
Guest Editors

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Keywords

crop improvement
genomics
transcriptomics
proteomics
metabolomics
metagenomics
metatranscriptomics
nutrigenomics
ionomics
lipidomics
phenomics
environmental omics
bioinformatics
machine learning

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Related Special Issue

Omics Approaches for Crop Improvement—Volume II in Agronomy (1 article)

Published Papers (11 papers)

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Editorial

Jump to: Research, Review

9 pages, 525 KiB

Open AccessEditorial

‘Omics’ Approaches for Crop Improvement

by Andrés J. Cortés, María Ángeles Castillejo and Roxana Yockteng

Agronomy 2023, 13(5), 1401; https://doi.org/10.3390/agronomy13051401 - 19 May 2023

Cited by 3 | Viewed by 3097

Abstract

The growing human population and climate change are imposing unprecedented challenges on the global food supply [...] Full article

(This article belongs to the Special Issue Omics Approaches for Crop Improvement)

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Research

Jump to: Editorial, Review

23 pages, 6372 KiB

Open AccessEditor’s ChoiceArticle

High-Throughput Canopy and Belowground Phenotyping of a Set of Peanut CSSLs Detects Lines with Increased Pod Weight and Foliar Disease Tolerance

by Davis Gimode, Ye Chu, Corley C. Holbrook, Daniel Fonceka, Wesley Porter, Iliyana Dobreva, Brody Teare, Henry Ruiz-Guzman, Dirk Hays and Peggy Ozias-Akins

Agronomy 2023, 13(5), 1223; https://doi.org/10.3390/agronomy13051223 - 26 Apr 2023

Cited by 2 | Viewed by 1884

Abstract

We deployed field-based high-throughput phenotyping (HTP) techniques to acquire trait data for a subset of a peanut chromosome segment substitution line (CSSL) population. Sensors mounted on an unmanned aerial vehicle (UAV) were used to derive various vegetative indices as well as canopy temperatures. A combination of aerial imaging and manual scoring showed that CSSL 100, CSSL 84, CSSL 111, and CSSL 15 had remarkably low tomato spotted wilt virus (TSWV) incidence, a devastating disease in South Georgia, USA. The four lines also performed well under leaf spot pressure. The vegetative indices showed strong correlations of up to 0.94 with visual disease scores, indicating that aerial phenotyping is a reliable way of selecting under disease pressure. Since the yield components of peanut are below the soil surface, we deployed ground penetrating radar (GPR) technology to detect pods non-destructively. Moderate correlations of up to 0.5 between pod weight and data acquired from GPR signals were observed. Both the manually acquired pod data and GPR variables highlighted the three lines, CSSL 84, CSSL 100, and CSSL 111, as the best-performing lines, with pod weights comparable to the cultivated check Tifguard. Through the combined application of manual and HTP techniques, this study reinforces the premise that chromosome segments from peanut wild relatives may be a potential source of valuable agronomic traits. Full article

(This article belongs to the Special Issue Omics Approaches for Crop Improvement)

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20 pages, 2790 KiB

Open AccessArticle

An Integration of Transcriptomic Data and Modular Gene Co-Expression Network Analysis Uncovers Drought Stress-Related Hub Genes in Transgenic Rice Overexpressing OsAbp57

by Muhammad-Redha Abdullah-Zawawi, Lay-Wen Tan, Zuraida Ab Rahman, Ismanizan Ismail and Zamri Zainal

Agronomy 2022, 12(8), 1959; https://doi.org/10.3390/agronomy12081959 - 19 Aug 2022

Cited by 3 | Viewed by 2238

Abstract

Auxin receptor plays a significant role in the plant auxin signalling pathway in response to abiotic stress. Recently, we found that transgenic rice overexpressing ABP57 had higher drought tolerance than the wild-type cultivar, MR219, due to the fact of its enhanced leaf photosynthetic rate and yields under drought stress. We performed a microarray study on this line to investigate the underlying mechanisms contributing to the observed phenotype. After microarray data filtering, 3596 genes were subjected to modular gene co-expression network (mGCN) development using CEMiTool, an R package. We identified highly related genes in 12 modules that could act to specific responses towards drought or any of the abiotic stress types. Gene set enrichment and overrepresentation analyses for modules extracted two highly upregulated modules that are involved in drought-related biological processes such as transmembrane transport of metal ions and response to oxidative stress. Finally, 123 hub genes were identified in all modules after integrating co-expression information with physical interaction data. In addition, the interplay of significant pathways between the metabolism of chlorophyll and flavonoid and the signalling pathways of MAPK, IAA, and SA inferred the concurrent involvement of stress tolerance response. Collectively, our findings seek new future directions for breeding strategies in rice tolerant improvements. Full article

