title: Genome-wide analysis of autophagy-associated genes in foxtail millet (Setaria italica L.) and characterization of the function of SiATG8a in conferring tolerance to nitrogen starvation in rice.
abstract: Autophagy is a cellular degradation process that is highly evolutionarily-conserved in yeast, plants, and animals. In plants, autophagy plays important roles in regulating intracellular degradation and recycling of amino acids in response to nutrient starvation, senescence, and other environmental stresses. Foxtail millet (Setaria italica) has strong resistance to stresses and has been proposed as an ideal material for use in the study of the physiological mechanisms of abiotic stress tolerance in plants. Although the genome sequence of foxtail millet (Setaria italica) is available, the characteristics and functions of abiotic stress-related genes remain largely unknown for this species.
  
  
  
  A total of 37 putative ATG (autophagy-associated genes) genes in the foxtail millet genome were identified. Gene duplication analysis revealed that both segmental and tandem duplication events have played significant roles in the expansion of the ATG gene family in foxtail millet. Comparative synteny mapping between the genomes of foxtail millet and rice suggested that the ATG genes in both species have common ancestors, as their ATG genes were primarily located in similar syntenic regions. Gene expression analysis revealed the induced expression of 31 SiATG genes by one or more phytohormone treatments, 26 SiATG genes by drought, salt and cold, 24 SiATG genes by darkness and 25 SiATG genes by nitrogen starvation. Results of qRT-PCR showing that among 37 SiATG genes, the expression level of SiATG8a was the highest after nitrogen starvation treatment 24 h, suggesting its potential role in tolerance to nutrient starvation. Moreover, the heterologous expression of SiATG8a in rice improved nitrogen starvation tolerance. Compared to wild type rice, the transgenic rice performed better and had higher aboveground total nitrogen content when the plants were grown under nitrogen starvation conditions.
  
  
  
  Our results deepen understanding about the characteristics and functions of ATG genes in foxtail millet and also identify promising new genetic resources that should be of use in future efforts to develop varieties of foxtail millet and other crop species that have resistance to nitrogen deficiency stress.
authors.affiliation: Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, 150025, China.
authors.forename: Weiwei
authors.identifier: 0000-0002-7108-5625
authors.initials: W
authors.lastname: Li
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China.
authors.forename: Ming
authors.initials: M
authors.lastname: Chen
authors.affiliation: College of Life Sciences, Northwest A&F University, Yangling, Shanxi, 712100, China.
authors.forename: Erhui
authors.initials: E
authors.lastname: Wang
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China.
authors.forename: Liqin
authors.initials: L
authors.lastname: Hu
authors.affiliation: Plant Biology and Crop Science Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
authors.forename: Malcolm J
authors.initials: MJ
authors.lastname: Hawkesford
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China.
authors.forename: Li
authors.initials: L
authors.lastname: Zhong
authors.affiliation: Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230000, China.
authors.forename: Zhu
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China.
authors.forename: Zhaoshi
authors.initials: Z
authors.lastname: Xu
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China.
authors.forename: Liancheng
authors.initials: L
authors.lastname: Li
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China.
authors.forename: Yongbin
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, 150025, China. kaku3008@126.com.
authors.forename: Changhong
authors.initials: C
authors.lastname: Guo
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China. mayouzhi@caas.cn.
authors.forename: Youzhi
authors.initials: Y
authors.lastname: Ma
mesh_terms: D001343:Autophagy / Q000235:genetics*; D000071190:Autophagy-Related Protein 8 Family / Q000235:genetics* / Q000378:metabolism; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D005091:Exons; D020440:Gene Duplication; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D055106:Genome-Wide Association Study; D007438:Introns; D009584:Nitrogen / Q000378:metabolism*; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010641:Phenotype; D010802:Phylogeny; D032983:Setaria Plant / Q000145:classification / Q000235:genetics*; D013312:Stress, Physiological
chemical_list: D000071190:Autophagy-Related Protein 8 Family; D009584:Nitrogen
keywords: Autophagy-associated genes; Expression pattern; Foxtail millet; Functional identification; Nitrogen starvation