Genome-Wide Identification and Analysis of NAC Transcription Factor Family in Two Diploid Wild Relatives of Cultivated Sweet Potato Uncovers Potential NAC Genes Related to Drought Tolerance

NAC (NAM, ATAF1/2, and CUC2) proteins play a pivotal role in modulating plant development and offer protection against biotic and abiotic stresses. Until now, no systematic knowledge of NAC family genes is available for the food security crop, sweet potato. Here, a comprehensive genome-wide survey of NAC domain-containing proteins identified 130 ItbNAC and 144 ItfNAC genes with full length sequences in the genomes of two diploid wild relatives of cultivated sweet potato, Ipomoea triloba and Ipomoea trifida, respectively. These genes were physically mapped onto 15 I. triloba and 16 I. trifida chromosomes, respectively. Phylogenetic analysis divided all 274 NAC proteins into 20 subgroups together with NAC transcription factors (TFs) from Arabidopsis. There were 9 and 15 tandem duplication events in the I. triloba and I. trifida genomes, respectively, indicating an important role of tandem duplication in sweet potato gene expansion and evolution. Moreover, synteny analysis suggested that most NAC genes in the two diploid sweet potato species had a similar origin and evolutionary process. Gene expression patterns based on RNA-Seq data in different tissues and in response to various hormone, biotic or abiotic treatments revealed their possible involvement in organ development and response to various biotic/abiotic stresses. The expression of 36 NAC TFs, which were upregulated in the five tissues and in response to mannitol treatment, was also determined by real-time quantitative polymerase chain reaction (RT-qPCR) in hexaploid cultivated sweet potato exposed to drought stress. Those results largely corroborated the expression profile of mannitol treatment uncovered by the RNA-Seq data. Some significantly up-regulated genes related to drought stress, such as ItbNAC110, ItbNAC114, ItfNAC15, ItfNAC28, and especially ItfNAC62, which had a conservative spatial conformation with a closely related paralogous gene, ANAC019, may be potential candidate genes for a sweet potato drought tolerance breeding program. This analysis provides comprehensive and systematic information about NAC family genes in two diploid wild relatives of cultivated sweet potato, and will provide a blueprint for their functional characterization and exploitation to improve the tolerance of sweet potato to abiotic stresses.

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Genome wide identification and characterization of light-harvesting Chloro a/b binding (LHC) genes reveals their potential role in enhancing drought tolerance in Gossypium hirsutum

Journal of Cotton Research ◽

10.1186/s42397-021-00090-8 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Teame Gereziher MEHARI ◽

Yanchao XU ◽

Richard Odongo MAGWANGA ◽

Muhammad Jawad UMER ◽

Joy Nyangasi KIRUNGU ◽

...

Keyword(s):

Drought Stress ◽

Gossypium Hirsutum ◽

Abiotic Stresses ◽

Substitution Rate ◽

Synonymous Substitution ◽

Synonymous Substitution Rate ◽

Drought Tolerant ◽

Genome Wide ◽

Identification And Characterization

Abstract Background Cotton is an important commercial crop for being a valuable source of natural fiber. Its production has undergone a sharp decline because of abiotic stresses, etc. Drought is one of the major abiotic stress causing significant yield losses in cotton. However, plants have evolved self-defense mechanisms to cope abiotic factors like drought, salt, cold, etc. The evolution of stress responsive transcription factors such as the trihelix, a nodule-inception-like protein (NLP), and the late embryogenesis abundant proteins have shown positive response in the resistance improvement to several abiotic stresses. Results Genome wide identification and characterization of the effects of Light-Harvesting Chloro a/b binding (LHC) genes were carried out in cotton under drought stress conditions. A hundred and nine proteins encoded by the LHC genes were found in the cotton genome, with 55, 27, and 27 genes found to be distributed in Gossypium hirsutum, G. arboreum, and G. raimondii, respectively. The proteins encoded by the genes were unevenly distributed on various chromosomes. The Ka/Ks (Non-synonymous substitution rate/Synonymous substitution rate) values were less than one, an indication of negative selection of the gene family. Differential expressions of genes showed that majority of the genes are being highly upregulated in the roots as compared with leaves and stem tissues. Most genes were found to be highly expressed in MR-85, a relative drought tolerant germplasm. Conclusion The results provide proofs of the possible role of the LHC genes in improving drought stress tolerance, and can be explored by cotton breeders in releasing a more drought tolerant cotton varieties.