(This article belongs to the Special Issue Omics Approaches for Crop Improvement)

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17 pages, 1190 KiB

Open AccessArticle

TMT-Based Quantitative Proteomic Analysis Reveals the Response of Tomato (Solanum lycopersicum L.) Seedlings to Ebb-and-Flow Subirrigation

by Kelei Wang, Muhammad Moaaz Ali, Tianxin Guo, Shiwen Su, Xianzhi Chen, Jian Xu and Faxing Chen

Agronomy 2022, 12(8), 1880; https://doi.org/10.3390/agronomy12081880 - 10 Aug 2022

Cited by 2 | Viewed by 1950

Abstract

Ebb-and-flow subirrigation (EFI) is a water-saving and environmentally friendly irrigation method that can effectively improve water use efficiency and promote plant growth. In this study, we elucidated the effects of ebb-and-flow subirrigation on the protein levels in tomato roots in comparison with top sprinkle irrigation (TSI) and used an integrated approach involving tandem mass tag (TMT) labeling, high-performance liquid chromatography (HPLC) fractionation, and mass-spectrometry (MS)-based analysis. A total of 8510 quantifiable proteins and 513 differentially accumulated proteins (DAPs) were identified, of which the expressions of 283 DAPs were up-regulated, and 230 DAPs were down-regulated in the EFI vs. TSI treatment comparison. According to proteomic data, we performed a systematic bioinformatics analysis of all the identified proteins and DAPs. The DAPs were most significantly associated with the terms ‘metabolic process’, ‘anchored component of membrane’, ‘oxidoreductase activity’, ‘phenylpropanoid biosynthesis’, and ‘biosynthesis of secondary metabolites’ according to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes enrichment (KEGG) analysis. The 272 DAPs were classified into 12 subcellular components according to their subcellular localization. Furthermore, the activities of SOD, POD, CAT, GR, and APX in tomato roots were remarkably increased under EFI, while the MDA content was decreased compared with TSI. Correlation analysis among activities of enzymes and their related DAPs showed that 30 DAPs might be responsible for the regulation of these enzymes. The results showed that ebb-and-flow subirrigation could induce a series of DAPs responses in tomato roots to be adapted to the new mode of water supply. Full article

(This article belongs to the Special Issue Omics Approaches for Crop Improvement)

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12 pages, 1600 KiB

Open AccessArticle

SNP Genotyping for Purity Assessment of a Forage Oat (Avena sativa L.) Variety from Colombia

by Luis Fernando Campuzano-Duque, Diego Bejarano-Garavito, Javier Castillo-Sierra, Daniel Ricardo Torres-Cuesta, Andrés J. Cortés and Matthew Wohlgemuth Blair

Agronomy 2022, 12(7), 1710; https://doi.org/10.3390/agronomy12071710 - 20 Jul 2022

