Genome-wide identification, classification and expression analysis of NAC family of genes in sorghum [Sorghum bicolor (L.) Moench]

Kadier, Yibadaiti; Zu, Yiyi; Dai, Qing-min; Ge, Song; Lin, Shi-wen; Qi-zhong, Sun; Pan, Jinbao; Lü, Min

doi:10.1007/s10725-017-0295-y

Cited by 40 publications

(22 citation statements)

References 44 publications

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“…The NAC TFs have an important contribution to plant adaptation to complex land environment [ 1 ]. Plants have large number of NAC genes, and this gene family consists of more than 100 members in most plants [ 4 , 29 , 74 ], which can be involved in growth and development of plants or be induced by environmental stress. The genome of P. mume adds resolution to comprehend the phylogenetic relationship and duplication patterns of NAC gene family in Prunus .…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of the NAC Transcription Factor Gene Family Reveals Differential Expression Patterns and Cold-Stress Responses in the Woody Plant Prunus mume

Zhuo

Zheng

Zhang

et al. 2018

Genes

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NAC transcription factors (TFs) participate in multiple biological processes, including biotic and abiotic stress responses, signal transduction and development. Cold stress can adversely impact plant growth and development, thereby limiting agricultural productivity. Prunus mume, an excellent horticultural crop, is widely cultivated in Asian countries. Its flower can tolerate freezing-stress in the early spring. To investigate the putative NAC genes responsible for cold-stress, we identified and analyzed 113 high-confidence PmNAC genes and characterized them by bioinformatics tools and expression profiles. These PmNACs were clustered into 14 sub-families and distributed on eight chromosomes and scaffolds, with the highest number located on chromosome 3. Duplicated events resulted in a large gene family; 15 and 8 pairs of PmNACs were the result of tandem and segmental duplicates, respectively. Moreover, three membrane-bound proteins (PmNAC59/66/73) and three miRNA-targeted genes (PmNAC40/41/83) were identified. Most PmNAC genes presented tissue-specific and time-specific expression patterns. Sixteen PmNACs (PmNAC11/19/20/23/41/48/58/74/75/76/78/79/85/86/103/111) exhibited down-regulation during flower bud opening and are, therefore, putative candidates for dormancy and cold-tolerance. Seventeen genes (PmNAC11/12/17/21/29/42/30/48/59/66/73/75/85/86/93/99/111) were highly expressed in stem during winter and are putative candidates for freezing resistance. The cold-stress response pattern of 15 putative PmNACs was observed under 4 °C at different treatment times. The expression of 10 genes (PmNAC11/20/23/40/42/48/57/60/66/86) was upregulated, while 5 genes (PmNAC59/61/82/85/107) were significantly inhibited. The putative candidates, thus identified, have the potential for breeding the cold-tolerant horticultural plants. This study increases our understanding of functions of the NAC gene family in cold tolerance, thereby potentially intensifying the molecular breeding programs of woody plants.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of the NAC Transcription Factor Gene Family Reveals Differential Expression Patterns and Cold-Stress Responses in the Woody Plant Prunus mume

Zhuo

Zheng

Zhang

et al. 2018

Genes

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“…NAC transcription factors were named for three genes initially discovered to contain NAC domains that contain N-terminal conserved motifs: NAM (no apical meristem), ATAF1 and -2, and CUC (cupshaped cotyledon) (Souer, van Houwelingen, Kloos, Mol, & Koes, 1996;Zhu et al, 2012). NAC transcription factors are unique to plants, and most plant species including sorghum encode >100 different NAC family members (Kadier et al, 2017). Phylogenetic analysis of grass genes encoding the SbNAC-D-like factors generated C4 grass and C3 grass groups (Supporting Information Figure S4).…”

Section: Phylogenetic Analysis Of Sbnac_dmentioning

confidence: 99%

Sorghum stem aerenchyma formation is regulated by SbNAC_D during internode development