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Spermine: Its Emerging Role in Regulating Drought Stress Responses in Plants

Cells ◽

10.3390/cells10020261 ◽

2021 ◽

Vol 10 (2) ◽

pp. 261

Author(s):

Md. Mahadi Hasan ◽

Milan Skalicky ◽

Mohammad Shah Jahan ◽

Md. Nazmul Hossain ◽

Zunaira Anwar ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Stress Responses ◽

Abiotic Stresses ◽

Defense Mechanisms ◽

Antioxidant Defense ◽

Severe Drought ◽

New Information ◽

Effects Of Drought

In recent years, research on spermine (Spm) has turned up a lot of new information about this essential polyamine, especially as it is able to counteract damage from abiotic stresses. Spm has been shown to protect plants from a variety of environmental insults, but whether it can prevent the adverse effects of drought has not yet been reported. Drought stress increases endogenous Spm in plants and exogenous application of Spm improves the plants’ ability to tolerate drought stress. Spm’s role in enhancing antioxidant defense mechanisms, glyoxalase systems, methylglyoxal (MG) detoxification, and creating tolerance for drought-induced oxidative stress is well documented in plants. However, the influences of enzyme activity and osmoregulation on Spm biosynthesis and metabolism are variable. Spm interacts with other molecules like nitric oxide (NO) and phytohormones such as abscisic acid, salicylic acid, brassinosteroids, and ethylene, to coordinate the reactions necessary for developing drought tolerance. This review focuses on the role of Spm in plants under severe drought stress. We have proposed models to explain how Spm interacts with existing defense mechanisms in plants to improve drought tolerance.

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A Novel WRKY Transcription Factor from Ipomoea trifida, ItfWRKY70, Confers Drought Tolerance in Sweet Potato

International Journal of Molecular Sciences ◽

10.3390/ijms23020686 ◽

2022 ◽

Vol 23 (2) ◽

pp. 686

Author(s):

Sifan Sun ◽

Xu Li ◽

Shaopei Gao ◽

Nan Nie ◽

Huan Zhang ◽

...

Keyword(s):

Drought Stress ◽

Transgenic Plants ◽

Drought Tolerance ◽

Sweet Potato ◽

Stress Responses ◽

Leaf Tissue ◽

Stomatal Aperture ◽

Ros Scavenging ◽

Ipomoea Trifida ◽

Positive Role

WRKY transcription factors are one of the important families in plants, and have important roles in plant growth, abiotic stress responses, and defense regulation. In this study, we isolated a WRKY gene, ItfWRKY70, from the wild relative of sweet potato Ipomoea trifida (H.B.K.) G. Don. This gene was highly expressed in leaf tissue and strongly induced by 20% PEG6000 and 100 μM abscisic acid (ABA). Subcellar localization analyses indicated that ItfWRKY70 was localized in the nucleus. Overexpression of ItfWRKY70 significantly increased drought tolerance in transgenic sweet potato plants. The content of ABA and proline, and the activity of SOD and POD were significantly increased, whereas the content of malondialdehyde (MDA) and H2O2 were decreased in transgenic plants under drought stress. Overexpression of ItfWRKY70 up-regulated the genes involved in ABA biosynthesis, stress-response, ROS-scavenging system, and stomatal aperture in transgenic plants under drought stress. Taken together, these results demonstrated that ItfWRKY70 plays a positive role in drought tolerance by accumulating the content of ABA, regulating stomatal aperture and activating the ROS scavenging system in sweet potato.

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Genome-Wide Identification, Evolutionary And Expression Analyses of LEA Gene Family In Peanut (Arachis Hypogaea L.)

10.21203/rs.3.rs-775523/v1 ◽

2021 ◽

Author(s):

RuoLan Huang ◽

Dong Xiao ◽

Xin Wang ◽

Yi Shen ◽

Jie Zhan ◽

...

