High-throughput discovery of plastid genes causing albino phenotypes in ornamental chimeric plants

Abstract

Chimeric plants composed of green and albino tissues have great ornamental value. To unveil the functional genes responsible for albino phenotypes in chimeric plants, we inspected the complete plastid genomes (plastomes) in green and albino leaf tissues from 23 ornamental chimeric plants belonging to 20 species, including monocots, dicots, and gymnosperms. In nine chimeric plants, plastomes were identical between green and albino tissues. Meanwhile, another 14 chimeric plants were heteroplasmic, showing a mutation between green and albino tissues. We identified 14 different point mutations in eight functional plastid genes related to plastid-encoded RNA polymerase (rpo) or photosystems which caused albinism in the chimeric plants. Among them, 12 were deleterious mutations in the target genes, in which early termination appeared due to small deletion-mediated frameshift or single nucleotide substitution. Another was single nucleotide substitution in an intron of the ycf3 and the other was a missense mutation in coding region of the rpoC2 gene. We inspected chlorophyll structure, protein functional model of the rpoC2, and expression levels of the related genes in green and albino tissues of Reynoutria japonica. A single amino acid change, histidine-to-proline substitution, in the rpoC2 protein may destabilize the peripheral helix of plastid-encoded RNA polymerase, impairing the biosynthesis of the photosynthesis system in the albino tissue of R. japonica chimera plant.

Transcriptome analysis reveals molecular mechanisms underlying chloroplast biogenesis in albino Agave angustifolia plantlets

“…NEP, an enzyme encoded by RpoTp nuclear gene, orchestrates the transcription of housekeeping genes, including the rpo complex subunits, particularly in the early stages of plastid development. Conversely, PEP, a bacterial‐type enzyme composed of subunits α, β, β' and β″ (encoded by plastome genes rpoA , rpoB , rpoC1 and rpoC2) and PAP proteins, becomes the primary player in transcribing photosynthesis genes during later stages (Liebers et al, 2017, Park et al, 2022). In both green and albino Agave plantlets, the rpo genes showed a substantial increase in their expression as the tissue transitioned from meristem to leaf.…”

“…The transition from NEP‐dependent to PEP‐dependent transcription is a critical checkpoint in chloroplast development (Liebers et al, 2017; Shimizu & Masuda, 2021). The shift from NEP to PEP regulation of transcription is well‐documented in various plant species, with NEP predominantly active during the early stages of plastid development, and PEP later taking the lead in transcribing photosynthesis genes (Loudya et al, 2021; Park et al, 2022; Qiu et al, 2022). However, this pattern seems distinct in Agave somaclonal variants, where NEP and PEP appear more expressed in leaf tissue than in the meristem.…”

Leaf variegation caused by plastome structural variation: an example from Dianella tasmanica

“…Variegation is common in plants and previous studies have identified spontaneous single-nucleotide mutations or single small insertions/deletions that are responsible for albinism in variegated plants [ 2 , 23 , 60 , 70 ]. However, in D. tasmanica it appears that intermolecular recombination mediated by a pair of 11-bp IRs leads to a 7094-bp deletion and thus the appearance of albinism.…”

“…Heteroplasmy in the shoot apical meristem (SAM) is thought to determine color patterns in variegated plants [ 16 , 23 , 24 , 70 , 87 ]. Similar to the situation in Figs 2A and 4B of Frank and Chitwood [ 16 ], the A-type plastome in variegated plants of D. tasmanica likely arises in SAM initial cells, and propagates throughout the second meristem layer (L2) by periclinal division, creating a uniform, genetically distinct stratum of cells.…”

“…However, variegated plants are a focus of plastome heteroplasmy studies because green sectors often contain cells with normal chloroplasts, while albino sectors contain cells with abnormal plastids [ 23 ]. Spontaneous mutations in the plastomes have been identified in albino mutants and variegated plants, such as Antirrhinum [ 79 ], Cryptomeria japonica [ 32 ], barley [ 47 , 48 ], sunflower [ 2 ], Oenothera [ 19 , 60 , 95 ], and many others [ 70 ]. These spontaneous mutations are typically either single-nucleotide substitutions or small insertions/deletions of 1–50 bp, which can often cause loss of function of a plastid gene.…”