Allele specific expression of Dof genes responding to hormones and abiotic stresses in sugarcane

Cai, Mingxing; Lin, Jishan; Li, Zeyun; Lin, Zhicong; Ma, Yaying; Wang, Yibin; Ming, Ray

doi:10.1371/journal.pone.0227716

Cited by 21 publications

(22 citation statements)

References 57 publications

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“…2 ). The quantity of SoDofs is lower than that of Arabidopsis (36) 27 , tomato (34) 42 , wheat (96) 43 , rice (30) 27 , potato (35) 44 , soybean (78) 28 , and sugarcane (29) 31 , but it is same to that of sugarbeet. This is because spinach separated with Arabidopsis just after the ancient whole-genome triplication and there was no whole-genome duplication in spinach genome 1 .…”

Section: Discussionmentioning

confidence: 95%

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Expression profiling of the Dof gene family under abiotic stresses in spinach

et al. 2021

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DNA-binding with one finger (Dof) are plant-specific transcription factors involved in numerous pathways of plant development, such as abiotic stresses responses. Although genome-wide analysis of Dof genes has been performed in many species, but these genes in spinach have not been analyzed yet. We performed a genome-wide analysis and characterization of Dof gene family in spinach (Spinacia oleracea L.). Twenty-two Dof genes were identified and classified into four groups with nine subgroups, which was further corroborated by gene structure and motif analyses. Ka/Ks analysis revealed that SoDofs were subjected to purifying selection. Using cis-acting elements analysis, SoDofs were involved in plant growth and development, plant hormones, and stress responses. Expression profiling demonstrated that SoDofs expressed in leaf and inflorescence, and responded to cold, heat, and drought stresses. SoDof22 expressed the highest level in male flowers and under cold stress. These results provided a genome-wide analysis of SoDof genes, their gender- and tissue-specific expression, and response to abiotic stresses. The knowledge and resources gained from these analyses will benefit spinach improvement.

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Section: Discussionmentioning

confidence: 95%

“…In recent years, with the sequencing of genome, the identification of Dof genes was widely researched in various plant species, such as Arabidopsis , rice 27 , soybean 28 , maize 29 , sorghum 30 , sugarcane 31 , and so on. The spinach draft genome was reported in 2017 1 , however, few gene families were analyzed for the genome.…”

Section: Introductionmentioning

confidence: 99%

Expression profiling of the Dof gene family under abiotic stresses in spinach

et al. 2021

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“…Allele-specific expression adds another layer to the complexity of interpreting gene expression in both autopolyploids and allopolyploids. For sugarcane, this phenomenon was investigated in genes with known functions (Cai et al ., 2020; De Mendonça Vilela et al ., 2017). As we evaluated a larger set of expressed genes, the ASEGs found in our study were associated with a wide range of functional roles, mostly with high level metabolic processes.…”

Section: Discussionmentioning

confidence: 99%

“…Allele expression has also been studied in combining the S. spontaneum genome (Zhang et al ., 2018) and transcriptomic datasets. Recently, Cai and colleagues (Cai et al ., 2020) used the upstream region of Dof transcription factors and found cis -elements associated with different functions in plants. Furthermore, these authors identified differences in upstream regions of the alleles of the same gene coding for a transcription factor.…”

Section: Discussionmentioning

confidence: 99%

“…Sforça and colleagues (Sforça et al ., 2019) also reported difficulties in observing all the haplotypes of a region, inferring missing haplotypes based on expression data when possible. Another approach used the tetraploid S. spontaneum genome (Zhang et al ., 2018) to investigate alleles of specific gene families (Cai et al ., 2020). These results show that expression of alleles from genes coding for the Dof transcription family differed depending on the tissues examined, the developmental stages or hormone treatments.…”

Section: Introductionmentioning

confidence: 99%

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Allele expression biases in mixed-ploid sugarcane accessions

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Garcia

et al. 2021

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Allele-specific expression (ASE) represents differences in the magnitude of expression between alleles of the same gene. This is not straightforward for polyploids, especially autopolyploids, as knowledge about the dose of each allele is required for accurate estimation of ASE. This is the case for the genomically complex Saccharum species, characterized by high levels of ploidy and aneuploidy. We used a Beta-Binomial model to test for allelic imbalance in Saccharum, with adaptations for mixed-ploid organisms. The hierarchical Beta-Binomial model was used to test if allele expression followed the expectation based on genomic allele dosage. The highest frequencies of ASE occurred in sugarcane hybrids, suggesting a possible influence of interspecific hybridization in these genotypes. For all accessions, ASEGs were less frequent than those with balanced allelic expression. These genes were related to a broad range of processes, mostly associated with general metabolism, organelles, responses to stress and responses to stimuli. In addition, the frequency of ASEGs in high-level functional terms was similar among the genotypes, with a few genes associated with more specific biological processes. We hypothesize that ASE in Saccharum is largely a genotype-specific phenomenon, as a large number of ASEGs were exclusive to individual accessions.

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