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Journal of Genetics

, Volume 97, Issue 5, pp 1083–1095 | Cite as

Genomewide identification of PPR gene family and prediction analysis on restorer gene in Gossypium

  • Nan Zhao
  • Yumei Wang
  • Jinping HuaEmail author
Research Article
  • 164 Downloads

Abstract

Pentatricopeptide repeat (PPR) gene family plays an essential role in the regulation of plant growth and organelle gene expression. Some PPR genes are related to fertility restoration in plant, but there is no detailed information in Gossypium. In the present study, we identified 482 and 433 PPR homologues in Gossypium raimondii (\(\hbox {D}_{5}\)) and G. arboreum (\(\hbox {A}_{2}\)) genomes, respectively. Most PPR homologues showed an even distribution on the whole chromosomes. Given an evolutionary analysis to PPR genes from G. raimondii (\(\hbox {D}_{5}\)), G. arboreum (\(\hbox {A}_{2}\)) and G. hirsutum genomes, eight PPR genes were clustered together with restoring genes of other species. Most cotton PPR genes were qualified with no intron, high proportion of \(\upalpha \)-helix and classical tertiary structure of PPR protein. Based on bioinformatics analyses, eight PPR genes were targeted in mitochondrion, encoding typical P subfamily protein with protein binding activity and organelle RNA metabolism in function. Further verified by RNA-seq and quantitative real-time PCR (qRT-PCR) analyses, two PPR candidate genes, Gorai.005G0470 (\(\hbox {D}_{5}\)) and Cotton_A_08373 (\(\hbox {A}_{2}\)), were upregulated in fertile line than sterile line. These results reveal new insights into PPR gene evolution in Gossypium.

Keywords

Gossypium PPR gene family phylogenetic analysis cytoplasmic male sterility restorer gene 

Notes

Acknowledgements

We are indebted to Dr. Anming Ding (Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China) for supplying HMMER matrix of PPR gene family in Arabidopsis (defined by Prof. Small Ian). We thank Dr. Zhen Su (State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China) for helpful advises and discussion. This work was supported by the National Natural Science Foundation of China (31671741) and National Key R & D Program for Crop Breeding (2016YFD0100203).

Supplementary material

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Supplementary material 1 (docx 1899 KB)

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Copyright information

© Indian Academy of Sciences 2018

Authors and Affiliations

  1. 1.Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingPeople’s Republic of China
  2. 2.Research Institute of Cash CropsHubei Academy of Agricultural SciencesWuhanPeople’s Republic of China

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