title: The transition from primary siRNAs to amplified secondary siRNAs that regulate chalcone synthase during development of Glycine max seed coats.
abstract: The I locus is a 27-kb inverted repeat cluster of chalcone synthase genes CHS1-3-4 that mediates siRNA down-regulation of CHS7 and CHS8 target mRNAs during seed development leading to yellow seed coats lacking anthocyanin pigments. Here, we report small RNA sequencing of ten stages of seed development from a few days post fertilization through maturity, revealing the amplification from primary to secondary short interfering RNAs (siRNAs) occurring during development. The young seed populations had a higher proportion of siRNAs representing the CHS1-3-4 gene family members, consistent with this region as the origin of the primary siRNAs. More intriguingly, the very young seed had a higher proportion of 22-nt CHS siRNAs than did the mid-maturation seed. We infer that the primary CHS siRNAs increase during development to levels sufficient to trigger amplification of secondary CHS siRNAs from the CHS7/8 target mRNAs, enabling the total levels of 21-nt CHS siRNAs to rise dramatically. Further, we demonstrate that the soybean system exhibits tissue-specific CHS siRNA production because primary CHS siRNA levels are not sufficient to trigger secondary amplification in tissues other than the seed coat.
authors.affiliation: Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America.
authors.forename: Young B
authors.initials: YB
authors.lastname: Cho
authors.forename: Sarah I
authors.initials: SI
authors.lastname: Jones
authors.forename: Lila
authors.initials: L
authors.lastname: Vodkin
mesh_terms: D000217:Acyltransferases / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D005784:Gene Amplification; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D007527:Isoenzymes / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D010858:Pigmentation / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics*; D012639:Seeds / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid; D013025:Glycine max / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D013997:Time Factors
chemical_list: D007527:Isoenzymes; D010940:Plant Proteins; D012333:RNA, Messenger; D018749:RNA, Plant; D034741:RNA, Small Interfering; D000217:Acyltransferases; C020141:flavanone synthetase