against UniProt and RefSeq or by longest ORF search. Microarray analysis The same RNA material was shared selleck chem inhibitor for use in the Illu mina sequencing and the microarray experiments and qRT PCR analysis. The rice 44K oligo microarray contained approximately 44,000 60 mer oligonucleotides synthesized on the basis of RAP annotation. For each microarray experiment, 400 ng of total RNAs was used for Cy3 or Cy5 labeled comple mentary RNA synthesis. DNA microarrays were hybridized for 16 h with 825 ng of Cy3 and Cy5 labeled probes from salinity stressed or unstressed plants. The microarray experiment was repeated with color swapping of Cy3 and Cy5. Agilent Feature Extraction Software was used to quantify microarray images.

Gene Spring software was used for background subtraction, LOWESS normalization, and extraction of normalized raw signal intensities for all probe sets from each array. Normalized raw signal inten sities were compared with the corresponding RPKM. Parts of the signals were removed for further analysis if they were not positive, significant, or above background levels. The hybridization experiments and array scanning were performed at an open laboratory run by the DNA Bank of the National Institute of Agrobiological Sciences. Quantitative RT PCR qRT PCR primers were designed on the basis of the anno tation of the RAP DB. One microgram of total RNA was reverse transcribed in a 20 uL reaction mixture of Transcriptor First Strand cDNA Synthesis Kit. qRT PCR was performed in a 20 uL reaction mixture containing 2�� SYBR Master Mix and 1 uL of cDNA template.

qRT PCR of three technical replicates for each sample was performed using a LightCycler480 System with its relative quantification software based on the delta delta Ct method. qRT PCR was performed for 10 s at 95 C, 5 s at 55 C, and 10 s at 72 C. The detection threshold cycle for each reaction was normalized against the expression level of the ubiquitin gene. Accession Numbers All primary Anacetrapib sequence read data have been submitted to DDBJ, and microarray data have been submitted to the GEO. Endosperm chalkiness is a varietal characteristic that negatively affects not only the appearance and milling properties but also the cooking texture and palatability of cooked rice. Chalky grains have a lower density of starch granules compared to vitreous ones, and are therefore more prone to breakage during milling.

In many rice producing areas, high chalkiness is a major concern that decreases grain quality. In http://www.selleckchem.com/products/U0126.html China, many early season indica and japonica varieties are of high grain endosperm chalkiness and their market values are seriously affected. Therefore, one of the goals in rice breeding is to reduce chalkiness in rice varieties. In rice grains, starch is the predominant storage substance that account for over 80% of the total dry mass. Starch in rice endosperm is composed of relatively unbranched amylose and highly branched amylopectin. Recent work showed that multiple factors contri bute to the formati