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Genetic Diversity of Plant Tolerance to Environmental Restraints

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (25 August 2022) | Viewed by 28879

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Special Issue Editors

Dr. Rudy Dolferus

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Guest Editor

Commonwealth Scientific & Industrial Research Organisation (CSIRO) Agr & Food, GPO Box 1700, Canberra, ACT 2601, Australia
Interests: plant molecular biology; plant genetics; plant growth regulators; response element; environmental stress

Dr. Olive Onyemaobi

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Co-Guest Editor

CSIRO Agriculture and Food, Floreat, WA 6014, Australia
Interests: agricultural plant science; botany; molecular biology

Special Issue Information

Dear Colleagues,

Land plants evolved from aquatic organisms about 475 million years ago, the conquest of land mass representing a major achievement made possible over time by genomic evolution (mutations, gene and genome duplications, polyploidy, transposons, etc.). Through this process, plants evolved complex networks of interacting genes to adapt to environmental conditions, and researchers have only just begun to unravel and understand these networks. In the 21st century, however, plants are facing a new challenge, where they have to adapt to a quickly changing environment. Global warming and extremes in temperature and water availability associated with climate change may require plants to adapt faster than their natural plasticity and/or mutation rate currently allow them to. This may cause the extinction of plant species, including staple food crops for human nutrition. The pressure is thus on for scientists to accelerate the identification of available genetic variation in plants linked to the capacity to adapt to environmental stressors and to unravel the underlying molecular and physiological basis. This Special Issue of Genes aims to provide a collection of papers that illustrate our current efforts in improving plant tolerance to environmental restraints.

Dr. Rudy Dolferus
Guest Editor
Dr. Olive Onyemaobi
Co-Guest Editor

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Keywords

plant tolerance
environmental stress
plant adaption
climate change
genome evolution
genetic variation
gene networks
stress physiology

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Published Papers (10 papers)

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Editorial

Jump to: Research, Review, Other

3 pages, 165 KiB

Open AccessEditorial

Editorial on Genetic Diversity of Plant Tolerance to Environmental Restraints

by Rudy Dolferus and Olive Onyemaobi

Genes 2023, 14(11), 1992; https://doi.org/10.3390/genes14111992 - 25 Oct 2023

Cited by 1 | Viewed by 825

Abstract

Environmental restraints like cold, drought and heat adversely affect growth and development in different ways and at different plant developmental stages, leading to reduced crop yield [...] Full article

(This article belongs to the Special Issue Genetic Diversity of Plant Tolerance to Environmental Restraints)

Research

Jump to: Editorial, Review, Other

24 pages, 4558 KiB

Open AccessArticle

Comparative Transcriptome Profiling Reveals Potential Candidate Genes, Transcription Factors, and Biosynthetic Pathways for Phosphite Response in Potato (Solanum tuberosum L.)

by Richard Dormatey, Tianyuan Qin, Yihao Wang, Benjamin Karikari, Simon Dontoro Dekomah, Youfang Fan, Zhenzhen Bi, Panfeng Yao, Kazim Ali, Chao Sun and Jiangping Bai

Genes 2022, 13(8), 1379; https://doi.org/10.3390/genes13081379 - 1 Aug 2022

Cited by 3 | Viewed by 2176

Abstract

The study was conducted with C31 and C80 genotypes of the potato (Solanum tuberosum L.), which are tolerant and susceptible to phosphite (Phi, H₂PO₃), respectively. To decipher the molecular mechanisms underlying tolerance and susceptibility to Phi in the potato, RNA sequencing was used to study the global transcriptional patterns of the two genotypes. Media were prepared with 0.25 and 0.50 mM Phi, No-phosphorus (P), and 1.25 mM (phosphate, Pi as control). The values of fragments per kilobase of exon per million mapped fragments of the samples were also subjected to a principal component analysis, grouping the biological replicates of each sample. Using stringent criteria, a minimum of 819 differential (DEGs) were detected in both C80-Phi-0.25_vs_C80-Phi-0.50 (comprising 517 upregulated and 302 downregulated) and C80-Phi-0.50_vs_C80-Phi-0.25 (comprising 302 upregulated and 517 downregulated) and a maximum of 5214 DEGs in both C31-Con_vs_C31-Phi-0.25 (comprising 1947 upregulated and 3267 downregulated) and C31-Phi-0.25_vs_C31-Con (comprising 3267 upregulated and 1947 downregulated). DEGs related to the ribosome, plant hormone signal transduction, photosynthesis, and plant–pathogen interaction performed important functions under Phi stress, as shown by the Kyoto Encyclopedia of Genes and Genomes annotation. The expressions of transcription factors increased significantly in C31 compared with C80. For example, the expressions of Soltu.DM.01G047240, Soltu.DM.08G015900, Soltu.DM.06G012130, and Soltu.DM.08G012710 increased under P deficiency conditions (Phi-0.25, Phi-0.50, and No-P) relative to the control (P sufficiency) in C31. This study adds to the growing body of transcriptome data on Phi stress and provides important clues to the Phi tolerance response of the C31 genotype. Full article

