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Agronomy
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Genetic Identification and Characterisation of Crop Agronomic Traits and Stress...
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Genetic Identification and Characterisation of Crop Agronomic Traits and Stress Resistance

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

Deadline for manuscript submissions: closed (25 November 2023) | Viewed by 15304

Special Issue Editors

Dr. Niharika Sharma

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Guest Editor
NSW Department of Primary Industries, Orange Agricultural Institute, 1447, Forest Road, Orange, NSW 2800, Australia
Interests: plant genomics; bioinformatics; omics data analysis
Special Issues, Collections and Topics in MDPI journals
Dr. Davinder Singh

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Guest Editor
Plant Breeding Institute, Faculty of Science, School of Life & Environmental Science, The University of Sydney, Cobbitty, NSW 2570, Australia
Interests: plant genetics and breeding
Special Issues, Collections and Topics in MDPI journals
Dr. Kalenahalli N. Yogendra

E-Mail Website
Guest Editor
International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad 502324, Telangana, India
Interests: plant biotechnology; metabolomics and proteomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

With the increasing global human population, there is a continuous demand for food supply and climate change scenarios pose an additional threat to agricultural production worldwide. Therefore, we rely on continuous genetic gains and genetically driven approaches for crop improvement. The identification of loci for agronomic traits and their genetic characterisation are crucial for breeding new varieties. The introduction of new adaptive alleles in diverse genetic backgrounds helps to improve grain yield or develop newer crop varieties to balance supply and demand globally. The availability of large-scale genomic resources provides an opportunity to discover genetic and molecular mechanisms behind plant responses to different environmental stresses. Integrating various omics technologies into routine breeding pipelines will support the delivery of cultivars with robust yield and improved quality. In this Special Issue, we aim to bring together research papers and reviews on using plant genetic and genomic resources for enhancing key agronomic traits in the current plant breeding scenario.

Dr. Niharika Sharma
Dr. Davinder Singh
Dr. Kalenahalli N. Yogendra
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • agronomic traits
  • crop improvement
  • breeding
  • abiotic/biotic stress
  • genetic characterisation

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Related Special Issue

Published Papers (7 papers)

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Editorial

Jump to: Research, Review

3 pages, 169 KiB  
Editorial
Genetic Identification and Characterisation of Crop Agronomic Traits and Stress Resistance
by Niharika Sharma, Davinder Singh and Kalenahalli Yogendra
Agronomy 2024, 14(3), 620; https://doi.org/10.3390/agronomy14030620 - 19 Mar 2024
Viewed by 901
Abstract
Enhancing crops’ agronomic traits and resilience to stress is crucial for promoting food security and sustainable agriculture, particularly during climate change and for the growing global population [...] Full article
(This article belongs to the Special Issue Genetic Identification and Characterisation of Crop Agronomic Traits and Stress Resistance)

