Tissue specificity of chalcone synthase short interfering RNAs (CHS siRNAs) that control seed color

We previously showed CHS siRNAs levels to be high in immature seed coats of seed with dominant alleles of the I locus that controls seed color (Tuteja et al., Plant Cell 2009; Cho et al., Plos One, 2013) and to be much lower in several other tissues sampled (Zabala et al., BMC Plant Biology 2012). Here, we examined 15 additional small RNA populations by high-throughput sequencing of developing seed coats of various stages from cultivars with the dominant I and i-i alleles that specify yellow seed coats or from spontaneous mutations to pigmented seed coats. The CHS siRNAs were tissue specific and found at high levels of up to 5700 normalized RPMs (reads per millions) in immature seed coats but were less than 6 RPMs in libraries from 21 non-seed coat samples including the embryonic axis, different stages of seedlings cotyledons, vegetative buds, and shoot tips, illustrating the tightly controlled tissue-specific expression of the CHS siRNAs in seed coats. Overall design: High-throughput sequencing was performed on different tissues and genotypes of soybean as listed in each sample.