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Genome-Wide Identification of the HMA Gene Family and Expression Analysis under Cd Stress in Barley.

ABSTRACT: In recent years, cadmium (Cd) pollution in soil has increased with increasing industrial activities, which has restricted crop growth and agricultural development. The heavy metal ATPase (HMA) gene family contributes to heavy metal stress resistance in plants. In this study, 21 HMA genes (HvHMAs) were identified in barley (Hordeumvulgare L., Hv) using bioinformatics methods. Based on phylogenetic analysis and domain distribution, barley HMA genes were divided into five groups (A-E), and complete analyses were performed in terms of physicochemical properties, structural characteristics, conserved domains, and chromosome localization. The expression pattern analysis showed that most HvHMA genes were expressed in barley and exhibited tissue specificity. According to the fragments per kilobase of exon per million fragments values in shoots from seedlings at the 10 cm shoot stage (LEA) and phylogenetic analysis, five HvHMA genes were selected for expression analysis under Cd stress. Among the five HvHMA genes, three (HvHMA1, HvHMA3, and HvHMA4) were upregulated and two (HvHMA2 and HvHMA6) were downregulated following Cd treatments. This study serves as a foundation for clarifying the functions of HvHMA proteins in the heavy metal stress resistance of barley.

SUBMITTER: Zhang C

PROVIDER: S-EPMC8468745 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundPlant non-specific lipid transfer proteins (nsLTPs), a group of small, basic ubiquitous proteins to participate in lipid transfer, cuticle formation and stress response, are involved in the regulation of plant growth and development. To date, although the nsLTP gene family of barley (Hordeum vulgare L.) has been preliminarily identified, it is still unclear in the recently completed genome database of barley and Qingke, and its transcriptional profiling under abiotic stress has not been elucidated as well.ResultsWe identified 40 barley nsLTP (HvLTP) genes through a strict screening strategy based on the latest barley genome and 35 Qingke nsLTP (HtLTP) orthologues using blastp, and these LTP genes were divided into four types (1, 2, D and G). At the same time, a comprehensive analysis of the physical and chemical characteristics, homology alignment, conserved motifs, gene structure and evolution of HvLTPs and HtLTPs further supported their similar nsLTP characteristics and classification. The genomic location of HvLTPs and HtLTPs showed that these genes were unevenly distributed, and obvious HvLTP and HtLTP gene clusters were found on the 7 chromosomes including six pairs of tandem repeats and one pair of segment repeats in the barley genome, indicating that these genes may be co-evolutionary and co-regulated. A spatial expression analysis showed that most HvLTPs and HtLTPs had different tissue-specific expression patterns. Moreover, the upstream cis-element analysis of HvLTPs and HtLTPs showed that there were many different stress-related transcriptional regulatory elements, and the expression pattern of HvLTPs and HtLTPs under abiotic stress also indicated that numerous HvLTP and HtLTP genes were related to the abiotic stress response. Taken together, these results may be due to the differences in promoters rather than by genes themselves resulting in different expression patterns under abiotic stress.ConclusionDue to a stringent screening and comprehensive analysis of the nsLTP gene family in barley and Qingke and its expression profile under abiotic stress, this study can be considered a useful source for the future studies of nsLTP genes in either barley or Qingke or for comparisons of different plant species.

Project description:IntroductionThe higher plant transcription factor C2H2 zinc finger protein (C2H2-ZFP) is essential for plant growth, development, and stress response. There are limited studies on C2H2-ZFP genes in sweetpotato, despite a substantial number of C2H2-ZFP genes having been systematically found in plants.MethodsIn this work, 178 C2H2-ZFP genes were found in sweetpotato, distributed randomly on 15 chromosomes, and given new names according to where they were located. These members of the zinc finger gene family are separated into six branches, as shown by the phylogenetic tree. 24 tandem repeats of IbZFP genes and 46 fragment repeats were identified, and a homology study revealed that IbZFP genes linked more regions with wild relative species of sweetpotato as well as rhizome plants like potato and cassava. And we analyzed the expression patterns of IbZFP genes during the early development of sweetpotato storage roots (SRs) and salt stress using transcriptome data, and identified 44 IbZFP genes that exhibited differences in expression levels during the early expansion of sweetpotato SRs in different varieties, and 92 IbZFP genes that exhibited differences in expression levels under salt stress in salt tolerant and salt sensitive sweetpotato varieties. Additionally, we cloned six IbZFP genes in sweetpotato and analyzed their expression patterns in different tissues, their expression patterns under abiotic stress and hormone treatment, and subcellular localization.Results and discussionThe results showed that the IbZFP genes had tissue specificity in sweetpotato and were induced to varying degrees by drought and salt stress. ABA and GA3 treatments also affected the expression of the IbZFP genes. We selected IbZFP105, which showed significant differences in expression levels under salt stress and ABA treatment, to be heterologously expressed in Arabidopsis thaliana. We found that IbZFP105 OE lines exhibited higher tolerance to salt stress and ABA stress. This indicates that IbZFP105 can enhance the salt tolerance of plants. These results systematically identified the evolution and expression patterns of members of the C2H2-ZFP gene family in sweetpotato, providing a theoretical basis for studying the role of IbZFP genes in the development of sweetpotato SRs and in resistance to stress.

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Genome-Wide Identification of the HMA Gene Family and Expression Analysis under Cd Stress in Barley.

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