(This article belongs to the Special Issue Genetic Diversity of Plant Tolerance to Environmental Restraints)

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14 pages, 2922 KiB

Open AccessEditor’s ChoiceArticle

WGCNA Analysis Identifies the Hub Genes Related to Heat Stress in Seedling of Rice (Oryza sativa L.)

by Yubo Wang, Yingfeng Wang, Xiong Liu, Jieqiang Zhou, Huabing Deng, Guilian Zhang, Yunhua Xiao and Wenbang Tang

Genes 2022, 13(6), 1020; https://doi.org/10.3390/genes13061020 - 6 Jun 2022

Cited by 20 | Viewed by 4378

Abstract

Frequent high temperature weather affects the growth and development of rice, resulting in the decline of seed–setting rate, deterioration of rice quality and reduction of yield. Although some high temperature tolerance genes have been cloned, there is still little success in solving the effects of high temperature stress in rice (Oryza sativa L.). Based on the transcriptional data of seven time points, the weighted correlation network analysis (WGCNA) method was used to construct a co–expression network of differentially expressed genes (DEGs) between the rice genotypes IR64 (tolerant to heat stress) and Koshihikari (susceptible to heat stress). There were four modules in both genotypes that were highly correlated with the time points after heat stress in the seedling. We further identified candidate hub genes through clustering and analysis of protein interaction network with known–core genes. The results showed that the ribosome and protein processing in the endoplasmic reticulum were the common pathways in response to heat stress between the two genotypes. The changes of starch and sucrose metabolism and the biosynthesis of secondary metabolites pathways are possible reasons for the sensitivity to heat stress for Koshihikari. Our findings provide an important reference for the understanding of high temperature response mechanisms and the cultivation of high temperature resistant materials. Full article

(This article belongs to the Special Issue Genetic Diversity of Plant Tolerance to Environmental Restraints)

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27 pages, 5298 KiB

Open AccessArticle

Estimating Effects of Radiation Frost on Wheat Using a Field-Based Frost Control Treatment to Stop Freezing Damage

by Brenton A. Leske and Thomas Ben Biddulph

Genes 2022, 13(4), 578; https://doi.org/10.3390/genes13040578 - 24 Mar 2022

Cited by 4 | Viewed by 2871 | Correction

Abstract

Crop phenotyping experiments have long struggled to have a reliable control treatment that excludes frost and associated freezing damage to plants. Previous attempts used a barrier, such as a removable shelter or cloth to exclude frost. However, these methods were labour intensive and varied in their effectiveness. An automated diesel heater was used to protect field plots of wheat (Triticum aestivum L.) from frost damage. In 2018 and 2019 there were 22 and 33 radiation frost events from July to October at the field site. The heater maintained canopy air temperature above freezing (>0 °C) for the duration of the frost (~6–8 h). Heated plots had 2–3 °C warmer minimum canopy air temperatures. Cold and chilling damage was still present in heated plots and represented 20–30% floret sterility; freezing damage in non-heated plots accounted for an additional 10–30% floret sterility. Grain mapping revealed: grain set in the apical spikelets is most affected by frost damage; proximal florets (G1 and G2) contribute the most to grain yield, but distal (G3 and G4) are important contributors to grain yield when sterility in proximal florets occurs. These results demonstrate that a plot heater is a useful tool to study frost-induced freezing damage in cereal crops, by way of preventing freezing damage in heated field plots for direct comparison to naturally frosted plots. This approach could be used to develop improved damage functions for crop simulation models through a dose and timing-response experiment for natural frost incidence on cereal crops in field plots. Full article

(This article belongs to the Special Issue Genetic Diversity of Plant Tolerance to Environmental Restraints)

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18 pages, 1900 KiB

Open AccessFeature PaperArticle

Drought, Low Nitrogen Stress, and Ultraviolet-B Radiation Effects on Growth, Development, and Physiology of Sweetpotato Cultivars during Early Season

by Purushothaman Ramamoorthy, Raju Bheemanahalli, Stephen L. Meyers, Mark W. Shankle and Kambham Raja Reddy