Casto

McKinley

et al. 2018

Plant Direct

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Sorghum bicolor is a drought‐resilient C4 grass used for production of grain, forage, sugar, and biomass. Sorghum genotypes capable of accumulating high levels of stem sucrose have solid stems that contain low levels of aerenchyma. The D ‐locus on SBI 06 modulates the extent of aerenchyma formation in sorghum stems and leaf midribs. A QTL aligned with this locus was identified and fine‐mapped in populations derived from BT x623* IS 320c, BT x623*R07007, and BT x623*Standard broomcorn. Analysis of coding polymorphisms in the fine‐mapped D ‐locus showed that genotypes that accumulate low levels of aerenchyma encode a truncated NAC transcription factor (Sobic.006G147400, SbNAC_d1 ), whereas parental lines that accumulate higher levels of stem aerenchyma encode full‐length NAC TF s ( SbNAC‐D ). During vegetative stem development, aerenchyma levels are low in nonelongated stem internodes, internode growing zones, and nodes. Aerenchyma levels increase in recently elongated internodes starting at the top of the internode near the center of the stem. SbNAC_D was expressed at low levels in nonelongated internodes and internode growing zones and at higher levels in regions of stem internodes that form aerenchyma. SbXCP1 , a gene encoding a cysteine protease involved in programmed cell death, was induced in SbNAC_D genotypes in parallel with aerenchyma formation in sorghum stems but not in SbNAC_d1 genotypes. Several sweet sorghum genotypes encode the recessive SbNAC_d1 allele and have low levels of stem aerenchyma. Based on these results, we propose that SbNAC_D is the D ‐gene identified by Hilton (1916) and that allelic variation in SbNAC_D modulates the extent of aerenchyma formation in sorghum stems.

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“…A myriad of genes is expressed in response to salt stress (Kadier et al, 2017;Yang et al, 2017). In the present study, the expression pattern of salinity stress-responsive genes, such NHX1, HKT1, SOS1, antioxidant-related (SOD1, CAT1 and POD1), osmolytes biosynthesis (P5CS), photosystem II-related (psbA), ABA-related (ABA2), were elucidated.…”

Section: Gene Expression Studiesmentioning

confidence: 85%

Impact of Salinity Stress on Membrane Status, Phytohormones, Antioxidant Defense System and Transcript Expression Pattern of Two Contrasting Sorghum Genotypes

Amoah

Berko

2020

Egypt. J. Agron.

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S ALINITY stress significantly impacts the growth, development and yield of sorghum. Knowledge about the productivity of sorghum under salinity stress condition is lagging, due to the marginally limited information about the physio-biochemical and molecular mechanisms underpinning salinity stress tolerance. The study aimed to investigate the physio-biochemical and molecular mechanisms associated with the differential responses under salinity stress condition in sorghum. To achieve our objectives, the physiological and biochemical salinity stress parameters, including membrane stability index, enzyme antioxidant activities, proline and chlorophyll contents, measured at the seedling stage, were elucidated to identify the salinity stress response status of the genotypes. The quantitative real-time polymerase chain reaction (qPCR) was perform to elucidate the expression pattern of different categories of genes under salinity stress in sorghum genotypes. From our results, enhanced enzyme antioxidant activities, membrane status, increased proline content and lower K + /Na + concentration under 300mM NaCl stress identified PI 585451 to be the most salinity stress-tolerant genotype. Nevertheless, increased MDA and Na + /K + level, lower proline, chlorophyll content and antioxidant enzyme activities in PI 585454 marked it to be sensitive to salinity stress. Besides, the transcript expression analysis of different genes, showed an upregulation in PI 585451 than in PI 585454. The results highlighted the differences in metabolic response to salinity stress that may play an important role in the provision of information, required for breeding and development of sorghum genotypes that are tolerant to salinity stress.

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Genome-wide identification, classification and expression analysis of NAC family of genes in sorghum [Sorghum bicolor (L.) Moench]

Cited by 40 publications

References 44 publications

Genome-Wide Analysis of the NAC Transcription Factor Gene Family Reveals Differential Expression Patterns and Cold-Stress Responses in the Woody Plant Prunus mume

Genome-Wide Analysis of the NAC Transcription Factor Gene Family Reveals Differential Expression Patterns and Cold-Stress Responses in the Woody Plant Prunus mume

Sorghum stem aerenchyma formation is regulated by SbNAC_D during internode development

Impact of Salinity Stress on Membrane Status, Phytohormones, Antioxidant Defense System and Transcript Expression Pattern of Two Contrasting Sorghum Genotypes

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