Parallel pigment and transcriptomic analysis of four barley Albina and Xantha mutants reveals the complex network of the chloroplast-dependent metabolism Chiara Campoli Æ Stefano Caffarri Æ Jan T. Svensson Æ Roberto Bassi Æ A. Michele Stanca Æ Luigi Cattivelli Æ Cristina Crosatti Received: 7 February 2008 / Accepted: 8 June 2009 / Published online: 26 June 2009 Ó Springer Science+Business Media B.V. 2009 Abstract We investigated the pigment composition and the transcriptome of albina (alb-e 16 and alb-f 17 ) and xantha (xan-s 46 and xan-b 12 ) barley mutants to provide an overall transcriptional picture of genes whose expression is inter- connected with chloroplast activities and to search for can- didate genes associated with the mutations. Beside those encoding plastid-localized proteins, more than 3,000 genes involved in non-chloroplast localized metabolism were up-/ down-regulated in the mutants revealing the network of chloroplast-dependent metabolic pathways. The alb-e 16 mutant was characterized by overaccumulation of proto- porphyrin IX upon ALA (5-amino levulinic acid) feeding and down-regulation of the gene encoding one subunit of Mg-chelatase, suggesting a block of the chlorophyll bio- synthetic pathway before Mg-protoporphyrin IX biosyn- thesis, while alb-f 17 overaccumulated Mg-protoporphyrin IX and repressed PorA expression, without alterations in Mg-chelatase mRNA level. The alb-f 17 mutant also showed overexpression of several genes involved in phytochrome and in phytochrome-dependent pathways. The results indi- cate that the down-regulation of Lhcb genes in alb-e 16 cannot be mediated by the accumulation of Mg-protoporphyrin IX. After ALA treatment, xan-s 46 showed overaccumulation of Mg-protoporphyrin IX, while the relative porphyrin com- position of xan-b 12 was similar to wild type. The transcripts encoding the components of several mitochondrial meta- bolic pathways were up-regulated in albina/xantha leaves to compensate for the absence of active chloroplasts. The mRNAs encoding gun3, gun4, and gun5 barley homologous genes showed significant expression variations and were used to search for co-expressed genes across all samples. These analyses provide additional evidences on a chloro- plast-dependent covariation of large sets of nuclear genes. Keywords Barley  Transcriptomic analysis  Albina/xantha mutants  Tetrapyrrole biosynthesis  Carotenoid biosynthesis Abbreviations ABA Abscisic acid ALA 5-Amino levulinic acid CAO Chlorophyll a oxigenase Chlide Chlorophyllide DVPchlide Divinylprotochlorophyllide Electronic supplementary material The online version of this article (doi:10.1007/s11103-009-9516-8) contains supplementary material, which is available to authorized users. C. Campoli  A. M. Stanca  L. Cattivelli  C. Crosatti (&) CRA Genomic Research Centre, Via S. Protaso 302, 29017 Fiorenzuola d’Arda (PC), Italy e-mail: cristina.crosatti@entecra.it S. Caffarri Laboratoire de Ge ´ne ´tique et Biophysique des Plantes De ´partement de Biologie, CEA, IBEB, SBVME, CNRS UMR Biologie Ve ´ge ´tale et Microbiologie Environnemetales, Universite ´ Aix-Marseille II, 163, Avenue de Luminy, 13009 Marseille, France J. T. Svensson Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA C. Campoli  R. Bassi Dipartimento Scientifico e Tecnologico, Universita ` di Verona, Strada Le Grazie 15, 37134 Verona, Italy Present Address: J. T. Svensson Department of Plant Biology and Biotechnology, VKR Center of Excellence Pro-Active Plants, University of Copenhagen, 1871 Frederiksberg C, Denmark 123 Plant Mol Biol (2009) 71:173–191 DOI 10.1007/s11103-009-9516-8