Glycine NPQ
Enhanced photoprotection in allopolyploid Glycine dolichocarpa
RNA-Seq transcript profiling of an allotetraploid, Glycine dolichocarpa (T2) and its diploid progenitors (G. tomentella, D3; and G. syndetika, D4) in order to explore the genetic basis of enhanced nonphotochemical quenching (NPQ) in the polyploid.     Three accessions of each species were grown under either limiting (125uE) or excess (800uE) light. At approx. 2 weeks of age, leaf tissue was pooled from 6 individuals per accession, and RNA was extracted using Qiagen RNeasy with on-column DNase treatment. RNA was used for Illumina single end library construction, following the Illumina mRNA sequencing protocol with the following modifications:1) two rounds of polyA selection were performed using Dynabeads mRNA DIRECT (Invitrogen); 2) RNA was fragmented for two minutes at 70C using the RNA fragmentation reagents kit (Ambion); and 3) Illumina PE adapters were replaced with custom-made adapters containing 3nt barcodes in order to facilitate multiplexing of samples. Libraries were sequenced on an Illumina GAIIx (86bp reads) or Hi-Seq (100bp reads).
Allopolyploidy is often associated with increased photosynthetic capacity as well as enhanced stress tolerance. Excess light is a ubiquitous plant stress associated with photosynthetic light harvesting. The capacity for nonphotochemical quenching (NPQmax) was higher in a recently formed natural allotetraploid (Glycine dolichocarpa, designated “T2”) than in its diploid progenitors (G. tomentella, “D3”; and G. syndetika, “D4”). This enhancement in NPQmax was due to an increase in energy-dependent quenching (qE) relative to D3, combined with an increase in zeaxanthin-dependent quenching (qZ) relative to D4. The RNA-Seq libraries in this study were produced to explore the genetic underpinnings of these phenotypes.