Genome-wide characterization and functional analysis of class III peroxidase gene family in soybean reveal regulatory roles of GsPOD40 in drought tolerance

Aleem, Muqadas; Riaz, Awais; Raza, Qasim; Aleem, Maida; Aslam, Muhammad; Kong, Keke; Atif, Rana Muhammad; Kashif, Muhammad; Bhat, Javaid Akhtar; Zhao, Tuanjie

doi:10.1016/j.ygeno.2021.11.016

Cited by 31 publications

(38 citation statements)

References 102 publications

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“…Ka and Ks analyses revealed that the evolution of POD genes was driven mainly by purifying selection and that only a few POD sequences may have experienced positive selection during the evolutionary period. Similar results were found in the study on the evolution of PODs in maize ( Wang Y et al, 2015 ), sweet orange ( Li et al, 2020 ), while in contrast with results in soybean ( Aleem et al, 2022 ), Arabidopsis ( Tognolli et al, 2002 ), and rice ( Passardi et al, 2004 ). Based on phylogenetic relationships, the NtPOD family was categorized into six subgroups.…”

Section: Discussionsupporting

confidence: 88%

“…In total, 210 class III peroxidase genes were identified in the tobacco genome. This number is larger than that of most reported species, such as Arabidopsis (73) ( Tognolli et al, 2002 ), rice (138) ( Passardi et al, 2004 ), maize (119) ( Wang Y et al, 2015 ), soybean (124) ( Aleem et al, 2022 ), polar (93) ( Ren et al, 2014 ), Chinese pear (94) ( Cao et al, 2016 ), carrot (102) ( Meng et al, 2021 ), and other diploid genome plants, but fewer than that in hexaploid wheat (374) ( Su et al, 2020 ). This indicates a considerable expansion of the POD gene family in tobacco and wheat compared to other plant species.…”

Section: Discussionmentioning

confidence: 75%

“…PODs have been shown to play a role in a broad range of physiological and developmental processes, including cell wall metabolism, lignification, auxin metabolism, stress tolerance, and defense response ( Pandey et al, 2017 ). To date, class III peroxidases have been investigated and characterized in a variety of plant species, including Arabidopsis ( Tognolli et al, 2002 ), cassava ( Wu et al, 2019 ), Chinese pear ( Cao et al, 2016 ), maize ( Wang Y et al, 2015 ), rice ( Passardi et al, 2004 ), orange ( Li et al, 2020 ), grapevine ( Xiao et al, 2020 ), and soybean ( Aleem et al, 2022 ). Some genetic evidences suggested that class III peroxidase is an abiotic stress-responsive enzyme in different plant species.…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Identification and Analysis of the Class III Peroxidase Gene Family in Tobacco (Nicotiana tabacum)

Cheng

Meng

et al. 2022

Front. Genet.

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Class III peroxidases (PODs) are plant-specific enzymes that play significant roles in plant physiological processes and stress responses. However, a comprehensive analysis of the POD gene family in tobacco has not yet been conducted. In this study, 210 non-redundant POD gene members (NtPODs) were identified in tobacco (Nicotiana tabacum) and distributed unevenly throughout 24 tobacco chromosomes. Phylogenetic analysis clustered these genes into six subgroups (I-VI). Gene structure and motif analyses showed the structural and functional diversity among the subgroups. Segmental duplication and purifying selection were the main factors affecting NtPOD gene evolution. Our analyses also suggested that NtPODs might be regulated by miRNAs and cis-acting regulatory elements of transcription factors that are involved in various biological processes. In addition, the expression patterns in different tissues and under various stress treatments were investigated. The results showed that the majority of NtPODs had tissue-specific expression patterns and may be involved in many biotic and abiotic responses. qRT-PCR analyses of different tissues and stress treatments were performed to verify transcriptome patterns. Expression of a green fluorescent protein-NtPOD fusion confirmed the plasma membrane localization of NtPOD121 and NtPOD4. Furthermore, 3D structures provided evidences of membrane-bound peroxidase. These findings provide useful information to better understand the evolution of the NtPOD gene family and lay the foundation for further studies on POD gene function in tobacco.

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Section: Discussionsupporting

confidence: 88%

Section: Discussionmentioning

confidence: 75%

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Identification and Analysis of the Class III Peroxidase Gene Family in Tobacco (Nicotiana tabacum)

Cheng

Meng

et al. 2022

Front. Genet.

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“…Genome-wide identification and characterization of important gene families are becoming main stream research approaches during recent years ( Ahmed et al, 2021 ; Aleem et al, 2022 ). Previously, comprehensive genome-wide analyses of MADS-box genes have been carried out in diverse plant species.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Diversity of MADS-Box Genes in Bread Wheat is Associated with its Rapid Global Adaptability

Raza¹,

Riaz²,

Atif

et al. 2022

Front. Genet.

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MADS-box gene family members play multifarious roles in regulating the growth and development of crop plants and hold enormous promise for bolstering grain yield potential under changing global environments. Bread wheat (Triticum aestivum L.) is a key stable food crop around the globe. Until now, the available information concerning MADS-box genes in the wheat genome has been insufficient. Here, a comprehensive genome-wide analysis identified 300 high confidence MADS-box genes from the publicly available reference genome of wheat. Comparative phylogenetic analyses with Arabidopsis and rice MADS-box genes classified the wheat genes into 16 distinct subfamilies. Gene duplications were mainly identified in subfamilies containing unbalanced homeologs, pointing towards a potential mechanism for gene family expansion. Moreover, a more rapid evolution was inferred for M-type genes, as compared with MIKC-type genes, indicating their significance in understanding the evolutionary history of the wheat genome. We speculate that subfamily-specific distal telomeric duplications in unbalanced homeologs facilitate the rapid adaptation of wheat to changing environments. Furthermore, our in-silico expression data strongly proposed MADS-box genes as active guardians of plants against pathogen insurgency and harsh environmental conditions. In conclusion, we provide an entire complement of MADS-box genes identified in the wheat genome that could accelerate functional genomics efforts and possibly facilitate bridging gaps between genotype-to-phenotype relationships through fine-tuning of agronomically important traits.

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“…Overexpression of Mn-SOD improved salt tolerance by inhibiting ROS accumulation in Arabidopsis thaliana plants [ 56 ]. Overexpression of GsPOD40 in soybean enhanced tolerance to drought stress through alleviation of ROS induced oxidative damage [ 57 ]. In this study, the expression levels of the ROS-scavenging system genes and the activity of SOD and POD were significantly increased, and the content of H 2 O 2 decreased in transgenic plants compared with WT under drought stress ( Figure 6 and Figure 8 ).…”

Section: Discussionmentioning

confidence: 99%

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

Sun

Gao

et al. 2022

IJMS

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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 characterization and functional analysis of class III peroxidase gene family in soybean reveal regulatory roles of GsPOD40 in drought tolerance

Cited by 31 publications

References 102 publications

Genome-Wide Identification and Analysis of the Class III Peroxidase Gene Family in Tobacco (Nicotiana tabacum)

Genome-Wide Identification and Analysis of the Class III Peroxidase Gene Family in Tobacco (Nicotiana tabacum)

Genome-Wide Diversity of MADS-Box Genes in Bread Wheat is Associated with its Rapid Global Adaptability

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

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