title: Genome-wide organization and expression profiling of the NAC transcription factor family in potato (Solanum tuberosum L.).
abstract: NAC [no apical meristem (NAM), Arabidopsis thaliana transcription activation factor [ATAF1/2] and cup-shaped cotyledon (CUC2)] proteins belong to one of the largest plant-specific transcription factor (TF) families and play important roles in plant development processes, response to biotic and abiotic cues and hormone signalling. Our genome-wide analysis identified 110 StNAC genes in potato encoding for 136 proteins, including 14 membrane-bound TFs. The physical map positions of StNAC genes on 12 potato chromosomes were non-random, and 40 genes were found to be distributed in 16 clusters. The StNAC proteins were phylogenetically clustered into 12 subgroups. Phylogenetic analysis of StNACs along with their Arabidopsis and rice counterparts divided these proteins into 18 subgroups. Our comparative analysis has also identified 36 putative TNAC proteins, which appear to be restricted to Solanaceae family. In silico expression analysis, using Illumina RNA-seq transcriptome data, revealed tissue-specific, biotic, abiotic stress and hormone-responsive expression profile of StNAC genes. Several StNAC genes, including StNAC072 and StNAC101that are orthologs of known stress-responsive Arabidopsis RESPONSIVE TO DEHYDRATION 26 (RD26) were identified as highly abiotic stress responsive. Quantitative real-time polymerase chain reaction analysis largely corroborated the expression profile of StNAC genes as revealed by the RNA-seq data. Taken together, this analysis indicates towards putative functions of several StNAC TFs, which will provide blue-print for their functional characterization and utilization in potato improvement.
authors: Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, HP 176061, India. anil@ihbt.res.in
authors: Anil Kumar
authors: AK
authors: Singh
authors: Vishal
authors: V
authors: Sharma
authors: Awadhesh Kumar
authors: AK
authors: Pal
authors: Vishal
authors: V
authors: Acharya
authors: Paramvir Singh
authors: PS
authors: Ahuja
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D055106:Genome-Wide Association Study; D008969:Molecular Sequence Data; D005810:Multigene Family; D012275:Oryza / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D020033:Protein Isoforms / Q000145:classification / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D011198:Solanum tuberosum / Q000235:genetics* / Q000378:metabolism; D013312:Stress, Physiological; D015534:Trans-Activators / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D010940:Plant Proteins; D020033:Protein Isoforms; C434490:StNAC protein, Solanum tuberosum; D015534:Trans-Activators
keywords: Illumina RNA-seq; NAC transcription factor; abiotic stress; genome-wide analysis; potato
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