Genome-Wide Identification and Analyses of Drought/Salt-Responsive Cytochrome P450 Genes in Medicago truncatula

Yin, Xia; Jiao, Yang; Ma, Lin; Su, Yan; Pang, Yongzhen

doi:10.3390/ijms22189957

Cited by 20 publications

(13 citation statements)

References 78 publications

(93 reference statements)

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“…On the other hand, the two other genes, HORVU7Hr1G101590 and HORVU7Hr1G103510 encode Cytochrome P450 superfamily protein and transducin/WD40 repeat-like superfamily protein (WD40), respectively. Both of these gene products participate in response to salt stress ( Mao et al., 2013 , Sun Z et al., 2018 , Sun et al., 2021 ; Xia et al., 2021 ; Xin et al., 2021 ). However, the detailed function of these genes concerning salt tolerance in barley remains to be investigated by gene-editing and gain-of-function-based genetic engineering.…”

Section: Discussionmentioning

confidence: 99%

Integrated GWAS and transcriptomic analysis reveal the candidate salt-responding genes regulating Na+/K+ balance in barley (Hordeum vulgare L.)

Meng²,

Zhu³

et al. 2023

Front. Plant Sci.

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Salt stress is one of the main abiotic stresses affecting crop yield and quality. Barley has strong salt tolerance, however, the underlying genetic basis is not fully clear, especially in the seedling stage. This study examined the ionic changes in barley core germplasms under the control and salt conditions. Genome-wide association study (GWAS) analysis revealed 54 significant SNPs from a pool of 25,342 SNPs distributed in 7 chromosomes (Chr) of the Illumina Barley 50K SNP array. These SNPs are associated with ion homeostasis traits, sodium (Na+) and potassium (K+) content, and Na+/K+ ratio representing five genomic regions on Chr 2, 4, 5, 6, and 7 in the leaves of worldwide barley accessions. And there are 3 SNP peaks located on the Chr 4, 6, and 7, which could be the “hot spots” regions for mining and identifying candidate genes for salt tolerance. Furthermore, 616 unique candidate genes were screened surrounding the significant SNPs, which are associated with transport proteins, protein kinases, binding proteins, and other proteins of unknown function. Meanwhile, transcriptomic analysis (RNA-Seq) was carried out to compare the salt-tolerant (CM72) and salt-sensitive (Gairdner) genotypes subjected to salt stress. And there was a greater accumulation of differentially expressed genes(DEGs) in Gairdner compared to CM72, mainly enriched in metabolic pathway, biosynthesis of secondary metabolites, photosynthesis, signal transduction,emphasizing the different transcriptional response in both genotypes following salt exposure. Combined GWAS and RNA-Seq analysis revealed 5 promising salt-responding genes (PGK2, BASS3, SINAT2, AQP, and SYT3) from the hot spot regions, which were verified between the salt-tolerant and salt-sensitive varieties by qRT-PCR. In all, these results provide candidate SNPs and genes responsible for salinity responding in barley, and a new idea for studying such genetic basis in similar crops.

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Section: Discussionmentioning

confidence: 99%

Integrated GWAS and transcriptomic analysis reveal the candidate salt-responding genes regulating Na+/K+ balance in barley (Hordeum vulgare L.)

Meng²,

Zhu³

et al. 2023

Front. Plant Sci.

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“…In the present study, a total of 687 BnCYP450 genes were identified from Brassica napus cultivar ZS11, which is assigned into 22 subfamilies and clustered into nine clans ( Table 1 ). The number of BnCYP450s was greater than those of Arabidopsis (251), Brassica rapa (354), Brassica oleracea (343), rice (355), apple (348), tomato (457), cotton (461), model legume (346), grape (236), and fewer than in wheat (1700) [ 22 , 23 , 24 , 25 , 27 , 28 ]. Some subfamilies and clans showed deep phylogenetic relationships.…”

Section: Discussionmentioning

confidence: 99%

“…The CYP450s catalyze a great number of NADPH- and/or O 2 -dependent oxygenation/hydroxylation reactions in many organisms [ 21 , 23 ]. The CYP450 genes are widely identified in most organisms, including bacteria, plants, animals, and humans [ 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 ]. In plants, the nomenclature of CYP450 genes is generally classified into two groups: A type and non-A type [ 21 , 22 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of the Cytochrome P450 Superfamily Genes and Targeted Editing of BnCYP704B1 Confers Male Sterility in Rapeseed

