Identification of nuclear genes controlling chlorophyll synthesis in barley by RNA-seq

Abstract

BackgroundAlbinism in plants is characterized by lack of chlorophyll and results in photosynthesis impairment, abnormal plant development and premature death. These abnormalities are frequently encountered in interspecific crosses and tissue culture experiments. Analysis of albino mutant phenotypes with full or partial chlorophyll deficiency can shed light on genetic determinants and molecular mechanisms of albinism. Here we report analysis of RNA-seq transcription profiling of barley (Hordeum vulgare L.) near-isogenic lines, one of which is a carrier of mutant allele of the Alm gene for albino lemma and pericarp phenotype (line i:BwAlm).Results1221 genome fragments have statistically significant changes in expression levels between lines i:BwAlm and Bowman, with 148 fragments having increased expression levels in line i:BwAlm, and 1073 genome fragments, including 42 plastid operons, having decreased levels of expression in line i:BwAlm. We detected functional dissimilarity between genes with higher and lower levels of expression in i:BwAlm line. Genes with lower level of expression in the i:BwAlm line are mostly associated with photosynthesis and chlorophyll synthesis, while genes with higher expression level are functionally associated with vesicle transport. Differentially expressed genes are shown to be involved in several metabolic pathways; the largest fraction of such genes was observed for the Calvin-Benson-Bassham cycle. Finally, de novo assembly of transcriptome contains several transcripts, not annotated in current H. vulgare genome version.ConclusionsOur results provide the new information about genes which could be involved in formation of albino lemma and pericarp phenotype. They demonstrate the interplay between nuclear and chloroplast genomes in this physiological process.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0926-x) contains supplementary material, which is available to authorized users.

Characterization of a Thermo-Inducible Chlorophyll-Deficient Mutant in Barley

“…Various leaf color mutants have been described in barley ( Gálová et al, 2000 ) but only a few genes controlling leaf color have been well characterized ( Liu Z.L. et al, 2008 ; Qin et al, 2015 ; Shmakov et al, 2016 ). In this study, we showed that V-V-Y is a thermo-inducible chlorophyll-deficient mutant at the seeding and tillering stages.…”

“…et al, 2008 ). Recently, genes controlling chlorophyll synthesis have been explored by RNA-seq in barley Alm gene near-isogenic lines ( Shmakov et al, 2016 ). However, the genes responsible for chlorophyll biosynthesis and biodegradation and leaf color formation are largely unknown in barley.…”

Improving the quality of barley transcriptome <i>de novo</i> assembling by using a hybrid approach for lines with varying spike and stem coloration

“…The data was obtained from NCBI SRA database BioProjects PRJNA342150 (libraries of NIL i:BwAlm and isogenic line Bowman) and PRJNA399215 (libraries of NIL BLP and isogenic line Bowman). In PRJNA342150 experiment, transcriptomes of NIL i:BwAlm, based on isogenic line Bowman, plants lemma and line Bowman, taken as a control, plants lemma were compared (Shmakov et al, 2016). For each of the lines three biological replicates were taken.…”

Novel genomic marker for the Alm locus in barley identified based on transcriptome analysis

“…Six short-read libraries were obtained by IonTorrent sequencing as described in Shmakov et al (2016). The libraries were filtered using PrinSeq-lite v 0.20.4 (Schmieder, Edwards, 2011).…”