Research

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17 pages, 3536 KiB  
Article
Comparison and Evaluation of Low-Temperature Tolerance of Different Soybean Cultivars during the Early-Growth Stage
by Xin Wang, Xiaomei Li, Qi Zhou, Shuang Song and Shoukun Dong
Agronomy 2023, 13(7), 1716; https://doi.org/10.3390/agronomy13071716 - 27 Jun 2023
Cited by 3 | Viewed by 1652
Abstract
Low temperatures have seriously affected crop growth owing to climate change and frequent extreme weather. Low-temperature disasters easily affect the early-growth stages of planted soybeans in Northeast China. In the present study, the comprehensive evaluation method using low-temperature (4 °C) simulation at soybean [...] Read more.
Low temperatures have seriously affected crop growth owing to climate change and frequent extreme weather. Low-temperature disasters easily affect the early-growth stages of planted soybeans in Northeast China. In the present study, the comprehensive evaluation method using low-temperature (4 °C) simulation at soybean germination and seedling stages was used to compare soybean cultivars. The results revealed that low temperatures inhibited the germination ability of soybean seeds and prolonged the average germination time (about 7–13 days under low temperatures). Simultaneously, low-temperature stress at the seedling stage decreased plant height and dry weight, but accumulated proline and soluble sugar. The soluble protein content of most cultivars decreased at low temperatures. Peroxidase activity was significantly decreased in henong70, suinong82, and heinong83, and opposite in the other cultivars. Additionally, MDA content increased in cultivars heinong69, dongnong42, and dongnong55. The final comprehensive evaluation showed that Suinong42 had better low-temperature tolerance, whereas Kendou40 was more sensitive to low temperatures. The grey correlation analysis also showed that dry weight and proline can be used as the target traits for cultivar improvement. Full article
(This article belongs to the Special Issue Genetic Identification and Characterisation of Crop Agronomic Traits and Stress Resistance)
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21 pages, 6767 KiB  
Article
Genome-Wide Association Study Using Genotyping by Sequencing for Bacterial Leaf Blight Resistance Loci in Local Thai Indica Rice
by Chananton Danaisilichaichon, Phanchita Vejchasarn, Sujin Patarapuwadol, Alessandro Tondelli, Giampiero Valè, Theerayut Toojinda and Chatchawan Jantasuriyarat
Agronomy 2023, 13(5), 1286; https://doi.org/10.3390/agronomy13051286 - 29 Apr 2023
Cited by 3 | Viewed by 2495
Abstract
Bacterial leaf blight (BLB) is a devastating disease caused by Xanthomonas oryzae pv. oryzae (Xoo), which poses a significant threat to global rice production. In this study, a genome-wide association study (GWAS) was conducted using the genotyping-by-sequencing (GBS) approach to identify [...] Read more.
Bacterial leaf blight (BLB) is a devastating disease caused by Xanthomonas oryzae pv. oryzae (Xoo), which poses a significant threat to global rice production. In this study, a genome-wide association study (GWAS) was conducted using the genotyping-by-sequencing (GBS) approach to identify candidate single nucleotide polymorphisms (SNPs) associated with BLB resistance genes. The study utilized 200 indica rice accessions inoculated with seven distinct Xoo isolates and filtered highly significant SNPs using a minor allele frequency (MAF) of >5% and a call rate of 75%. Four statistical models were used to explore potential SNPs associated with BLB resistance, resulting in the identification of 32 significant SNPs on chromosomes 1–8 and 12 in the rice genome. Additionally, 179 genes were located within ±100 kb of the SNP region, of which 49 were selected as candidate genes based on their known functions in plant defense mechanisms. Several candidate genes were identified, including two genes in the same linkage disequilibrium (LD) decay as the well-known BLB resistance gene (Xa1). These findings represent a valuable resource for conducting further functional studies and developing novel breeding strategies to enhance the crop’s resistance to this disease. Full article
(This article belongs to the Special Issue Genetic Identification and Characterisation of Crop Agronomic Traits and Stress Resistance)
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19 pages, 12386 KiB  
Article
Effect of NaCl on Morphophysiological and Biochemical Responses in Gossypium hirsutum L.
by Sabahat Shaheen, Muhammad Baber, Sidra Aslam, Seema Aslam, Mehak Shaheen, Raheela Waheed, Hyojin Seo and Muhammad Tehseen Azhar
Agronomy 2023, 13(4), 1012; https://doi.org/10.3390/agronomy13041012 - 30 Mar 2023
Cited by 6 | Viewed by 1571
Abstract
Soil salinity is increasing due to several factors such as climate change and areas with uneven rainfall. This increase in level of salinity compelled the cotton breeders to develop a new germplasm that exhibit the suitable for salty soil. This study aimed to [...] Read more.
Soil salinity is increasing due to several factors such as climate change and areas with uneven rainfall. This increase in level of salinity compelled the cotton breeders to develop a new germplasm that exhibit the suitable for salty soil. This study aimed to determine the salt tolerance of 50 accessions of Gossypium hirsutum in hydroponic conditions having three levels of NaCl, i.e., 0 mM, 150 mM, and 200 mM. The experiment was carried out in a completely randomized design with a factorial arrangement. Morphological, physiological, and biochemical attributes were estimated in these genotypes. The Na+/K+ ratio was determined by dry digestion method. Salt-susceptible and -tolerant genotypes were identified by biplot and cluster analysis. The genotypes showed significant differences for morphophysiological and biochemical parameters. In control, Cyto-515 showed enhanced growth with shoot length (30.20 cm), root length (20.63 cm), fresh shoot weight (2.34 g), and fresh root weight (0.93 g), while under 150 mM and 200 mM salinity levels, MNH-992 had the maximum root length (15.67 cm) and shoot length (24.67 cm). At a 150 mM salinity level, maximum levels of antioxidants were found in Kehkshan and CIM-595, while at a 200 mM salinity level, AA-703, CIM-595, and Kehkshan showed maximum values of antioxidants. The highest Na+/K+ ratio was observed in VH-363 and FH-114, while Kehkshan had lowest Na+/K+ ratio. The biplot analysis revealed that Kehkshan, CIM-595, VH-330, Cyto-178, MNH-992, and Cyto-515 were widely dispersed and distant from the origin, and exhibiting variability for morphophysiological and biochemical traits under the salt stress. In terms of performance across the treatments, accessions MNH-992, Kehkshan, Cyto-515, and CIM-595 performed significantly better. Peroxidase activity, proline contents, H2O2 determination, and Na+/K+ ratio were shown to be useful for the salt tolerance selection criteria. The potential of such salt tolerant accessions (MNH-992, Kehkshan, Cyto-515, and CIM-595) could be assessed after planting in salt affected areas and could be used in breeding programs for the development of diverse salt tolerant new genotypes of upland cotton. Full article