Wang

Zhang

Song

et al. 2023

Plants

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The cytochrome P450 (CYP450) monooxygenase superfamily, which is involved in the biosynthesis pathways of many primary and secondary metabolites, plays prominent roles in plant growth and development. However, systemic information about CYP450s in Brassica napus (BnCYP450) was previously undiscovered and their biological significance are far from understood. Members of clan 86 CYP450s, such as CYP704Bs, are essential for the formation of pollen exine in plant male reproduction, and the targeted mutagenesis of CYP704B genes has been used to create new male sterile lines in many crops. In the present study, a total of 687 BnCYP450 genes were identified in Brassica napus cultivar “Zhongshuang 11” (ZS11), which has nearly 2.8-fold as many CYP450 members as in Arabidopsis thaliana. It is rationally estimated since Brassica napus is a tetraploid oil plant with a larger genome compared with Arabidopsis thaliana. The BnCYP450 genes were divided into 47 subfamilies and clustered into nine clans. Phylogenetic relationship analysis reveals that CYP86 clan consists of four subfamilies and 109 BnCYP450s. Members of CYP86 clan genes display specific expression profiles in different tissues and in response to ABA and abiotic stresses. Two BnCYP450s within the CYP704 subfamily from CYP86 clan, BnCYP704B1a and BnCYP704B1b, display high similarity to MS26 (Male Sterility 26, also known as CYP704B1). These two BnCYP704B1 genes were specifically expressed in young buds. We then simultaneously knocked-out these two BnCYP704B1 genes through a clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) genome engineering system. The edited plants displayed a pollenless, sterile phenotype in mature anthers, suggesting that we successfully reproduced genic male sterility (GMS, also known as nuclear male sterility) lines in Brassica napus. This study provides a systemic view of BnCYP450s and offers a strategy to facilitate the commercial utility of the CRISPR/Cas9 system for the rapid generation of GMS in rapeseed via knocking-out GMS controlling genes.

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“…Previous studies have shown that the NF-YB subfamily plays key role in improving drought tolerance in plants such as Arabidopsis [13], tobacco [18], and maize [19]. Gene families such as P450 [23], HD-ZIP [24], SRS [25], and PcG [26] in Medicago have been identified. These families are related to abiotic stress and growth, but the NF-YB gene family has not yet been reported.…”

Section: Introductionmentioning

confidence: 99%

Identification and Characterization of Abiotic Stress–Responsive NF-YB Family Genes in Medicago

Jiao

et al. 2022

IJMS

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Nuclear factor YB (NF-YB) are plant-specific transcription factors that play a critical regulatory role in plant growth and development as well as in plant resistance against various stresses. In this study, a total of 49 NF-YB genes were identified from the genomes of Medicago truncatula and Medicago sativa. Multiple sequence alignment analysis showed that all of these NF-YB members contain DNA binding domain, NF-YA interaction domain and NF-YC interaction domain. Phylogenetic analysis suggested that these NF-YB proteins could be classified into five distinct clusters. We also analyzed the exon–intron organizations and conserved motifs of these NF-YB genes and their deduced proteins. We also found many stress-related cis-acting elements in their promoter region. In addition, analyses on genechip for M. truncatula and transcriptome data for M. sativa indicated that these NF-YB genes exhibited a distinct expression pattern in various tissues; many of these could be induced by drought and/or salt treatments. In particular, RT-qPCR analysis revealed that the expression levels of gene pairs MsNF-YB27/MtNF-YB15 and MsNF-YB28/MtNF-YB16 were significantly up-regulated under NaCl and mannitol treatments, indicating that they are most likely involved in salt and drought stress response. Taken together, our study on NF-YB family genes in Medicago is valuable for their functional characterization, as well as for the application of NF-YB genes in genetic breeding for high-yield and high-resistance alfalfa.

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Genome-Wide Identification and Analyses of Drought/Salt-Responsive Cytochrome P450 Genes in Medicago truncatula

Cited by 20 publications

References 78 publications

Integrated GWAS and transcriptomic analysis reveal the candidate salt-responding genes regulating Na+/K+ balance in barley (Hordeum vulgare L.)

Integrated GWAS and transcriptomic analysis reveal the candidate salt-responding genes regulating Na+/K+ balance in barley (Hordeum vulgare L.)

Genome-Wide Identification of the Cytochrome P450 Superfamily Genes and Targeted Editing of BnCYP704B1 Confers Male Sterility in Rapeseed

Identification and Characterization of Abiotic Stress–Responsive NF-YB Family Genes in Medicago

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