Identification of QTLs and Candidate Genes Related to Flower Traits and Bolting Time in Raphanus sativus

Radish flower color, bolting time, and flowering time are important traits for attracting certain pollinators and affect fleshy root quality. In this study, an analysis of the anthocyanidins in radish flowers by high-performance liquid chromatography revealed that differences in the cyanidin content are likely to be associated with the variability in radish flower colors (i.e., purple and white petals). A quantitative trait loci (QTL) analysis identified nine QTLs on three Raphanus sativus linkage groups. Three QTLs—qRFC1, qRBT1, and qRFT1—which were consistently detected and explained a high proportion of the observed variation (10.30% to 34.57%), were considered as the major QTLs responsible for flower color, bolting time, and flowering time, respectively. A total of 16 and 11 candidate genes within the major QTL regions for flower color and bolting/flowering times, respectively, were preliminarily annotated. Six genes (Rs018140, Rs018950, Rs019220, Rs020080, Rs020590, and Rs021450) related to flower color were differentially expressed in the parental lines. On the basis of nucleotide and amino acid sequence diversity between the parental lines, Rs314940, Rs315000, Rs315310, and Rs315960 were identified as candidate genes mediating the radish bolting and flowering times. This study revealed the genetic complexity of the radish flower color, bolting time, and flowering time traits. The identified candidate genes in the QTL regions may be useful for radish breeding programs and also for functional characterization in radish.

Multiple Loci Control Variation in Plasticity to Foliar Shade Throughout Development in Arabidopsis thaliana

The shade avoidance response is a set of developmental changes exhibited by plants to avoid shading by competitors, and is an important model of adaptive plant plasticity. While the mechanisms of sensing shading by other plants are well-known and appear conserved across plants, less is known about the developmental mechanisms that result in the diverse array of morphological and phenological responses to shading. This is particularly true for traits that appear later in plant development. Here we use a nested association mapping (NAM) population of Arabidopsis thaliana to decipher the genetic architecture of the shade avoidance response in late-vegetative and reproductive plants. We focused on four traits: bolting time, rosette size, inflorescence growth rate, and inflorescence size, found plasticity in each trait in response to shade, and detected 17 total QTL; at least one of which is a novel locus not previously identified for shade responses in Arabidopsis. Using path analysis, we dissected each colocalizing QTL into direct effects on each trait and indirect effects transmitted through direct effects on earlier developmental traits. Doing this separately for each of the seven NAM populations in each environment, we discovered considerable heterogeneity among the QTL effects across populations, suggesting allelic series at multiple QTL or interactions between QTL and the genetic background or the environment. Our results provide insight into the development and variation in shade avoidance responses in Arabidopsis, and emphasize the value of directly modeling the relationships among traits when studying the genetics of complex developmental syndromes.

Gene Expression Changes Occurring at Bolting Time are Associated with Leaf Senescence in Arabidopsis

In plants, the vegetative to reproductive phase transition (termed bolting in Arabidopsis) generally precedes age-dependent leaf senescence (LS). Many studies describe a temporal link between bolting time and LS, as plants that bolt early, senesce early, and plants that bolt late, senesce late. However, the molecular mechanisms underlying this relationship are unknown and are potentially agriculturally important, as they may allow for the development of crops that can overcome early LS caused by stress-related early phase transition. We hypothesized that gene expression changes associated with bolting time were regulating LS. We used a mutant that displays both early bolting and early LS as a model to test this hypothesis. An RNA-seq time series experiment was completed to compare the early bolting mutant to vegetative WT plants of the same age. This allowed us to identify bolting time-associated genes (BAGs) expressed in an older rosette leaf at the time of inflorescence emergence. The BAG list contains many well characterized LS regulators (ORE1, WRKY45, NAP, WRKY28), and GO analysis revealed enrichment for LS and LS-related processes. These bolting associated LS regulators likely contribute to the temporal coupling of bolting time to LS.