Deep sequencing reveals the complex and coordinated transcriptional regulation of genes related to grain quality in rice cultivars

<p>Abstract</p> <p>Background</p> <p>Milling yield and eating quality are two important grain quality traits in rice. To identify the genes involved in these two traits, we performed a deep transcriptional analysis of developing seeds using both massively parallel signature sequencing (MPSS) and sequencing-by-synthesis (SBS). Five MPSS and five SBS libraries were constructed from 6-day-old developing seeds of Cypress (high milling yield), LaGrue (low milling yield), Ilpumbyeo (high eating quality), YR15965 (low eating quality), and Nipponbare (control).</p> <p>Results</p> <p>The transcriptomes revealed by MPSS and SBS had a high correlation co-efficient (0.81 to 0.90), and about 70% of the transcripts were commonly identified in both types of the libraries. SBS, however, identified 30% more transcripts than MPSS. Among the highly expressed genes in Cypress and Ilpumbyeo, over 100 conserved <it>cis </it>regulatory elements were identified. Numerous specifically expressed transcription factor (TF) genes were identified in Cypress (282), LaGrue (312), Ilpumbyeo (363), YR15965 (260), and Nipponbare (357). Many key grain quality-related genes (i.e., genes involved in starch metabolism, aspartate amino acid metabolism, storage and allergenic protein synthesis, and seed maturation) that were expressed at high levels underwent alternative splicing and produced antisense transcripts either in Cypress or Ilpumbyeo. Further, a time course RT-PCR analysis confirmed a higher expression level of genes involved in starch metabolism such as those encoding ADP glucose pyrophosphorylase (AGPase) and granule bound starch synthase I (GBSS I) in Cypress than that in LaGrue during early seed development.</p> <p>Conclusion</p> <p>This study represents the most comprehensive analysis of the developing seed transcriptome of rice available to date. Using two high throughput sequencing methods, we identified many differentially expressed genes that may affect milling yield or eating quality in rice. Many of the identified genes are involved in the biosynthesis of starch, aspartate family amino acids, and storage proteins. Some of the differentially expressed genes could be useful for the development of molecular markers if they are located in a known QTL region for milling yield or eating quality in the rice genome. Therefore, our comprehensive and deep survey of the developing seed transcriptome in five rice cultivars has provided a rich genomic resource for further elucidating the molecular basis of grain quality in rice.</p

Infrared polarimetry of Mrk 231: scattering off hot dust grains in the central core

We present high-angular (0.17−0.35 arcsec) resolution imaging polarimetric observations of Mrk 231 in the 3.1 µm filter using MMT-Pol on the 6.5-m MMT, and in the 8.7 µm, 10.3 µm, and 11.6 µm filters using CanariCam on the 10.4-m Gran Telescopio CANARIAS. In combination with already published observations, we compile the 1−12 µm total and polarized nuclear spectral energy distribution (SED). The total flux SED in the central 400 pc is explained as the combination of 1) a hot (731 ± 4 K) dusty structure, directly irradiated by the central engine, which is at 1.6 ± 0.1 pc away and attributed to be in the pc-scale polar region, 2) an optically-thick, smooth and disk-like dusty structure (‘torus’) with an inclination of 48 ± 23◦ surrounding the central engine, and 3) an extinguished (AV = 36 ± 5 mag) starburst component. The polarized SED decreases from 0.77 ± 0.14 per cent at 1.2 µm to 0.31 ± 0.15 per cent at 11.6 µm and follows a power-law function, λ ∼0.57. The polarization angle remains constant (∼108◦ ) in the 1−12 µm wavelength range. The dominant polarization mechanism is explained as scattering off hot dust grains in the pc-scale polar regions

Infrared polarimetry of Mrk 231: scattering off hot dust grains in the central core

We present high-angular (0.17−0.35 arcsec) resolution imaging polarimetric observations of Mrk 231 in the 3.1 µm filter using MMT-Pol on the 6.5-m MMT, and in the 8.7 µm, 10.3 µm, and 11.6 µm filters using CanariCam on the 10.4-m Gran Telescopio CANARIAS. In combination with already published observations, we compile the 1−12 µm total and polarized nuclear spectral energy distribution (SED). The total flux SED in the central 400 pc is explained as the combination of 1) a hot (731 ± 4 K) dusty structure, directly irradiated by the central engine, which is at 1.6 ± 0.1 pc away and attributed to be in the pc-scale polar region, 2) an optically-thick, smooth and disk-like dusty structure (‘torus’) with an inclination of 48 ± 23◦ surrounding the central engine, and 3) an extinguished (AV = 36 ± 5 mag) starburst component. The polarized SED decreases from 0.77 ± 0.14 per cent at 1.2 µm to 0.31 ± 0.15 per cent at 11.6 µm and follows a power-law function, λ ∼0.57. The polarization angle remains constant (∼108◦ ) in the 1−12 µm wavelength range. The dominant polarization mechanism is explained as scattering off hot dust grains in the pc-scale polar regions