title: Comparative Transcriptome Analysis of White and Purple Potato to Identify Genes Involved in Anthocyanin Biosynthesis.
abstract: BACKGROUND
  The potato (Solanum tuberosum) cultivar 'Xin Daping' is tetraploid with white skin and white flesh, while the cultivar 'Hei Meiren' is also tetraploid with purple skin and purple flesh. Comparative transcriptome analysis of white and purple cultivars was carried out using high-throughput RNA sequencing in order to further understand the mechanism of anthocyanin biosynthesis in potato.
  
  
  RESULTS
  By aligning transcript reads to the recently published diploid potato genome and de novo assembly, 209 million paired-end Illumina RNA-seq reads from these tetraploid cultivars were assembled on to 60,930 transcripts, of which 27,754 (45.55%) are novel transcripts and 9393 alternative transcripts. Using a comparison of the RNA-sequence datasets, multiple versions of the genes encoding anthocyanin biosynthetic steps and regulatory transcription factors were identified. Other novel genes potentially involved in anthocyanin biosynthesis in potato tubers were also discovered. Real-time qPCR validation of candidate genes revealed good correlation with the transcriptome data. SNPs (Single Nucleotide Polymorphism) and indels were predicted and validated for the transcription factors MYB AN1 and bHLH1 and the biosynthetic gene anthocyanidin 3-O-glucosyltransferase (UFGT).
  
  
  CONCLUSIONS
  These results contribute to our understanding of the molecular mechanism of white and purple potato development, by identifying differential responses of biosynthetic gene family members together with the variation in structural genes and transcription factors in this highly heterozygous crop. This provides an excellent platform and resource for future genetic and functional genomic research.
authors.affiliation: Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China.
authors.forename: Yuhui
authors.initials: Y
authors.lastname: Liu
authors.affiliation: The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Auckland, New Zealand.
authors.forename: Kui
authors.initials: K
authors.lastname: Lin-Wang
authors.affiliation: The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Auckland, New Zealand.
authors.forename: Cecilia
authors.initials: C
authors.lastname: Deng
authors.affiliation: The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Auckland, New Zealand.
authors.forename: Ben
authors.initials: B
authors.lastname: Warran
authors.affiliation: Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China.
authors.forename: Li
authors.initials: L
authors.lastname: Wang
authors.affiliation: Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Yu
authors.affiliation: Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China; College of Horticulture, Gansu Agricultural University, Lanzhou, China.
authors.forename: Hongyu
authors.initials: H
authors.lastname: Yang
authors.affiliation: College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.affiliation: The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Auckland, New Zealand.
authors.forename: Richard V
authors.initials: RV
authors.lastname: Espley
authors.affiliation: Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China; College of Horticulture, Gansu Agricultural University, Lanzhou, China.
authors.forename: Junlian
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China.
authors.forename: Di
authors.initials: D
authors.lastname: Wang
authors.affiliation: The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research) Mt Albert, Auckland, New Zealand; School of Biological Sciences, University of Auckland, Auckland, New Zealand.
authors.forename: Andrew C
authors.initials: AC
authors.lastname: Allan
mesh_terms: D000872:Anthocyanins / Q000096:biosynthesis*; D053898:Biosynthetic Pathways; D016000:Cluster Analysis; D019295:Computational Biology; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D054643:INDEL Mutation; D058977:Molecular Sequence Annotation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D011198:Solanum tuberosum / Q000235:genetics* / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D000872:Anthocyanins