(This article belongs to the Special Issue Genetic Identification and Characterisation of Crop Agronomic Traits and Stress Resistance)
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20 pages, 3141 KiB  
Article
Estimation of Drought Tolerance Indices in Upland Cotton under Water Deficit Conditions
by Sidra Aslam, Syed Bilal Hussain, Muhammad Baber, Sabahat Shaheen, Seema Aslam, Raheela Waheed, Hyojin Seo and Muhammad Tehseen Azhar
Agronomy 2023, 13(4), 984; https://doi.org/10.3390/agronomy13040984 - 27 Mar 2023
Cited by 9 | Viewed by 2309
Abstract
Cotton is a precious commodity that offers raw material to the textile industry. This crop is grown in tropical and sub-tropical regions of the world. Abiotic stresses exerts negative impact on cotton production, but water scarcity has the worst impact. It is rising [...] Read more.
Cotton is a precious commodity that offers raw material to the textile industry. This crop is grown in tropical and sub-tropical regions of the world. Abiotic stresses exerts negative impact on cotton production, but water scarcity has the worst impact. It is rising due to current situation, in which global warming is producing a decrease in precipitation while an increase in evapo-transpiration is causing an agricultural drought. Thus, it is a difficult task for cotton breeders to identify cotton lines that can respond to areas with limited water supplies without lowering yields and might be utilized as suitable parents in a breeding program to produce drought-tolerant indices. The primary objective of this research was the estimation of drought tolerance indices in upland cotton under water deficit conditions. For this purpose, fifty accessions of upland cotton were assessed for their ability to tolerate the water stress under three conditions, namely control, 50% FC, and 75% FC. These genotypes showed significant variations based on morpho-physiological and biochemical characteristics. At control conditions, these genotypes exhibited enhanced growth and better performance. Whereas, the behavior of some indices under 75% FC showed less growth as compared to control, while under the 50% FC highly significant reductions were observed among genotypes. The genotypes that are resistant to drought and those that are susceptible were found using the K-means cluster and biplot analysis. In terms of performance, the genotypes namely Cyto-515, CIM-595, FH-142, and IR-3701 exhibited relatively better in all the treatments and low excised leaf water loss, high relative water contents, chlorophyll contents, free proline contents, and peroxidase activity were observed to be useful selection criteria for drought resistance. These identified genotypes namely, Cyto-515, CIM-595, FH-142, and IR-3701 may be grown in water deficit areas of the country to assess their potential, could be used in breeding programs for development of germplasm suitable for water stress conditions. Full article
(This article belongs to the Special Issue Genetic Identification and Characterisation of Crop Agronomic Traits and Stress Resistance)
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21 pages, 3196 KiB  
Article
Agro-Morphological, Yield and Biochemical Responses of Selected Wheat (Triticum aestivum L.) Genotypes to Salt Stress
by Arpita Sen, Md. Moshiul Islam, Erin Zaman, Uttam Kumar Ghosh, Milia Bente Momtaz, Md. Ariful Islam, Tahmina Akter Urmi, Md. Abdullah Al Mamun, Md. Mamunur Rahman, Mohammed Zia Uddin Kamal, G. K. M. Mustafizur Rahman, M. Moynul Haque and Yoshiyuki Murata
Agronomy 2022, 12(12), 3027; https://doi.org/10.3390/agronomy12123027 - 30 Nov 2022
Cited by 6 | Viewed by 2143
Abstract
Wheat is affected by various biotic and abiotic stresses, especially salinity, which reduces the growth and yield drastically. With this view, an experiment was conducted to observe genotypic differences in agro-morphological, yield, and biochemical responses to salinity. Experimental variables consisted of five salt-tolerant [...] Read more.
Wheat is affected by various biotic and abiotic stresses, especially salinity, which reduces the growth and yield drastically. With this view, an experiment was conducted to observe genotypic differences in agro-morphological, yield, and biochemical responses to salinity. Experimental variables consisted of five salt-tolerant genotypes (G 13, G 20-1, G 9, G 22, G 20-2), one susceptible genotype (G 24) and one standard check variety (BARI ghom 25), which assigned to four levels of salinity with electrical conductivities 0, 4, 8 and 12 dS m−1. Irrespective of genotypes, salinity stress significantly decreased the yield and yield attributes. However, maximum total tillers plant−1, effective tillers plant−1, number of grains spike−1, and grain yield plant−1 was found in salt tolerant genotype G 20-2, followed by genotypes G 13, G 20-1, and the lowest was observed in salt-susceptible genotype G 24. The lowest reduction percentage of yield and yield attributes were also observed in salt tolerant genotype G 20-2 followed by genotypes G 13, G 20-2, and the maximum reduction percentage was found in salt-susceptible genotype G 24. Results showed that the highest amount of proline, glycinebetaine, soluble sugar and soluble protein content were observed in salt-tolerant genotype G 20-2, followed by genotypes G 13, G 20-1, and the minimum was found in salt-susceptible genotype G 24. On the other hand, the lowest hydrogen peroxide (H2O2) and melondealdehyde (MDA) accumulation was detected in the same salt-tolerant genotype G 20-2, followed by G 13, G 20-1, and the maximum was observed in salt-susceptible genotype G 24. Therefore, higher accumulations of compatible solute in the tolerant genotypes reduce the oxidative stress, and provide the higher yield. Full article
(This article belongs to the Special Issue Genetic Identification and Characterisation of Crop Agronomic Traits and Stress Resistance)
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Review