Keyword(s):

Salicylic Acid ◽

Abiotic Stress ◽

Stress Response ◽

Gene Family ◽

Segmental Duplication ◽

Abiotic Stresses ◽

Tandem Duplication ◽

Critical Role ◽

Recognition Sites ◽

Genome Wide

Abstract Background: Late embryogenesis abundant (LEA) proteins are a group of highly hydrophilic glycine-rich proteins, which accumulate in the late stage of seed maturation and are associated with many abiotic stresses. However, few peanut LEA genes had been reported, and the research on the number, location, structure, molecular phylogeny and expression of AhLEAs was very limited. Results: In this study, 126 LEA genes were identified in the peanut genome through genome-wide analysis and were further divided into eight groups. Sequence analysis showed that most of the AhLEAs (85.7 %) had no or only one intron. LEA genes were randomly distributed on 20 chromosomes. Compared with tandem duplication, segmental duplication played a more critical role in AhLEAs amplication, and 93 segmental duplication AhLEAs and 5 pairs of tandem duplication genes were identified. Synteny analysis showed that some AhLEAs genes come from a common ancestor, and genome rearrangement and translocation occurred among these genomes. Almost all promoters of LEAs contain ABRE, MYB recognition sites, MYC recognition sites, and ERE cis-acting elements, suggesting that the LEA genes were involved in stress response. Gene expression analyses revealed that most of the LEAs were expressed in the late stages of peanut embryonic development. LEA3 (AH16G06810.1, AH06G03960.1), and Dehydrin (AH07G18700.1, AH17G19710.1) were highly expressed in roots, stems, leaves and flowers. Moreover, 100 AhLEAs were involved in response to drought, low-temperature, or Al stresses. Some LEAs that were regulated by different abiotic stresses were also regulated by hormones including ABA, brassinolide, ethylene and salicylic acid. Interestingly, AhLEAs that were up-regulated by ethylene and salicylic acid showed obvious subfamily preferences.Conclusions: AhLEAs are involved in abiotic stress response, and segmental duplication plays an important role in the evolution and amplification of AhLEAs. The genome-wide identification, classification, evolutionary and expression analyses of the AhLEA gene family provide a foundation for further exploring the LEA genes’ function in response to abiotic stress in peanuts.

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Physiological Responses under Drought Stress of Improved Drought-Tolerant Rice Lines and their Parents

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha46211188 ◽

2018 ◽

Vol 46 (2) ◽

pp. 679-687 ◽

Cited By ~ 6

Author(s):

Preeyanuch LARKUNTHOD ◽

Noppawan NOUNJAN ◽

Jonaliza L SIANGLIW ◽

Theerayut TOOJINDA ◽

Jirawat SANITCHON ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Water Status ◽

Physiological Responses ◽

High Water ◽

Recurrent Parent ◽

Potential Candidate ◽

Substitution Lines ◽

Chromosome Segment Substitution Lines ◽

Drought Tolerant

Many of the economically important rice cultivars including ‘Khao Dawk Mali 105’ (KDML105) or jasmine rice, one of the world’s famous rice exported from Thailand suffers from drought due to erratic rainfalls and limited irrigation. To improve drought tolerance and reserve genetic background of KDML105, chromosome segment substitution lines (CSSL) containing drought tolerant quantitative trait loci (DT-QTL) has been previously developed by backcrossing between KDML105 and drought tolerant donor, IR58586-F2-CA-143 (DH212). To understand the physiological responses related to drought tolerance in CSSL lines compared to parents, two CSSLs namely CSSL1-16 and CSSL1-18, respectively were used in this study. Twenty-one-d-old hydroponically grown plants were subjected to 20% PEG for 0, 7, 14 d and then recovered from stress for 3 d. The results indicated that CSSL lines especially, CSSL1-16 showed better performance under drought stress compared to their recurrent parent. Drought tolerance superior CSSL1-16 line was indicated by high water status (high relative water content and leaf water potential), good osmotic adjustment, high proline and greater membrane stability. Moreover, this line was able to resume growth after stress recovery whereas other lines/cultivar could not recover. Similarly, drought tolerant donor showed high water status suggesting that well-maintained plant water status was associated with drought tolerant trait. It could be concluded that the highest drought tolerant line was CSSL1-16 followed by DH212, CSSL1-18 and KDML105. It would be interesting to go further into introgressed section in CSSL1-16 to identify potential candidate genes in DT-QTL for breeding drought tolerant rice in the future.

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Isolation of genes/quantitative trait loci for drought stress tolerance in maize.

Molecular breeding in wheat, maize and sorghum: strategies for improving abiotic stress tolerance and yield ◽

10.1079/9781789245431.0015 ◽

2021 ◽

pp. 267-281

Author(s):

Pardeep Kumar ◽

Mukesh Choudhary ◽

B. S. Jat ◽

M. C. Dagla ◽

Vishal Singh ◽

...

