Genome-wide identification and characterization of the BES/BZR gene family in wheat and foxtail millet

Liú, Dan; Cui, Yanjiao; Zhao, Zilong; Li, Suying; Liang, Dan; Wang, Conglei; Feng, Gang; Wang, Jianhe; Liu, Zhengli

doi:10.1186/s12864-021-08002-5

Cited by 14 publications

(15 citation statements)

References 44 publications

(63 reference statements)

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“…The total RNA extraction, cDNA synthesis and qRT-PCR analysis were performed as described previously [60]. All primers applied in qRT-PCR were listed in electronic supplementary material, table S11.…”

Section: Methodsmentioning

confidence: 99%

Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet ( Setaria italica (L.) P. Beauv.)

et al. 2022

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A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was performed. Comparisons between the varieties revealed that 70 genes were commonly differentially expressed. Moreover, the ratio of net photosynthetic rate under shaded environment to that under light environment could be used as an indicator of shade tolerance. Subsequently, weighted gene co-expression network analysis was employed to construct a co-expression network and modules were correlated with this ratio. A total of 375 genes were identified as potentially relevant to shade tolerance, among which nine genes were also present in the 70 differentially expressed genes, which implied that they were good candidates for genes involved in shade tolerance. Our results provide valuable resources for elucidation of the molecular mechanisms underlying shade tolerance and will contribute to breeding of shade-tolerant foxtail millet that are adapted to the shaded environment under chestnut trees.

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Section: Methodsmentioning

confidence: 99%

Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet ( Setaria italica (L.) P. Beauv.)

et al. 2022

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“…Furthermore, a recent study identified 56 Laccase family members linked to lignin metabolism ( Simões et al, 2020 ). In addition, various other gene families involved in multiple stress responses, disease resistance, seed storage or transport, such as WD40 ( Mishra et al, 2014 ), 14–3-3 ( Kumar et al, 2015 ), ZIP ( Alagarasan et al, 2017 ), SOD ( Wang et al, 2018c ), OASTL ( Liu et al, 2019b ), ATG ( Li et al, 2016a , b ), LIM ( Yang et al, 2019 ), CDPK ( Yu et al, 2018 ), NBS-LRR ( Zhao et al, 2016 ), CNL ( Andersen and Nepal, 2017b ), SSP ( Gaur et al, 2018 ), MADS-box ( Zhao et al, 2021a ), BES/BZR ( Liu et al, 2021 ), SNARE ( Wang et al, 2021a ), and PTI1 ( Huangfu et al, 2021 ; Supplementary Table 3 ). Genome-wide identification and in silico analysis of phosphate transporter 1 gene ( PHT 1 ) in Setaria viridis depicted 12 PHT 1 gene families for phosphorous uptake ( Ceasar, 2019 ).…”

Section: Omics Resources In Setariamentioning

confidence: 99%

Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects

et al. 2022

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Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C4 photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.

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“…Thus, the availability of foxtail millet genome information provided excellent opportunity for researchers to initiate whole-genome annotation and perform comparative genomic study in foxtail millet [ 5 ]. Until now, foxtail millet has gained popularity among millet research community and several gene families such as AP2/ERF [ 1 ], GRAS [ 2 ], NF-Y [ 3 ], LecRLKs [ 4 ], NAC [ 6 ], WD40 [ 7 ], MYB [ 8 ], PPR [ 9 ], HSP [ 10 ], CDPK [ 11 ], BES/BZR [ 12 ], and MADS-Box [ 13 ] have been identified and characterized to investigate their role in plant abiotic stress tolerance.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification, molecular evolution and expression analysis of the non-specific lipid transfer protein (nsLTP) family in Setaria italica

Fan

Guo

et al. 2022

BMC Plant Biol

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Background Foxtail millet (Setaria italica L.) is a millet species with high tolerance to stressful environments. Plant non-specific lipid transfer proteins (nsLTPs) are a kind of small, basic proteins involved in many biological processes. So far, the genome of S. italica has been fully sequenced, and a comprehensive understanding of the evolution and expression of the nsLTP family is still lacking in foxtail millet. Results Forty-five nsLTP genes were identified in S. italica and clustered into 5 subfamilies except three single genes (SinsLTP38, SinsLTP7, and SinsLTP44). The proportion of SinsLTPs was different in each subfamily, and members within the same subgroup shared conserved exon–intron structures. Besides, 5 SinsLTP duplication events were investigated. Both tandem and segmental duplication contributed to nsLTP expansion in S. italica, and the duplicated SinsLTPs had mainly undergone purifying selection pressure, which suggested that the function of the duplicated SinsLTPs might not diverge much. Moreover, we identified the nsLTP members in 5 other monocots, and 41, 13, 10, 4, and 1 orthologous gene pairs were identified between S. italica and S. viridis, S. bicolor, Z. mays, O. sativa, and B. distachyon, respectively. The functional divergence within the nsLTP orthologous genes might be limited. In addition, the tissue-specific expression patterns of the SinsLTPs were investigated, and the expression profiles of the SinsLTPs in response to abiotic stress were analyzed, all the 10 selected SinsLTPs were responsive to drought, salt, and cold stress. Among the selected SinsLTPs, 2 paired duplicated genes shared almost equivalent expression profiles, suggesting that these duplicated genes might retain some essential functions during subsequent evolution. Conclusions The present study provided the first systematic analysis for the phylogenetic classification, conserved domain and gene structure, expansion pattern, and expression profile of the nsLTP family in S. italica. These findings could pave a way for further comparative genomic and evolution analysis of nsLTP family in foxtail millet and related monocots, and lay the foundation for the functional analysis of the nsLTPs in S. italica.

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Genome-wide identification and characterization of the BES/BZR gene family in wheat and foxtail millet

Cited by 14 publications

References 44 publications

Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet ( Setaria italica (L.) P. Beauv.)

Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet ( Setaria italica (L.) P. Beauv.)

Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects

Genome-wide identification, molecular evolution and expression analysis of the non-specific lipid transfer protein (nsLTP) family in Setaria italica

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