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Transcriptome sequencing and whole genome expression profiling of hexaploid sweetpotato under salt stress.

ABSTRACT: BACKGROUND:Purple-fleshed sweetpotato (PFSP) is one of the most important crops in the word which helps to bridge the food gap and contribute to solve the malnutrition problem especially in developing countries. Salt stress is seriously limiting its production and distribution. Due to lacking of reference genome, transcriptome sequencing is offering a rapid approach for crop improvement with promising agronomic traits and stress adaptability. RESULTS:Five cDNA libraries were prepared from the third true leaf of hexaploid sweetpotato at seedlings stage (Xuzi-8 cultivar) treated with 200?mM NaCl for 0, 1, 6, 12, 48?h. Using second and third generation technology, Illumina sequencing generated 170,344,392 clean high-quality long reads that were assembled into 15,998 unigenes with an average length 2178 base pair and 96.55% of these unigenes were functionally annotated in the NR protein database. A number of 537 unigenes failed to hit any homologs which may be considered as novel genes. The current results indicated that sweetpotato plants behavior during the first hour of salt stress was different than the other three time points. Furthermore, expression profiling analysis identified 4, 479, 281, 508 significantly expressed unigenes in salt stress treated samples at the different time points including 1, 6, 12, 48?h, respectively as compared to control. In addition, there were 4, 1202, 764 and 2195 transcription factors differentially regulated DEGs by salt stress at different time points including 1, 6, 12, 48?h of salt stress. Validation experiment was done using 6 randomly selected unigenes and the results was in agree with the DEG results. Protein kinases include many genes which were found to play a vital role in phosphorylation process and act as a signal transductor/ receptor proteins in membranes. These findings suggest that salt stress tolerance in hexaploid sweetpotato plants may be mainly affected by TFs, PKs, Protein Detox and hormones related genes which contribute to enhance salt tolerance. CONCLUSION:These transcriptome sequencing data of hexaploid sweetpotato under salt stress conditions can provide a valuable resource for sweetpotato breeding research and focus on novel insights into hexaploid sweetpotato responses to salt stress. In addition, it offers new candidate genes or markers that can be used as a guide to the future studies attempting to breed salt tolerance sweetpotato cultivars.

SUBMITTER: Arisha MH

PROVIDER: S-EPMC7057664 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Transcriptome sequencing and whole genome expression profiling of hexaploid sweetpotato under salt stress.

Arisha Mohamed Hamed MH Aboelnasr Hesham H Ahmad Muhammad Qadir MQ Liu Yaju Y Tang Wei W Gao Runfei R Yan Hui H Kou Meng M Wang Xin X Zhang Yungang Y Li Qiang Q

BMC genomics 20200304 1

<h4>Background</h4>Purple-fleshed sweetpotato (PFSP) is one of the most important crops in the word which helps to bridge the food gap and contribute to solve the malnutrition problem especially in developing countries. Salt stress is seriously limiting its production and distribution. Due to lacking of reference genome, transcriptome sequencing is offering a rapid approach for crop improvement with promising agronomic traits and stress adaptability.<h4>Results</h4>Five cDNA libraries were prepa ...[more]

PMID: 32131729

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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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Transcriptome sequencing and whole genome expression profiling of hexaploid sweetpotato under salt stress.

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Transcriptome sequencing and whole genome expression profiling of hexaploid sweetpotato under salt stress.

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