Keyword(s):

Drought Stress ◽

Quantitative Trait Loci ◽

Drought Tolerance ◽

Stress Tolerance ◽

Quantitative Trait ◽

Wild Relatives ◽

Drought Stress Tolerance ◽

Expression Studies ◽

Trait Loci ◽

Breeding Programmes

Abstract This chapter focuses on target traits for drought stress, progress in mapping for drought tolerance-associated genes/QTLs identification and expression studies and introgression strategies followed by the possibilities of integrating the concept of speed breeding in maize drought breeding programmes for better utilization of wild relatives.

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Genome-wide investigation of the AP2/ERF gene family in ginger: evolution and expression profiling during development and abiotic stresses

BMC Plant Biology ◽

10.1186/s12870-021-03329-3 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Haitao Xing ◽

Yusong Jiang ◽

Yong Zou ◽

Xiaoling Long ◽

Xiaoli Wu ◽

...

Keyword(s):

Gene Structure ◽

Abiotic Stresses ◽

Growth And Development ◽

Expression Profiles ◽

Rna Seq ◽

Qrt Pcr ◽

Genome Wide ◽

Evolutionary Features ◽

Erf Family

Abstract Background AP2/ERF transcription factors (TFs) constitute one of the largest TF families in plants, which play crucial roles in plant metabolism, growth, and development as well as biotic and abiotic stresses responses. Although the AP2/ERF family has been thoroughly identified in many plant species and several AP2/ERF TFs have been functionally characterized, little is known about this family in ginger (Zingiber officinale Roscoe), an important affinal drug and diet vegetable. Recent completion of the ginger genome sequencing provides an opportunity to investigate the expression profiles of AP2/ERF genes in ginger on a genome-wide basis. Results A total of 163 AP2/ERF genes were obtained in the Z.officinale genome and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. Phylogenetic analysis divided them into three subfamilies, of which 35 belonged to the AP2 subfamily, 120 to ERF, three to RAV, and five to Sololist, respectively, which is in accordance with the number of conserved domains and gene structure analysis. A total of 10 motifs were detected in ZoAP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes. The chromosomal localization, gene structure, and conserved protein motif analyses, as well as the characterization of gene duplication events provided deep insight into the evolutionary features of these ZoAP2/ERF genes. The expression profiles derived from the RNA-seq data and quantitative reserve transcription (qRT-PCR) analysis of ZoAP2/ERFs during development and responses to abiotic stresses were investigated in ginger. Conclusion A comprehensive analysis of the AP2/ERF gene expression patterns in various tissues by RNA-seq and qRT-PCR showed that they played an important role in the growth and development of ginger, and genes that might regulate rhizome and flower development were preliminary identified. In additionally, the ZoAP2/ERF family genes that responded to abiotic stresses were also identified. This study is the first time to identify the ZoAP2/ERF family, which contributes to research on evolutionary characteristics and better understanding the molecular basis for development and abiotic stress response, as well as further functional characterization of ZoAP2/ERF genes with an aim of ginger crop improvement.

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Response of Tibetan Wild Barley Genotypes to Drought Stress and Identification of Quantitative Trait Loci by Genome-Wide Association Analysis

International Journal of Molecular Sciences ◽

10.3390/ijms20030791 ◽

2019 ◽

Vol 20 (3) ◽

pp. 791

Author(s):

Mian Zhang ◽

Man-Man Fu ◽

Cheng-Wei Qiu ◽

Fangbin Cao ◽

Zhong-Hua Chen ◽

...

Keyword(s):