Cited by 1 | Viewed by 2816

Abstract

Single nucleotide polymorphism (SNP) markers have multiple applications in plant breeding of small grains. They are used for the selection of divergent parents, the identification of genetic variants and marker-assisted selection. However, the use of SNPs in varietal purity assessment is under-reported, especially for multi-line varieties from the public sector. In the case of variety evaluation, these genetic markers are tools for maintaining varietal distinctness, uniformity and stability needed for cultivar release of multi-line or pure-line varieties of inbred crops. The objective of this research was to evaluate the purity and relationships of one original (AV-25) and two multi-line sub-populations (AV25-T and AV25-S) of the inbreeding species, oats (Avena sativa L.). Both sub-populations could be useful as forages in the central highland region of Colombia (>2000 masl), such as in the departments of Boyacá and Cundinamarca, even though they were derived from an original composite mixture widely used in the mountainsides of the southern department of Nariño named Avena 25. Representative single plant selections (SPS) from the two sub-populations were grown together with SPS harvests from off-type plants (early and late) and plants from the original AV25 composite mixture, to determine their genetic similarity. Plants were genotyped by DNA extraction of a plateful of 96 individual plant samples and SNPs were detected for an Illumina Infinium 6K Chip assay. The data were used for the analysis of genetic structure and population relationships. The grouping observed based on the genetic data indicated that AV25-T and AV25-S were homogeneous populations and somewhat divergent in their genetic profile compared to the original AV25-C mix. In addition, to the two commercial, certified oat varieties (Cajicá and Cayuse) were different from these. The early and late selections were probable contaminants and could be discarded. We concluded that the use of SNP markers is an appropriate tool for ensuring genetic purity of oat varieties. Full article

(This article belongs to the Special Issue Omics Approaches for Crop Improvement)

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18 pages, 2079 KiB

Open AccessArticle

Photosystem II Repair Cycle in Faba Bean May Play a Role in Its Resistance to Botrytis fabae Infection

by María Ángeles Castillejo, Ángel M. Villegas-Fernández, Tamara Hernández-Lao and Diego Rubiales

Agronomy 2021, 11(11), 2247; https://doi.org/10.3390/agronomy11112247 - 6 Nov 2021

Cited by 4 | Viewed by 2365

Abstract

Chocolate spot, which is caused by the necrotrophic fungus Botrytis fabae, is a major foliar disease occurring worldwide and dramatically reducing crop yields in faba bean (Vicia faba). Although chemical control of this disease is an option, it has serious economic and environmental drawbacks that make resistant cultivars a more sensible choice. The molecular mechanisms behind the defense against B. fabae are poorly understood. In this work, we studied the leave proteome in two faba bean genotypes that respond differently to B. fabae in order to expand the available knowledge on such mechanisms. For this purpose, we used two-dimensional gel electrophoresis (2DE) in combination with Matrix-Assisted Laser Desorption/Ionization (MALDI-TOF/TOF). Univariate statistical analysis of the gels revealed 194 differential protein spots, 102 of which were identified by mass spectrometry. Most of the spots belonged to proteins in the energy and primary metabolism, degradation, redox or response to stress functional groups. The MS results were validated with assays of protease activity in gels. Overall, they suggest that the two genotypes may respond to B. fabae with a different PSII protein repair cycle mechanism in the chloroplast. The differences in resistance to B. fabae may be the result of a metabolic imbalance in the susceptible genotype and of a more efficient chloroplast detoxification system in the resistant genotype at the early stages of infection. Full article

(This article belongs to the Special Issue Omics Approaches for Crop Improvement)

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22 pages, 1493 KiB

Open AccessEditor’s ChoiceArticle

Multi-Environment Yield Components in Advanced Common Bean (Phaseolus vulgaris L.) × Tepary Bean (P. acutifolius A. Gray) Interspecific Lines for Heat and Drought Tolerance

by Esteban Burbano-Erazo, Rommel Igor León-Pacheco, Carina Cecilia Cordero-Cordero, Felipe López-Hernández, Andrés J. Cortés and Adriana Patricia Tofiño-Rivera

Agronomy 2021, 11(10), 1978; https://doi.org/10.3390/agronomy11101978 - 30 Sep 2021