Genes 2022, 13(1), 156; https://doi.org/10.3390/genes13010156 - 16 Jan 2022

Cited by 17 | Viewed by 3967

Abstract

Drought, ultraviolet-B (UV-B), and nitrogen stress are significant constraints for sweetpotato productivity. Their impact on plant growth and development can be acute, resulting in low productivity. Identifying phenotypes that govern stress tolerance in sweetpotatoes is highly desirable to develop elite cultivars with better yield. Ten sweetpotato cultivars were grown under nonstress (100% replacement of evapotranspiration (ET)), drought-stress (50% replacement of ET), UV-B (10 kJ), and low-nitrogen (20% LN) conditions. Various shoot and root morphological, physiological, and gas-exchange traits were measured at the early stage of the crop growth to assess its performance and association with the storage root number. All three stress factors caused significant changes in the physiological and root- and shoot-related traits. Drought stress reduced most shoot developmental traits (29%) to maintain root growth. UV-B stress increased the accumulation of plant pigments and decreased the photosynthetic rate. Low-nitrogen treatment decreased shoot growth (11%) and increased the root traits (18%). The highly stable and productive cultivars under all four treatments were identified using multitrait stability index analysis and weighted average of absolute scores (WAASB) analyses. Further, based on the total stress response indices, ‘Evangeline’, ‘O’Henry’, and ‘Beauregard B-14’ were identified as vigorous under drought; ‘Evangeline’, ‘Orleans’, and ‘Covington’ under UV-B; and ‘Bonita’, ‘Orleans’, and ‘Beauregard B-14’ cultivars showed greater tolerance to low nitrogen. The cultivars ‘Vardaman’ and ‘NC05-198’ recorded a low tolerance index across stress treatments. This information could help determine which plant phenotypes are desirable under stress treatment for better productivity. The cultivars identified as tolerant, sensitive, and well-adapted within and across stress treatments can be used as source materials for abiotic stress tolerance breeding programs. Full article

(This article belongs to the Special Issue Genetic Diversity of Plant Tolerance to Environmental Restraints)

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19 pages, 905 KiB

Open AccessArticle

Gene Expression Profiles Suggest a Better Cold Acclimation of Polyploids in the Alpine Species Ranunculus kuepferi (Ranunculaceae)

by Eleni Syngelaki, Claudia Paetzold and Elvira Hörandl

Genes 2021, 12(11), 1818; https://doi.org/10.3390/genes12111818 - 18 Nov 2021

Cited by 13 | Viewed by 2508

Abstract

Alpine habitats are shaped by harsh abiotic conditions and cold climates. Temperature stress can affect phenotypic plasticity, reproduction, and epigenetic profiles, which may affect acclimation and adaptation. Distribution patterns suggest that polyploidy seems to be advantageous under cold conditions. Nevertheless, whether temperature stress can induce gene expression changes in different cytotypes, and how the response is initialized through gene set pathways and epigenetic control remain vague for non-model plants. The perennial alpine plant Ranunculus kuepferi was used to investigate the effect of cold stress on gene expression profiles. Diploid and autotetraploid individuals were exposed to cold and warm conditions in climate growth chambers and analyzed via transcriptome sequencing and qRT-PCR. Overall, cold stress changed gene expression profiles of both cytotypes and induced cold acclimation. Diploids changed more gene set pathways than tetraploids, and suppressed pathways involved in ion/cation homeostasis. Tetraploids mostly activated gene set pathways related to cell wall and plasma membrane. An epigenetic background for gene regulation in response to temperature conditions is indicated. Results suggest that perennial alpine plants can respond to temperature extremes via altered gene expression. Tetraploids are better acclimated to cold conditions, enabling them to colonize colder climatic areas in the Alps. Full article

(This article belongs to the Special Issue Genetic Diversity of Plant Tolerance to Environmental Restraints)

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37 pages, 9194 KiB

Open AccessArticle

Reproductive Stage Drought Tolerance in Wheat: Importance of Stomatal Conductance and Plant Growth Regulators

by Olive Onyemaobi, Harriet Sangma, Gagan Garg, Xiaomei Wallace, Sue Kleven, Pipob Suwanchaikasem, Ute Roessner and Rudy Dolferus