Genetic Variation ◽

Drought Stress ◽

Drought Tolerance ◽

Quantitative Trait ◽

Wild Barley ◽

Genome Wide Association ◽

Dart Markers ◽

Tibetan Wild Barley ◽

Genome Wide ◽

Barley Genotypes

Tibetan wild barley has been identified to show large genetic variation and stress tolerance. A genome-wide association (GWA) analysis was performed to detect quantitative trait loci (QTLs) for drought tolerance using 777 Diversity Array Technology (DArT) markers and morphological and physiological traits of 166 Tibetan wild barley accessions in both hydroponic and pot experiments. Large genotypic variation for these traits was found; and population structure and kinship analysis identified three subpopulations among these barley genotypes. The average LD (linkage disequilibrium) decay distance was 5.16 cM, with the minimum on 6H (0.03 cM) and the maximum on 4H (23.48 cM). A total of 91 DArT markers were identified to be associated with drought tolerance-related traits, with 33, 26, 16, 1, 3, and 12 associations for morphological traits, H+K+-ATPase activity, antioxidant enzyme activities, malondialdehyde (MDA) content, soluble protein content, and potassium concentration, respectively. Furthermore, 7 and 24 putative candidate genes were identified based on the reference Meta-QTL map and by searching the Barleymap. The present study implicated that Tibetan annual wild barley from Qinghai–Tibet Plateau is rich in genetic variation for drought stress. The QTLs detected by genome-wide association analysis could be used in marker-assisting breeding for drought-tolerant barley genotypes and provide useful information for discovery and functional analysis of key genes in the future.

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Defining the function of SUMO system in pod development and abiotic stresses in Peanut

BMC Plant Biology ◽

10.1186/s12870-019-2136-9 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Yiyang Liu ◽

Jiao Zhu ◽

Sheng Sun ◽

Feng Cui ◽

Yan Han ◽

...

Keyword(s):

Abiotic Stresses ◽

Developmental Process ◽

Expression Patterns ◽

Rna Seq ◽

Specific Expression ◽

Genome Wide ◽

Pod Development ◽

Core Components ◽

Arachis Duranensis ◽

New Strategies

Abstract Background Posttranslational modification of proteins by small ubiquitin like modifier (SUMO) proteins play an important role during the developmental process and in response to abiotic stresses in plants. However, little is known about SUMOylation in peanut (Arachis hypogaea L.), one of the world’s major food legume crops. In this study, we characterized the SUMOylation system from the diploid progenitor genomes of peanut, Arachis duranensis (AA) and Arachis ipaensis (BB). Results Genome-wide analysis revealed the presence of 40 SUMO system genes in A. duranensis and A. ipaensis. Our results showed that peanut also encodes a novel class II isotype of the SCE1, which was previously reported to be uniquely present in cereals. RNA-seq data showed that the core components of the SUMOylation cascade SUMO1/2 and SCE1 genes exhibited pod-specific expression patterns, implying coordinated regulation during pod development. Furthermore, both transcripts and conjugate profiles revealed that SUMOylation has significant roles during the pod development. Moreover, dynamic changes in the SUMO conjugates were observed in response to abiotic stresses. Conclusions The identification and organization of peanut SUMO system revealed SUMOylation has important roles during stress defense and pod development. The present study will serve as a resource for providing new strategies to enhance agronomic yield and reveal the mechanism of peanut pod development.

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Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava

Scientific Reports ◽

10.1038/srep45981 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 38

Author(s):

Shuxia Li ◽

Xiang Yu ◽

Ning Lei ◽

Zhihao Cheng ◽

Pingjuan Zhao ◽

...

Keyword(s):

Drought Stress ◽

Experimental Studies ◽

Growth And Yield ◽

Rna Seq ◽

Functional Prediction ◽

Systematic Screening ◽

Cellular Processes ◽

Genome Wide ◽

Young Leaves ◽

And Control

Abstract Cold and drought stresses seriously affect cassava (Manihot esculenta) plant growth and yield. Recently, long noncoding RNAs (lncRNAs) have emerged as key regulators of diverse cellular processes in mammals and plants. To date, no systematic screening of lncRNAs under abiotic stress and their regulatory roles in cassava has been reported. In this study, we present the first reference catalog of 682 high-confidence lncRNAs based on analysis of strand-specific RNA-seq data from cassava shoot apices and young leaves under cold, drought stress and control conditions. Among them, 16 lncRNAs were identified as putative target mimics of cassava known miRNAs. Additionally, by comparing with small RNA-seq data, we found 42 lncNATs and sense gene pairs can generate nat-siRNAs. We identified 318 lncRNAs responsive to cold and/or drought stress, which were typically co-expressed concordantly or discordantly with their neighboring genes. Trans-regulatory network analysis suggested that many lncRNAs were associated with hormone signal transduction, secondary metabolites biosynthesis, and sucrose metabolism pathway. The study provides an opportunity for future computational and experimental studies to uncover the functions of lncRNAs in cassava.

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