Cited by 38 | Viewed by 3965

Abstract

Heat and drought are major stresses that significantly reduce seed yield of the common bean (Phaseolus vulgaris L.). In turn, this affects the profitability of the crop in climatic-vulnerable tropical arid regions, which happen to be the poorest and in most need of legume proteins. Therefore, it is imperative to broaden the sources of heat and drought resistance in the common bean by examining closely related species from warmer and drier environments (i.e., Tepary bean, P. acutifolius A. Gray), while harnessing such variation, typically polygenic, throughout advanced interspecific crossing schemes. As part of this study, interspecific congruity backcrosses for high temperature and drought tolerance conditions were characterized across four localities in coastal Colombia. Genotypes with high values of CO₂ assimilation (>24 µmol CO₂ m⁻² s⁻¹), promising yield scores (>19 g/plant), and high seed mineral content (Fe > 100 mg/kg) were identified at the warmest locality, Motilonia. At the driest locality, Caribia, one intercrossed genotype (i.e., 85) and the P. acutifolius G40001 control exhibited sufficient yield for commercial production (17.76 g/plant and 12.76 g/plant, respectively). Meanwhile, at southernmost Turipaná and Carmen de Bolívar localities, two clusters of genotypes exhibited high mean yield scores with 33.31 g/plant and 17.89 g/plant, respectively, and one genotype had an increased Fe content (109.7 mg/kg). Overall, a multi-environment AMMI analysis revealed that genotypes 13, 27, 82, and 84 were environmentally stable with higher yield scores compared to the Tepary control G40001. Ultimately, this study allows us to conclude that advanced common bean × Tepary bean interspecific congruity backcrosses are capable of pyramiding sufficient polygenic tolerance responses for the extreme weather conditions of coastal Colombia, which are likely to worsen due to climate change. Furthermore, some particular recombination events (i.e., genotype 68) show that there may be potential to couple breeding for heat and drought tolerance with Fe mineral biofortification, despite a prevalent trade-off, as a way to fight malnutrition of marginalized communities in tropical regions. Full article

(This article belongs to the Special Issue Omics Approaches for Crop Improvement)

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18 pages, 9575 KiB

Open AccessEditor’s ChoiceArticle

Magnesium transporter Gene Family: Genome-Wide Identification and Characterization in Theobroma cacao, Corchorus capsularis, and Gossypium hirsutum of Family Malvaceae

by Parviz Heidari, Abdullah, Sahar Faraji and Peter Poczai

Agronomy 2021, 11(8), 1651; https://doi.org/10.3390/agronomy11081651 - 19 Aug 2021

Cited by 45 | Viewed by 3909

Abstract

Magnesium (Mg) is an element involved in various key cellular processes in plants. Mg transporter (MGT) genes play an important role in magnesium distribution and ionic balance maintenance. Here, MGT family members were identified and characterized in three species of the plant family Malvaceae, Theobroma cacao, Corchorus capsularis, and Gossypium hirsutum, to improve our understanding of their structure, regulatory systems, functions, and possible interactions. We identified 18, 41, and 16 putative non-redundant MGT genes from the genome of T. cacao, G. hirsutum, and C. capsularis, respectively, which clustered into three groups the maximum likelihood tree. Several segmental/tandem duplication events were determined between MGT genes. MGTs appear to have evolved slowly under a purifying selection. Analysis of gene promoter regions showed that MGTs have a high potential to respond to biotic/abiotic stresses and hormones. The expression patterns of MGT genes revealed a possible role in response to P. megakarya fungi in T. cacao, whereas MGT genes showed differential expression in various tissues and response to several abiotic stresses, including cold, salt, drought, and heat stress in G. hirsutum. The co-expression network of MGTs indicated that genes involved in auxin-responsive lipid metabolism, cell wall organization, and photoprotection can interact with MGTs. Full article

(This article belongs to the Special Issue Omics Approaches for Crop Improvement)

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20 pages, 7662 KiB

Open AccessEditor’s ChoiceArticle

The GASA Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome Wide Identification and Expression Analysis

by Abdullah, Sahar Faraji, Furrukh Mehmood, Hafiz Muhammad Talha Malik, Ibrar Ahmed, Parviz Heidari and Peter Poczai

Agronomy 2021, 11(7), 1425; https://doi.org/10.3390/agronomy11071425 - 16 Jul 2021

Cited by 45 | Viewed by 6318

Abstract

The gibberellic acid-stimulated Arabidopsis (GASA/GAST) gene family is widely distributed in plants and involved in various physiological and biological processes. These genes also provide resistance to abiotic and biotic stresses, including antimicrobial, antiviral, and antifungal. We are interested in characterizing the GASA gene family and determining its role in various physiological and biological process in Theobroma cacao. Here, we report 17 tcGASA genes distributed on six chromosomes in T. cacao. The gene structure, promoter region, protein structure and biochemical properties, expression, and phylogenetics of all tcGASAs were analyzed. Phylogenetic analyses divided tcGASA proteins into five groups. Among 17 tcGASA genes, nine segmentally duplicating genes were identified which formed four pairs and cluster together in phylogenetic tree. Differential expression analyses revealed that most of the tcGASA genes showed elevated expression in the seeds (cacao food), implying their role in seed development. The differential expression of tcGASAs was recorded between the tolerant and susceptible cultivars of cacao, which indicating their possible role as fungal resistant. Our findings provide new insight into the function, evolution, and regulatory system of the GASA family genes in T.cacao and may suggest new target genes for development of fungi-resistant cacao varieties in breeding programs. Full article

