Genome-Wide Identification, Characterization, and Expression Profiling of Eukaryotic-Specific UBP Family Genes in Brassica rapa

Karamat, Umer; Tabusam, Javaria; Khan, Muhammad Khalil Ullah; Awan, Muhammad Jawad Akbar; Zulfiqar, Sumer; Du, Wenchao; Farooq, Muhammad

doi:10.1007/s00344-022-10820-0

Cited by 6 publications

(2 citation statements)

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“…5A). The results indicate that the TaGW2 genes have a domain of the Ring U-box superfamily that functions as an E3 ubiquitin ligase and involves speci c post-translational modi cation of proteins known as ubiquitination 20,21 . The TaD27 genes contain the DUF4033 superfamily domain that has been reported in rice, chrysanthemum, and Arabidopsis thaliana and proven to be involved in shoot branching through biosynthesis of strigolactones 22,23 , while TaCKX2.1 and TaCKX2.2 genes possess cytokinin-binding superfamily domains and involved in the inactivation of plant growth hormone-cytokinin 12 .…”

Section: Domain Analysis Of Yield-related Negative Regulatorsmentioning

confidence: 99%

Deciphering the differential expression patterns of yield-related negative regulators in hexaploid wheat and F1 hybrids at different growth stages

Awan,

Farooq,

Naqvi

et al. 2023

Preprint

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Being a major source of protein and calories in the human diet, bread wheat is cultivated worldwide, and its yield is showing dwindling notion due to various environmental challenges. Hexaploid bread wheat underwent a series of polyploidization events through interspecific hybridizations that conferred adaptive plasticity and resulted in duplication and neofunctionalization of major agronomic genes. Interestingly the genetic architecture of polyploid wheat not only confers adaptive plasticity but also offers huge genetic diversity. However, the contribution of different gene copies (homeologs) encoded from different subgenomes (A, B, D) at different growth stages remained unexplored. In this study, we assessed the differential expression profiles of yield-related negative regulators in elite cultivars of wheat and their F1 hybrids and identified various cis-regulatory signatures that might influence these expression patterns. Furthermore, the differential and preferential expression patterns of the homeologs showed dynamic expression profiles of A, B, and D subgenomes at six different growth stages, portraying the different homeolog-dominance at the same stage in the different cultivars and their F1 hybrids. Based on the expression profiling, hybrid progenies of elite cultivars were developed that showed better heterosis such as up to 17% increase in the average number of grains and up to 50% increase in average thousand grains weight as compared to mid-parents and the F2 segregating populations demonstrated varying yields from high-yielding parents. These results suggest the significance of dynamic transcriptional expression patterns and the regulatory signatures of major genes that can substantially contribute and provide insights for the selective introduction of better cultivars into hybrid breeding programs which can be harnessed for the improvement of future wheat.

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Section: Domain Analysis Of Yield-related Negative Regulatorsmentioning

confidence: 99%

Deciphering the differential expression patterns of yield-related negative regulators in hexaploid wheat and F1 hybrids at different growth stages

Awan,

Farooq,

Naqvi

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

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“…To date, the UBP family members have been identified in many plants, such as Arabidopsis thaliana, Oryza sativa, Triticum aestivum, Phyllostachys edulis, and Brassica rapa [10][11][12][13][14]. The biological functions of many UBP members have been elucidated (mostly from research results for A. thaliana), shedding light on their important roles under abiotic stresses as well as in plant growth and development [7].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification, Characterization, and Expression Analysis under Abiotic Stresses of the UBP Gene Family in Rice (Oryza sativa L.)

Zou,

Li,

Yin

et al. 2023

Agronomy

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The ubiquitin-specific protease (UBP) family represents a type of deubiquitinase (DUB) that plays a significant role in plant abiotic stress responses, growth, and development. Although UBP genes have been characterized in many species, a genome-wide systematic analysis and the potential functions under abiotic stresses have not yet been reported in rice (Oryza sativa L.). In this study, we identified 21 UBP gene family members in the genome of rice, all of which had UCH domains containing short but highly conserved Cys-box and His-box. The DUF4220 and DUF594 domains, which are found in monocotyledonous plants, were unique. Phylogenetic analysis suggested that OsUBP7 and OsUBP12 genes had the closest genetic relationships with AtUBP12 and AtUBP13, implying that OsUBP7 and OsUBP12 might have similar biological functions to AtUBP12 and AtUBP13. Synteny analysis revealed that OsUBP genes were expanded through segmental duplication under purifying selection. Meanwhile, they had closer evolutionary relationships with monocotyledonous plants. Additionally, all OsUBP genes had an ABRE cis-element, which was related to abscisic acid (ABA) stress hormone response. Protein interaction analysis suggested that OsUBP22 might modulate gene regulation through OsGCN5- and OsADA2-mediated chromatin modification, and OsUBP10 might regulate salt stress through modulating OsDNA2_4 stability. Specifically, the expression profiles and the transcriptional levels of 11 representative OsUBPs suggested the potential important functions of OsUBP9 and OsUBP17 under drought and cold stresses. Taken together, our study provided a systematic analysis of OsUBPs and preliminarily explored their potential roles under abiotic stresses. Our results lay a foundation for further research on the functions of the OsUBP gene family under abiotic stresses.

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Genome-wide identification and analysis of UBP gene family in Quercus robur

Song,

Zhang,

2024

Trees

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Genome-Wide Identification, Characterization, and Expression Profiling of Eukaryotic-Specific UBP Family Genes in Brassica rapa

Cited by 6 publications

References 70 publications

Deciphering the differential expression patterns of yield-related negative regulators in hexaploid wheat and F1 hybrids at different growth stages

Deciphering the differential expression patterns of yield-related negative regulators in hexaploid wheat and F1 hybrids at different growth stages

Genome-Wide Identification, Characterization, and Expression Analysis under Abiotic Stresses of the UBP Gene Family in Rice (Oryza sativa L.)

Genome-wide identification and analysis of UBP gene family in Quercus robur

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