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31 pages, 4469 KiB  
Review
Molecular Basis and Engineering Strategies for Transcription Factor-Mediated Reproductive-Stage Heat Tolerance in Crop Plants
by Niharika Sharma, Lakshay Sharma, Dhanyakumar Onkarappa, Kalenahalli Yogendra, Jayakumar Bose and Rita A. Sharma
Agronomy 2024, 14(1), 159; https://doi.org/10.3390/agronomy14010159 - 10 Jan 2024
Cited by 1 | Viewed by 2550
Abstract
Heat stress (HS) is a major threat to crop productivity and is expected to be more frequent and severe due to climate change challenges. The predicted increase in global temperature requires us to understand the dimensions of HS experienced by plants, particularly during [...] Read more.
Heat stress (HS) is a major threat to crop productivity and is expected to be more frequent and severe due to climate change challenges. The predicted increase in global temperature requires us to understand the dimensions of HS experienced by plants, particularly during reproductive stages, as crop productivity is majorly dependent on the success of plant reproduction. The impact of HS on crop productivity is relatively less-studied than the other abiotic stresses, such as drought and salinity. Plants have evolved diverse mechanisms to perceive, transduce, respond, and adapt to HS at the molecular, biochemical, and physiological levels. Unraveling these complex mechanisms underlying plant HS response and tolerance would facilitate designing well-informed and effective strategies to engineer HS tolerance in crop plants. In this review, we concisely discuss the molecular impact of HS on plant reproductive processes and yield, with major emphasis on transcription factors. Moreover, we offer vital strategies (encompassing omics studies, genetic engineering and more prominently gene editing techniques) that can be used to engineer transcription factors for enhancing heat tolerance. Further, we highlight critical shortcomings and knowledge gaps in HS tolerance research that should guide future research investigations. Judicious studies and a combination of these strategies could speed up the much-needed development of HS-resilient crop cultivars. Full article
(This article belongs to the Special Issue Genetic Identification and Characterisation of Crop Agronomic Traits and Stress Resistance)
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