(This article belongs to the Special Issue Omics Approaches for Crop Improvement)

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20 pages, 4622 KiB

Open AccessEditor’s ChoiceArticle

Marker-Assisted Backcross Breeding for Improvement of Submergence Tolerance and Grain Yield in the Popular Rice Variety ‘Maudamani’

by Elssa Pandit, Swapnil Pawar, Saumya Ranjan Barik, Shakti Prakash Mohanty, Jitendriya Meher and Sharat Kumar Pradhan

Agronomy 2021, 11(7), 1263; https://doi.org/10.3390/agronomy11071263 - 22 Jun 2021

Cited by 16 | Viewed by 3862

Abstract

Submergence stress due to flash floods reduces rice yield drastically in sensitive varieties. Maudamani is a high yielding popular rice variety but is highly susceptible to submergence stress. The selection of progenies carrying Sub1 and GW5 (wide-grain) enhanced the submergence stress tolerance and grain yield of theMaudamani variety by following the marker-assisted backcross breeding method. Foreground screening detected 14 BC1F1, 17 BC2F1, and 12 BC3F1 backcross progenies that carried the target QTLs for submergence tolerance and grain width. Background screening was performed in the progenies carrying the target QTL and enhanced the recovery of a recipient parent’s genome by upto 96.875% in the BC3 pyramided line. The BC3F1 plant containing the highest recipient parent genome content and the target QTLs was self-pollinated. In BC3F2 generation, the target QTLs the Sub1 and GW5 (wide-grain) alleles and recipient parent’s yield component QTL OsSPL14 were tracked for homozygous states in the progenies. Seven pyramided lines showed tolerance to submergence for 14 days and higher grain yield than both the parents. The pyramided lines were similar to the recipient parent for the majority of the studied morphological and quality traits. The pyramided lines are useful as cultivars and can serve as potential donors for transfer of Sub1, OsSPL14, Gn1a, GW5 (wide-grain), and SCM2 QTLs. Full article

(This article belongs to the Special Issue Omics Approaches for Crop Improvement)

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Review

Jump to: Editorial, Research

17 pages, 10151 KiB

Open AccessReview

A Review of Omics Technologies and Bioinformatics to Accelerate Improvement of Papaya Traits

by Rabiatul-Adawiah Zainal-Abidin, Insyirah-Hannah Ruhaizat-Ooi and Sarahani Harun

Agronomy 2021, 11(7), 1356; https://doi.org/10.3390/agronomy11071356 - 1 Jul 2021

Cited by 6 | Viewed by 5033

Abstract

Papaya (Carica papaya) is an economically important fruit crop that is mostly planted in tropical and subtropical regions. Major diseases of papaya, such as the papaya dieback disease (PDD), papaya ringspot virus (PRSV) disease, and papaya sticky disease (PSD), have caused large yield and economic losses in papaya-producing countries worldwide. Postharvest losses have also contributed to the decline in papaya production. Hence, there is an urgent need to secure the production of papaya for a growing world population. Integration of omics resources in crop breeding is anticipated in order to facilitate better-designed crops in the breeding programme. In papaya research, the application of omics and bioinformatics approaches are gradually increased and are underway. Hence, this review focuses on addressing omics technologies and bioinformatics that are used in papaya research. To date, four traits of the papaya have been studied using omics and bioinformatics approaches, which include its ripening process, abiotic stress, disease resistance, and fruit quality (i.e., sweetness, fruit shape, and fruit size). This review also highlights the potential of genetics and genomics data, as well as the systems biology approach that can be applied in a papaya-breeding programme in the near future. Full article

(This article belongs to the Special Issue Omics Approaches for Crop Improvement)

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