- © 2014 American Society of Plant Biologists. All Rights Reserved.
Abstract
Variation in inflorescence development is an important target of selection for numerous crop species, including many members of the Poaceae (grasses). In Asian rice (Oryza sativa), inflorescence (panicle) architecture is correlated with yield and grain-quality traits. However, many rice breeders continue to use composite phenotypes in selection pipelines, because measuring complex, branched panicles requires a significant investment of resources. We developed an open-source phenotyping platform, PANorama, which measures multiple architectural and branching phenotypes from images simultaneously. PANorama automatically extracts skeletons from images, allows users to subdivide axes into individual internodes, and thresholds away structures, such as awns, that normally interfere with accurate panicle phenotyping. PANorama represents an improvement in both efficiency and accuracy over existing panicle imaging platforms, and flexible implementation makes PANorama capable of measuring a range of organs from other plant species. Using high-resolution phenotypes, a mapping population of recombinant inbred lines, and a dense single-nucleotide polymorphism data set, we identify, to our knowledge, the largest number of quantitative trait loci (QTLs) for panicle traits ever reported in a single study. Several areas of the genome show pleiotropic clusters of panicle QTLs, including a region near the rice Green Revolution gene SEMIDWARF1. We also confirm that multiple panicle phenotypes are distinctly different among a small collection of diverse rice varieties. Taken together, these results suggest that clusters of small-effect QTLs may be responsible for varietal or subpopulation-specific panicle traits, representing a significant opportunity for rice breeders selecting for yield performance across different genetic backgrounds.
Glossary
- PI
- panicle initiation
- IM
- inflorescence meristem
- PBM
- primary branch meristem
- QTL
- quantitative trait locus
- RIL
- recombinant inbred line
- PL
- panicle length
- GUI
- graphical user interface
- EP
- extrusion point
- IMAP
- initial main axis point
- FMAP
- final main axis point
- MAPD
- mean absolute percentage deviation
- MPE
- mean percentage error
- PBL
- primary branch length
- NN
- internode number
- DTH
- days to heading
- PN
- panicle number
- EL
- exsertion length
- LOD
- log10 of the odds
- cM
- centimorgan
- NL
- internode length
- GWAS
- genome-wide association studies
- PVE
- percentage variance explained
- RL
- rachis length
- BpN
- average number of branches per node
- PBN
- primary branch number
- Received February 25, 2014.
- Accepted April 1, 2014.
- Published April 2, 2014.