Genes 2021, 12(11), 1742; https://doi.org/10.3390/genes12111742 - 29 Oct 2021

Cited by 25 | Viewed by 3806

Abstract

Drought stress requires plants to adjust their water balance to maintain tissue water levels. Isohydric plants (‘water-savers’) typically achieve this through stomatal closure, while anisohydric plants (‘water-wasters’) use osmotic adjustment and maintain stomatal conductance. Isohydry or anisohydry allows plant species to adapt to different environments. In this paper we show that both mechanisms occur in bread wheat (Triticum aestivum L.). Wheat lines with reproductive drought-tolerance delay stomatal closure and are temporarily anisohydric, before closing stomata and become isohydric at higher threshold levels of drought stress. Drought-sensitive wheat is isohydric from the start of the drought treatment. The capacity of the drought-tolerant line to maintain stomatal conductance correlates with repression of ABA synthesis in spikes and flag leaves. Gene expression profiling revealed major differences in the drought response in spikes and flag leaves of both wheat lines. While the isohydric drought-sensitive line enters a passive growth mode (arrest of photosynthesis, protein translation), the tolerant line mounts a stronger stress defence response (ROS protection, LEA proteins, cuticle synthesis). The drought response of the tolerant line is characterised by a strong response in the spike, displaying enrichment of genes involved in auxin, cytokinin and ethylene metabolism/signalling. While isohydry may offer advantages for longer term drought stress, anisohydry may be more beneficial when drought stress occurs during the critical stages of wheat spike development, ultimately improving grain yield. Full article

(This article belongs to the Special Issue Genetic Diversity of Plant Tolerance to Environmental Restraints)

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19 pages, 2035 KiB

Open AccessArticle

Transcriptional Changes in Pearl Millet Leaves under Heat Stress

by Dejun Huang, Min Sun, Ailing Zhang, Jishan Chen, Jian Zhang, Chuang Lin, Huan Zhang, Xiaowen Lu, Xiaoshan Wang, Haidong Yan, Jianan Tang and Linkai Huang

Genes 2021, 12(11), 1716; https://doi.org/10.3390/genes12111716 - 28 Oct 2021

Cited by 18 | Viewed by 2842

Abstract

High-temperature stress negatively affects the growth and development of plants, and therefore threatens global agricultural safety. Cultivating stress-tolerant plants is the current objective of plant breeding programs. Pearl millet is a multi-purpose plant, commonly used as a forage but also an important food staple. This crop is very heat-resistant and has a higher net assimilation rate than corn under high-temperature stress. However, the response of heat resistant pearl millet has so far not been studied at the transcriptional level. In this study, transcriptome sequencing of pearl millet leaves exposed to different lengths of heat treatment (1 h, 48 h and 96 h) was conducted in order to investigate the molecular mechanisms of the heat stress response and to identify key genes related to heat stress. The results showed that the amount of heat stress-induced DEGs in leaves differs with the length of exposure to high temperatures. The highest value of DEGs (8286) was observed for the group exposed to heat stress for 96 h, while the other two treatments showed lower DEGs values of 4659 DEGs after 1 h exposure and 3981 DEGs after 48 h exposure to heat stress. The DEGs were mainly synthesized in protein folding pathways under high-temperature stress after 1 h exposure. Moreover, a large number of genes encoding ROS scavenging enzymes were activated under heat stress for 1 h and 48 h treatments. The flavonoid synthesis pathway of pearl millet was enriched after heat stress for 96 h. This study analyzed the transcription dynamics under short to long-term heat stress to provide a theoretical basis for the heat resistance response of pearl millet. Full article

(This article belongs to the Special Issue Genetic Diversity of Plant Tolerance to Environmental Restraints)

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Review

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12 pages, 1848 KiB

Open AccessReview

Source-To-Sink Transport of Sugar and Its Role in Male Reproductive Development

by Jingbin Li, Yu-Jin Kim and Dabing Zhang

Genes 2022, 13(8), 1323; https://doi.org/10.3390/genes13081323 - 25 Jul 2022

Cited by 10 | Viewed by 3357

Abstract

Sucrose is produced in leaf mesophyll cells via photosynthesis and exported to non-photosynthetic sink tissues through the phloem. The molecular basis of source-to-sink long-distance transport in cereal crop plants is of importance due to its direct influence on grain yield—pollen grains, essential for male fertility, are filled with sugary starch, and rely on long-distance sugar transport from source leaves. Here, we overview sugar partitioning via phloem transport in rice, especially where relevant for male reproductive development. Phloem loading and unloading in source leaves and sink tissues uses a combination of the symplastic, apoplastic, and/or polymer trapping pathways. The symplastic and polymer trapping pathways are passive processes, correlated with source activity and sugar gradients. In contrast, apoplastic phloem loading/unloading involves active processes and several proteins, including SUcrose Transporters (SUTs), Sugars Will Eventually be Exported Transporters (SWEETs), Invertases (INVs), and MonoSaccharide Transporters (MSTs). Numerous transcription factors combine to create a complex network, such as DNA binding with One Finger 11 (DOF11), Carbon Starved Anther (CSA), and CSA2, which regulates sugar metabolism in normal male reproductive development and in response to changes in environmental signals, such as photoperiod. Full article

(This article belongs to the Special Issue Genetic Diversity of Plant Tolerance to Environmental Restraints)

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